From 91e2772a86de66d95119f8ea694fe3eb8a848f48 Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Thu, 26 Jun 2025 09:21:12 +0200 Subject: [PATCH 1/7] visual summary module --- R/visual_summary.R | 291 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 291 insertions(+) create mode 100644 R/visual_summary.R diff --git a/R/visual_summary.R b/R/visual_summary.R new file mode 100644 index 00000000..91f1ca32 --- /dev/null +++ b/R/visual_summary.R @@ -0,0 +1,291 @@ +#' Data correlations evaluation module +#' +#' @param id Module id +#' +#' @name data-missings +#' @returns Shiny ui module +#' @export +visual_summary_ui <- function(id) { + ns <- shiny::NS(id) + + shiny::tagList( + shiny::plotOutput(outputId = ns("visual_plot"), height = "70vh") + ) +} + +visual_summary_server <- function(id, + data_r=shiny::reactive(NULL), + ...) { + shiny::moduleServer( + id = id, + module = function(input, output, session) { + # ns <- session$ns + rv <- shiny::reactiveValues(data = NULL) + + shiny::bindEvent(shiny::observe({ + data <- data_r() + rv$data <- data + # vars_num <- vapply(data, \(.x){ + # is.numeric(.x) || is_datetime(.x) + # }, logical(1)) + # vars_num <- names(vars_num)[vars_num] + # shinyWidgets::updateVirtualSelect( + # inputId = "variable", + # choices = vars_num, + # selected = if (isTruthy(input$variable)) input$variable else vars_num[1] + # ) + }), data_r(), input$hidden) + + # datar <- if (is.reactive(data)) data else reactive(data) + + + # apexcharter::renderApexchart({ + # missings_apex_plot(datar(), ...) + # }) + output$visual_plot <- shiny::renderPlot(expr = { + visual_summary(data = rv$data,...) + }) + } + ) +} + +visual_summary_demo_app <- function() { + ui <- shiny::fluidPage( + shiny::actionButton( + inputId = "modal_missings", + label = "Visual summary", + width = "100%", + disabled = FALSE + ) + ) + server <- function(input, output, session) { + data_demo <- mtcars + data_demo[sample(1:32, 10), "cyl"] <- NA + data_demo[sample(1:32, 8), "vs"] <- NA + + visual_summary_server(id = "data", data = shiny::reactive(data_demo)) + + observeEvent(input$modal_missings, { + tryCatch( + { + modal_visual_summary(id = "data") + }, + error = function(err) { + showNotification(paste0("We encountered the following error browsing your data: ", err), type = "err") + } + ) + }) + } + shiny::shinyApp(ui, server) +} + +visual_summary_demo_app() + + +modal_visual_summary <- function(id, + title = "Visual overview of data classes and missing observations", + easyClose = TRUE, + size = "xl", + footer = NULL, + ...) { + showModal(modalDialog( + title = tagList(title, datamods:::button_close_modal()), + visual_summary_ui(id = id), + easyClose = easyClose, + size = size, + footer = footer + )) +} + + +## Slow with many observations... + +#' Plot missings and class with apexcharter +#' +#' @param data data frame +#' +#' @returns An [apexchart()] `htmlwidget` object. +#' @export +#' +#' @examples +#' data_demo <- mtcars +#' data_demo[2:4, "cyl"] <- NA +#' rbind(data_demo, data_demo, data_demo, data_demo) |> missings_apex_plot() +#' data_demo |> missings_apex_plot() +#' mtcars |> missings_apex_plot(animation = TRUE) +#' # dplyr::storms |> missings_apex_plot() +#' visdat::vis_dat(dplyr::storms) +missings_apex_plot <- function(data, animation = FALSE, ...) { + l <- data_summary_gather(data, ...) + + df_plot <- l$data + + out <- apexcharter::apex( + data = df_plot, + type = "heatmap", + mapping = apexcharter::aes(x = variable, y = rows, fill = valueType_num), + ... + ) |> + apexcharter::ax_stroke(width = NULL) |> + apexcharter::ax_plotOptions( + heatmap = apexcharter::heatmap_opts( + radius = 0, + enableShades = FALSE, + colorScale = list( + ranges = l$labels + ), + useFillColorAsStroke = TRUE + ) + ) |> + apexcharter::ax_dataLabels(enabled = FALSE) |> + apexcharter::ax_tooltip( + enabled = FALSE, + intersect = FALSE + ) + + if (!isTRUE(animation)) { + out <- out |> + apexcharter::ax_chart(animations = list(enabled = FALSE)) + } + + out +} + + + +#' Ggplot2 data summary visualisation based on visdat::vis_dat. +#' +#' @param data data +#' @param ... optional arguments passed to data_summary_gather() +#' +#' @returns ggplot2 object +#' @export +#' +#' @examples +#' data_demo <- mtcars +#' data_demo[sample(1:32, 10), "cyl"] <- NA +#' data_demo[sample(1:32, 8), "vs"] <- NA +#' visual_summary(data_demo) +#' visual_summary(data_demo, palette.fun = scales::hue_pal()) +#' visual_summary(dplyr::storms) +#' visual_summary(dplyr::storms, summary.fun = data_type) +visual_summary <- function(data, legend.title = "Data class", ...) { + l <- data_summary_gather(data, ...) + + df <- l$data + + df$valueType <- factor(df$valueType, levels = names(l$colors)) + df$variable <- factor(df$variable, levels = unique_short(names(data))) + + ggplot2::ggplot(data = df, ggplot2::aes(x = variable, y = rows)) + + ggplot2::geom_raster(ggplot2::aes(fill = valueType)) + + ggplot2::theme_minimal() + + ggplot2::theme(axis.text.x = ggplot2::element_text( + angle = 45, + vjust = 1, hjust = 1 + )) + + ggplot2::scale_fill_manual(values = l$colors) + + ggplot2::labs(x = "", y = "Observations") + + ggplot2::scale_y_reverse() + + ggplot2::theme(axis.text.x = ggplot2::element_text(hjust = 0.5)) + + ggplot2::guides(colour = "none") + + ggplot2::guides(fill = ggplot2::guide_legend(title = legend.title)) + + # change the limits etc. + ggplot2::guides(fill = ggplot2::guide_legend(title = "Type")) + + # add info about the axes + ggplot2::scale_x_discrete(position = "top") + + ggplot2::theme(axis.text.x = ggplot2::element_text(hjust = 0)) + + ggplot2::theme( + panel.grid.major = ggplot2::element_blank(), + panel.grid.minor = ggplot2::element_blank(), + text = ggplot2::element_text(size = 18), + plot.title = ggplot2::element_blank() + ) +} + +#' Data summary for printing visual summary +#' +#' @param data data.frame +#' @param fun summary function. Default is "class" +#' @param palette.fun optionally use specific palette functions. First argument +#' has to be the length. +#' +#' @returns data.frame +#' @export +#' +#' @examples +#' mtcars |> data_summary_gather() +data_summary_gather <- function(data, summary.fun = class, palette.fun = viridisLite::viridis) { + df_plot <- setNames(data, unique_short(names(data))) |> + purrr::map_df(\(x){ + ifelse(is.na(x), + yes = NA, + no = glue::glue_collapse(summary.fun(x), + sep = "\n" + ) + ) + }) |> + dplyr::mutate(rows = dplyr::row_number()) |> + tidyr::pivot_longer( + cols = -rows, + names_to = "variable", values_to = "valueType", values_transform = list(valueType = as.character) + ) |> + dplyr::arrange(rows, variable, valueType) + + + df_plot$valueType_num <- df_plot$valueType |> + forcats::as_factor() |> + as.numeric() + + df_plot$valueType[is.na(df_plot$valueType)] <- "NA" + df_plot$valueType_num[is.na(df_plot$valueType_num)] <- max(df_plot$valueType_num, na.rm = TRUE) + 1 + + labels <- setNames(unique(df_plot$valueType_num), unique(df_plot$valueType)) |> sort() + + if (any(df_plot$valueType == "NA")) { + colors <- setNames(c(palette.fun(length(labels) - 1), "#999999"), names(labels)) + } else { + colors <- setNames(palette.fun(length(labels)), names(labels)) + } + + + label_list <- labels |> + purrr::imap(\(.x, .i){ + list( + from = .x, + to = .x, + color = colors[[.i]], + name = .i + ) + }) |> + setNames(NULL) + + list(data = df_plot, colors = colors, labels = label_list) +} + + + +#' Create unique short names of character vector items based on index +#' +#' @description +#' The function will prefer original names, and only append index to long +#' strings. +#' +#' +#' @param data character vector +#' @param max maximum final name length +#' +#' @returns character vector +#' @export +#' +#' @examples +#' c("kahdleidnsallskdj", "hej") |> unique_short() +unique_short <- function(data, max = 15) { + purrr::imap(data, \(.x, .i){ + if (nchar(.x) > max) { + glue::glue("{substr(.x,1,(max-(nchar(.i)+1)))}_{.i}") + } else { + .x + } + }) |> unlist() +} From fde1a5014066998ac7b3e63aa3fa49a45e7df175 Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Thu, 26 Jun 2025 09:21:42 +0200 Subject: [PATCH 2/7] helper functions for nivce labels and FreesearchR color palette --- R/theme.R | 15 +++++++++++++-- man/FreesearchR_palette.Rd | 20 ++++++++++++++++++++ man/unique_short.Rd | 23 +++++++++++++++++++++++ man/visual_summary.Rd | 28 ++++++++++++++++++++++++++++ 4 files changed, 84 insertions(+), 2 deletions(-) create mode 100644 man/FreesearchR_palette.Rd create mode 100644 man/unique_short.Rd create mode 100644 man/visual_summary.Rd diff --git a/R/theme.R b/R/theme.R index 7f8c7f75..2bcc2699 100644 --- a/R/theme.R +++ b/R/theme.R @@ -46,7 +46,7 @@ FreesearchR_colors <- function(choose = NULL) { secondary = "#FF6F61", success = "#00C896", warning = "#FFB100", - danger = "#FF3A2F", + danger = "#CC2E25", extra = "#8A4FFF", info = "#11A0EC", bg = "#FFFFFF", @@ -60,7 +60,18 @@ FreesearchR_colors <- function(choose = NULL) { } } - +#' Use the FreesearchR colors +#' +#' @param n number of colors +#' +#' @returns character vector +#' @export +#' +#' @examples +#' FreesearchR_palette(n=7) +FreesearchR_palette <- function(n){ + rep_len(FreesearchR_colors(),n) +} diff --git a/man/FreesearchR_palette.Rd b/man/FreesearchR_palette.Rd new file mode 100644 index 00000000..f0033c2c --- /dev/null +++ b/man/FreesearchR_palette.Rd @@ -0,0 +1,20 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/theme.R +\name{FreesearchR_palette} +\alias{FreesearchR_palette} +\title{Use the FreesearchR colors} +\usage{ +FreesearchR_palette(n) +} +\arguments{ +\item{n}{number of colors} +} +\value{ +character vector +} +\description{ +Use the FreesearchR colors +} +\examples{ +FreesearchR_palette(n=7) +} diff --git a/man/unique_short.Rd b/man/unique_short.Rd new file mode 100644 index 00000000..6a9d7b18 --- /dev/null +++ b/man/unique_short.Rd @@ -0,0 +1,23 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/visual_summary.R +\name{unique_short} +\alias{unique_short} +\title{Create unique short names of character vector items based on index} +\usage{ +unique_short(data, max = 15) +} +\arguments{ +\item{data}{character vector} + +\item{max}{maximum final name length} +} +\value{ +character vector +} +\description{ +The function will prefer original names, and only append index to long +strings. +} +\examples{ +c("kahdleidnsallskdj", "hej") |> unique_short() +} diff --git a/man/visual_summary.Rd b/man/visual_summary.Rd new file mode 100644 index 00000000..4a508ea7 --- /dev/null +++ b/man/visual_summary.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/visual_summary.R +\name{visual_summary} +\alias{visual_summary} +\title{Ggplot2 data summary visualisation based on visdat::vis_dat.} +\usage{ +visual_summary(data, legend.title = "Data class", ...) +} +\arguments{ +\item{data}{data} + +\item{...}{optional arguments passed to data_summary_gather()} +} +\value{ +ggplot2 object +} +\description{ +Ggplot2 data summary visualisation based on visdat::vis_dat. +} +\examples{ +data_demo <- mtcars +data_demo[sample(1:32, 10), "cyl"] <- NA +data_demo[sample(1:32, 8), "vs"] <- NA +visual_summary(data_demo) +visual_summary(data_demo, palette.fun = scales::hue_pal()) +visual_summary(dplyr::storms) +visual_summary(dplyr::storms, summary.fun = data_type) +} From da37710d6b1741cef772ee96bac946cdfd5530c7 Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Thu, 26 Jun 2025 09:22:00 +0200 Subject: [PATCH 3/7] docs --- man/data-missings.Rd | 9 ++++++++- man/data_summary_gather.Rd | 29 +++++++++++++++++++++++++++++ man/missings_apex_plot.Rd | 2 +- 3 files changed, 38 insertions(+), 2 deletions(-) create mode 100644 man/data_summary_gather.Rd diff --git a/man/data-missings.Rd b/man/data-missings.Rd index 510d78b0..f3f908df 100644 --- a/man/data-missings.Rd +++ b/man/data-missings.Rd @@ -1,14 +1,17 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/missings-module.R +% Please edit documentation in R/missings-module.R, R/visual_summary.R \name{data-missings} \alias{data-missings} \alias{data_missings_ui} \alias{data_missings_server} +\alias{visual_summary_ui} \title{Data correlations evaluation module} \usage{ data_missings_ui(id) data_missings_server(id, data, variable, ...) + +visual_summary_ui(id) } \arguments{ \item{id}{Module id} @@ -21,7 +24,11 @@ data_missings_server(id, data, variable, ...) Shiny ui module shiny server module + +Shiny ui module } \description{ +Data correlations evaluation module + Data correlations evaluation module } diff --git a/man/data_summary_gather.Rd b/man/data_summary_gather.Rd new file mode 100644 index 00000000..f904afbf --- /dev/null +++ b/man/data_summary_gather.Rd @@ -0,0 +1,29 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/visual_summary.R +\name{data_summary_gather} +\alias{data_summary_gather} +\title{Data summary for printing visual summary} +\usage{ +data_summary_gather( + data, + summary.fun = class, + palette.fun = viridisLite::viridis +) +} +\arguments{ +\item{data}{data.frame} + +\item{palette.fun}{optionally use specific palette functions. First argument +has to be the length.} + +\item{fun}{summary function. Default is "class"} +} +\value{ +data.frame +} +\description{ +Data summary for printing visual summary +} +\examples{ +mtcars |> data_summary_gather() +} diff --git a/man/missings_apex_plot.Rd b/man/missings_apex_plot.Rd index c9474534..bcf076ed 100644 --- a/man/missings_apex_plot.Rd +++ b/man/missings_apex_plot.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/missings-module.R +% Please edit documentation in R/visual_summary.R \name{missings_apex_plot} \alias{missings_apex_plot} \title{Plot missings and class with apexcharter} From c7a9467b471b1b528c4f3267f49f2b6320ed673f Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Thu, 26 Jun 2025 09:22:21 +0200 Subject: [PATCH 4/7] slimmed missings evaluation module --- R/missings-module.R | 149 +++++--------------------------------------- 1 file changed, 17 insertions(+), 132 deletions(-) diff --git a/R/missings-module.R b/R/missings-module.R index 53ea9298..71791ac6 100644 --- a/R/missings-module.R +++ b/R/missings-module.R @@ -34,7 +34,8 @@ data_missings_server <- function(id, variabler <- if (is.reactive(variable)) variable else reactive(variable) rv <- shiny::reactiveValues( - data = NULL + data = NULL, + table = NULL ) rv$data <- shiny::reactive({ @@ -65,15 +66,25 @@ data_missings_server <- function(id, shiny::req(variabler) if (is.null(variabler()) || variabler() == "" || !variabler() %in% names(datar())) { + if (anyNA(datar())){ + title <- "No variable chosen for analysis" + } else { title <- "No missing observations" + } } else { - title <- paste("Missing vs non-missing observations in", variabler()) + title <- glue::glue("Missing vs non-missing observations in the variable **'{variabler()}'**") } - rv$data() |> + out <- rv$data() |> gtsummary::as_gt() |> gt::tab_header(title = gt::md(title)) + + rv$table <- out + + out }) + + return(reactive(rv$table)) } ) } @@ -100,10 +111,12 @@ missing_demo_app <- function() { data_missings_server(id = "data", data = data_demo, variable = shiny::reactive(input$missings_var)) + visual_summary_server(id = "visual", data = data_demo) + observeEvent(input$modal_missings, { tryCatch( { - modal_visual_missings(data = data_demo, id = "modal_missings") + modal_visual_summary(id = "visual") }, error = function(err) { showNotification(paste0("We encountered the following error browsing your data: ", err), type = "err") @@ -117,137 +130,9 @@ missing_demo_app <- function() { missing_demo_app() -modal_visual_missings <- function(data, - title = "Visual overview of data classes and missing observations", - easyClose = TRUE, - size = "xl", - footer = NULL, - ...) { - datar <- if (is.reactive(data)) data else reactive(data) - - showModal(modalDialog( - title = tagList(title, datamods:::button_close_modal()), - tags$div( - # apexcharter::renderApexchart({ - # missings_apex_plot(datar(), ...) - # }) - shiny::renderPlot({ - visdat::vis_dat(datar(),sort_type = FALSE) + - ggplot2::guides(fill = ggplot2::guide_legend(title = "Data class")) + - # ggplot2::theme_void() + - ggplot2::theme( - # legend.position = "none", - panel.grid.major = ggplot2::element_blank(), - panel.grid.minor = ggplot2::element_blank(), - # axis.text.y = element_blank(), - # axis.title.y = element_blank(), - text = ggplot2::element_text(size = 18), - # axis.text = ggplot2::element_blank(), - # panel.background = ggplot2::element_rect(fill = "white"), - # plot.background = ggplot2::element_rect(fill = "white"), - # panel.border = ggplot2::element_blank() - plot.title = ggplot2::element_blank() - ) - }) - ), - easyClose = easyClose, - size = size, - footer = footer - )) -} -## Slow with many observations... - -#' Plot missings and class with apexcharter -#' -#' @param data data frame -#' -#' @returns An [apexchart()] `htmlwidget` object. -#' @export -#' -#' @examples -#' data_demo <- mtcars -#' data_demo[2:4, "cyl"] <- NA -#' rbind(data_demo, data_demo, data_demo, data_demo) |> missings_apex_plot() -#' data_demo |> missings_apex_plot() -#' mtcars |> missings_apex_plot(animation = TRUE) -#' # dplyr::storms |> missings_apex_plot() -#' visdat::vis_dat(dplyr::storms) -missings_apex_plot <- function(data, animation = FALSE, ...) { - browser() - - df_plot <- purrr::map_df(data, \(x){ - ifelse(is.na(x), - yes = NA, - no = glue::glue_collapse(class(x), - sep = "\n" - ) - ) - }) %>% - dplyr::mutate(rows = dplyr::row_number()) %>% - tidyr::pivot_longer( - cols = -rows, - names_to = "variable", values_to = "valueType", values_transform = list(valueType = as.character) - ) %>% - dplyr::arrange(rows, variable, valueType) - df_plot$valueType_num <- df_plot$valueType |> - forcats::as_factor() |> - as.numeric() - df_plot$valueType[is.na(df_plot$valueType)] <- "NA" - df_plot$valueType_num[is.na(df_plot$valueType_num)] <- max(df_plot$valueType_num, na.rm = TRUE) + 1 - - labels <- setNames(unique(df_plot$valueType_num), unique(df_plot$valueType)) - - if (any(df_plot$valueType == "NA")) { - colors <- setNames(c(viridisLite::viridis(n = length(labels) - 1), "#999999"), names(labels)) - } else { - colors <- setNames(viridisLite::viridis(n = length(labels)), names(labels)) - } - - - label_list <- labels |> - purrr::imap(\(.x, .i){ - list( - from = .x, - to = .x, - color = colors[[.i]], - name = .i - ) - }) |> - setNames(NULL) - - out <- apexcharter::apex( - data = df_plot, - type = "heatmap", - mapping = apexcharter::aes(x = variable, y = rows, fill = valueType_num), - ... - ) %>% - apexcharter::ax_stroke(width = NULL) |> - apexcharter::ax_plotOptions( - heatmap = apexcharter::heatmap_opts( - radius = 0, - enableShades = FALSE, - colorScale = list( - ranges = label_list - ), - useFillColorAsStroke = TRUE - ) - ) %>% - apexcharter::ax_dataLabels(enabled = FALSE) |> - apexcharter::ax_tooltip( - enabled = FALSE, - intersect = FALSE - ) - - if (!isTRUE(animation)) { - out <- out |> - apexcharter::ax_chart(animations = list(enabled = FALSE)) - } - - out -} From 4c42636faaca7e3bcdd1d542a5918ff268f16a2b Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Thu, 26 Jun 2025 09:22:30 +0200 Subject: [PATCH 5/7] docs --- DESCRIPTION | 3 +- NAMESPACE | 5 + NEWS.md | 2 +- R/hosted_version.R | 2 +- R/sysdata.rda | Bin 2757 -> 2785 bytes SESSION.md | 4 + inst/apps/FreesearchR/app.R | 556 ++++++++++++++++--------- inst/apps/FreesearchR/www/web_data.rds | Bin 3564988 -> 1737943 bytes 8 files changed, 371 insertions(+), 201 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index cebd5484..46be9506 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -64,8 +64,7 @@ Imports: RcppArmadillo, ggcorrplot, shinyjs, - emmeans, - visdat + emmeans Suggests: styler, devtools, diff --git a/NAMESPACE b/NAMESPACE index 2e380700..34c6092e 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -3,6 +3,7 @@ S3method(cut_var,default) S3method(cut_var,hms) S3method(plot,tbl_regression) +export(FreesearchR_palette) export(add_class_icon) export(add_sparkline) export(align_axes) @@ -32,6 +33,7 @@ export(data_correlations_ui) export(data_description) export(data_missings_server) export(data_missings_ui) +export(data_summary_gather) export(data_summary_server) export(data_summary_ui) export(data_type) @@ -121,12 +123,15 @@ export(supported_plots) export(symmetrical_scale_x_log10) export(tbl_merge) export(type_icons) +export(unique_short) export(update_factor_server) export(update_factor_ui) export(update_variables_server) export(update_variables_ui) export(vectorSelectInput) export(vertical_stacked_bars) +export(visual_summary) +export(visual_summary_ui) export(wide2long) export(winbox_create_column) export(winbox_update_factor) diff --git a/NEWS.md b/NEWS.md index 3ac90ee6..a92e676b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,6 @@ # FreesearchR 25.6.3 -- *NEW* First go at introducing more options to evaluate missings. This has introduced a new dependency to use the visdat package and visualisation. The solution includes the option to visualise data classes and missingness as well as comparisons of variables by missing outcome variable or not to determine the nature of missingness. +- *NEW* Introducing more options to evaluate missing observations. Inspired by the [visdat()] function from the {visdat} package, a specialised function has been introduced to easily visualise data classes and missing observations in the data set. This highly increases the options to visually get an overview of the data and to assess the pattern of missing data. Also under Evaluate, a comparison module has been introduced to compare the distribution of observations across variables depending on the missing vs non-missing in a specified variable. - *FIX* The REDCap import module has been updated visually and the PAI token is now hidden as a password. 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variable = shiny::reactive(input$missings_var)) + visual_summary_server(id = "visual", data = data_demo) + observeEvent(input$modal_missings, { tryCatch( { - modal_visual_missings(data = data_demo, id = "modal_missings") + modal_visual_summary(id = "visual") }, error = function(err) { showNotification(paste0("We encountered the following error browsing your data: ", err), type = "err") @@ -4778,140 +4791,12 @@ missing_demo_app <- function() { missing_demo_app() -modal_visual_missings <- function(data, - title = "Visual overview of data classes and missing observations", - easyClose = TRUE, - size = "xl", - footer = NULL, - ...) { - datar <- if (is.reactive(data)) data else reactive(data) - - showModal(modalDialog( - title = tagList(title, datamods:::button_close_modal()), - tags$div( - # apexcharter::renderApexchart({ - # missings_apex_plot(datar(), ...) - # }) - shiny::renderPlot({ - visdat::vis_dat(datar(),sort_type = FALSE) + - ggplot2::guides(fill = ggplot2::guide_legend(title = "Data class")) + - # ggplot2::theme_void() + - ggplot2::theme( - # legend.position = "none", - panel.grid.major = ggplot2::element_blank(), - panel.grid.minor = ggplot2::element_blank(), - # axis.text.y = element_blank(), - # axis.title.y = element_blank(), - text = ggplot2::element_text(size = 18), - # axis.text = ggplot2::element_blank(), - # panel.background = ggplot2::element_rect(fill = "white"), - # plot.background = ggplot2::element_rect(fill = "white"), - # panel.border = ggplot2::element_blank() - plot.title = ggplot2::element_blank() - ) - }) - ), - easyClose = easyClose, - size = size, - footer = footer - )) -} -## Slow with many observations... - -#' Plot missings and class with apexcharter -#' -#' @param data data frame -#' -#' @returns An [apexchart()] `htmlwidget` object. -#' @export -#' -#' @examples -#' data_demo <- mtcars -#' data_demo[2:4, "cyl"] <- NA -#' rbind(data_demo, data_demo, data_demo, data_demo) |> missings_apex_plot() -#' data_demo |> missings_apex_plot() -#' mtcars |> missings_apex_plot(animation = TRUE) -#' # dplyr::storms |> missings_apex_plot() -#' visdat::vis_dat(dplyr::storms) -missings_apex_plot <- function(data, animation = FALSE, ...) { - browser() - - df_plot <- purrr::map_df(data, \(x){ - ifelse(is.na(x), - yes = NA, - no = glue::glue_collapse(class(x), - sep = "\n" - ) - ) - }) %>% - dplyr::mutate(rows = dplyr::row_number()) %>% - tidyr::pivot_longer( - cols = -rows, - names_to = "variable", values_to = "valueType", values_transform = list(valueType = as.character) - ) %>% - dplyr::arrange(rows, variable, valueType) - df_plot$valueType_num <- df_plot$valueType |> - forcats::as_factor() |> - as.numeric() - df_plot$valueType[is.na(df_plot$valueType)] <- "NA" - df_plot$valueType_num[is.na(df_plot$valueType_num)] <- max(df_plot$valueType_num, na.rm = TRUE) + 1 - - labels <- setNames(unique(df_plot$valueType_num), unique(df_plot$valueType)) - - if (any(df_plot$valueType == "NA")) { - colors <- setNames(c(viridisLite::viridis(n = length(labels) - 1), "#999999"), names(labels)) - } else { - colors <- setNames(viridisLite::viridis(n = length(labels)), names(labels)) - } - - - label_list <- labels |> - purrr::imap(\(.x, .i){ - list( - from = .x, - to = .x, - color = colors[[.i]], - name = .i - ) - }) |> - setNames(NULL) - - out <- apexcharter::apex( - data = df_plot, - type = "heatmap", - mapping = apexcharter::aes(x = variable, y = rows, fill = valueType_num), - ... - ) %>% - apexcharter::ax_stroke(width = NULL) |> - apexcharter::ax_plotOptions( - heatmap = apexcharter::heatmap_opts( - radius = 0, - enableShades = FALSE, - colorScale = list( - ranges = label_list - ), - useFillColorAsStroke = TRUE - ) - ) %>% - apexcharter::ax_dataLabels(enabled = FALSE) |> - apexcharter::ax_tooltip( - enabled = FALSE, - intersect = FALSE - ) - - if (!isTRUE(animation)) { - out <- out |> - apexcharter::ax_chart(animations = list(enabled = FALSE)) - } - - out -} ######## @@ -8278,7 +8163,7 @@ FreesearchR_colors <- function(choose = NULL) { secondary = "#FF6F61", success = "#00C896", warning = "#FFB100", - danger = "#FF3A2F", + danger = "#CC2E25", extra = "#8A4FFF", info = "#11A0EC", bg = "#FFFFFF", @@ -8292,7 +8177,18 @@ FreesearchR_colors <- function(choose = NULL) { } } - +#' Use the FreesearchR colors +#' +#' @param n number of colors +#' +#' @returns character vector +#' @export +#' +#' @examples +#' FreesearchR_palette(n=7) +FreesearchR_palette <- function(n){ + rep_len(FreesearchR_colors(),n) +} @@ -9443,6 +9339,303 @@ clean_date <- function(data) { } +######## +#### Current file: /Users/au301842/FreesearchR/R//visual_summary.R +######## + +#' Data correlations evaluation module +#' +#' @param id Module id +#' +#' @name data-missings +#' @returns Shiny ui module +#' @export +visual_summary_ui <- function(id) { + ns <- shiny::NS(id) + + shiny::tagList( + shiny::plotOutput(outputId = ns("visual_plot"), height = "70vh") + ) +} + +visual_summary_server <- function(id, + data_r=shiny::reactive(NULL), + ...) { + shiny::moduleServer( + id = id, + module = function(input, output, session) { + # ns <- session$ns + rv <- shiny::reactiveValues(data = NULL) + + shiny::bindEvent(shiny::observe({ + data <- data_r() + rv$data <- data + # vars_num <- vapply(data, \(.x){ + # is.numeric(.x) || is_datetime(.x) + # }, logical(1)) + # vars_num <- names(vars_num)[vars_num] + # shinyWidgets::updateVirtualSelect( + # inputId = "variable", + # choices = vars_num, + # selected = if (isTruthy(input$variable)) input$variable else vars_num[1] + # ) + }), data_r(), input$hidden) + + # datar <- if (is.reactive(data)) data else reactive(data) + + + # apexcharter::renderApexchart({ + # missings_apex_plot(datar(), ...) + # }) + output$visual_plot <- shiny::renderPlot(expr = { + visual_summary(data = rv$data,...) + }) + } + ) +} + +visual_summary_demo_app <- function() { + ui <- shiny::fluidPage( + shiny::actionButton( + inputId = "modal_missings", + label = "Visual summary", + width = "100%", + disabled = FALSE + ) + ) + server <- function(input, output, session) { + data_demo <- mtcars + data_demo[sample(1:32, 10), "cyl"] <- NA + data_demo[sample(1:32, 8), "vs"] <- NA + + visual_summary_server(id = "data", data = shiny::reactive(data_demo)) + + observeEvent(input$modal_missings, { + tryCatch( + { + modal_visual_summary(id = "data") + }, + error = function(err) { + showNotification(paste0("We encountered the following error browsing your data: ", err), type = "err") + } + ) + }) + } + shiny::shinyApp(ui, server) +} + +visual_summary_demo_app() + + +modal_visual_summary <- function(id, + title = "Visual overview of data classes and missing observations", + easyClose = TRUE, + size = "xl", + footer = NULL, + ...) { + showModal(modalDialog( + title = tagList(title, datamods:::button_close_modal()), + visual_summary_ui(id = id), + easyClose = easyClose, + size = size, + footer = footer + )) +} + + +## Slow with many observations... + +#' Plot missings and class with apexcharter +#' +#' @param data data frame +#' +#' @returns An [apexchart()] `htmlwidget` object. +#' @export +#' +#' @examples +#' data_demo <- mtcars +#' data_demo[2:4, "cyl"] <- NA +#' rbind(data_demo, data_demo, data_demo, data_demo) |> missings_apex_plot() +#' data_demo |> missings_apex_plot() +#' mtcars |> missings_apex_plot(animation = TRUE) +#' # dplyr::storms |> missings_apex_plot() +#' visdat::vis_dat(dplyr::storms) +missings_apex_plot <- function(data, animation = FALSE, ...) { + l <- data_summary_gather(data, ...) + + df_plot <- l$data + + out <- apexcharter::apex( + data = df_plot, + type = "heatmap", + mapping = apexcharter::aes(x = variable, y = rows, fill = valueType_num), + ... + ) |> + apexcharter::ax_stroke(width = NULL) |> + apexcharter::ax_plotOptions( + heatmap = apexcharter::heatmap_opts( + radius = 0, + enableShades = FALSE, + colorScale = list( + ranges = l$labels + ), + useFillColorAsStroke = TRUE + ) + ) |> + apexcharter::ax_dataLabels(enabled = FALSE) |> + apexcharter::ax_tooltip( + enabled = FALSE, + intersect = FALSE + ) + + if (!isTRUE(animation)) { + out <- out |> + apexcharter::ax_chart(animations = list(enabled = FALSE)) + } + + out +} + + + +#' Ggplot2 data summary visualisation based on visdat::vis_dat. +#' +#' @param data data +#' @param ... optional arguments passed to data_summary_gather() +#' +#' @returns ggplot2 object +#' @export +#' +#' @examples +#' data_demo <- mtcars +#' data_demo[sample(1:32, 10), "cyl"] <- NA +#' data_demo[sample(1:32, 8), "vs"] <- NA +#' visual_summary(data_demo) +#' visual_summary(data_demo, palette.fun = scales::hue_pal()) +#' visual_summary(dplyr::storms) +#' visual_summary(dplyr::storms, summary.fun = data_type) +visual_summary <- function(data, legend.title = "Data class", ...) { + l <- data_summary_gather(data, ...) + + df <- l$data + + df$valueType <- factor(df$valueType, levels = names(l$colors)) + df$variable <- factor(df$variable, levels = unique_short(names(data))) + + ggplot2::ggplot(data = df, ggplot2::aes(x = variable, y = rows)) + + ggplot2::geom_raster(ggplot2::aes(fill = valueType)) + + ggplot2::theme_minimal() + + ggplot2::theme(axis.text.x = ggplot2::element_text( + angle = 45, + vjust = 1, hjust = 1 + )) + + ggplot2::scale_fill_manual(values = l$colors) + + ggplot2::labs(x = "", y = "Observations") + + ggplot2::scale_y_reverse() + + ggplot2::theme(axis.text.x = ggplot2::element_text(hjust = 0.5)) + + ggplot2::guides(colour = "none") + + ggplot2::guides(fill = ggplot2::guide_legend(title = legend.title)) + + # change the limits etc. + ggplot2::guides(fill = ggplot2::guide_legend(title = "Type")) + + # add info about the axes + ggplot2::scale_x_discrete(position = "top") + + ggplot2::theme(axis.text.x = ggplot2::element_text(hjust = 0)) + + ggplot2::theme( + panel.grid.major = ggplot2::element_blank(), + panel.grid.minor = ggplot2::element_blank(), + text = ggplot2::element_text(size = 18), + plot.title = ggplot2::element_blank() + ) +} + +#' Data summary for printing visual summary +#' +#' @param data data.frame +#' @param fun summary function. Default is "class" +#' @param palette.fun optionally use specific palette functions. First argument +#' has to be the length. +#' +#' @returns data.frame +#' @export +#' +#' @examples +#' mtcars |> data_summary_gather() +data_summary_gather <- function(data, summary.fun = class, palette.fun = viridisLite::viridis) { + df_plot <- setNames(data, unique_short(names(data))) |> + purrr::map_df(\(x){ + ifelse(is.na(x), + yes = NA, + no = glue::glue_collapse(summary.fun(x), + sep = "\n" + ) + ) + }) |> + dplyr::mutate(rows = dplyr::row_number()) |> + tidyr::pivot_longer( + cols = -rows, + names_to = "variable", values_to = "valueType", values_transform = list(valueType = as.character) + ) |> + dplyr::arrange(rows, variable, valueType) + + + df_plot$valueType_num <- df_plot$valueType |> + forcats::as_factor() |> + as.numeric() + + df_plot$valueType[is.na(df_plot$valueType)] <- "NA" + df_plot$valueType_num[is.na(df_plot$valueType_num)] <- max(df_plot$valueType_num, na.rm = TRUE) + 1 + + labels <- setNames(unique(df_plot$valueType_num), unique(df_plot$valueType)) |> sort() + + if (any(df_plot$valueType == "NA")) { + colors <- setNames(c(palette.fun(length(labels) - 1), "#999999"), names(labels)) + } else { + colors <- setNames(palette.fun(length(labels)), names(labels)) + } + + + label_list <- labels |> + purrr::imap(\(.x, .i){ + list( + from = .x, + to = .x, + color = colors[[.i]], + name = .i + ) + }) |> + setNames(NULL) + + list(data = df_plot, colors = colors, labels = label_list) +} + + + +#' Create unique short names of character vector items based on index +#' +#' @description +#' The function will prefer original names, and only append index to long +#' strings. +#' +#' +#' @param data character vector +#' @param max maximum final name length +#' +#' @returns character vector +#' @export +#' +#' @examples +#' c("kahdleidnsallskdj", "hej") |> unique_short() +unique_short <- function(data, max = 15) { + purrr::imap(data, \(.x, .i){ + if (nchar(.x) > max) { + glue::glue("{substr(.x,1,(max-(nchar(.i)+1)))}_{.i}") + } else { + .x + } + }) |> unlist() +} + + ######## #### Current file: /Users/au301842/FreesearchR/R//wide2long.R ######## @@ -9796,7 +9989,7 @@ ui_elements <- list( shiny::column( width = 3, shiny::actionButton( - inputId = "modal_missings", + inputId = "modal_visual_overview", label = "Visual overview", width = "100%", disabled = TRUE @@ -10323,6 +10516,7 @@ server <- function(input, output, session) { rv <- shiny::reactiveValues( list = list(), regression = NULL, + missings = NULL, ds = NULL, local_temp = NULL, ready = NULL, @@ -10342,28 +10536,6 @@ server <- function(input, output, session) { ######### ############################################################################## - ## This does not render correctly apparently due to css and load order - # output$source <- shiny::renderUI({ - # - # choices <- c( - # "File upload" = "file", - # "REDCap server export" = "redcap", - # "Local or sample data" = "env" - # ) - # - # if (isTRUE(is_local)){ - # choices <- choices[c(1,3)] - # } - # - # shinyWidgets::radioGroupButtons( - # inputId = "source", - # selected = "file", - # choices = choices, - # size = "lg" - # ) - # }) - - data_file <- import_file_server( id = "file_import", show_data_in = "popup", @@ -10386,16 +10558,6 @@ server <- function(input, output, session) { rv$code <- modifyList(x = rv$code, list(import = from_redcap$code())) }) - ## This is used to ensure the reactive data is retrieved - # output$redcap_prev <- DT::renderDT( - # { - # DT::datatable(head(from_redcap$data(), 5), - # caption = "First 5 observations" - # ) - # }, - # server = TRUE - # ) - from_env <- datamods::import_globalenv_server( id = "env", trigger_return = "change", @@ -10410,11 +10572,20 @@ server <- function(input, output, session) { rv$code <- modifyList(x = rv$code, list(import = from_env$name())) }) + visual_summary_server( + id = "initial_summary", + data_r = shiny::reactive({ + shiny::req(rv$data_temp) + default_parsing(rv$data_temp) + }), + palette.fun = FreesearchR_palette + ) + observeEvent(input$modal_initial_view, { tryCatch( { - modal_visual_missings( - data = default_parsing(rv$data_temp), + modal_visual_summary( + id = "initial_summary", footer = NULL, size = "xl" ) @@ -10497,12 +10668,12 @@ server <- function(input, output, session) { if (is.null(rv$data_original) | NROW(rv$data_original) == 0) { shiny::updateActionButton(inputId = "act_start", disabled = TRUE) shiny::updateActionButton(inputId = "modal_browse", disabled = TRUE) - shiny::updateActionButton(inputId = "modal_missings", disabled = TRUE) + shiny::updateActionButton(inputId = "modal_visual_overview", disabled = TRUE) shiny::updateActionButton(inputId = "act_eval", disabled = TRUE) } else { shiny::updateActionButton(inputId = "act_start", disabled = FALSE) shiny::updateActionButton(inputId = "modal_browse", disabled = FALSE) - shiny::updateActionButton(inputId = "modal_missings", disabled = FALSE) + shiny::updateActionButton(inputId = "modal_visual_overview", disabled = FALSE) shiny::updateActionButton(inputId = "act_eval", disabled = FALSE) } }) @@ -10548,7 +10719,6 @@ server <- function(input, output, session) { ) }) - ######### ######### Modifications ######### @@ -10741,11 +10911,20 @@ server <- function(input, output, session) { ) }) - observeEvent(input$modal_missings, { + visual_summary_server( + id = "visual_overview", + data_r = shiny::reactive({ + shiny::req(rv$data_filtered) + REDCapCAST::fct_drop(rv$data_filtered) + }), + palette.fun = FreesearchR_palette + ) + + observeEvent(input$modal_visual_overview, { tryCatch( { - modal_visual_missings( - data = REDCapCAST::fct_drop(rv$data_filtered), + modal_visual_summary( + id = "visual_overview", footer = "Here is an overview of how your data is interpreted, and where data is missing. Use this information to consider if data is missing at random or if some observations are missing systematically wich may be caused by an observation bias.", size = "xl" ) @@ -10756,7 +10935,6 @@ server <- function(input, output, session) { ) }) - output$original_str <- renderPrint({ str(rv$data_original) }) @@ -10779,7 +10957,6 @@ server <- function(input, output, session) { shiny::req(rv$data_filtered) rv$list$table1 <- NULL - # rv$regression <- NULL } ) @@ -10904,7 +11081,7 @@ server <- function(input, output, session) { rv$list$table1 <- rlang::exec(create_baseline, !!!append_list(rv$list$data, parameters, "data")) }) - rv$code$table1 <- glue::glue("FreesearchR::create_baseline(data,{list2str(parameters)})") + rv$code$table1 <- glue::glue("FreesearchR::create_baseline(df,{list2str(parameters)})") } ) @@ -10951,12 +11128,12 @@ server <- function(input, output, session) { label = "Select variable to stratify analysis", data = shiny::reactive({ shiny::req(rv$data_filtered) - rv$data_filtered[apply(rv$data_filtered,2,anyNA)] + rv$data_filtered[apply(rv$data_filtered, 2, anyNA)] })() ) }) - data_missings_server( + rv$missings <- data_missings_server( id = "missingness", data = shiny::reactive(rv$data_filtered), variable = shiny::reactive(input$missings_var) @@ -10979,22 +11156,6 @@ server <- function(input, output, session) { rv$regression <- regression_server("regression", data = shiny::reactive(rv$list$data)) - # shiny::observeEvent(rv$regression, { - # browser() - # if (shiny::is.reactive(rv$regression)) { - # rv$list$regression <- rv$regression() - # } else { - # rv$list$regression <- rv$regression - # } - # # rv$list$regression <- rv$regression() - # }) - - # output$regression_models <- renderText({ - # req(rv$list$regression) - # browser() - # names(rv$list$regression) - # }) - ############################################################################## ######### ######### Page navigation @@ -11051,6 +11212,7 @@ server <- function(input, output, session) { format <- ifelse(type == "docx", "word_document", "odt_document") rv$list$regression <- rv$regression() + rv$list$missings <- rv$missings() shiny::withProgress(message = "Generating the report. 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zhJW?9`vRl55@Q(FjP(*|W&;?7@Gpk8GPG5`5;1{5{C++yVjDwSWwqr|!nUl?)`>OG z=o9B`W8H5|pPO$jZ1~E|x%t)Q4Xe$bn_p|KC3eiLrw*^jhxKKj$s0f^e7{Asct%ly z7W8g`2uMR{vGi<%egRr6BU(YH5+W-Y(F(dAN9K3CxX`yqLIGGb)>>}B{S%9c#aS;3 zid@WyR`3QbsT|w+$k$~x zmKriwOX-g>0Xh{|O93C15Yt2766iWg*v5#~B)ZC)S9p4gzDH2jkdtUDaqX`lOPWD` zO}8rgNo-Kk>gy8CgSw6eY-)+RM(?1mCF*JcLtRVM>D>Y`AR$;Ts>Km~K)Zn1k5N>h zQwg&lBU(XMkz5(k%7|8(0|Tv}E5kz#xR{l{7pGD&ks-3h1`xou6VOT`_E9g`L|BZwFm2xq7gK{y5fJC`CrUB(*3=6S$jndj`W|J6E z`zs?_!Edy`_K!9LM(>O0@c()U`xCFUm^ab_f`g`WD1aV?w}rspaC??KItCtIHp07aU^u3&JX?x&;v@v66ON>mbh9*X?bJaZ%&TLY;A7z967Yu=rk|1+RKZL zm7YWSKiaJ$hnAKXFSa_Z)k4>uzNJCWWU5Qs?LMB#;AbN1ZslcpW@dTyZT7>pr}$`k z`FvyTu^v7-@PW05*IJLR_3S?Q___Jj<&BLeJWoR6NcDBNv9f-#v9`I|1oLhGSc*nd zTL(GQs From 4f0a17d821c23218562e22daa61d041f52143224 Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Thu, 26 Jun 2025 10:17:24 +0200 Subject: [PATCH 6/7] publishing with docker --- .github/workflows/docker-build.yml | 49 + CITATION.cff | 13 - DESCRIPTION | 3 +- R/sysdata.rda | Bin 2785 -> 2769 bytes SESSION.md | 10 +- app_docker/.dockerignore | 6 + app_docker/Dockerfile | 12 + app_docker/app.R | 11275 ++++++++++++++++++++++++++ app_docker/www/FreesearchR-logo.png | Bin 0 -> 22712 bytes app_docker/www/favicon.ico | Bin 0 -> 15086 bytes app_docker/www/favicon.png | Bin 0 -> 28511 bytes app_docker/www/favicon.svg | 3 + app_docker/www/intro.html | 438 + app_docker/www/intro.md | 31 + app_docker/www/references.bib | 11 + app_docker/www/report.rmd | 83 + app_docker/www/style.css | 125 + app_docker/www/umami-app.html | 1 + app_docker/www/web_data.rds | Bin 0 -> 1737943 bytes renv.lock | 48 - 20 files changed, 12040 insertions(+), 68 deletions(-) create mode 100644 .github/workflows/docker-build.yml create mode 100644 app_docker/.dockerignore create mode 100644 app_docker/Dockerfile create mode 100644 app_docker/app.R create mode 100644 app_docker/www/FreesearchR-logo.png create mode 100755 app_docker/www/favicon.ico create mode 100644 app_docker/www/favicon.png create mode 100755 app_docker/www/favicon.svg create mode 100644 app_docker/www/intro.html create mode 100644 app_docker/www/intro.md create mode 100644 app_docker/www/references.bib create mode 100644 app_docker/www/report.rmd create mode 100644 app_docker/www/style.css create mode 100644 app_docker/www/umami-app.html create mode 100644 app_docker/www/web_data.rds diff --git a/.github/workflows/docker-build.yml b/.github/workflows/docker-build.yml new file mode 100644 index 00000000..3cd45b8b --- /dev/null +++ b/.github/workflows/docker-build.yml @@ -0,0 +1,49 @@ +name: Build and Push Docker Image +permissions: + contents: read + packages: write + +on: + # push: + # branches: + # - main + # - master + release: + types: [published] + workflow_dispatch: + +jobs: + build: + runs-on: ubuntu-latest + + steps: + - name: Checkout code + uses: actions/checkout@v3 + + - name: Setup Docker Buildx + uses: docker/setup-buildx-action@v2 + + - name: Login to GitHub Container Registry + uses: docker/login-action@v2 + with: + registry: ghcr.io + username: ${{ github.actor }} + password: ${{ secrets.GITHUB_TOKEN }} + + - name: Define lowercase variables + id: vars + run: | + REPO_OWNER_LOWER=$(echo "$GITHUB_REPOSITORY_OWNER" | tr '[:upper:]' '[:lower:]') + REPO_NAME_LOWER=$(echo "$GITHUB_REPOSITORY" | cut -d'/' -f2 | tr '[:upper:]' '[:lower:]') + echo "REPO_OWNER_LOWER=$REPO_OWNER_LOWER" >> $GITHUB_ENV + echo "REPO_NAME_LOWER=$REPO_NAME_LOWER" >> $GITHUB_ENV + + - name: Build and push Docker image + uses: docker/build-push-action@v4 + with: + context: . + file: app_docker/Dockerfile + push: true + tags: | + ghcr.io/${{ env.REPO_OWNER_LOWER }}/${{ env.REPO_NAME_LOWER }}:latest + ghcr.io/${{ env.REPO_OWNER_LOWER }}/${{ env.REPO_NAME_LOWER }}:${{ github.sha }} diff --git a/CITATION.cff b/CITATION.cff index ed962eb8..fbe84208 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1002,19 +1002,6 @@ references: email: russell-lenth@uiowa.edu year: '2025' doi: 10.32614/CRAN.package.emmeans -- type: software - title: visdat - abstract: 'visdat: Preliminary Visualisation of Data' - notes: Imports - url: https://docs.ropensci.org/visdat/ - repository: https://CRAN.R-project.org/package=visdat - authors: - - family-names: Tierney - given-names: Nicholas - email: nicholas.tierney@gmail.com - orcid: https://orcid.org/0000-0003-1460-8722 - year: '2025' - doi: 10.32614/CRAN.package.visdat - type: software title: styler abstract: 'styler: Non-Invasive Pretty Printing of R Code' diff --git a/DESCRIPTION b/DESCRIPTION index 46be9506..439b7312 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -79,7 +79,8 @@ Suggests: testthat (>= 3.0.0), shinytest, covr, - cffr + cffr, + shiny2docker URL: https://github.com/agdamsbo/FreesearchR, https://agdamsbo.github.io/FreesearchR/, https://app.FreesearchR.org/ BugReports: https://github.com/agdamsbo/FreesearchR/issues VignetteBuilder: knitr diff --git a/R/sysdata.rda b/R/sysdata.rda index 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c(list(data = data), fun.args)) + return(out) +} + + + +#' Create a baseline table +#' +#' @param data data +#' @param ... passed as fun.arg to baseline_table() +#' @param strat.var grouping/strat variable +#' @param add.p add comparison/p-value +#' @param add.overall add overall column +#' +#' @returns gtsummary table list object +#' @export +#' +#' @examples +#' mtcars |> create_baseline(by.var = "gear", add.p = "yes" == "yes") +#' create_baseline(default_parsing(mtcars), by.var = "am", add.p = FALSE, add.overall = FALSE, theme = "lancet") +create_baseline <- function(data, ..., by.var, add.p = FALSE, add.overall = FALSE, theme = c("jama", "lancet", "nejm", "qjecon")) { + theme <- match.arg(theme) + + if (by.var == "none" | !by.var %in% names(data)) { + by.var <- NULL + } + + ## These steps are to handle logicals/booleans, that messes up the order of columns + ## Has been reported and should be fixed soon (02042025) + + if (!is.null(by.var)) { + if (identical("logical", class(data[[by.var]]))) { + data[by.var] <- as.character(data[[by.var]]) + } + } + + suppressMessages(gtsummary::theme_gtsummary_journal(journal = theme)) + + args <- list(...) + + parameters <- list( + data = data, + fun.args = list(by = by.var, ...) + ) + + out <- do.call( + baseline_table, + parameters + ) + + + if (!is.null(by.var)) { + if (isTRUE(add.overall)) { + out <- out |> gtsummary::add_overall() + } + if (isTRUE(add.p)) { + out <- out |> + gtsummary::add_p() |> + gtsummary::bold_p() + } + } + + out +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//contrast_text.R +######## + +#' @title Contrast Text Color +#' @description Calculates the best contrast text color for a given +#' background color. +#' @param background A hex/named color value that represents the background. +#' @param light_text A hex/named color value that represents the light text +#' color. +#' @param dark_text A hex/named color value that represents the dark text color. +#' @param threshold A numeric value between 0 and 1 that is used to determine +#' the luminance threshold of the background color for text color. +#' @param method A character string that specifies the method for calculating +#' the luminance. Three different methods are available: +#' c("relative","perceived","perceived_2") +#' @param ... parameter overflow. Ignored. +#' @details +#' This function aids in deciding the font color to print on a given background. +#' The function is based on the example provided by teppo: +#' https://stackoverflow.com/a/66669838/21019325. +#' The different methods provided are based on the methods outlined in the +#' StackOverflow thread: +#' https://stackoverflow.com/questions/596216/formula-to-determine-perceived-brightness-of-rgb-color +#' @return A character string that contains the best contrast text color. +#' @examples +#' contrast_text(c("#F2F2F2", "blue")) +#' +#' contrast_text(c("#F2F2F2", "blue"), method="relative") +#' @export +#' +#' +contrast_text <- function(background, + light_text = 'white', + dark_text = 'black', + threshold = 0.5, + method = "perceived_2", + ...) { + if (method == "relative") { + luminance <- + c(c(.2126, .7152, .0722) %*% grDevices::col2rgb(background) / 255) + } else if (method == "perceived") { + luminance <- + c(c(.299, .587, .114) %*% grDevices::col2rgb(background) / 255) + } else if (method == "perceived_2") { + luminance <- c(sqrt(colSums(( + c(.299, .587, .114) * grDevices::col2rgb(background) + ) ^ 2)) / 255) + } + + ifelse(luminance < threshold, + light_text, + dark_text) +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//correlations-module.R +######## + +#' Data correlations evaluation module +#' +#' @param id Module id. (Use 'ns("id")') +#' +#' @name data-correlations +#' @returns Shiny ui module +#' @export +data_correlations_ui <- function(id, ...) { + ns <- shiny::NS(id) + + shiny::tagList( + shiny::textOutput(outputId = ns("suggest")), + shiny::plotOutput(outputId = ns("correlation_plot"), ...) + ) +} + + +#' +#' @param data data +#' @param color.main main color +#' @param color.sec secondary color +#' @param ... arguments passed to toastui::datagrid +#' +#' @name data-correlations +#' @returns shiny server module +#' @export +data_correlations_server <- function(id, + data, + include.class = NULL, + cutoff = .7, + ...) { + shiny::moduleServer( + id = id, + module = function(input, output, session) { + # ns <- session$ns + + rv <- shiny::reactiveValues( + data = NULL + ) + + rv$data <- shiny::reactive({ + shiny::req(data) + if (!is.null(include.class)) { + filter <- sapply(data(), class) %in% include.class + out <- data()[filter] + } else { + out <- data() + } + # out |> dplyr::mutate(dplyr::across(tidyselect::everything(),as.numeric)) + sapply(out,as.numeric) + # as.numeric() + }) + + # rv <- list() + # rv$data <- mtcars + + output$suggest <- shiny::renderPrint({ + shiny::req(rv$data) + shiny::req(cutoff) + pairs <- correlation_pairs(rv$data(), threshold = cutoff()) + + more <- ifelse(nrow(pairs) > 1, "from each pair ", "") + + if (nrow(pairs) == 0) { + out <- glue::glue("No variables have a correlation measure above the threshold.") + } else { + out <- pairs |> + apply(1, \(.x){ + glue::glue("'{.x[1]}'x'{.x[2]}'({round(as.numeric(.x[3]),2)})") + }) |> + (\(.x){ + glue::glue("The following variable pairs are highly correlated: {sentence_paste(.x)}.\nConsider excluding one {more}from the dataset to ensure variables are independent.") + })() + } + out + }) + + output$correlation_plot <- shiny::renderPlot({ + ggcorrplot::ggcorrplot(cor(rv$data())) + + # ggplot2::theme_void() + + ggplot2::theme( + # legend.position = "none", + legend.title = ggplot2::element_text(size = 20), + legend.text = ggplot2::element_text(size = 14), + # panel.grid.major = element_blank(), + # panel.grid.minor = element_blank(), + # axis.text.y = element_blank(), + # axis.title.y = element_blank(), + axis.text.x = ggplot2::element_text(size = 20), + axis.text.y = ggplot2::element_text(size = 20), + # text = element_text(size = 5), + # plot.title = element_blank(), + # panel.background = ggplot2::element_rect(fill = "white"), + # plot.background = ggplot2::element_rect(fill = "white"), + panel.border = ggplot2::element_blank() + ) + # psych::pairs.panels(rv$data()) + }) + } + ) +} + +correlation_pairs <- function(data, threshold = .8) { + data <- as.data.frame(data)[!sapply(as.data.frame(data), is.character)] + data <- sapply(data,\(.x)if (is.factor(.x)) as.numeric(.x) else .x) |> as.data.frame() + # data <- data |> dplyr::mutate(dplyr::across(dplyr::where(is.factor), as.numeric)) + cor <- Hmisc::rcorr(as.matrix(data)) + r <- cor$r %>% as.table() + d <- r |> + as.data.frame() |> + dplyr::filter(abs(Freq) > threshold, Freq != 1) + + d[1:2] |> + apply(1, \(.x){ + sort(unname(.x)) + }, + simplify = logical(1) + ) |> + duplicated() |> + (\(.x){ + d[!.x, ] + })() |> + setNames(c("var1", "var2", "cor")) +} + +sentence_paste <- function(data, and.str = "and") { + and.str <- gsub(" ", "", and.str) + if (length(data) < 2) { + data + } else if (length(data) == 2) { + paste(data, collapse = glue::glue(" {and.str} ")) + } else if (length(data) > 2) { + paste(paste(data[-length(data)], collapse = ", "), data[length(data)], sep = glue::glue(" {and.str} ")) + } +} + + + + + + +######## +#### Current file: /Users/au301842/FreesearchR/R//create-column-mod.R +######## + +#' @title Create new column +#' +#' @description +#' This module allow to enter an expression to create a new column in a `data.frame`. +#' +#' +#' @param id Module's ID. +#' +#' @return A [shiny::reactive()] function returning the data. +#' +#' @note User can only use a subset of function: `r paste(list_allowed_operations(), collapse=", ")`. +#' You can add more operations using the `allowed_operations` argument, for example if you want to allow to use package lubridate, you can do: +#' ```r +#' c(list_allowed_operations(), getNamespaceExports("lubridate")) +#' ``` +#' +#' @export +#' +#' @importFrom htmltools tagList tags css +#' +#' @name create-column +#' +#' @example examples/create_column_module_demo.R +create_column_ui <- function(id) { + ns <- NS(id) + htmltools::tagList( + # datamods:::html_dependency_datamods(), + # html_dependency_FreesearchR(), + shiny::tags$head( + shiny::tags$link(rel = "stylesheet", type = "text/css", href = "FreesearchR/inst/assets/css/FreesearchR.css") + ), + # tags$head( + # # Note the wrapping of the string in HTML() + # tags$style(HTML(" + # /* modified from esquisse for data types */ + # .btn-column-categorical { + # background-color: #EF562D; + # color: #FFFFFF; + # } + # .btn-column-continuous { + # background-color: #0C4C8A; + # color: #FFFFFF; + # } + # .btn-column-dichotomous { + # background-color: #97D5E0; + # color: #FFFFFF; + # } + # .btn-column-datetime { + # background-color: #97D5E0; + # color: #FFFFFF; + # } + # .btn-column-id { + # background-color: #848484; + # color: #FFFFFF; + # } + # .btn-column-text { + # background-color: #2E2E2E; + # color: #FFFFFF; + # }")) + # ), + fluidRow( + column( + width = 6, + textInput( + inputId = ns("new_column"), + label = i18n("New column name:"), + value = "new_column1", + width = "100%" + ) + ), + column( + width = 6, + shinyWidgets::virtualSelectInput( + inputId = ns("group_by"), + label = i18n("Group calculation by:"), + choices = NULL, + multiple = TRUE, + disableSelectAll = TRUE, + hasOptionDescription = TRUE, + width = "100%" + ) + ) + ), + shiny::textAreaInput( + inputId = ns("expression"), + label = i18n("Enter an expression to define new column:"), + value = "", + width = "100%", + rows = 6 + ), + tags$i( + class = "d-block", + phosphoricons::ph("info"), + datamods::i18n("Click on a column name to add it to the expression:") + ), + uiOutput(outputId = ns("columns")), + uiOutput(outputId = ns("feedback")), + tags$div( + style = htmltools::css( + display = "grid", + gridTemplateColumns = "3fr 1fr", + columnGap = "10px", + margin = "10px 0" + ), + actionButton( + inputId = ns("compute"), + label = tagList( + phosphoricons::ph("gear"), i18n("Create column") + ), + class = "btn-outline-primary", + width = "100%" + ), + actionButton( + inputId = ns("remove"), + label = tagList( + phosphoricons::ph("trash") + ), + class = "btn-outline-danger", + width = "100%" + ) + ) + ) +} + +#' @param data_r A [shiny::reactive()] function returning a `data.frame`. +#' @param allowed_operations A `list` of allowed operations, see below for details. +#' +#' @export +#' +#' @rdname create-column +#' +create_column_server <- function(id, + data_r = reactive(NULL), + allowed_operations = list_allowed_operations()) { + moduleServer( + id, + function(input, output, session) { + ns <- session$ns + + info_alert <- shinyWidgets::alert( + status = "info", + phosphoricons::ph("question"), + datamods::i18n("Choose a name for the column to be created or modified,"), + datamods::i18n("then enter an expression before clicking on the button above to validate or on "), + phosphoricons::ph("trash"), datamods::i18n("to delete it.") + ) + + rv <- reactiveValues( + data = NULL, + feedback = info_alert + ) + + observeEvent(input$hidden, rv$feedback <- info_alert) + + bindEvent(observe({ + data <- data_r() + shinyWidgets::updateVirtualSelect( + inputId = "group_by", + choices = make_choices_with_infos(data) + ) + }), data_r(), input$hidden) + + observeEvent(data_r(), rv$data <- data_r()) + + output$feedback <- renderUI(rv$feedback) + + output$columns <- renderUI({ + data <- req(rv$data) + mapply( + label = names(data), + data = data, + FUN = btn_column, + MoreArgs = list(inputId = ns("add_column")), + SIMPLIFY = FALSE + ) + }) + + observeEvent(input$add_column, { + updateTextAreaInput( + session = session, + inputId = "expression", + value = paste0(input$expression, input$add_column) + ) + }) + + observeEvent(input$new_column, { + if (input$new_column == "") { + rv$feedback <- shinyWidgets::alert( + status = "warning", + phosphoricons::ph("warning"), datamods::i18n("New column name cannot be empty") + ) + } + }) + + observeEvent(input$remove, { + rv$data[[input$new_column]] <- NULL + }) + observeEvent(input$compute, { + rv$feedback <- try_compute_column( + expression = input$expression, + name = input$new_column, + rv = rv, + allowed_operations = allowed_operations, + by = input$group_by + ) + }) + + return(reactive(rv$data)) + } + ) +} + +#' @export +#' +#' @rdname create-column +# @importFrom methods getGroupMembers +list_allowed_operations <- function() { + c( + "(", "c", + # getGroupMembers("Arith"), + c("+", "-", "*", "^", "%%", "%/%", "/"), + # getGroupMembers("Compare"), + c("==", ">", "<", "!=", "<=", ">="), + # getGroupMembers("Logic"), + c("&", "|"), + # getGroupMembers("Math"), + c( + "abs", "sign", "sqrt", "ceiling", "floor", "trunc", "cummax", + "cummin", "cumprod", "cumsum", "exp", "expm1", "log", "log10", + "log2", "log1p", "cos", "cosh", "sin", "sinh", "tan", "tanh", + "acos", "acosh", "asin", "asinh", "atan", "atanh", "cospi", "sinpi", + "tanpi", "gamma", "lgamma", "digamma", "trigamma" + ), + # getGroupMembers("Math2"), + c("round", "signif"), + # getGroupMembers("Summary"), + c("max", "min", "range", "prod", "sum", "any", "all"), + "pmin", "pmax", "mean", + "paste", "paste0", "substr", "nchar", "trimws", + "gsub", "sub", "grepl", "ifelse", "length", + "as.numeric", "as.character", "as.integer", "as.Date", "as.POSIXct", + "as.factor", "factor" + ) +} + + +#' @inheritParams shiny::modalDialog +#' @export +#' +#' @importFrom shiny showModal modalDialog textInput +#' @importFrom htmltools tagList +#' +#' @rdname create-column +modal_create_column <- function(id, + title = i18n("Create a new column"), + easyClose = TRUE, + size = "l", + footer = NULL) { + ns <- NS(id) + showModal(modalDialog( + title = tagList(title, datamods:::button_close_modal()), + create_column_ui(id), + tags$div( + style = "display: none;", + textInput(inputId = ns("hidden"), label = NULL, value = datamods:::genId()) + ), + easyClose = easyClose, + size = size, + footer = footer + )) +} + +#' @inheritParams shinyWidgets::WinBox +#' @export +#' +#' @importFrom shinyWidgets WinBox wbOptions wbControls +#' @importFrom htmltools tagList +#' @rdname create-column +winbox_create_column <- function(id, + title = i18n("Create a new column"), + options = shinyWidgets::wbOptions(), + controls = shinyWidgets::wbControls()) { + ns <- NS(id) + WinBox( + title = title, + ui = tagList( + create_column_ui(id), + tags$div( + style = "display: none;", + textInput(inputId = ns("hidden"), label = NULL, value = datamods:::genId()) + ) + ), + options = modifyList( + shinyWidgets::wbOptions(height = "550px", modal = TRUE), + options + ), + controls = controls, + auto_height = FALSE + ) +} + + +try_compute_column <- function(expression, + name, + rv, + allowed_operations, + by = NULL) { + parsed <- try(parse(text = expression, keep.source = FALSE), silent = TRUE) + if (inherits(parsed, "try-error")) { + return(datamods:::alert_error(attr(parsed, "condition")$message)) + } + funs <- unlist(c(extract_calls(parsed), lapply(parsed, extract_calls)), recursive = TRUE) + if (!are_allowed_operations(funs, allowed_operations)) { + return(datamods:::alert_error(datamods::i18n("Some operations are not allowed"))) + } + if (!isTruthy(by)) { + result <- try( + rlang::eval_tidy(rlang::parse_expr(expression), data = rv$data), + silent = TRUE + ) + } else { + result <- try( + { + dt <- as.data.table(rv$data) + new_col <- NULL + dt[, new_col := rlang::eval_tidy(rlang::parse_expr(expression), data = .SD), by = by] + dt$new_col + }, + silent = TRUE + ) + } + if (inherits(result, "try-error")) { + return(alert_error(attr(result, "condition")$message)) + } + adding_col <- try(rv$data[[name]] <- result, silent = TRUE) + if (inherits(adding_col, "try-error")) { + return(alert_error(attr(adding_col, "condition")$message)) + } + code <- if (!isTruthy(by)) { + rlang::call2("mutate", !!!rlang::set_names(list(rlang::parse_expr(expression)), name)) + } else { + rlang::call2( + "mutate", + !!!rlang::set_names(list(rlang::parse_expr(expression)), name), + !!!list(.by = rlang::expr(c(!!!rlang::syms(by)))) + ) + } + attr(rv$data, "code") <- Reduce( + f = function(x, y) rlang::expr(!!x %>% !!y), + x = c(attr(rv$data, "code"), code) + ) + shinyWidgets::alert( + status = "success", + phosphoricons::ph("check"), datamods::i18n("Column added!") + ) +} + +are_allowed_operations <- function(x, allowed_operations) { + all( + x %in% allowed_operations + ) +} + + +extract_calls <- function(exp) { + if (is.call(exp)) { + return(list( + as.character(exp[[1L]]), + lapply(exp[-1L], extract_calls) + )) + } +} + +alert_error <- function(text) { + alert( + status = "danger", + phosphoricons::ph("bug"), text + ) +} + + +btn_column <- function(label, data, inputId) { + icon <- get_var_icon(data, "class") + type <- data_type(data) + tags$button( + type = "button", + class = paste0("btn btn-column-", type), + style = htmltools::css( + "--bs-btn-padding-y" = ".25rem", + "--bs-btn-padding-x" = ".5rem", + "--bs-btn-font-size" = ".75rem", + "margin-bottom" = "5px" + ), + if (!is.null(icon)) icon, + label, + onclick = sprintf( + "Shiny.setInputValue('%s', '%s', {priority: 'event'})", + inputId, label + ) + ) +} + +make_choices_with_infos <- function(data) { + lapply( + X = seq_along(data), + FUN = function(i) { + nm <- names(data)[i] + values <- data[[nm]] + icon <- get_var_icon(values, "class") + # icon <- if (inherits(values, "character")) { + # phosphoricons::ph("text-aa") + # } else if (inherits(values, "factor")) { + # phosphoricons::ph("list-bullets") + # } else if (inherits(values, c("numeric", "integer"))) { + # phosphoricons::ph("hash") + # } else if (inherits(values, c("Date"))) { + # phosphoricons::ph("calendar") + # } else if (inherits(values, c("POSIXt"))) { + # phosphoricons::ph("clock") + # } else { + # NULL + # } + description <- if (is.atomic(values)) { + paste(i18n("Unique values:"), data.table::uniqueN(values)) + } else { + "" + } + list( + label = htmltools::doRenderTags(tagList( + icon, nm + )), + value = nm, + description = description + ) + } + ) +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//custom_SelectInput.R +######## + +#' A selectizeInput customized for data frames with column labels +#' +#' @description +#' Copied and modified from the IDEAFilter package +#' Adds the option to select "none" which is handled later +#' +#' @param inputId passed to \code{\link[shiny]{selectizeInput}} +#' @param label passed to \code{\link[shiny]{selectizeInput}} +#' @param data \code{data.frame} object from which fields should be populated +#' @param selected default selection +#' @param ... passed to \code{\link[shiny]{selectizeInput}} +#' @param col_subset a \code{vector} containing the list of allowable columns to select +#' @param placeholder passed to \code{\link[shiny]{selectizeInput}} options +#' @param onInitialize passed to \code{\link[shiny]{selectizeInput}} options +#' @param none_label label for "none" item +#' @param maxItems max number of items +#' +#' @return a \code{\link[shiny]{selectizeInput}} dropdown element +#' +#' @importFrom shiny selectizeInput +#' @export +#' +columnSelectInput <- function(inputId, label, data, selected = "", ..., + col_subset = NULL, placeholder = "", onInitialize, none_label="No variable selected",maxItems=NULL) { + datar <- if (is.reactive(data)) data else reactive(data) + col_subsetr <- if (is.reactive(col_subset)) col_subset else reactive(col_subset) + + labels <- Map(function(col) { + json <- sprintf( + IDEAFilter:::strip_leading_ws(' + { + "name": "%s", + "label": "%s", + "dataclass": "%s", + "datatype": "%s" + }'), + col, + attr(datar()[[col]], "label") %||% "", + IDEAFilter:::get_dataFilter_class(datar()[[col]]), + data_type(datar()[[col]]) + ) + }, col = names(datar())) + + if (!"none" %in% names(datar())){ + labels <- c("none"=list(sprintf('\n {\n \"name\": \"none\",\n \"label\": \"%s\",\n \"dataclass\": \"\",\n \"datatype\": \"\"\n }',none_label)),labels) + choices <- setNames(names(labels), labels) + choices <- choices[match(if (length(col_subsetr()) == 0 || isTRUE(col_subsetr() == "")) names(datar()) else col_subsetr(), choices)] + } else { + choices <- setNames(names(datar()), labels) + choices <- choices[match(if (length(col_subsetr()) == 0 || isTRUE(col_subsetr() == "")) choices else col_subsetr(), choices)] + } + + shiny::selectizeInput( + inputId = inputId, + label = label, + choices = choices, + selected = selected, + ..., + options = c( + list(render = I("{ + // format the way that options are rendered + option: function(item, escape) { + item.data = JSON.parse(item.label); + return '

'; + }, + + // avoid data vomit splashing on screen when an option is selected + item: function(item, escape) { + item.data = JSON.parse(item.label); + return '
' + + escape(item.data.name) + + '
'; + } + }")), + if (!is.null(maxItems)) list(maxItems=maxItems) + ) + ) +} + + +#' A selectizeInput customized for named vectors +#' +#' @param inputId passed to \code{\link[shiny]{selectizeInput}} +#' @param label passed to \code{\link[shiny]{selectizeInput}} +#' @param choices A named \code{vector} from which fields should be populated +#' @param selected default selection +#' @param ... passed to \code{\link[shiny]{selectizeInput}} +#' @param placeholder passed to \code{\link[shiny]{selectizeInput}} options +#' @param onInitialize passed to \code{\link[shiny]{selectizeInput}} options +#' +#' @returns a \code{\link[shiny]{selectizeInput}} dropdown element +#' @export +#' +#' @examples +#' if (shiny::interactive()) { +#' shinyApp( +#' ui = fluidPage( +#' shiny::uiOutput("select"), +#' tableOutput("data") +#' ), +#' server = function(input, output) { +#' output$select <- shiny::renderUI({ +#' vectorSelectInput( +#' inputId = "variable", label = "Variable:", +#' data = c( +#' "Cylinders" = "cyl", +#' "Transmission" = "am", +#' "Gears" = "gear" +#' ) +#' ) +#' }) +#' +#' output$data <- renderTable( +#' { +#' mtcars[, c("mpg", input$variable), drop = FALSE] +#' }, +#' rownames = TRUE +#' ) +#' } +#' ) +#' } +vectorSelectInput <- function(inputId, + label, + choices, + selected = "", + ..., + placeholder = "", + onInitialize) { + datar <- if (shiny::is.reactive(choices)) data else shiny::reactive(choices) + + labels <- sprintf( + IDEAFilter:::strip_leading_ws(' + { + "name": "%s", + "label": "%s" + }'), + datar(), + names(datar()) %||% "" + ) + + choices_new <- stats::setNames(datar(), labels) + + shiny::selectizeInput( + inputId = inputId, + label = label, + choices = choices_new, + selected = selected, + ..., + options = c( + list(render = I("{ + // format the way that options are rendered + option: function(item, escape) { + item.data = JSON.parse(item.label); + return '
' + + '
' + + escape(item.data.name) + ' ' + + '
' + + (item.data.label != '' ? '
' + escape(item.data.label) + '
' : '') + + '
'; + }, + + // avoid data vomit splashing on screen when an option is selected + item: function(item, escape) { + item.data = JSON.parse(item.label); + return '
' + + escape(item.data.name) + + '
'; + } + }")) + ) + ) +} + + + + +######## +#### Current file: /Users/au301842/FreesearchR/R//cut-variable-dates.R +######## + +#' Extended cutting function with fall-back to the native base::cut +#' +#' @param x an object inheriting from class "hms" +#' @param ... passed on +#' +#' @export +#' @name cut_var +cut_var <- function(x, ...) { + UseMethod("cut_var") +} + +#' @export +#' @name cut_var +cut_var.default <- function(x, ...) { + base::cut(x, ...) +} + +#' @name cut_var +#' +#' @return factor +#' @export +#' +#' @examples +#' readr::parse_time(c("01:00:20", "03:00:20", "01:20:20", "08:20:20", "21:20:20", "03:02:20")) |> cut_var(2) +#' readr::parse_time(c("01:00:20", "03:00:20", "01:20:20", "08:20:20", "21:20:20", "03:02:20")) |> cut_var("min") +#' readr::parse_time(c("01:00:20", "03:00:20", "01:20:20", "08:20:20", "21:20:20", "03:02:20")) |> cut_var(breaks = "hour") +#' readr::parse_time(c("01:00:20", "03:00:20", "01:20:20", "08:20:20", "21:20:20", "03:02:20")) |> cut_var(breaks = hms::as_hms(c("01:00:00", "03:01:20", "9:20:20"))) +#' d_t <- readr::parse_time(c("01:00:20", "03:00:20", "01:20:20", "03:02:20", NA)) +#' f <- d_t |> cut_var(2) +#' readr::parse_time(c("01:00:20", "03:00:20", "01:20:20", "03:02:20", NA)) |> cut_var(breaks = lubridate::as_datetime(c(hms::as_hms(levels(f)), hms::as_hms(max(d_t, na.rm = TRUE) + 1))), right = FALSE) +cut_var.hms <- function(x, breaks, ...) { + ## as_hms keeps returning warnings on tz(); ignored + suppressWarnings({ + if (hms::is_hms(breaks)) { + breaks <- lubridate::as_datetime(breaks) + } + x <- lubridate::as_datetime(x) + out <- cut_var.POSIXt(x, breaks = breaks, ...) + attr(out, which = "brks") <- hms::as_hms(lubridate::as_datetime(attr(out, which = "brks"))) + attr(out, which = "levels") <- as.character(hms::as_hms(lubridate::as_datetime(attr(out, which = "levels")))) + }) + out +} + +#' @name cut_var +#' @param x an object inheriting from class "POSIXt" or "Date" +#' +#' @examples +#' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(2) +#' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks = "weekday") +#' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks = "month_only") +#' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks=NULL,format = "%A-%H") +#' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks=NULL,format = "%W") +cut_var.POSIXt <- function(x, breaks, right = FALSE, include.lowest = TRUE, start.on.monday = TRUE, ...) { + breaks_o <- breaks + args <- list(...) + # browser() + if (is.numeric(breaks)) { + breaks <- quantile( + x, + probs = seq(0, 1, 1 / breaks), + right = right, + include.lowest = include.lowest, + na.rm = TRUE + ) + } + + if ("format" %in% names(args)){ + assertthat::assert_that(is.character(args$format)) + out <- forcats::as_factor(format(x,format=args$format)) + } else if (identical(breaks, "weekday")) { + ## This is + ds <- as.Date(1:7) |> + (\(.x){ + sort_by(format(.x,"%A"),as.numeric(format(.x,"%w"))) + })() + + if (start.on.monday) { + ds <- ds[c(7, 1:6)] + } + out <- factor(weekdays(x), levels = ds) |> forcats::fct_drop() + } else if (identical(breaks, "month_only")) { + ## Simplest way to create a vector of all months in order + ## which will also follow the locale of the machine + ms <- paste0("1970-", 1:12, "-01") |> + as.Date() |> + months() + + out <- factor(months(x), levels = ms) |> forcats::fct_drop() + } else { + ## Doesn't really work very well for breaks other than the special character cases as right border is excluded + out <- base::cut.POSIXt(x, breaks = breaks, right = right, ...) |> forcats::fct_drop() + # browser() + } + l <- levels(out) + if (is.numeric(breaks_o)) { + l <- breaks + } else if (is.character(breaks) && length(breaks) == 1 && !(identical(breaks, "weekday") | identical(breaks, "month_only"))) { + if (include.lowest) { + if (right) { + l <- c(l, min(as.character(x))) + } else { + l <- c(l, max(as.character(x))) + } + } + } else if (length(l) < length(breaks_o)) { + l <- breaks_o + } + + attr(out, which = "brks") <- l + out +} + +#' @name cut_var +#' @param x an object inheriting from class "POSIXct" +cut_var.POSIXct <- cut_var.POSIXt + +#' @name cut_var +#' @param x an object inheriting from class "POSIXct" +#' +#' @examples +#' as.Date(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(2) +#' as.Date(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks = "weekday") +#' as.Date(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(format = "%W") +cut_var.Date <- function(x, breaks=NULL, start.on.monday = TRUE, ...) { + args <- list(...) + + if ("format" %in% names(args)){ + assertthat::assert_that(is.character(args$format)) + out <- forcats::as_factor(format(x,format=args$format)) + } else if (identical(breaks, "weekday")) { + ds <- as.Date(1:7) |> + (\(.x){ + sort_by(format(.x,"%A"),as.numeric(format(.x,"%w"))) + })() + + if (start.on.monday) { + ds <- ds[c(7, 1:6)] + } + out <- factor(weekdays(x), levels = ds) |> forcats::fct_drop() + } else if (identical(breaks, "month_only")) { + ms <- paste0("1970-", 1:12, "-01") |> + as.Date() |> + months() + + out <- factor(months(x), levels = ms) |> forcats::fct_drop() + } else { + ## Doesn't really work very well for breaks other than the special character cases as right border is excluded + out <- base::cut.Date(x, breaks = breaks, ...) |> forcats::fct_drop() + # browser() + } + out +} + +#' Test class +#' +#' @param data data +#' @param class.vec vector of class names to test +#' +#' @return factor +#' @export +#' +#' @examples +#' \dontrun{ +#' vapply(REDCapCAST::redcapcast_data, \(.x){ +#' is_any_class(.x, c("hms", "Date", "POSIXct", "POSIXt")) +#' }, logical(1)) +#' } +is_any_class <- function(data, class.vec) { + any(class(data) %in% class.vec) +} + +#' Test is date/datetime/time +#' +#' @param data data +#' +#' @return factor +#' @export +#' +#' @examples +#' vapply(REDCapCAST::redcapcast_data, is_datetime, logical(1)) +is_datetime <- function(data) { + is_any_class(data, class.vec = c("hms", "Date", "POSIXct", "POSIXt")) +} + +#' @title Module to Convert Numeric to Factor +#' +#' @description +#' This module contain an interface to cut a numeric into several intervals. +#' +#' +#' @param id Module ID. +#' +#' @return A [shiny::reactive()] function returning the data. +#' @export +#' +#' @importFrom shiny NS fluidRow column numericInput checkboxInput checkboxInput plotOutput uiOutput +#' @importFrom shinyWidgets virtualSelectInput +#' @importFrom toastui datagridOutput2 +#' +#' @name cut-variable +#' +cut_variable_ui <- function(id) { + ns <- NS(id) + tagList( + shiny::fluidRow( + column( + width = 3, + shinyWidgets::virtualSelectInput( + inputId = ns("variable"), + label = datamods:::i18n("Variable to cut:"), + choices = NULL, + width = "100%" + ) + ), + column( + width = 3, + shiny::uiOutput(ns("cut_method")) + ), + column( + width = 3, + numericInput( + inputId = ns("n_breaks"), + label = datamods:::i18n("Number of breaks:"), + value = 3, + min = 2, + max = 12, + width = "100%" + ) + ), + column( + width = 3, + checkboxInput( + inputId = ns("right"), + label = datamods:::i18n("Close intervals on the right"), + value = TRUE + ), + checkboxInput( + inputId = ns("include_lowest"), + label = datamods:::i18n("Include lowest value"), + value = TRUE + ) + ) + ), + conditionalPanel( + condition = "input.method == 'fixed'", + ns = ns, + uiOutput(outputId = ns("slider_fixed")) + ), + plotOutput(outputId = ns("plot"), width = "100%", height = "270px"), + toastui::datagridOutput2(outputId = ns("count")), + actionButton( + inputId = ns("create"), + label = tagList(phosphoricons::ph("scissors"), datamods:::i18n("Create factor variable")), + class = "btn-outline-primary float-end" + ), + tags$div(class = "clearfix") + ) +} + +#' @param data_r A [shiny::reactive()] function returning a `data.frame`. +#' +#' @export +#' +#' @importFrom shiny moduleServer observeEvent reactive req bindEvent renderPlot +#' @importFrom shinyWidgets updateVirtualSelect noUiSliderInput +#' @importFrom toastui renderDatagrid2 datagrid grid_colorbar +#' @importFrom rlang %||% call2 set_names expr syms +#' @importFrom classInt classIntervals +#' +#' @rdname cut-variable +cut_variable_server <- function(id, data_r = reactive(NULL)) { + moduleServer( + id, + function(input, output, session) { + rv <- reactiveValues(data = NULL, new_var_name = NULL) + + bindEvent(observe({ + data <- data_r() + rv$data <- data + vars_num <- vapply(data, \(.x){ + is.numeric(.x) || is_datetime(.x) + }, logical(1)) + vars_num <- names(vars_num)[vars_num] + shinyWidgets::updateVirtualSelect( + inputId = "variable", + choices = vars_num, + selected = if (isTruthy(input$variable)) input$variable else vars_num[1] + ) + }), data_r(), input$hidden) + + output$slider_fixed <- renderUI({ + data <- req(data_r()) + variable <- req(input$variable) + req(hasName(data, variable)) + + if (is_datetime(data[[variable]])) { + brks <- cut_var(data[[variable]], + breaks = input$n_breaks + )$brks + } else { + brks <- classInt::classIntervals( + var = data[[variable]], + n = input$n_breaks, + style = "quantile" + )$brks + } + + if (is_datetime(data[[variable]])) { + lower <- min(data[[variable]], na.rm = TRUE) + } else { + lower <- floor(min(data[[variable]], na.rm = TRUE)) + } + + if (is_datetime(data[[variable]])) { + upper <- max(data[[variable]], na.rm = TRUE) + } else { + upper <- ceiling(max(data[[variable]], na.rm = TRUE)) + } + + + shinyWidgets::noUiSliderInput( + inputId = session$ns("fixed_brks"), + label = datamods:::i18n("Fixed breaks:"), + min = lower, + max = upper, + value = brks, + color = datamods:::get_primary_color(), + width = "100%" + ) + }) + + output$cut_method <- renderUI({ + data <- req(data_r()) + variable <- req(input$variable) + + choices <- c( + # "fixed", + # "quantile" + ) + + if (any(c("hms","POSIXct") %in% class(data[[variable]]))) { + choices <- c(choices, "hour") + } else if (any(c("POSIXt", "Date") %in% class(data[[variable]]))) { + choices <- c( + choices, + "day", + "weekday", + "week", + # "week_only", + "month", + "month_only", + "quarter", + "year" + ) + } else { + choices <- c( + choices, + "fixed", + "quantile", + # "sd", + # "equal", + # "pretty", + # "kmeans", + # "hclust", + # "bclust", + # "fisher", + # "jenks", + "headtails" # , + # "maximum", + # "box" + ) + } + + choices <- unique(choices) + + shinyWidgets::virtualSelectInput( + inputId = session$ns("method"), + label = datamods:::i18n("Method:"), + choices = choices, + selected = NULL, + width = "100%" + ) + }) + + + breaks_r <- reactive({ + data <- req(data_r()) + variable <- req(input$variable) + req(hasName(data, variable)) + req(input$n_breaks, input$method) + if (input$method == "fixed") { + req(input$fixed_brks) + if (any(c("hms", "POSIXct") %in% class(data[[variable]]))) { + # cut.POSIXct <- cut.POSIXt + f <- cut_var(data[[variable]], breaks = input$fixed_brks) + list(var = f, brks = levels(f)) + } else { + classInt::classIntervals( + var = as.numeric(data[[variable]]), + n = input$n_breaks, + style = "fixed", + fixedBreaks = input$fixed_brks + ) + } + } else if (input$method == "quantile") { + req(input$fixed_brks) + if (any(c("hms", "POSIXt") %in% class(data[[variable]]))) { + # cut.POSIXct <- cut.POSIXt + f <- cut_var(data[[variable]], breaks = input$n_breaks) + list(var = f, brks = levels(f)) + } else { + classInt::classIntervals( + var = as.numeric(data[[variable]]), + n = input$n_breaks, + style = "quantile" + ) + } + } else if (input$method %in% c( + "day", + "weekday", + "week", + "month", + "month_only", + "quarter", + "year" + )) { + # To enable datetime cutting + # cut.POSIXct <- cut.POSIXt + f <- cut_var(data[[variable]], breaks = input$method) + list(var = f, brks = levels(f)) + } else if (input$method %in% c("hour")) { + # To enable datetime cutting + # cut.POSIXct <- cut.POSIXt + f <- cut_var(data[[variable]], breaks = "hour") + list(var = f, brks = levels(f)) + # } else if (input$method %in% c("week_only")) { + # # As a proof of concept a single option to use "format" parameter + # # https://www.stat.berkeley.edu/~s133/dates.html + # f <- cut_var(data[[variable]], format = "%W") + # list(var = f, brks = levels(f)) + } else { + classInt::classIntervals( + var = as.numeric(data[[variable]]), + n = input$n_breaks, + style = input$method + ) + } + }) + + output$plot <- renderPlot({ + data <- req(data_r()) + variable <- req(input$variable) + plot_histogram(data, variable, breaks = breaks_r()$brks, color = datamods:::get_primary_color()) + # plot_histogram(data = breaks_r()$var, breaks = breaks_r()$brks, color = datamods:::get_primary_color()) + }) + + + data_cutted_r <- reactive({ + req(input$method) + data <- req(data_r()) + variable <- req(input$variable) + + + if (input$method %in% c("day", "weekday", "week", "month", "month_only", "quarter", "year", "hour")) { + breaks <- input$method + } else { + breaks <- breaks_r()$brks + } + + parameters <- list( + x = data[[variable]], + breaks = breaks, + include.lowest = input$include_lowest, + right = input$right + ) + + new_variable <- tryCatch( + { + rlang::exec(cut_var, !!!parameters) + }, + error = function(err) { + showNotification(paste0("We encountered the following error creating your report: ", err), type = "err") + } + ) + + # new_variable <- do.call( + # cut, + # parameters + # ) + + + data <- append_column(data, column = new_variable, name = paste0(variable, "_cut"), index = "right") + + # setNames(paste0(variable, "_cut")) + # + # data <- dplyr::bind_cols(data, new_variable, .name_repair = "unique_quiet") + + # rv$new_var_name <- names(data)[length(data)] + # browser() + + # browser() + code <- rlang::call2( + "append_column", + !!!list( + column = rlang::call2("cut_var", + !!!modifyList(parameters, list(x = as.symbol(paste0("data$", variable)))), + .ns = "FreesearchR"), + name = paste0(variable, "_cut"), index = "right" + ), + .ns = "FreesearchR" + ) + attr(data, "code") <- code + + # attr(data, "code") <- Reduce( + # f = function(x, y) expr(!!x %>% !!y), + # x = c(attr(data, "code"), code) + # ) + data + }) + + output$count <- toastui::renderDatagrid2({ + # shiny::req(rv$new_var_name) + data <- req(data_cutted_r()) + # variable <- req(input$variable) + count_data <- as.data.frame( + table( + breaks = data[[length(data)]], + useNA = "ifany" + ), + responseName = "count" + ) + gridTheme <- getOption("datagrid.theme") + if (length(gridTheme) < 1) { + datamods:::apply_grid_theme() + } + on.exit(toastui::reset_grid_theme()) + grid <- toastui::datagrid( + data = count_data, + colwidths = "guess", + theme = "default", + bodyHeight = "auto" + ) + grid <- toastui::grid_columns(grid, className = "font-monospace") + toastui::grid_colorbar( + grid, + column = "count", + label_outside = TRUE, + label_width = "40px", + bar_bg = datamods:::get_primary_color(), + from = c(0, max(count_data$count) + 1) + ) + }) + + data_returned_r <- observeEvent(input$create, { + rv$data <- data_cutted_r() + }) + return(reactive(rv$data)) + } + ) +} + + + +#' @inheritParams shiny::modalDialog +#' @export +#' +#' @importFrom shiny showModal modalDialog textInput +#' @importFrom htmltools tagList +#' +#' @rdname cut-variable +modal_cut_variable <- function(id, + title = datamods:::i18n("Convert Numeric to Factor"), + easyClose = TRUE, + size = "l", + footer = NULL) { + ns <- NS(id) + showModal(modalDialog( + title = tagList(title, datamods:::button_close_modal()), + cut_variable_ui(id), + tags$div( + style = "display: none;", + textInput(inputId = ns("hidden"), label = NULL, value = datamods:::genId()) + ), + easyClose = easyClose, + size = size, + footer = footer + )) +} + + +#' @importFrom graphics abline axis hist par plot.new plot.window +plot_histogram <- function(data, column=NULL, bins = 30, breaks = NULL, color = "#112466") { + if (is.vector(data)){ + x <- data + } else { + x <- data[[column]] + + } + x <- as.numeric(x) + op <- par(mar = rep(1.5, 4)) + on.exit(par(op)) + plot.new() + plot.window(xlim = range(pretty(x)), ylim = range(pretty(hist(x, breaks = bins, plot = FALSE)$counts))) + abline(v = pretty(x), col = "#D8D8D8") + abline(h = pretty(hist(x, breaks = bins, plot = FALSE)$counts), col = "#D8D8D8") + hist(x, breaks = bins, xlim = range(pretty(x)), xaxs = "i", yaxs = "i", col = color, add = TRUE) + axis(side = 1, at = pretty(x), pos = 0) + axis(side = 2, at = pretty(hist(x, breaks = bins, plot = FALSE)$counts), pos = min(pretty(x))) + abline(v = breaks, col = "#FFFFFF", lty = 1, lwd = 1.5) + abline(v = breaks, col = "#2E2E2E", lty = 2, lwd = 1.5) +} + + + +######## +#### Current file: /Users/au301842/FreesearchR/R//data_plots.R +######## + +# source(here::here("functions.R")) + +#' Data correlations evaluation module +#' +#' @param id Module id. (Use 'ns("id")') +#' +#' @name data-plots +#' @returns Shiny ui module +#' @export +#' +data_visuals_ui <- function(id, tab_title = "Plots", ...) { + ns <- shiny::NS(id) + + # bslib::navset_bar( + list( + + # Sidebar with a slider input + sidebar = bslib::sidebar( + bslib::accordion( + multiple = FALSE, + bslib::accordion_panel( + title = "Creating plot", + icon = bsicons::bs_icon("graph-up"), + shiny::uiOutput(outputId = ns("primary")), + shiny::helpText('Only non-text variables are available for plotting. Go the "Data" to reclass data to plot.'), + shiny::tags$br(), + shiny::uiOutput(outputId = ns("type")), + shiny::uiOutput(outputId = ns("secondary")), + shiny::uiOutput(outputId = ns("tertiary")), + shiny::br(), + shiny::actionButton( + inputId = ns("act_plot"), + label = "Plot", + width = "100%", + icon = shiny::icon("palette"), + disabled = FALSE + ), + shiny::helpText('Adjust settings, then press "Plot".') + ), + # bslib::accordion_panel( + # title = "Advanced", + # icon = bsicons::bs_icon("gear") + # ), + bslib::accordion_panel( + title = "Download", + icon = bsicons::bs_icon("download"), + shinyWidgets::noUiSliderInput( + inputId = ns("height_slide"), + label = "Plot height (mm)", + min = 50, + max = 300, + value = 100, + step = 1, + format = shinyWidgets::wNumbFormat(decimals = 0), + color = datamods:::get_primary_color(), + inline = TRUE + ), + # shiny::numericInput( + # inputId = ns("height_numeric"), + # label = "Plot height (mm)", + # min = 50, + # max = 300, + # value = 100 + # ), + shinyWidgets::noUiSliderInput( + inputId = ns("width"), + label = "Plot width (mm)", + min = 50, + max = 300, + value = 100, + step = 1, + format = shinyWidgets::wNumbFormat(decimals = 0), + color = datamods:::get_primary_color() + ), + shiny::selectInput( + inputId = ns("plot_type"), + label = "File format", + choices = list( + "png", + "tiff", + "eps", + "pdf", + "jpeg", + "svg" + ) + ), + shiny::br(), + # Button + shiny::downloadButton( + outputId = ns("download_plot"), + label = "Download plot", + icon = shiny::icon("download") + ) + ) + ) + ), + bslib::nav_panel( + title = tab_title, + shiny::plotOutput(ns("plot"), height = "70vh"), + shiny::tags$br(), + shiny::tags$br(), + shiny::htmlOutput(outputId = ns("code_plot")) + ) + ) +} + + +#' +#' @param data data +#' @param ... ignored +#' +#' @name data-plots +#' @returns shiny server module +#' @export +data_visuals_server <- function(id, + data, + ...) { + shiny::moduleServer( + id = id, + module = function(input, output, session) { + ns <- session$ns + + rv <- shiny::reactiveValues( + plot.params = NULL, + plot = NULL, + code = NULL + ) + + # ## --- New attempt + # + # rv$plot.params <- shiny::reactive({ + # get_plot_options(input$type) |> purrr::pluck(1) + # }) + # + # c(output, + # list(shiny::renderUI({ + # columnSelectInput( + # inputId = ns("primary"), + # data = data, + # placeholder = "Select variable", + # label = "Response variable", + # multiple = FALSE + # ) + # }), + # shiny::renderUI({ + # shiny::req(input$primary) + # # browser() + # + # if (!input$primary %in% names(data())) { + # plot_data <- data()[1] + # } else { + # plot_data <- data()[input$primary] + # } + # + # plots <- possible_plots( + # data = plot_data + # ) + # + # plots_named <- get_plot_options(plots) |> + # lapply(\(.x){ + # stats::setNames(.x$descr, .x$note) + # }) + # + # vectorSelectInput( + # inputId = ns("type"), + # selected = NULL, + # label = shiny::h4("Plot type"), + # choices = Reduce(c, plots_named), + # multiple = FALSE + # ) + # }), + # shiny::renderUI({ + # shiny::req(input$type) + # + # cols <- c( + # rv$plot.params()[["secondary.extra"]], + # all_but( + # colnames(subset_types( + # data(), + # rv$plot.params()[["secondary.type"]] + # )), + # input$primary + # ) + # ) + # + # columnSelectInput( + # inputId = ns("secondary"), + # data = data, + # selected = cols[1], + # placeholder = "Please select", + # label = if (isTRUE(rv$plot.params()[["secondary.multi"]])) "Additional variables" else "Secondary variable", + # multiple = rv$plot.params()[["secondary.multi"]], + # maxItems = rv$plot.params()[["secondary.max"]], + # col_subset = cols, + # none_label = "No variable" + # ) + # }), + # shiny::renderUI({ + # shiny::req(input$type) + # columnSelectInput( + # inputId = ns("tertiary"), + # data = data, + # placeholder = "Please select", + # label = "Grouping variable", + # multiple = FALSE, + # col_subset = c( + # "none", + # all_but( + # colnames(subset_types( + # data(), + # rv$plot.params()[["tertiary.type"]] + # )), + # input$primary, + # input$secondary + # ) + # ), + # none_label = "No stratification" + # ) + # }) + # )|> setNames(c("primary","type","secondary","tertiary")),keep.null = TRUE) + + + output$primary <- shiny::renderUI({ + shiny::req(data()) + columnSelectInput( + inputId = ns("primary"), + col_subset = names(data())[sapply(data(), data_type) != "text"], + data = data, + placeholder = "Select variable", + label = "Response variable", + multiple = FALSE + ) + }) + + # shiny::observeEvent(data, { + # if (is.null(data()) | NROW(data()) == 0) { + # shiny::updateActionButton(inputId = ns("act_plot"), disabled = TRUE) + # } else { + # shiny::updateActionButton(inputId = ns("act_plot"), disabled = FALSE) + # } + # }) + + + output$type <- shiny::renderUI({ + shiny::req(input$primary) + shiny::req(data()) + # browser() + + if (!input$primary %in% names(data())) { + plot_data <- data()[1] + } else { + plot_data <- data()[input$primary] + } + + plots <- possible_plots( + data = plot_data + ) + + plots_named <- get_plot_options(plots) |> + lapply(\(.x){ + stats::setNames(.x$descr, .x$note) + }) + + vectorSelectInput( + inputId = ns("type"), + selected = NULL, + label = shiny::h4("Plot type"), + choices = Reduce(c, plots_named), + multiple = FALSE + ) + }) + + rv$plot.params <- shiny::reactive({ + get_plot_options(input$type) |> purrr::pluck(1) + }) + + output$secondary <- shiny::renderUI({ + shiny::req(input$type) + + cols <- c( + rv$plot.params()[["secondary.extra"]], + all_but( + colnames(subset_types( + data(), + rv$plot.params()[["secondary.type"]] + )), + input$primary + ) + ) + + columnSelectInput( + inputId = ns("secondary"), + data = data, + selected = cols[1], + placeholder = "Please select", + label = if (isTRUE(rv$plot.params()[["secondary.multi"]])) "Additional variables" else "Secondary variable", + multiple = rv$plot.params()[["secondary.multi"]], + maxItems = rv$plot.params()[["secondary.max"]], + col_subset = cols, + none_label = "No variable" + ) + }) + + output$tertiary <- shiny::renderUI({ + shiny::req(input$type) + columnSelectInput( + inputId = ns("tertiary"), + data = data, + placeholder = "Please select", + label = "Grouping variable", + multiple = FALSE, + col_subset = c( + "none", + all_but( + colnames(subset_types( + data(), + rv$plot.params()[["tertiary.type"]] + )), + input$primary, + input$secondary + ) + ), + none_label = "No stratification" + ) + }) + + shiny::observeEvent(input$act_plot, + { + if (NROW(data()) > 0) { + tryCatch( + { + parameters <- list( + type = rv$plot.params()[["fun"]], + pri = input$primary, + sec = input$secondary, + ter = input$tertiary + ) + + shiny::withProgress(message = "Drawing the plot. Hold tight for a moment..", { + rv$plot <- rlang::exec(create_plot, !!!append_list(data(), parameters, "data")) + }) + + rv$code <- glue::glue("FreesearchR::create_plot(data,{list2str(parameters)})") + }, + # warning = function(warn) { + # showNotification(paste0(warn), type = "warning") + # }, + error = function(err) { + showNotification(paste0(err), type = "err") + } + ) + } + }, + ignoreInit = TRUE + ) + + output$code_plot <- shiny::renderUI({ + shiny::req(rv$code) + prismCodeBlock(paste0("#Plotting\n", rv$code)) + }) + + shiny::observeEvent( + list( + data() + ), + { + shiny::req(data()) + + rv$plot <- NULL + } + ) + + output$plot <- shiny::renderPlot({ + # shiny::req(rv$plot) + # rv$plot + if (!is.null(rv$plot)) { + rv$plot + } else { + return(NULL) + } + }) + + # shiny::observeEvent(input$height_numeric, { + # shinyWidgets::updateNoUiSliderInput(session, ns("height_slide"), value = input$height_numeric) + # }, ignoreInit = TRUE) + # shiny::observeEvent(input$height_slide, { + # shiny::updateNumericInput(session, ns("height_numeric"), value = input$height_slide) + # }, ignoreInit = TRUE) + + + output$download_plot <- shiny::downloadHandler( + filename = shiny::reactive({ + paste0("plot.", input$plot_type) + }), + content = function(file) { + if (inherits(rv$plot,"patchwork")){ + plot <- rv$plot + } else if (inherits(rv$plot,"ggplot")){ + plot <- rv$plot + }else { + plot <- rv$plot[[1]] + + } + # browser() + shiny::withProgress(message = "Drawing the plot. Hold on for a moment..", { + ggplot2::ggsave( + filename = file, + plot = plot, + width = input$width, + height = input$height_slide, + dpi = 300, + units = "mm", scale = 2 + ) + }) + } + ) + + + shiny::observe( + return(rv$plot) + ) + } + ) +} + +#' Select all from vector but +#' +#' @param data vector +#' @param ... exclude +#' +#' @returns vector +#' @export +#' +#' @examples +#' all_but(1:10, c(2, 3), 11, 5) +all_but <- function(data, ...) { + data[!data %in% c(...)] +} + +#' Easily subset by data type function +#' +#' @param data data +#' @param types desired types +#' @param type.fun function to get type. Default is outcome_type +#' +#' @returns vector +#' @export +#' +#' @examples +#' default_parsing(mtcars) |> subset_types("ordinal") +#' default_parsing(mtcars) |> subset_types(c("dichotomous", "categorical")) +#' #' default_parsing(mtcars) |> subset_types("factor",class) +subset_types <- function(data, types, type.fun = data_type) { + data[sapply(data, type.fun) %in% types] +} + + +#' Implemented functions +#' +#' @description +#' Library of supported functions. The list name and "descr" element should be +#' unique for each element on list. +#' +#' - descr: Plot description +#' +#' - primary.type: Primary variable data type (continuous, dichotomous or ordinal) +#' +#' - secondary.type: Secondary variable data type (continuous, dichotomous or ordinal) +#' +#' - secondary.extra: "none" or NULL to have option to choose none. +#' +#' - tertiary.type: Tertiary variable data type (continuous, dichotomous or ordinal) +#' +#' +#' @returns list +#' @export +#' +#' @examples +#' supported_plots() |> str() +supported_plots <- function() { + list( + plot_hbars = list( + fun = "plot_hbars", + descr = "Stacked horizontal bars", + note = "A classical way of visualising the distribution of an ordinal scale like the modified Ranking Scale and known as Grotta bars", + primary.type = c("dichotomous", "categorical"), + secondary.type = c("dichotomous", "categorical"), + secondary.multi = FALSE, + tertiary.type = c("dichotomous", "categorical"), + secondary.extra = "none" + ), + plot_violin = list( + fun = "plot_violin", + descr = "Violin plot", + note = "A modern alternative to the classic boxplot to visualise data distribution", + primary.type = c("datatime", "continuous", "dichotomous", "categorical"), + secondary.type = c("dichotomous", "categorical"), + secondary.multi = FALSE, + secondary.extra = "none", + tertiary.type = c("dichotomous", "categorical") + ), + # plot_ridge = list( + # descr = "Ridge plot", + # note = "An alternative option to visualise data distribution", + # primary.type = "continuous", + # secondary.type = c("dichotomous" ,"categorical"), + # tertiary.type = c("dichotomous" ,"categorical"), + # secondary.extra = NULL + # ), + plot_sankey = list( + fun = "plot_sankey", + descr = "Sankey plot", + note = "A way of visualising change between groups", + primary.type = c("dichotomous", "categorical"), + secondary.type = c("dichotomous", "categorical"), + secondary.multi = FALSE, + secondary.extra = NULL, + tertiary.type = c("dichotomous", "categorical") + ), + plot_scatter = list( + fun = "plot_scatter", + descr = "Scatter plot", + note = "A classic way of showing the association between to variables", + primary.type = c("datatime", "continuous"), + secondary.type = c("datatime", "continuous", "categorical"), + secondary.multi = FALSE, + tertiary.type = c("dichotomous", "categorical"), + secondary.extra = NULL + ), + plot_box = list( + fun = "plot_box", + descr = "Box plot", + note = "A classic way to plot data distribution by groups", + primary.type = c("datatime", "continuous", "dichotomous", "categorical"), + secondary.type = c("dichotomous", "categorical"), + secondary.multi = FALSE, + tertiary.type = c("dichotomous", "categorical"), + secondary.extra = "none" + ), + plot_euler = list( + fun = "plot_euler", + descr = "Euler diagram", + note = "Generate area-proportional Euler diagrams to display set relationships", + primary.type = c("dichotomous", "categorical"), + secondary.type = c("dichotomous", "categorical"), + secondary.multi = TRUE, + secondary.max = 4, + tertiary.type = c("dichotomous", "categorical"), + secondary.extra = NULL + ) + ) +} + +#' Get possible regression models +#' +#' @param data data +#' +#' @returns character vector +#' @export +#' +#' @examples +#' mtcars |> +#' default_parsing() |> +#' dplyr::pull("cyl") |> +#' possible_plots() +#' +#' mtcars |> +#' default_parsing() |> +#' dplyr::select("mpg") |> +#' possible_plots() +possible_plots <- function(data) { + # browser() + # data <- if (is.reactive(data)) data() else data + if (is.data.frame(data)) { + data <- data[[1]] + } + + type <- data_type(data) + + if (type == "unknown") { + out <- type + } else { + out <- supported_plots() |> + lapply(\(.x){ + if (type %in% .x$primary.type) { + .x$descr + } + }) |> + unlist() + } + unname(out) +} + +#' Get the function options based on the selected function description +#' +#' @param data vector +#' +#' @returns list +#' @export +#' +#' @examples +#' ls <- mtcars |> +#' default_parsing() |> +#' dplyr::pull(mpg) |> +#' possible_plots() |> +#' (\(.x){ +#' .x[[1]] +#' })() |> +#' get_plot_options() +get_plot_options <- function(data) { + descrs <- supported_plots() |> + lapply(\(.x){ + .x$descr + }) |> + unlist() + supported_plots() |> + (\(.x){ + .x[match(data, descrs)] + })() +} + + + +#' Wrapper to create plot based on provided type +#' +#' @param data data.frame +#' @param pri primary variable +#' @param sec secondary variable +#' @param ter tertiary variable +#' @param type plot type (derived from possible_plots() and matches custom function) +#' @param ... ignored for now +#' +#' @name data-plots +#' +#' @returns ggplot2 object +#' @export +#' +#' @examples +#' create_plot(mtcars, "plot_violin", "mpg", "cyl") |> attributes() +create_plot <- function(data, type, pri, sec, ter = NULL, ...) { + if (!is.null(sec)) { + if (!any(sec %in% names(data))) { + sec <- NULL + } + } + + if (!is.null(ter)) { + if (!ter %in% names(data)) { + ter <- NULL + } + } + + parameters <- list( + pri = pri, + sec = sec, + ter = ter, + ... + ) + + out <- do.call( + type, + modifyList(parameters,list(data=data)) + ) + + code <- rlang::call2(type,!!!parameters,.ns = "FreesearchR") + + attr(out,"code") <- code + out +} + +#' Print label, and if missing print variable name +#' +#' @param data vector or data frame +#' @param var variable name. Optional. +#' +#' @returns character string +#' @export +#' +#' @examples +#' mtcars |> get_label(var = "mpg") +#' mtcars |> get_label() +#' mtcars$mpg |> get_label() +#' gtsummary::trial |> get_label(var = "trt") +#' gtsummary::trial$trt |> get_label() +#' 1:10 |> get_label() +get_label <- function(data, var = NULL) { + # data <- if (is.reactive(data)) data() else data + if (!is.null(var) & is.data.frame(data)) { + data <- data[[var]] + } + out <- REDCapCAST::get_attr(data = data, attr = "label") + if (is.na(out)) { + if (is.null(var)) { + out <- deparse(substitute(data)) + } else { + if (is.symbol(var)) { + out <- gsub('\"', "", deparse(substitute(var))) + } else { + out <- var + } + } + } + out +} + + +#' Line breaking at given number of characters for nicely plotting labels +#' +#' @param data string +#' @param lineLength maximum line length +#' @param fixed flag to force split at exactly the value given in lineLength. +#' Default is FALSE, only splitting at spaces. +#' +#' @returns character string +#' @export +#' +#' @examples +#' "Lorem ipsum... you know the routine" |> line_break() +#' paste(sample(letters[1:10], 100, TRUE), collapse = "") |> line_break(force = TRUE) +line_break <- function(data, lineLength = 20, force = FALSE) { + if (isTRUE(force)) { + gsub(paste0("(.{1,", lineLength, "})(\\s|[[:alnum:]])"), "\\1\n", data) + } else { + paste(strwrap(data, lineLength), collapse = "\n") + } + ## https://stackoverflow.com/a/29847221 +} + + +#' Wrapping +#' +#' @param data list of ggplot2 objects +#' @param tag_levels passed to patchwork::plot_annotation if given. Default is NULL +#' +#' @returns list of ggplot2 objects +#' @export +#' +wrap_plot_list <- function(data, tag_levels = NULL) { + if (ggplot2::is_ggplot(data[[1]])) { + if (length(data) > 1) { + out <- data |> + (\(.x){ + if (rlang::is_named(.x)) { + purrr::imap(.x, \(.y, .i){ + .y + ggplot2::ggtitle(.i) + }) + } else { + .x + } + })() |> + align_axes() |> + patchwork::wrap_plots(guides = "collect", axes = "collect", axis_titles = "collect") + if (!is.null(tag_levels)) { + out <- out + patchwork::plot_annotation(tag_levels = tag_levels) + } + } else { + out <- data + } + } else { + cli::cli_abort("Can only wrap lists of {.cls ggplot} objects") + } + out +} + + +#' Aligns axes between plots +#' +#' @param ... ggplot2 objects or list of ggplot2 objects +#' +#' @returns list of ggplot2 objects +#' @export +#' +align_axes <- function(...) { + # https://stackoverflow.com/questions/62818776/get-axis-limits-from-ggplot-object + # https://github.com/thomasp85/patchwork/blob/main/R/plot_multipage.R#L150 + if (ggplot2::is_ggplot(..1)) { + ## Assumes list of ggplots + p <- list(...) + } else if (is.list(..1)) { + ## Assumes list with list of ggplots + p <- ..1 + } else { + cli::cli_abort("Can only align {.cls ggplot} objects or a list of them") + } + + yr <- clean_common_axis(p, "y") + + xr <- clean_common_axis(p, "x") + + suppressWarnings({ + p |> purrr::map(~ .x + ggplot2::xlim(xr) + ggplot2::ylim(yr)) + }) +} + +#' Extract and clean axis ranges +#' +#' @param p plot +#' @param axis axis. x or y. +#' +#' @returns vector +#' @export +#' +clean_common_axis <- function(p, axis) { + purrr::map(p, ~ ggplot2::layer_scales(.x)[[axis]]$get_limits()) |> + unlist() |> + (\(.x){ + if (is.numeric(.x)) { + range(.x) + } else { + as.character(.x) + } + })() |> + unique() +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//data-import.R +######## + +data_import_ui <- function(id) { + ns <- shiny::NS(id) + + shiny::fluidRow( + shiny::column(width = 2), + shiny::column( + width = 8, + shiny::h4("Choose your data source"), + shiny::br(), + shinyWidgets::radioGroupButtons( + inputId = "source", + selected = "env", + choices = c( + "File upload" = "file", + "REDCap server export" = "redcap", + "Local or sample data" = "env" + ), + width = "100%" + ), + shiny::helpText("Upload a file from your device, get data directly from REDCap or select a sample data set for testing from the app."), + shiny::br(), + shiny::br(), + shiny::conditionalPanel( + condition = "input.source=='file'", + import_file_ui( + id = ns("file_import"), + layout_params = "dropdown", + title = "Choose a datafile to upload", + file_extensions = c(".csv", ".tsv", ".txt", ".xls", ".xlsx", ".rds", ".sas7bdat", ".ods", ".dta") + ) + ), + shiny::conditionalPanel( + condition = "input.source=='redcap'", + m_redcap_readUI(id = ns("redcap_import")) + ), + shiny::conditionalPanel( + condition = "input.source=='env'", + datamods::import_globalenv_ui(id = ns("env"), title = NULL) + ), + shiny::conditionalPanel( + condition = "input.source=='redcap'", + DT::DTOutput(outputId = ns("redcap_prev")) + ) + ) + ) + } + + +data_import_server <- function(id) { + module <- function(input, output, session) { + ns <- session$ns + + rv <- shiny::reactiveValues( + data_temp = NULL, + code = list() + ) + + data_file <- import_file_server( + id = ns("file_import"), + show_data_in = "popup", + trigger_return = "change", + return_class = "data.frame" + ) + + shiny::observeEvent(data_file$data(), { + shiny::req(data_file$data()) + + rv$data_temp <- data_file$data() + rv$code <- append_list(data = data_file$code(), list = rv$code, index = "import") + }) + + data_redcap <- m_redcap_readServer( + id = "redcap_import" + ) + + shiny::observeEvent(data_redcap(), { + # rv$data_original <- purrr::pluck(data_redcap(), "data")() + rv$data_temp <- data_redcap() + }) + + from_env <- datamods::import_globalenv_server( + id = "env", + trigger_return = "change", + btn_show_data = FALSE, + reset = reactive(input$hidden) + ) + + shiny::observeEvent(from_env$data(), { + shiny::req(from_env$data()) + + rv$data_temp <- from_env$data() + # rv$code <- append_list(data = from_env$code(),list = rv$code,index = "import") + }) + + return(list( + # status = reactive(temporary_rv$status), + # name = reactive(temporary_rv$name), + # code = reactive(temporary_rv$code), + data = shiny::reactive(rv$data_temp) + )) + + } + + shiny::moduleServer( + id = id, + module = module + ) + + } + + +#' Test app for the data-import module +#' +#' @rdname data-import +#' +#' @examples +#' \dontrun{ +#' data_import_demo_app() +#' } +data_import_demo_app <- function() { + ui <- shiny::fluidPage( + data_import_ui("data_import"), + toastui::datagridOutput2(outputId = "table"), + DT::DTOutput("data_summary") + ) + server <- function(input, output, session) { + imported <- shiny::reactive(data_import_server(id = "data_import")) + + # output$data_summary <- DT::renderDataTable( + # { + # shiny::req(data_val$data) + # data_val$data + # }, + # options = list( + # scrollX = TRUE, + # pageLength = 5 + # ) + # ) + output$table <- toastui::renderDatagrid2({ + req(imported$data) + toastui::datagrid( + data = head(imported$data, 5), + theme = "striped", + colwidths = "guess", + minBodyHeight = 250 + ) + }) + + } + shiny::shinyApp(ui, server) +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//data-summary.R +######## + +#' Data summary module +#' +#' @param id Module id. (Use 'ns("id")') +#' +#' @name data-summary +#' @returns Shiny ui module +#' @export +data_summary_ui <- function(id) { + ns <- NS(id) + + toastui::datagridOutput(outputId = ns("tbl_summary")) +} + + +#' +#' @param data data +#' @param color.main main color +#' @param color.sec secondary color +#' @param ... arguments passed to create_overview_datagrid +#' +#' @name data-summary +#' @returns shiny server module +#' @export +data_summary_server <- function(id, + data, + color.main, + color.sec, + ...) { + shiny::moduleServer( + id = id, + module = function(input, output, session) { + ns <- session$ns + + output$tbl_summary <- + toastui::renderDatagrid( + { + shiny::req(data()) + data() |> + overview_vars() |> + create_overview_datagrid(...) |> + add_sparkline( + column = "vals", + color.main = color.main, + color.sec = color.sec + ) + } + ) + + } + ) +} + +#' Add sparkline to datagrid +#' +#' @param grid grid +#' @param column clumn to transform +#' +#' @returns datagrid +#' @export +#' +#' @examples +#' grid <- mtcars |> +#' default_parsing() |> +#' overview_vars() |> +#' toastui::datagrid() |> +#' add_sparkline() +#' grid +add_sparkline <- function(grid, column = "vals", color.main = "#2a8484", color.sec = "#84EF84") { + out <- toastui::grid_sparkline( + grid = grid, + column = column, + renderer = function(data) { + data_cl <- class(data) + if (all(sapply(data,is.na))){ + type <- "line" + ds <- data.frame(x = NA, y = NA) + horizontal <- FALSE + } else if (identical(data_cl, "factor")) { + type <- "column" + s <- summary(data) + ds <- data.frame(x = names(s), y = s) + horizontal <- FALSE + } else if (identical(data_cl, "logical")) { + type <- "column" + s <- table(data) + ds <- data.frame(x = names(s), y = as.vector(s)) + horizontal <- FALSE + } else if (any(c("numeric", "integer") %in% data_cl)) { + if (is_consecutive(data)) { + type <- "line" + ds <- data.frame(x = NA, y = NA) + horizontal <- FALSE + } else { + type <- "box" + ds <- data.frame(x = 1, y = data) + horizontal <- TRUE + } + } else if (any(c("Date", "POSIXct", "POSIXt", "hms", "difftime") %in% data_cl)) { + type <- "line" + ds <- data.frame(x = seq_along(data), y = data) + horizontal <- FALSE + } else { + type <- "line" + ds <- data.frame(x = NA, y = NA) + horizontal <- FALSE + } + apexcharter::apex( + ds, + apexcharter::aes(x, y), + type = type, + auto_update = TRUE + ) |> + apexcharter::ax_chart(sparkline = list(enabled = TRUE)) |> + apexcharter::ax_plotOptions( + boxPlot = apexcharter::boxplot_opts(color.upper = color.sec, color.lower = color.main), + bar = apexcharter::bar_opts(horizontal = horizontal) + ) |> + apexcharter::ax_colors( + c(color.main, color.sec) + ) + } + ) + + toastui::grid_columns( + grid = out, + columns = column, + minWidth = 200 + ) +} + +#' Checks if elements in vector are equally spaced as indication of ID +#' +#' @param data vector +#' +#' @returns logical +#' @export +#' +#' @examples +#' 1:10 |> is_consecutive() +#' sample(1:100,40) |> is_consecutive() +is_consecutive <- function(data){ + suppressWarnings(length(unique(diff(as.numeric(data))))==1) +} + +#' Create a data overview data.frame ready for sparklines +#' +#' @param data data +#' +#' @returns data.frame +#' @export +#' +#' @examples +#' mtcars |> overview_vars() +overview_vars <- function(data) { + data <- as.data.frame(data) + + dplyr::tibble( + icon = get_classes(data), + class = icon, + name = names(data), + n_missing = unname(colSums(is.na(data))), + p_complete = 1 - n_missing / nrow(data), + n_unique = get_n_unique(data), + vals = as.list(data) + ) +} + +#' Create a data overview datagrid +#' +#' @param data data +#' +#' @returns datagrid +#' @export +#' +#' @examples +#' mtcars |> +#' overview_vars() |> +#' create_overview_datagrid() +create_overview_datagrid <- function(data,...) { + # browser() + gridTheme <- getOption("datagrid.theme") + if (length(gridTheme) < 1) { + datamods:::apply_grid_theme() + } + on.exit(toastui::reset_grid_theme()) + + col.names <- names(data) + + std_names <- c( + "Name" = "name", + "Icon" = "icon", + "Class" = "class", + "Type" = "type", + "Missings" = "n_missing", + "Complete" = "p_complete", + "Unique" = "n_unique", + "Distribution" = "vals" + ) + + headers <- lapply(col.names, \(.x){ + if (.x %in% std_names) { + names(std_names)[match(.x, std_names)] + } else { + .x + } + }) |> unlist() + + grid <- toastui::datagrid( + data = data, + theme = "default", + colwidths = "fit", + ... + ) + + grid <- toastui::grid_columns( + grid = grid, + columns = col.names, + header = headers, + resizable = TRUE + ) + + grid <- toastui::grid_columns( + grid = grid, + columns = "vals", + width = 120 + ) + + grid <- toastui::grid_columns( + grid = grid, + columns = "icon", + header = " ", + align = "center",sortable = FALSE, + width = 40 + ) + + grid <- add_class_icon( + grid = grid, + column = "icon", + fun = class_icons + ) + + grid <- toastui::grid_format( + grid = grid, + "p_complete", + formatter = toastui::JS("function(obj) {return (obj.value*100).toFixed(0) + '%';}") + ) + + ## This could obviously be extended, which will added even more complexity. + + grid <- toastui::grid_filters( + grid = grid, + column = "name", + # columns = unname(std_names[std_names!="vals"]), + showApplyBtn = FALSE, + showClearBtn = TRUE, + type = "text" + ) + + + return(grid) +} + +#' Convert class grid column to icon +#' +#' @param grid grid +#' @param column column +#' +#' @returns datagrid +#' @export +#' +#' @examples +#' mtcars |> +#' overview_vars() |> +#' toastui::datagrid() |> +#' add_class_icon() +add_class_icon <- function(grid, column = "class", fun=class_icons) { + out <- toastui::grid_format( + grid = grid, + column = column, + formatter = function(value) { + lapply( + X = value, + FUN = fun + ) + } + ) + + toastui::grid_columns( + grid = out, + header = NULL, + columns = column, + width = 60 + ) +} + + +#' Get data class icons +#' +#' @param x character vector of data classes +#' +#' @returns list +#' @export +#' +#' @examples +#' "numeric" |> class_icons()|> str() +#' mtcars |> sapply(class) |> class_icons() |> str() +class_icons <- function(x) { + if (length(x)>1){ + lapply(x,class_icons) + } else { + if (identical(x, "numeric")) { + shiny::icon("calculator") + } else if (identical(x, "factor")) { + shiny::icon("chart-simple") + } else if (identical(x, "integer")) { + shiny::icon("arrow-down-1-9") + } else if (identical(x, "character")) { + shiny::icon("arrow-down-a-z") + } else if (identical(x, "logical")) { + shiny::icon("toggle-off") + } else if (any(c("Date", "POSIXt") %in% x)) { + shiny::icon("calendar-days") + } else if (any("POSIXct", "hms") %in% x) { + shiny::icon("clock") + } else { + shiny::icon("table") + }} +} + +#' Get data type icons +#' +#' @param x character vector of data classes +#' +#' @returns list +#' @export +#' +#' @examples +#' "ordinal" |> type_icons() +#' default_parsing(mtcars) |> sapply(data_type) |> type_icons() +type_icons <- function(x) { + if (length(x)>1){ + lapply(x,class_icons) + } else { + if (identical(x, "continuous")) { + shiny::icon("calculator") + } else if (identical(x, "categorical")) { + shiny::icon("chart-simple") + } else if (identical(x, "ordinal")) { + shiny::icon("arrow-down-1-9") + } else if (identical(x, "text")) { + shiny::icon("arrow-down-a-z") + } else if (identical(x, "dichotomous")) { + shiny::icon("toggle-off") + } else if (identical(x,"datetime")) { + shiny::icon("calendar-days") + } else if (identical(x,"id")) { + shiny::icon("id-card") + } else { + shiny::icon("table") + } + } +} + +#' Easily get variable icon based on data type or class +#' +#' @param data variable or data frame +#' @param class.type "type" or "class". Default is "class" +#' +#' @returns svg icon +#' @export +#' +#' @examples +#' mtcars[1] |> get_var_icon("class") +#' default_parsing(mtcars) |> get_var_icon() +get_var_icon <- function(data,class.type=c("class","type")){ + if (is.data.frame(data)){ + lapply(data,get_var_icon) + } else { + + class.type <- match.arg(class.type) + + switch(class.type, + type = { + type_icons(data_type(data)) + }, + class = { + class(data)[1] |> class_icons() + } + ) +} + +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//datagrid-infos-mod.R +######## + + +#' Display a table in a window +#' +#' @param data a data object (either a `matrix` or a `data.frame`). +#' @param title Title to be displayed in window. +#' @param show_classes Show variables classes under variables names in table header. +#' @param type Display table in a pop-up with [shinyWidgets::show_alert()], +#' in modal window with [shiny::showModal()] or in a WinBox window with [shinyWidgets::WinBox()]. +#' @param options Arguments passed to [toastui::datagrid()]. +#' @param width Width of the window, only used if `type = "popup"` or `type = "winbox"`. +#' @param ... Additional options, such as `wbOptions = wbOptions()` or `wbControls = wbControls()`. +#' +#' @note +#' If you use `type = "winbox"`, you'll need to use `shinyWidgets::html_dependency_winbox()` somewhere in your UI. +#' +#' @return No value. +#' @export +#' +show_data <- function(data, + title = NULL, + options = NULL, + show_classes = TRUE, + type = c("popup", "modal", "winbox"), + width = "65%", + ...) { # nocov start + type <- match.arg(type) + data <- as.data.frame(data) + args <- list(...) + gridTheme <- getOption("datagrid.theme") + if (length(gridTheme) < 1) { + datamods:::apply_grid_theme() + } + on.exit(toastui::reset_grid_theme()) + + if (is.null(options)) + options <- list() + + options$height <- 500 + options$minBodyHeight <- 400 + options$data <- data + options$theme <- "default" + options$colwidths <- "guess" + options$guess_colwidths_opts <- list(min_width = 90, max_width = 400, mul = 1, add = 10) + if (isTRUE(show_classes)) + options$summary <- construct_col_summary(data) + datatable <- rlang::exec(toastui::datagrid, !!!options) + datatable <- toastui::grid_columns(datatable, className = "font-monospace") + if (identical(type, "winbox")) { + stopifnot( + "You need shinyWidgets >= 0.8.4" = packageVersion("shinyWidgets") >= "0.8.4" + ) + wb_options <- if (is.null(args$wbOptions)) { + shinyWidgets::wbOptions( + height = "600px", + width = width, + modal = TRUE + ) + } else { + modifyList( + shinyWidgets::wbOptions( + height = "600px", + width = width, + modal = TRUE + ), + args$wbOptions + ) + } + wb_controls <- if (is.null(args$wbControls)) { + shinyWidgets::wbControls() + } else { + args$wbControls + } + shinyWidgets::WinBox( + title = title, + ui = datatable, + options = wb_options, + controls = wb_controls, + padding = "0 5px" + ) + } else if (identical(type, "popup")) { + shinyWidgets::show_alert( + title = NULL, + text = tags$div( + if (!is.null(title)) { + tagList( + tags$h3(title), + tags$hr() + ) + }, + style = "color: #000 !important;", + datatable + ), + closeOnClickOutside = TRUE, + showCloseButton = TRUE, + btn_labels = NA, + html = TRUE, + width = width + ) + } else { + showModal(modalDialog( + title = tagList( + datamods:::button_close_modal(), + title + ), + tags$div( + style = htmltools::css(minHeight = htmltools::validateCssUnit(options$height)), + toastui::renderDatagrid2(datatable) + ), + size = "xl", + footer = NULL, + easyClose = TRUE + )) + } +} # nocov end + + + +#' @importFrom htmltools tagList tags css +describe_col_char <- function(x, with_summary = TRUE) { + tags$div( + style = htmltools::css(padding = "3px 0", fontSize = "x-small"), + tags$div( + style = htmltools::css(fontStyle = "italic"), + get_var_icon(x), + # phosphoricons::ph("text-aa"), + "character" + ), + if (with_summary) { + tagList( + tags$hr(style = htmltools::css(margin = "3px 0")), + tags$div( + datamods:::i18n("Unique:"), length(unique(x)) + ), + tags$div( + datamods:::i18n("Missing:"), sum(is.na(x)) + ), + tags$div( + style = htmltools::css(whiteSpace = "normal", wordBreak = "break-all"), + datamods:::i18n("Most Common:"), gsub( + pattern = "'", + replacement = "\u07F4", + x = names(sort(table(x), decreasing = TRUE))[1] + ) + ), + tags$div( + "\u00A0" + ) + ) + } + ) +} + +fmt_p <- function(val, tot) { + paste0(round(val / tot * 100, 1), "%") +} + +describe_col_factor <- function(x, with_summary = TRUE) { + count <- sort(table(x, useNA = "always"), decreasing = TRUE) + total <- sum(count) + one <- count[!is.na(names(count))][1] + two <- count[!is.na(names(count))][2] + missing <- count[is.na(names(count))] + tags$div( + style = htmltools::css(padding = "3px 0", fontSize = "x-small"), + tags$div( + style = htmltools::css(fontStyle = "italic"), + get_var_icon(x), + # phosphoricons::ph("list-bullets"), + "factor" + ), + if (with_summary) { + tagList( + tags$hr(style = htmltools::css(margin = "3px 0")), + tags$div( + names(one), ":", fmt_p(one, total) + ), + tags$div( + names(two), ":", fmt_p(two, total) + ), + tags$div( + "Missing", ":", fmt_p(missing, total) + ), + tags$div( + "\u00A0" + ) + ) + } + ) +} + +describe_col_num <- function(x, with_summary = TRUE) { + tags$div( + style = htmltools::css(padding = "3px 0", fontSize = "x-small"), + tags$div( + style = htmltools::css(fontStyle = "italic"), + get_var_icon(x), + # phosphoricons::ph("hash"), + "numeric" + ), + if (with_summary) { + tagList( + tags$hr(style = htmltools::css(margin = "3px 0")), + tags$div( + datamods:::i18n("Min:"), round(min(x, na.rm = TRUE), 2) + ), + tags$div( + datamods:::i18n("Mean:"), round(mean(x, na.rm = TRUE), 2) + ), + tags$div( + datamods:::i18n("Max:"), round(max(x, na.rm = TRUE), 2) + ), + tags$div( + datamods:::i18n("Missing:"), sum(is.na(x)) + ) + ) + } + ) +} + + +describe_col_date <- function(x, with_summary = TRUE) { + tags$div( + style = htmltools::css(padding = "3px 0", fontSize = "x-small"), + tags$div( + style = htmltools::css(fontStyle = "italic"), + get_var_icon(x), + # phosphoricons::ph("calendar"), + "date" + ), + if (with_summary) { + tagList( + tags$hr(style = htmltools::css(margin = "3px 0")), + tags$div( + datamods:::i18n("Min:"), min(x, na.rm = TRUE) + ), + tags$div( + datamods:::i18n("Max:"), max(x, na.rm = TRUE) + ), + tags$div( + datamods:::i18n("Missing:"), sum(is.na(x)) + ), + tags$div( + "\u00A0" + ) + ) + } + ) +} + +describe_col_datetime <- function(x, with_summary = TRUE) { + tags$div( + style = htmltools::css(padding = "3px 0", fontSize = "x-small"), + tags$div( + style = htmltools::css(fontStyle = "italic"), + get_var_icon(x), + # phosphoricons::ph("clock"), + "datetime" + ), + if (with_summary) { + tagList( + tags$hr(style = htmltools::css(margin = "3px 0")), + tags$div( + datamods:::i18n("Min:"), min(x, na.rm = TRUE) + ), + tags$div( + datamods:::i18n("Max:"), max(x, na.rm = TRUE) + ), + tags$div( + datamods:::i18n("Missing:"), sum(is.na(x)) + ), + tags$div( + "\u00A0" + ) + ) + } + ) +} + + +describe_col_other <- function(x, with_summary = TRUE) { + tags$div( + style = htmltools::css(padding = "3px 0", fontSize = "x-small"), + tags$div( + style = htmltools::css(fontStyle = "italic"), + get_var_icon(x), + # phosphoricons::ph("clock"), + paste(class(x), collapse = ", ") + ), + if (with_summary) { + tagList( + tags$hr(style = htmltools::css(margin = "3px 0")), + tags$div( + datamods:::i18n("Unique:"), length(unique(x)) + ), + tags$div( + datamods:::i18n("Missing:"), sum(is.na(x)) + ), + tags$div( + "\u00A0" + ), + tags$div( + "\u00A0" + ) + ) + } + ) +} + +construct_col_summary <- function(data) { + list( + position = "top", + height = 90, + columnContent = lapply( + X = setNames(names(data), names(data)), + FUN = function(col) { + values <- data[[col]] + content <- if (inherits(values, "character")) { + describe_col_char(values) + } else if (inherits(values, "factor")) { + describe_col_factor(values) + } else if (inherits(values, c("numeric", "integer"))) { + describe_col_num(values) + } else if (inherits(values, c("Date"))) { + describe_col_date(values) + } else if (inherits(values, c("POSIXt"))) { + describe_col_datetime(values) + } else { + describe_col_other(values) + } + list( + template = toastui::JS( + "function(value) {", + sprintf( + "return '%s';", + gsub(replacement = "", pattern = "\n", x = htmltools::doRenderTags(content)) + ), + "}" + ) + ) + } + ) + ) +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//helpers.R +######## + +#' Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' +#' +#' @description +#' This function follows the idea from this comment: https://stackoverflow.com/questions/38983179/do-call-a-function-in-r-without-loading-the-package +#' @param x function or function name +#' +#' @return function or character vector +#' @export +#' +#' @examples +#' getfun("stats::lm") +getfun <- function(x) { + if ("character" %in% class(x)) { + if (length(grep("::", x)) > 0) { + parts <- strsplit(x, "::")[[1]] + requireNamespace(parts[1]) + getExportedValue(parts[1], parts[2]) + } + } else { + x + } +} + +#' Wrapper to save data in RDS, load into specified qmd and render +#' +#' @param data list to pass to qmd +#' @param ... Passed to `quarto::quarto_render()` +#' +#' @return output file name +#' @export +#' +write_quarto <- function(data, ...) { + # Exports data to temporary location + # + # I assume this is more secure than putting it in the www folder and deleting + # on session end + + # temp <- base::tempfile(fileext = ".rds") + # readr::write_rds(data, file = here) + + readr::write_rds(data, file = "www/web_data.rds") + + ## Specifying a output path will make the rendering fail + ## Ref: https://github.com/quarto-dev/quarto-cli/discussions/4041 + ## Outputs to the same as the .qmd file + quarto::quarto_render( + execute_params = list(data.file = "web_data.rds"), + # execute_params = list(data.file = temp), + ... + ) +} + +write_rmd <- function(data, ..., params.args=NULL) { + # Exports data to temporary location + # + # I assume this is more secure than putting it in the www folder and deleting + # on session end + + # temp <- base::tempfile(fileext = ".rds") + # readr::write_rds(data, file = here) + + readr::write_rds(data, file = "www/web_data.rds") + + ## Specifying a output path will make the rendering fail + ## Ref: https://github.com/quarto-dev/quarto-cli/discussions/4041 + ## Outputs to the same as the .qmd file + rmarkdown::render( + params = modifyList(list(data.file = "web_data.rds",version=app_version()),params.args), + # execute_params = list(data.file = temp), + ... + ) +} + +#' Flexible file import based on extension +#' +#' @param file file name +#' @param consider.na character vector of strings to consider as NAs +#' +#' @return tibble +#' @export +#' +#' @examples +#' read_input("https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/data/sample.csv") +read_input <- function(file, consider.na = c("NA", '""', "")) { + ext <- tools::file_ext(file) + + if (ext == "csv") { + df <- readr::read_csv(file = file, na = consider.na) + } else if (ext %in% c("xls", "xlsx")) { + df <- readxl::read_excel(file = file, na.strings = consider.na) + } else if (ext == "dta") { + df <- haven::read_dta(file = file) + } else if (ext == "ods") { + df <- readODS::read_ods(path = file) + } else if (ext == "rds") { + df <- readr::read_rds(file = file) + } else { + stop("Input file format has to be on of: + '.csv', '.xls', '.xlsx', '.dta', '.ods' or '.rds'") + } + + df +} + +#' Convert string of arguments to list of arguments +#' +#' @description +#' Idea from the answer: https://stackoverflow.com/a/62979238 +#' +#' @param string string to convert to list to use with do.call +#' +#' @return list +#' @export +#' +#' @examples +#' argsstring2list("A=1:5,b=2:4") +#' +argsstring2list <- function(string) { + eval(parse(text = paste0("list(", string, ")"))) +} + + +#' Factorize variables in data.frame +#' +#' @param data data.frame +#' @param vars variables to force factorize +#' +#' @return data.frame +#' @export +#' +#' @examples +#' factorize(mtcars, names(mtcars)) +factorize <- function(data, vars) { + if (!is.null(vars)) { + data |> + dplyr::mutate( + dplyr::across( + dplyr::all_of(vars), + REDCapCAST::as_factor + ) + ) + } else { + data + } +} + +dummy_Imports <- function() { + list( + MASS::as.fractions(), + broom::augment(), + broom.helpers::all_categorical(), + here::here(), + cardx::all_of(), + parameters::ci(), + DT::addRow(), + bslib::accordion() + ) + # https://github.com/hadley/r-pkgs/issues/828 +} + + +#' Title +#' +#' @param data data +#' @param output.format output +#' @param filename filename +#' @param ... passed on +#' +#' @returns data +#' @export +#' +file_export <- function(data, output.format = c("df", "teal", "list"), filename, ...) { + output.format <- match.arg(output.format) + + filename <- gsub("-", "_", filename) + + if (output.format == "teal") { + out <- within( + teal_data(), + { + assign(name, value |> + dplyr::bind_cols(.name_repair = "unique_quiet") |> + default_parsing()) + }, + value = data, + name = filename + ) + + datanames(out) <- filename + } else if (output.format == "df") { + out <- data |> + default_parsing() + } else if (output.format == "list") { + out <- list( + data = data, + name = filename + ) + + out <- c(out, ...) + } + + out +} + + +#' Default data parsing +#' +#' @param data data +#' +#' @returns data.frame or tibble +#' @export +#' +#' @examples +#' mtcars |> str() +#' mtcars |> +#' default_parsing() |> +#' str() +#' head(starwars, 5) |> str() +#' starwars |> +#' default_parsing() |> +#' head(5) |> +#' str() +default_parsing <- function(data) { + name_labels <- lapply(data, \(.x) REDCapCAST::get_attr(.x, attr = "label")) + # browser() + out <- data |> + setNames(make.names(names(data), unique = TRUE)) |> + ## Temporary step to avoid nested list and crashing + remove_nested_list() |> + REDCapCAST::parse_data() |> + REDCapCAST::as_factor() |> + REDCapCAST::numchar2fct(numeric.threshold = 8, character.throshold = 10) |> + REDCapCAST::as_logical() |> + REDCapCAST::fct_drop() + + set_column_label(out, setNames(name_labels, names(out)), overwrite = FALSE) + + # purrr::map2( + # out, + # name_labels[names(name_labels) %in% names(out)], + # \(.x, .l){ + # if (!(is.na(.l) | .l == "")) { + # REDCapCAST::set_attr(.x, .l, attr = "label") + # } else { + # attr(x = .x, which = "label") <- NULL + # .x + # } + # # REDCapCAST::set_attr(data = .x, label = .l,attr = "label", overwrite = FALSE) + # } + # ) |> dplyr::bind_cols() +} + +#' Remove empty/NA attributes +#' +#' @param data data +#' +#' @returns data of same class as input +#' @export +#' +#' @examples +#' ds <- mtcars |> +#' lapply(\(.x) REDCapCAST::set_attr(.x, label = NA, attr = "label")) |> +#' dplyr::bind_cols() +#' ds |> +#' remove_empty_attr() |> +#' str() +#' mtcars |> +#' lapply(\(.x) REDCapCAST::set_attr(.x, label = NA, attr = "label")) |> +#' remove_empty_attr() |> +#' str() +#' +remove_empty_attr <- function(data) { + if (is.data.frame(data)) { + data |> + lapply(remove_empty_attr) |> + dplyr::bind_cols() + } else if (is.list(data)) { + data |> lapply(remove_empty_attr) + } else { + attributes(data)[is.na(attributes(data))] <- NULL + data + } +} + +#' Removes columns with completenes below cutoff +#' +#' @param data data frame +#' @param cutoff numeric +#' +#' @returns data frame +#' @export +#' +#' @examples +#' data.frame(a = 1:10, b = NA, c = c(2, NA)) |> remove_empty_cols(cutoff = .5) +remove_empty_cols <- function(data, cutoff = .7) { + filter <- apply(X = data, MARGIN = 2, FUN = \(.x){ + sum(as.numeric(!is.na(.x))) / length(.x) + }) >= cutoff + data[filter] +} + + +#' Append list with named index +#' +#' @param data data to add to list +#' @param list list +#' @param index index name +#' +#' @returns list +#' @export +#' +#' @examples +#' ls_d <- list(test = c(1:20)) +#' ls_d <- list() +#' data.frame(letters[1:20], 1:20) |> append_list(ls_d, "letters") +#' letters[1:20] |> append_list(ls_d, "letters") +append_list <- function(data, list, index) { + ## This will overwrite and not warn + ## Not very safe, but convenient to append code to list + if (index %in% names(list)) { + list[[index]] <- data + out <- list + } else { + out <- setNames(c(list, list(data)), c(names(list), index)) + } + out +} + + +#' Get missingsness fraction +#' +#' @param data data +#' +#' @returns numeric vector +#' @export +#' +#' @examples +#' c(NA, 1:10, rep(NA, 3)) |> missing_fraction() +missing_fraction <- function(data) { + NROW(data[is.na(data)]) / NROW(data) +} + + + +#' Ultra short data dascription +#' +#' @param data +#' +#' @returns character vector +#' @export +#' +#' @examples +#' data.frame( +#' sample(1:8, 20, TRUE), +#' sample(c(1:8, NA), 20, TRUE) +#' ) |> data_description() +data_description <- function(data, data_text = "Data") { + data <- if (shiny::is.reactive(data)) data() else data + + n <- nrow(data) + n_var <- ncol(data) + n_complete <- sum(complete.cases(data)) + p_complete <- n_complete / n + + sprintf( + "%s has %s observations and %s variables, with %s (%s%%) complete cases.", + data_text, + n, + n_var, + n_complete, + signif(100 * p_complete, 3) + ) +} + + +#' Filter function to filter data set by variable type +#' +#' @param data data frame +#' @param type vector of data types (recognised: data_types) +#' +#' @returns data.frame +#' @export +#' +#' @examples +#' default_parsing(mtcars) |> +#' data_type_filter(type = c("categorical", "continuous")) |> +#' attributes() +#' default_parsing(mtcars) |> +#' data_type_filter(type = NULL) |> +#' attributes() +#' \dontrun{ +#' default_parsing(mtcars) |> data_type_filter(type = c("test", "categorical", "continuous")) +#' } +data_type_filter <- function(data, type) { + ## Please ensure to only provide recognised data types + assertthat::assert_that(all(type %in% names(data_types()))) + + if (!is.null(type)) { + out <- data[data_type(data) %in% type] + code <- rlang::call2("data_type_filter", !!!list(type = type), .ns = "FreesearchR") + attr(out, "code") <- code + } else { + out <- data + } + out +} + +#' Drop-in replacement for the base::sort_by with option to remove NAs +#' +#' @param x x +#' @param y y +#' @param na.rm remove NAs +#' @param ... passed to base_sort_by +#' +#' @returns vector +#' @export +#' +#' @examples +#' sort_by(c("Multivariable", "Univariable"), c("Univariable", "Minimal", "Multivariable")) +sort_by <- function(x, y, na.rm = FALSE, ...) { + out <- base::sort_by(x, y, ...) + if (na.rm == TRUE) { + out[!is.na(out)] + } else { + out + } +} + + +get_ggplot_label <- function(data, label) { + assertthat::assert_that(ggplot2::is_ggplot(data)) + data$labels[[label]] +} + + +#' Return if available +#' +#' @param data vector +#' @param default assigned value for missings +#' +#' @returns vector +#' @export +#' +#' @examples +#' NULL |> if_not_missing("new") +#' c(2, "a", NA) |> if_not_missing() +#' "See" |> if_not_missing() +if_not_missing <- function(data, default = NULL) { + if (length(data) > 1) { + Reduce(c, lapply(data, if_not_missing)) + } else if (is.na(data) || is.null(data)) { + return(default) + } else { + return(data) + } +} + + +#' Merge list of expressions +#' +#' @param data list +#' +#' @returns expression +#' @export +#' +#' @examples +#' list( +#' rlang::call2(.fn = "select", !!!list(c("cyl", "disp")), .ns = "dplyr"), +#' rlang::call2(.fn = "default_parsing", .ns = "FreesearchR") +#' ) |> merge_expression() +merge_expression <- function(data) { + Reduce( + f = function(x, y) rlang::expr(!!x %>% !!y), + x = data + ) +} + +#' Reduce character vector with the native pipe operator or character string +#' +#' @param data list +#' +#' @returns character string +#' @export +#' +#' @examples +#' list( +#' "mtcars", +#' rlang::call2(.fn = "select", !!!list(c("cyl", "disp")), .ns = "dplyr"), +#' rlang::call2(.fn = "default_parsing", .ns = "FreesearchR") +#' ) |> +#' lapply(expression_string) |> +#' pipe_string() |> +#' expression_string("data<-") +pipe_string <- function(data, collapse = "|>\n") { + if (is.list(data)) { + Reduce( + f = function(x, y) glue::glue("{x}{collapse}{y}"), + x = data + ) + } else { + data + } +} + +#' Deparses expression as string, substitutes native pipe and adds assign +#' +#' @param data expression +#' +#' @returns string +#' @export +#' +#' @examples +#' list( +#' as.symbol(paste0("mtcars$", "mpg")), +#' rlang::call2(.fn = "select", !!!list(c("cyl", "disp")), .ns = "dplyr"), +#' rlang::call2(.fn = "default_parsing", .ns = "FreesearchR") +#' ) |> +#' merge_expression() |> +#' expression_string() +expression_string <- function(data, assign.str = "") { + exp.str <- if (is.call(data)) deparse(data) else data + # browser() + out <- paste0(assign.str, gsub("%>%", "|>\n", paste(gsub('"', "'", paste(exp.str, collapse = "")), collapse = ""))) + gsub(" |`", "", out) +} + + +#' Very simple function to remove nested lists, like when uploading .rds +#' +#' @param data data +#' +#' @returns data.frame +#' @export +#' +#' @examples +#' dplyr::tibble(a = 1:10, b = rep(list("a"), 10)) |> remove_nested_list() +#' dplyr::tibble(a = 1:10, b = rep(list(c("a", "b")), 10)) |> as.data.frame() +remove_nested_list <- function(data) { + data[!sapply(data, is.list)] +} + + + + +#' (Re)label columns in data.frame +#' +#' @param data data.frame to be labelled +#' @param label named list or vector +#' +#' @returns data.frame +#' @export +#' +#' @examples +#' ls <- list("mpg" = "", "cyl" = "Cylinders", "disp" = "", "hp" = "", "drat" = "", "wt" = "", "qsec" = "", "vs" = "", "am" = "", "gear" = "", "carb" = "") +#' ls2 <- c("mpg" = "", "cyl" = "Cylinders", "disp" = "", "hp" = "Horses", "drat" = "", "wt" = "", "qsec" = "", "vs" = "", "am" = "", "gear" = "", "carb" = "") +#' ls3 <- c("mpg" = "", "cyl" = "", "disp" = "", "hp" = "Horses", "drat" = "", "wt" = "", "qsec" = "", "vs" = "", "am" = "", "gear" = "", "carb" = "") +#' mtcars |> +#' set_column_label(ls) |> +#' set_column_label(ls2) |> +#' set_column_label(ls3) +#' rlang::expr(FreesearchR::set_column_label(label = !!ls3)) |> expression_string() +set_column_label <- function(data, label, overwrite = TRUE) { + purrr::imap(data, function(.data, .name) { + ls <- if (is.list(label)) unlist(label) else label + ls[ls == ""] <- NA + if (.name %in% names(ls)) { + out <- REDCapCAST::set_attr(.data, unname(ls[.name]), attr = "label", overwrite = overwrite) + remove_empty_attr(out) + } else { + .data + } + }) |> dplyr::bind_cols(.name_repair = "unique_quiet") +} + + +#' Append a column to a data.frame +#' +#' @param data data +#' @param column new column (vector) or data.frame with 1 column +#' @param name new name (pre-fix) +#' @param index desired location. May be "left", "right" or numeric index. +#' +#' @returns data.frame +#' @export +#' +#' @examples +#' mtcars |> +#' dplyr::mutate(mpg_cut = mpg) |> +#' append_column(mtcars$mpg, "mpg_cutter") +append_column <- function(data, column, name, index = "right") { + assertthat::assert_that(NCOL(column) == 1) + assertthat::assert_that(length(index) == 1) + + if (index == "right") { + index <- ncol(data) + 1 + } else if (index == "left") { + index <- 1 + } else if (is.numeric(index)) { + if (index > ncol(data)) { + index <- ncol(data) + 1 + } + } else { + index <- ncol(data) + 1 + } + + ## Identifying potential naming conflicts + nm_conflicts <- names(data)[startsWith(names(data), name)] + ## Simple attemt to create new unique name + if (length(nm_conflicts) > 0) { + name <- glue::glue("{name}_{length(nm_conflicts)+1}") + } + ## If the above not achieves a unique name, the generic approach is used + if (name %in% names(data)) { + name <- make.names(c(name, names(data)), unique = TRUE)[1] + } + new_df <- setNames(data.frame(column), name) + + list( + data[seq_len(index - 1)], + new_df, + if (!index > ncol(data)) data[index:ncol(data)] + ) |> + dplyr::bind_cols() +} + + + +#' Test if element is identical to the previous +#' +#' @param data data. vector, data.frame or list +#' @param no.name logical to remove names attribute before testing +#' +#' @returns logical vector +#' @export +#' +#' @examples +#' c(1, 1, 2, 3, 3, 2, 4, 4) |> is_identical_to_previous() +#' mtcars[c(1, 1, 2, 3, 3, 2, 4, 4)] |> is_identical_to_previous() +#' list(1, 1, list(2), "A", "a", "a") |> is_identical_to_previous() +is_identical_to_previous <- function(data, no.name = TRUE) { + if (is.data.frame(data)) { + lagged <- data.frame(FALSE, data[seq_len(length(data) - 1)]) + } else { + lagged <- c(FALSE, data[seq_len(length(data) - 1)]) + } + + vapply(seq_len(length(data)), \(.x){ + if (isTRUE(no.name)) { + identical(unname(lagged[.x]), unname(data[.x])) + } else { + identical(lagged[.x], data[.x]) + } + }, FUN.VALUE = logical(1)) +} + + +#' Simplified version of the snakecase packages to_snake_case +#' +#' @param data character string vector +#' +#' @returns vector +#' @export +#' +#' @examples +#' c("foo bar", "fooBar21", "!!Foo'B'a-r", "foo_bar", "F OO bar") |> simple_snake() +simple_snake <- function(data){ + gsub("[\\s+]","_",gsub("[^\\w\\s:-]", "", tolower(data), perl=TRUE), perl=TRUE) +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//hosted_version.R +######## + +hosted_version <- function()'v25.6.3-250626' + + +######## +#### Current file: /Users/au301842/FreesearchR/R//html_dependency_freesearchr.R +######## + +html_dependency_FreesearchR <- function() { + htmltools::htmlDependency( + name = "FreesearchR", + version = packageVersion("FreesearchR"), + src = list(href = "FreesearchR", file = "assets"), + package = "FreesearchR", + stylesheet = "css/FreesearchR.css" + ) +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//import-file-ext.R +######## + +#' @title Import data from a file +#' +#' @description Let user upload a file and import data +#' +#' @param preview_data Show or not a preview of the data under the file input. +#' @param file_extensions File extensions accepted by [shiny::fileInput()], can also be MIME type. +#' @param layout_params How to display import parameters : in a dropdown button or inline below file input. +#' +#' @export +#' +#' @name import-file +#' +#' +import_file_ui <- function(id, + title = "", + preview_data = TRUE, + file_extensions = c(".csv", ".txt", ".xls", ".xlsx", ".rds", ".fst", ".sas7bdat", ".sav"), + layout_params = c("dropdown", "inline")) { + ns <- shiny::NS(id) + + if (!is.null(layout_params)) { + layout_params <- match.arg(layout_params) + } + + if (isTRUE(title)) { + title <- shiny::tags$h4( + datamods:::i18n("Import a file"), + class = "datamods-title" + ) + } + + + params_ui <- shiny::fluidRow( + shiny::column( + width = 6, + shinyWidgets::numericInputIcon( + inputId = ns("skip_rows"), + label = datamods:::i18n("Rows to skip before reading data:"), + value = 0, + min = 0, + icon = list("n ="), + size = "sm", + width = "100%" + ), + shiny::tagAppendChild( + shinyWidgets::textInputIcon( + inputId = ns("na_label"), + label = datamods:::i18n("Missing values character(s):"), + value = "NA,,'',na", + icon = list("NA"), + size = "sm", + width = "100%" + ), + shiny::helpText(phosphoricons::ph("info"), datamods:::i18n("if several use a comma (',') to separate them")) + ) + ), + shiny::column( + width = 6, + shinyWidgets::textInputIcon( + inputId = ns("dec"), + label = datamods:::i18n("Decimal separator:"), + value = ".", + icon = list("0.00"), + size = "sm", + width = "100%" + ), + selectInputIcon( + inputId = ns("encoding"), + label = datamods:::i18n("Encoding:"), + choices = c( + "UTF-8" = "UTF-8", + "Latin1" = "latin1" + ), + icon = phosphoricons::ph("text-aa"), + size = "sm", + width = "100%" + ) + ) + ) + + file_ui <- shiny::tagAppendAttributes( + shiny::fileInput( + inputId = ns("file"), + label = datamods:::i18n("Upload a file:"), + buttonLabel = datamods:::i18n("Browse..."), + placeholder = datamods:::i18n("No file selected; maximum file size is 5 mb"), + accept = file_extensions, + width = "100%", + ## A solution to allow multiple file upload is being considered + multiple = FALSE + ), + class = "mb-0" + ) + if (identical(layout_params, "dropdown")) { + file_ui <- shiny::tags$div( + style = htmltools::css( + display = "grid", + gridTemplateColumns = "1fr 50px", + gridColumnGap = "10px" + ), + file_ui, + shiny::tags$div( + class = "shiny-input-container", + shiny::tags$label( + class = "control-label", + `for` = ns("dropdown_params"), + "...", + style = htmltools::css(visibility = "hidden") + ), + shinyWidgets::dropMenu( + shiny::actionButton( + inputId = ns("dropdown_params"), + label = phosphoricons::ph("gear", title = "Parameters"), + width = "50px", + class = "px-1" + ), + params_ui + ) + ) + ) + } + shiny::tags$div( + class = "datamods-import", + datamods:::html_dependency_datamods(), + title, + file_ui, + if (identical(layout_params, "inline")) params_ui, + shiny::tags$div( + class = "hidden", + id = ns("sheet-container"), + shinyWidgets::pickerInput( + inputId = ns("sheet"), + label = datamods:::i18n("Select sheet to import:"), + choices = NULL, + width = "100%", + multiple = TRUE + ) + ), + shiny::tags$div( + id = ns("import-placeholder"), + shinyWidgets::alert( + id = ns("import-result"), + status = "info", + shiny::tags$b(datamods:::i18n("No file selected:")), + sprintf(datamods:::i18n("You can import %s files"), paste(file_extensions, collapse = ", ")), + dismissible = TRUE + ) + ), + if (isTRUE(preview_data)) { + toastui::datagridOutput2(outputId = ns("table")) + }, + shiny::uiOutput( + outputId = ns("container_confirm_btn"), + style = "margin-top: 20px;" + ), + tags$div( + style = htmltools::css(display = "none"), + shiny::checkboxInput( + inputId = ns("preview_data"), + label = NULL, + value = isTRUE(preview_data) + ) + ) + ) +} + +#' +#' @export +#' +#' +#' @rdname import-file +import_file_server <- function(id, + btn_show_data = TRUE, + show_data_in = c("popup", "modal"), + trigger_return = c("button", "change"), + return_class = c("data.frame", "data.table", "tbl_df", "raw"), + reset = reactive(NULL)) { + read_fns <- list( + ods = "import_ods", + dta = "import_dta", + csv = "import_delim", + tsv = "import_delim", + txt = "import_delim", + xls = "import_xls", + xlsx = "import_xls", + rds = "import_rds" + ) + + trigger_return <- match.arg(trigger_return) + return_class <- match.arg(return_class) + + module <- function(input, output, session) { + ns <- session$ns + imported_rv <- shiny::reactiveValues(data = NULL, name = NULL) + temporary_rv <- shiny::reactiveValues(data = NULL, name = NULL, status = NULL, sheets = 1) + + shiny::observeEvent(reset(), { + temporary_rv$data <- NULL + temporary_rv$name <- NULL + temporary_rv$status <- NULL + }) + + output$container_confirm_btn <- shiny::renderUI({ + if (identical(trigger_return, "button")) { + datamods:::button_import() + } + }) + + shiny::observeEvent(input$file, { + ## Several steps are taken to ensure no errors on changed input file + temporary_rv$sheets <- 1 + if (isTRUE(is_workbook(input$file$datapath))) { + if (isTRUE(is_excel(input$file$datapath))) { + temporary_rv$sheets <- readxl::excel_sheets(input$file$datapath) + } else if (isTRUE(is_ods(input$file$datapath))) { + temporary_rv$sheets <- readODS::ods_sheets(input$file$datapath) + } + selected <- temporary_rv$sheets[1] + + shinyWidgets::updatePickerInput( + session = session, + inputId = "sheet", + selected = selected, + choices = temporary_rv$sheets + ) + datamods:::showUI(paste0("#", ns("sheet-container"))) + } else { + datamods:::hideUI(paste0("#", ns("sheet-container"))) + } + }) + + observeEvent( + list( + input$file, + input$sheet, + input$skip_rows, + input$dec, + input$encoding, + input$na_label + ), + { + req(input$file) + + if (!all(input$sheet %in% temporary_rv$sheets)) { + sheets <- 1 + } else { + sheets <- input$sheet + } + + extension <- tools::file_ext(input$file$datapath) + + parameters <- list( + file = input$file$datapath, + sheet = sheets, + skip = input$skip_rows, + dec = input$dec, + encoding = input$encoding, + na.strings = datamods:::split_char(input$na_label) + ) + + parameters <- parameters[which(names(parameters) %in% rlang::fn_fmls_names(get(read_fns[[extension]])))] + # parameters <- parameters[which(names(parameters) %in% rlang::fn_fmls_names(read_fns[[extension]]))] + imported <- try(rlang::exec(read_fns[[extension]], !!!parameters), silent = TRUE) + code <- rlang::call2(read_fns[[extension]], !!!modifyList(parameters, list(file = input$file$name)), .ns = "FreesearchR") + + if (inherits(imported, "try-error")) { + imported <- try(rlang::exec(rio::import, !!!parameters[1]), silent = TRUE) + code <- rlang::call2("import", !!!list(file = input$file$name), .ns = "rio") + } + + if (inherits(imported, "try-error") || NROW(imported) < 1) { + datamods:::toggle_widget(inputId = "confirm", enable = FALSE) + datamods:::insert_error(mssg = datamods:::i18n(attr(imported, "condition")$message)) + temporary_rv$status <- "error" + temporary_rv$data <- NULL + temporary_rv$name <- NULL + temporary_rv$code <- NULL + } else { + datamods:::toggle_widget(inputId = "confirm", enable = TRUE) + + datamods:::insert_alert( + selector = ns("import"), + status = "success", + datamods:::make_success_alert( + imported, + trigger_return = trigger_return, + btn_show_data = btn_show_data, + extra = if (isTRUE(input$preview_data)) datamods:::i18n("First five rows are shown below:") + ) + ) + temporary_rv$status <- "success" + temporary_rv$data <- imported + temporary_rv$name <- input$file$name + temporary_rv$code <- code + } + }, + ignoreInit = TRUE + ) + + observeEvent(input$see_data, { + tryCatch( + { + datamods:::show_data(default_parsing(temporary_rv$data), title = datamods:::i18n("Imported data"), type = show_data_in) + }, + # warning = function(warn) { + # showNotification(warn, type = "warning") + # }, + error = function(err) { + showNotification(err, type = "err") + } + ) + }) + + output$table <- toastui::renderDatagrid2({ + req(temporary_rv$data) + tryCatch( + { + toastui::datagrid( + data = setNames(head(temporary_rv$data, 5), make.names(names(temporary_rv$data), unique = TRUE)), + theme = "striped", + colwidths = "guess", + minBodyHeight = 250 + ) + }, + error = function(err) { + showNotification(err, type = "err") + } + ) + }) + + observeEvent(input$confirm, { + imported_rv$data <- temporary_rv$data + imported_rv$name <- temporary_rv$name + imported_rv$code <- temporary_rv$code + }) + + if (identical(trigger_return, "button")) { + return(list( + status = reactive(temporary_rv$status), + name = reactive(imported_rv$name), + code = reactive(imported_rv$code), + data = reactive(datamods:::as_out(imported_rv$data, return_class)) + )) + } else { + return(list( + status = reactive(temporary_rv$status), + name = reactive(temporary_rv$name), + code = reactive(temporary_rv$code), + data = reactive(datamods:::as_out(temporary_rv$data, return_class)) + )) + } + } + + moduleServer( + id = id, + module = module + ) +} + +# utils ------------------------------------------------------------------- + +is_excel <- function(path) { + isTRUE(tools::file_ext(path) %in% c("xls", "xlsx")) +} + +is_ods <- function(path) { + isTRUE(tools::file_ext(path) %in% c("ods")) +} + +is_sas <- function(path) { + isTRUE(tools::file_ext(path) %in% c("sas7bdat")) +} + +is_workbook <- function(path) { + is_excel(path) || is_ods(path) +} + + +# File import functions --------------------------------------------------- + +#' Wrapper to ease data file import +#' +#' @param file path to the file +#' @param sheet for Excel files, sheet to read +#' @param skip number of row to skip +#' @param encoding file encoding +#' @param na.strings character(s) to interpret as missing values. +#' +#' +#' @name import-file-type +#' +#' @returns data.frame +#' @export +#' +import_delim <- function(file, skip, encoding, na.strings) { + data.table::fread( + file = file, + na.strings = na.strings, + skip = skip, + check.names = TRUE, + encoding = encoding, + data.table = FALSE, + logical01 = TRUE, + logicalYN = TRUE, + keepLeadingZeros = TRUE + ) +} + + +#' @name import-file-type +#' +#' @returns data.frame +#' @export +#' +import_xls <- function(file, sheet, skip, na.strings) { + tryCatch( + { + ## If sheet is null, this allows purrr::map to run + if (is.null(sheet)) sheet <- 1 + + sheet |> + purrr::map(\(.x){ + readxl::read_excel( + path = file, + sheet = .x, + na = na.strings, + skip = skip, + .name_repair = "unique_quiet", + trim_ws = TRUE + ) + + # openxlsx2::read_xlsx( + # file = file, + # sheet = .x, + # skip_empty_rows = TRUE, + # start_row = skip - 1, + # na.strings = na.strings + # ) + }) |> + purrr::reduce(dplyr::full_join) + }, + # warning = function(warn) { + # showNotification(paste0(warn), type = "warning") + # }, + error = function(err) { + showNotification(paste0(err), type = "err") + } + ) +} + + +#' @name import-file-type +#' +#' @returns data.frame +#' @export +#' +import_ods <- function(file, sheet, skip, na.strings) { + tryCatch( + { + if (is.null(sheet)) sheet <- 1 + sheet |> + purrr::map(\(.x){ + readODS::read_ods( + path = file, + sheet = .x, + skip = skip, + na = na.strings + ) + }) |> + purrr::reduce(dplyr::full_join) + }, + # warning = function(warn) { + # showNotification(paste0(warn), type = "warning") + # }, + error = function(err) { + showNotification(paste0(err), type = "err") + } + ) +} + +#' @name import-file-type +#' +#' @returns data.frame +#' @export +#' +import_dta <- function(file) { + haven::read_dta( + file = file, + .name_repair = "unique_quiet" + ) +} + +#' @name import-file-type +#' +#' @returns data.frame +#' @export +#' +import_rds <- function(file) { + readr::read_rds( + file = file + ) +} + +#' @title Create a select input control with icon(s) +#' +#' @description Extend form controls by adding text or icons before, +#' after, or on both sides of a classic `selectInput`. +#' +#' @inheritParams shiny::selectInput +#' +#' @return A numeric input control that can be added to a UI definition. +#' @export +#' +#' @importFrom shiny restoreInput +#' @importFrom htmltools tags validateCssUnit css +#' +selectInputIcon <- function(inputId, + label, + choices, + selected = NULL, + multiple = FALSE, + selectize = TRUE, + size = NULL, + width = NULL, + icon = NULL) { + selected <- shiny::restoreInput(id = inputId, default = selected) + shiny::tags$div( + class = "form-group shiny-input-container", + shinyWidgets:::label_input(inputId, label), + style = htmltools:::css(width = htmltools:::validateCssUnit(width)), + shiny::tags$div( + class = "input-group", + class = shinyWidgets:::validate_size(size), + shinyWidgets:::markup_input_group(icon, "left", theme_func = shiny::getCurrentTheme), + shiny::tags$select( + id = inputId, + class = "form-control select-input-icon", + shiny:::selectOptions(choices, selected, inputId, selectize) + ), + shinyWidgets:::markup_input_group(icon, "right", theme_func = shiny::getCurrentTheme) + ), + shinyWidgets:::html_dependency_input_icons() + ) +} + + +#' Test app for the import_file module +#' +#' @rdname import-file_module +#' +#' @examples +#' \dontrun{ +#' import_file_demo_app() +#' } +import_file_demo_app <- function() { + ui <- shiny::fluidPage( + # theme = bslib::bs_theme(version = 5L), + # theme = bslib::bs_theme(version = 5L, preset = "bootstrap"), + shiny::tags$h3("Import data from a file"), + shiny::fluidRow( + shiny::column( + width = 4, + import_file_ui( + id = "myid", + file_extensions = c(".csv", ".tsv", ".txt", ".xls", ".xlsx", ".rds", ".sas7bdat", ".ods", ".dta"), + layout_params = "dropdown" # "inline" # or "dropdown" + ) + ), + shiny::column( + width = 8, + shiny::tags$b("Import status:"), + shiny::verbatimTextOutput(outputId = "status"), + shiny::tags$b("Name:"), + shiny::verbatimTextOutput(outputId = "name"), + shiny::tags$b("Code:"), + shiny::verbatimTextOutput(outputId = "code"), + shiny::tags$b("Data:"), + shiny::verbatimTextOutput(outputId = "data") + ) + ) + ) + server <- function(input, output, session) { + imported <- import_file_server( + id = "myid", + show_data_in = "popup", + trigger_return = "change", + return_class = "data.frame" + ) + + output$status <- shiny::renderPrint({ + imported$status() + }) + output$name <- shiny::renderPrint({ + imported$name() + }) + output$code <- shiny::renderPrint({ + imported$code() + }) + output$data <- shiny::renderPrint({ + imported$data() + }) + } + shiny::shinyApp(ui, server) +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//launch_FreesearchR.R +######## + +#' Easily launch the FreesearchR app +#' +#' @description +#' All data.frames in the global environment will be accessible through the app. +#' +#' @param ... passed on to `shiny::runApp()` +#' +#' @returns shiny app +#' @export +#' +#' @examples +#' \dontrun{ +#' data(mtcars) +#' launch_FreesearchR(launch.browser = TRUE) +#' } +launch_FreesearchR <- function(...){ + appDir <- system.file("apps", "FreesearchR", package = "FreesearchR") + if (appDir == "") { + stop("Could not find the app directory. Try re-installing `FreesearchR`.", call. = FALSE) + } + + a <- shiny::runApp(appDir = paste0(appDir,"/app.R"), ...) + return(invisible(a)) +} + + + +######## +#### Current file: /Users/au301842/FreesearchR/R//missings-module.R +######## + +#' Data correlations evaluation module +#' +#' @param id Module id +#' +#' @name data-missings +#' @returns Shiny ui module +#' @export +data_missings_ui <- function(id) { + ns <- shiny::NS(id) + + shiny::tagList( + gt::gt_output(outputId = ns("missings_table")) + ) +} + + +#' +#' @param data data +#' @param output.format output format +#' +#' @name data-missings +#' @returns shiny server module +#' @export +data_missings_server <- function(id, + data, + variable, + ...) { + shiny::moduleServer( + id = id, + module = function(input, output, session) { + # ns <- session$ns + + datar <- if (is.reactive(data)) data else reactive(data) + variabler <- if (is.reactive(variable)) variable else reactive(variable) + + rv <- shiny::reactiveValues( + data = NULL, + table = NULL + ) + + rv$data <- shiny::reactive({ + df_tbl <- datar() + by_var <- variabler() + + tryCatch( + { + if (!is.null(by_var) && by_var != "" && by_var %in% names(df_tbl)) { + df_tbl[[by_var]] <- ifelse(is.na(df_tbl[[by_var]]), "Missing", "Non-missing") + + out <- gtsummary::tbl_summary(df_tbl, by = by_var) |> + gtsummary::add_p() + } else { + out <- gtsummary::tbl_summary(df_tbl) + } + }, + error = function(err) { + showNotification(paste0("Error: ", err), type = "err") + } + ) + + out + }) + + output$missings_table <- gt::render_gt({ + shiny::req(datar) + shiny::req(variabler) + + if (is.null(variabler()) || variabler() == "" || !variabler() %in% names(datar())) { + if (anyNA(datar())){ + title <- "No variable chosen for analysis" + } else { + title <- "No missing observations" + } + } else { + title <- glue::glue("Missing vs non-missing observations in the variable **'{variabler()}'**") + } + + out <- rv$data() |> + gtsummary::as_gt() |> + gt::tab_header(title = gt::md(title)) + + rv$table <- out + + out + }) + + return(reactive(rv$table)) + } + ) +} + + +missing_demo_app <- function() { + ui <- shiny::fluidPage( + shiny::actionButton( + inputId = "modal_missings", + label = "Browse data", + width = "100%", + disabled = FALSE + ), + shiny::selectInput( + inputId = "missings_var", + label = "Select variable to stratify analysis", choices = c("cyl", "vs") + ), + data_missings_ui("data") + ) + server <- function(input, output, session) { + data_demo <- mtcars + data_demo[sample(1:32, 10), "cyl"] <- NA + data_demo[sample(1:32, 8), "vs"] <- NA + + data_missings_server(id = "data", data = data_demo, variable = shiny::reactive(input$missings_var)) + + visual_summary_server(id = "visual", data = data_demo) + + observeEvent(input$modal_missings, { + tryCatch( + { + modal_visual_summary(id = "visual") + }, + error = function(err) { + showNotification(paste0("We encountered the following error browsing your data: ", err), type = "err") + } + ) + }) + } + shiny::shinyApp(ui, server) +} + +missing_demo_app() + + + + + + + + + + +######## +#### Current file: /Users/au301842/FreesearchR/R//plot_box.R +######## + +#' Beautiful box plot(s) +#' +#' @returns ggplot2 object +#' @export +#' +#' @name data-plots +#' +#' @examples +#' mtcars |> plot_box(pri = "mpg", sec = "cyl", ter = "gear") +#' mtcars |> +#' default_parsing() |> +#' plot_box(pri = "mpg", sec = "cyl", ter = "gear") +plot_box <- function(data, pri, sec, ter = NULL) { + if (!is.null(ter)) { + ds <- split(data, data[ter]) + } else { + ds <- list(data) + } + + out <- lapply(ds, \(.ds){ + plot_box_single( + data = .ds, + pri = pri, + sec = sec + ) + }) + + wrap_plot_list(out) +} + + + + +#' Create nice box-plots +#' +#' @name data-plots +#' +#' @returns ggplot object +#' @export +#' +#' @examples +#' mtcars |> plot_box_single("mpg") +#' mtcars |> plot_box_single("mpg","cyl") +plot_box_single <- function(data, pri, sec=NULL, seed = 2103) { + set.seed(seed) + + if (is.null(sec)) { + sec <- "All" + data[[sec]] <- sec + } + + discrete <- !data_type(data[[sec]]) %in% "continuous" + + data |> + ggplot2::ggplot(ggplot2::aes(x = !!dplyr::sym(pri), y = !!dplyr::sym(sec), fill = !!dplyr::sym(sec), group = !!dplyr::sym(sec))) + + ggplot2::geom_boxplot(linewidth = 1.8, outliers = FALSE) + + ## THis could be optional in future + ggplot2::geom_jitter(color = "black", size = 2, alpha = 0.9, width = 0.1, height = .2) + + ggplot2::coord_flip() + + viridis::scale_fill_viridis(discrete = discrete, option = "D") + + # ggplot2::theme_void() + + ggplot2::theme_bw(base_size = 24) + + ggplot2::theme( + legend.position = "none", + # panel.grid.major = element_blank(), + # panel.grid.minor = element_blank(), + # axis.text.y = element_blank(), + # axis.title.y = element_blank(), + # text = ggplot2::element_text(size = 20), + # axis.text = ggplot2::element_blank(), + # plot.title = element_blank(), + panel.background = ggplot2::element_rect(fill = "white"), + plot.background = ggplot2::element_rect(fill = "white"), + panel.border = ggplot2::element_blank(), + panel.grid.major = ggplot2::element_blank(), + panel.grid.minor = ggplot2::element_blank(), + axis.line = ggplot2::element_line(colour = "black"), + axis.ticks = ggplot2::element_line(colour = "black") + ) +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//plot_euler.R +######## + +#' Area proportional venn diagrams +#' +#' @description +#' THis is slightly modified from https://gist.github.com/danlooo/d23d8bcf8856c7dd8e86266097404ded +#' +#' This functions uses eulerr::euler to plot area proportional venn diagramms +#' but plots it using ggplot2 +#' +#' @param combinations set relationships as a named numeric vector, matrix, or +#' data.frame(See `eulerr::euler`) +#' @param show_quantities whether to show number of intersecting elements +#' @param show_labels whether to show set names +#' @param ... further arguments passed to eulerr::euler +ggeulerr <- function( + combinations, + show_quantities = TRUE, + show_labels = TRUE, + ...) { + # browser() + data <- + eulerr::euler(combinations = combinations, ...) |> + plot(quantities = show_quantities) |> + purrr::pluck("data") + + + tibble::as_tibble(data$ellipses, rownames = "Variables") |> + ggplot2::ggplot() + + ggforce::geom_ellipse( + mapping = ggplot2::aes( + x0 = h, y0 = k, a = a, b = b, angle = 0, fill = Variables + ), + alpha = 0.5, + linewidth = 1.5 + ) + + ggplot2::geom_text( + data = { + data$centers |> + dplyr::mutate( + label = labels |> purrr::map2(quantities, ~ { + if (!is.na(.x) && !is.na(.y) && show_labels) { + paste0(.x, "\n", sprintf(.y, fmt = "%.2g")) + } else if (!is.na(.x) && show_labels) { + .x + } else if (!is.na(.y)) { + .y + } else { + "" + } + }) + ) + }, + mapping = ggplot2::aes(x = x, y = y, label = label), + size = 8 + ) + + ggplot2::theme(panel.grid = ggplot2::element_blank()) + + ggplot2::coord_fixed() + + ggplot2::scale_fill_hue() +} + +#' Easily plot euler diagrams +#' +#' @param data data +#' @param x name of main variable +#' @param y name of secondary variables +#' @param z grouping variable +#' @param seed seed +#' +#' @returns patchwork object +#' @export +#' +#' @examples +#' data.frame( +#' A = sample(c(TRUE, TRUE, FALSE), 50, TRUE), +#' B = sample(c("A", "C"), 50, TRUE), +#' C = sample(c(TRUE, FALSE, FALSE, FALSE), 50, TRUE), +#' D = sample(c(TRUE, FALSE, FALSE, FALSE), 50, TRUE) +#' ) |> plot_euler("A", c("B", "C"), "D", seed = 4) +#' mtcars |> plot_euler("vs", "am", seed = 1) +plot_euler <- function(data, pri, sec, ter = NULL, seed = 2103) { + set.seed(seed = seed) + if (!is.null(ter)) { + ds <- split(data, data[ter]) + } else { + ds <- list(data) + } + + out <- lapply(ds, \(.x){ + .x[c(pri, sec)] |> + as.data.frame() |> + na.omit() |> + plot_euler_single() + }) + + # names(out) + wrap_plot_list(out) + # patchwork::wrap_plots(out, guides = "collect") +} + +#' Easily plot single euler diagrams +#' +#' @returns ggplot2 object +#' @export +#' +#' @examples +#' data.frame( +#' A = sample(c(TRUE, TRUE, FALSE), 50, TRUE), +#' B = sample(c("A", "C"), 50, TRUE), +#' C = sample(c(TRUE, FALSE, FALSE, FALSE), 50, TRUE), +#' D = sample(c(TRUE, FALSE, FALSE, FALSE), 50, TRUE) +#' ) |> plot_euler_single() +#' mtcars[c("vs", "am")] |> plot_euler_single() +plot_euler_single <- function(data) { + # if (any("categorical" %in% data_type(data))){ + # shape <- "ellipse" + # } else { + # shape <- "circle" + # } + + data |> + ggeulerr(shape = "circle") + + ggplot2::theme_void() + + ggplot2::theme( + legend.position = "none", + # panel.grid.major = element_blank(), + # panel.grid.minor = element_blank(), + # axis.text.y = element_blank(), + # axis.title.y = element_blank(), + text = ggplot2::element_text(size = 20), + axis.text = ggplot2::element_blank(), + # plot.title = element_blank(), + # panel.background = ggplot2::element_rect(fill = "white"), + plot.background = ggplot2::element_rect(fill = "white"), + panel.border = ggplot2::element_blank() + ) +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//plot_hbar.R +######## + +#' Nice horizontal stacked bars (Grotta bars) +#' +#' @returns ggplot2 object +#' @export +#' +#' @name data-plots +#' +#' @examples +#' mtcars |> plot_hbars(pri = "carb", sec = "cyl") +#' mtcars |> plot_hbars(pri = "carb", sec = NULL) +plot_hbars <- function(data, pri, sec, ter = NULL) { + out <- vertical_stacked_bars(data = data, score = pri, group = sec, strata = ter) + + out +} + + +#' Vertical stacked bar plot wrapper +#' +#' @param data data.frame +#' @param score outcome variable +#' @param group grouping variable +#' @param strata stratifying variable +#' @param t.size text size +#' +#' @return ggplot2 object +#' @export +#' +vertical_stacked_bars <- function(data, + score = "full_score", + group = "pase_0_q", + strata = NULL, + t.size = 10, + l.color = "black", + l.size = .5, + draw.lines = TRUE) { + if (is.null(group)) { + df.table <- data[c(score, group, strata)] |> + dplyr::mutate("All" = 1) |> + table() + group <- "All" + draw.lines <- FALSE + } else { + df.table <- data[c(score, group, strata)] |> + table() + } + + p <- df.table |> + rankinPlot::grottaBar( + scoreName = score, + groupName = group, + textColor = c("black", "white"), + strataName = strata, + textCut = 6, + textSize = 20, + printNumbers = "none", + lineSize = l.size, + returnData = TRUE + ) + + colors <- viridisLite::viridis(nrow(df.table)) + contrast_cut <- + sum(contrast_text(colors, threshold = .3) == "white") + + score_label <- data |> get_label(var = score) + group_label <- data |> get_label(var = group) + + p |> + (\(.x){ + .x$plot + + ggplot2::geom_text( + data = .x$rectData[which(.x$rectData$n > + 0), ], + size = t.size, + fontface = "plain", + ggplot2::aes( + x = group, + y = p_prev + 0.49 * p, + color = as.numeric(score) > contrast_cut, + # label = paste0(sprintf("%2.0f", 100 * p),"%"), + label = sprintf("%2.0f", 100 * p) + ) + ) + + ggplot2::labs(fill = score_label) + + ggplot2::scale_fill_manual(values = rev(colors)) + + ggplot2::theme( + legend.position = "bottom", + axis.title = ggplot2::element_text(), + ) + + ggplot2::xlab(group_label) + + ggplot2::ylab(NULL) + # viridis::scale_fill_viridis(discrete = TRUE, direction = -1, option = "D") + })() +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//plot_ridge.R +######## + +#' Plot nice ridge plot +#' +#' @returns ggplot2 object +#' @export +#' +#' @name data-plots +#' +#' @examples +#' mtcars |> +#' default_parsing() |> +#' plot_ridge(x = "mpg", y = "cyl") +#' mtcars |> plot_ridge(x = "mpg", y = "cyl", z = "gear") +plot_ridge <- function(data, x, y, z = NULL, ...) { + if (!is.null(z)) { + ds <- split(data, data[z]) + } else { + ds <- list(data) + } + + out <- lapply(ds, \(.ds){ + ggplot2::ggplot(.ds, ggplot2::aes(x = !!dplyr::sym(x), y = !!dplyr::sym(y), fill = !!dplyr::sym(y))) + + ggridges::geom_density_ridges() + + ggridges::theme_ridges() + + ggplot2::theme(legend.position = "none") |> rempsyc:::theme_apa() + }) + + patchwork::wrap_plots(out) +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//plot_sankey.R +######## + +#' Readying data for sankey plot +#' +#' @name data-plots +#' +#' @returns data.frame +#' @export +#' +#' @examples +#' ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = sample(c(letters[1:4], NA), 100, TRUE, prob = c(rep(.23, 4), .08))) +#' ds |> sankey_ready("first", "last") +#' ds |> sankey_ready("first", "last", numbers = "percentage") +#' data.frame( +#' g = sample(LETTERS[1:2], 100, TRUE), +#' first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), +#' last = sample(c(TRUE, FALSE, FALSE), 100, TRUE) +#' ) |> +#' sankey_ready("first", "last") +sankey_ready <- function(data, pri, sec, numbers = "count", ...) { + ## TODO: Ensure ordering x and y + + ## Ensure all are factors + data[c(pri, sec)] <- data[c(pri, sec)] |> + dplyr::mutate(dplyr::across(!dplyr::where(is.factor), forcats::as_factor)) + + out <- dplyr::count(data, !!dplyr::sym(pri), !!dplyr::sym(sec), .drop = FALSE) + + out <- out |> + dplyr::group_by(!!dplyr::sym(pri)) |> + dplyr::mutate(gx.sum = sum(n)) |> + dplyr::ungroup() |> + dplyr::group_by(!!dplyr::sym(sec)) |> + dplyr::mutate(gy.sum = sum(n)) |> + dplyr::ungroup() + + if (numbers == "count") { + out <- out |> dplyr::mutate( + lx = factor(paste0(!!dplyr::sym(pri), "\n(n=", gx.sum, ")")), + ly = factor(paste0(!!dplyr::sym(sec), "\n(n=", gy.sum, ")")) + ) + } else if (numbers == "percentage") { + out <- out |> dplyr::mutate( + lx = factor(paste0(!!dplyr::sym(pri), "\n(", round((gx.sum / sum(n)) * 100, 1), "%)")), + ly = factor(paste0(!!dplyr::sym(sec), "\n(", round((gy.sum / sum(n)) * 100, 1), "%)")) + ) + } + + if (is.factor(data[[pri]])) { + index <- match(levels(data[[pri]]), str_remove_last(levels(out$lx), "\n")) + out$lx <- factor(out$lx, levels = levels(out$lx)[index]) + } + + if (is.factor(data[[sec]])) { + index <- match(levels(data[[sec]]), str_remove_last(levels(out$ly), "\n")) + out$ly <- factor(out$ly, levels = levels(out$ly)[index]) + } + + out +} + +str_remove_last <- function(data, pattern = "\n") { + strsplit(data, split = pattern) |> + lapply(\(.x)paste(unlist(.x[[-length(.x)]]), collapse = pattern)) |> + unlist() +} + +#' Beautiful sankey plot with option to split by a tertiary group +#' +#' @returns ggplot2 object +#' @export +#' +#' @name data-plots +#' +#' @examples +#' ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE))) +#' ds |> plot_sankey("first", "last") +#' ds |> plot_sankey("first", "last", color.group = "sec") +#' ds |> plot_sankey("first", "last", ter = "g", color.group = "sec") +#' mtcars |> +#' default_parsing() |> +#' plot_sankey("cyl", "gear", "am", color.group = "pri") +#' ## In this case, the last plot as the secondary variable in wrong order +#' ## Dont know why... +#' mtcars |> +#' default_parsing() |> +#' plot_sankey("cyl", "gear", "vs", color.group = "pri") +plot_sankey <- function(data, pri, sec, ter = NULL, color.group = "pri", colors = NULL) { + if (!is.null(ter)) { + ds <- split(data, data[ter]) + } else { + ds <- list(data) + } + + out <- lapply(ds, \(.ds){ + plot_sankey_single(.ds, pri = pri, sec = sec, color.group = color.group, colors = colors) + }) + + patchwork::wrap_plots(out) +} + +#' Beautiful sankey plot +#' +#' @param color.group set group to colour by. "x" or "y". +#' @param colors optinally specify colors. Give NA color, color for each level +#' in primary group and color for each level in secondary group. +#' @param ... passed to sankey_ready() +#' +#' @returns ggplot2 object +#' @export +#' +#' @examples +#' ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE))) +#' ds |> plot_sankey_single("first", "last") +#' ds |> plot_sankey_single("first", "last", color.group = "sec") +#' data.frame( +#' g = sample(LETTERS[1:2], 100, TRUE), +#' first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), +#' last = sample(c(TRUE, FALSE, FALSE), 100, TRUE) +#' ) |> +#' plot_sankey_single("first", "last", color.group = "pri") +#' mtcars |> +#' default_parsing() |> +#' plot_sankey_single("cyl", "vs", color.group = "pri") +plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), colors = NULL, ...) { + color.group <- match.arg(color.group) + + data_orig <- data + data[c(pri, sec)] <- data[c(pri, sec)] |> + dplyr::mutate(dplyr::across(dplyr::where(is.factor), forcats::fct_drop)) + + # browser() + + data <- data |> sankey_ready(pri = pri, sec = sec, ...) + + na.color <- "#2986cc" + box.color <- "#1E4B66" + + if (is.null(colors)) { + if (color.group == "sec") { + main.colors <- viridisLite::viridis(n = length(levels(data_orig[[sec]]))) + ## Only keep colors for included levels + main.colors <- main.colors[match(levels(data[[sec]]), levels(data_orig[[sec]]))] + + secondary.colors <- rep(na.color, length(levels(data[[pri]]))) + label.colors <- Reduce(c, lapply(list(secondary.colors, rev(main.colors)), contrast_text)) + } else { + main.colors <- viridisLite::viridis(n = length(levels(data_orig[[pri]]))) + ## Only keep colors for included levels + main.colors <- main.colors[match(levels(data[[pri]]), levels(data_orig[[pri]]))] + + secondary.colors <- rep(na.color, length(levels(data[[sec]]))) + label.colors <- Reduce(c, lapply(list(rev(main.colors), secondary.colors), contrast_text)) + } + colors <- c(na.color, main.colors, secondary.colors) + } else { + label.colors <- contrast_text(colors) + } + + group_labels <- c(get_label(data, pri), get_label(data, sec)) |> + sapply(line_break) |> + unname() + + p <- ggplot2::ggplot(data, ggplot2::aes(y = n, axis1 = lx, axis2 = ly)) + + if (color.group == "sec") { + p <- p + + ggalluvial::geom_alluvium( + ggplot2::aes( + fill = !!dplyr::sym(sec) # , + ## Including will print strings when levels are empty + # color = !!dplyr::sym(sec) + ), + width = 1 / 16, + alpha = .8, + knot.pos = 0.4, + curve_type = "sigmoid" + ) + ggalluvial::geom_stratum(ggplot2::aes(fill = !!dplyr::sym(sec)), + size = 2, + width = 1 / 3.4 + ) + } else { + p <- p + + ggalluvial::geom_alluvium( + ggplot2::aes( + fill = !!dplyr::sym(pri) # , + # color = !!dplyr::sym(pri) + ), + width = 1 / 16, + alpha = .8, + knot.pos = 0.4, + curve_type = "sigmoid" + ) + ggalluvial::geom_stratum(ggplot2::aes(fill = !!dplyr::sym(pri)), + size = 2, + width = 1 / 3.4 + ) + } + + ## Will fail to use stat="stratum" if library is not loaded. + library(ggalluvial) + p + + ggplot2::geom_text( + stat = "stratum", + ggplot2::aes(label = after_stat(stratum)), + colour = label.colors, + size = 8, + lineheight = 1 + ) + + ggplot2::scale_x_continuous( + breaks = 1:2, + labels = group_labels + ) + + ggplot2::scale_fill_manual(values = colors[-1], na.value = colors[1]) + + # ggplot2::scale_color_manual(values = main.colors) + + ggplot2::theme_void() + + ggplot2::theme( + legend.position = "none", + # panel.grid.major = element_blank(), + # panel.grid.minor = element_blank(), + # axis.text.y = element_blank(), + # axis.title.y = element_blank(), + axis.text.x = ggplot2::element_text(size = 20), + # text = element_text(size = 5), + # plot.title = element_blank(), + # panel.background = ggplot2::element_rect(fill = "white"), + plot.background = ggplot2::element_rect(fill = "white"), + panel.border = ggplot2::element_blank() + ) +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//plot_scatter.R +######## + +#' Beautiful violin plot +#' +#' @returns ggplot2 object +#' @export +#' +#' @name data-plots +#' +#' @examples +#' mtcars |> plot_scatter(pri = "mpg", sec = "wt") +plot_scatter <- function(data, pri, sec, ter = NULL) { + if (is.null(ter)) { + rempsyc::nice_scatter( + data = data, + predictor = sec, + response = pri, + xtitle = get_label(data, var = sec), + ytitle = get_label(data, var = pri) + ) + } else { + rempsyc::nice_scatter( + data = data, + predictor = sec, + response = pri, + group = ter, + xtitle = get_label(data, var = sec), + ytitle = get_label(data, var = pri) + ) + } +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//plot_violin.R +######## + +#' Beatiful violin plot +#' +#' @returns ggplot2 object +#' @export +#' +#' @name data-plots +#' +#' @examples +#' mtcars |> plot_violin(pri = "mpg", sec = "cyl", ter = "gear") +plot_violin <- function(data, pri, sec, ter = NULL) { + if (!is.null(ter)) { + ds <- split(data, data[ter]) + } else { + ds <- list(data) + } + + out <- lapply(ds, \(.ds){ + rempsyc::nice_violin( + data = .ds, + group = sec, + response = pri, + xtitle = get_label(data, var = sec), + ytitle = get_label(data, var = pri) + ) + }) + + wrap_plot_list(out) + # patchwork::wrap_plots(out,guides = "collect") +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//plot-download-module.R +######## + +plot_download_ui <- regression_ui <- function(id, ...) { + ns <- shiny::NS(id) + + shiny::tagList( + shinyWidgets::noUiSliderInput( + inputId = ns("plot_height"), + label = "Plot height (mm)", + min = 50, + max = 300, + value = 100, + step = 1, + format = shinyWidgets::wNumbFormat(decimals = 0), + color = datamods:::get_primary_color() + ), + shinyWidgets::noUiSliderInput( + inputId = ns("plot_width"), + label = "Plot width (mm)", + min = 50, + max = 300, + value = 100, + step = 1, + format = shinyWidgets::wNumbFormat(decimals = 0), + color = datamods:::get_primary_color() + ), + shiny::selectInput( + inputId = ns("plot_type"), + label = "File format", + choices = list( + "png", + "tiff", + "eps", + "pdf", + "jpeg", + "svg" + ) + ), + shiny::br(), + # Button + shiny::downloadButton( + outputId = ns("download_plot"), + label = "Download plot", + icon = shiny::icon("download") + ) + ) +} + +plot_download_server <- function(id, + data, + file_name = "reg_plot", + ...) { + shiny::moduleServer( + id = id, + module = function(input, output, session) { + # ns <- session$ns + + + + output$download_plot <- shiny::downloadHandler( + filename = paste0(file_name, ".", input$plot_type), + content = function(file) { + shiny::withProgress(message = "Saving the plot. Hold on for a moment..", { + ggplot2::ggsave( + filename = file, + plot = data, + width = input$plot_width, + height = input$plot_height, + dpi = 300, + units = "mm", scale = 2 + ) + }) + } + ) + } + ) +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//redcap_read_shiny_module.R +######## + +#' Shiny module to browser and export REDCap data +#' +#' @param id Namespace id +#' @param include_title logical to include title +#' +#' @rdname redcap_read_shiny_module +#' +#' @return shiny ui element +#' @export +m_redcap_readUI <- function(id, title = TRUE, url = NULL) { + ns <- shiny::NS(id) + + if (isTRUE(title)) { + title <- shiny::tags$h4( + "Import data from REDCap", + class = "redcap-module-title" + ) + } + + server_ui <- shiny::tagList( + shiny::tags$h4("REDCap server"), + shiny::textInput( + inputId = ns("uri"), + label = "Web address", + value = if_not_missing(url, "https://redcap.your.institution/"), + width = "100%" + ), + shiny::helpText("Format should be either 'https://redcap.your.institution/' or 'https://your.institution/redcap/'"), + # shiny::textInput( + # inputId = ns("api"), + # label = "API token", + # value = "", + # width = "100%" + # ), + shiny::passwordInput( + inputId = ns("api"), + label = "API token", + value = "", + width = "100%" + ), + shiny::helpText("The token is a string of 32 numbers and letters."), + shiny::br(), + shiny::br(), + shiny::actionButton( + inputId = ns("data_connect"), + label = "Connect", + icon = shiny::icon("link", lib = "glyphicon"), + width = "100%", + disabled = TRUE + ), + shiny::br(), + shiny::br(), + tags$div( + id = ns("connect-placeholder"), + shinyWidgets::alert( + id = ns("connect-result"), + status = "info", + tags$p(phosphoricons::ph("info", weight = "bold"), "Please fill in server address (URI) and API token, then press 'Connect'.") + ), + dismissible = TRUE + ), + shiny::br() + ) + + filter_ui <- + shiny::tagList( + # width = 6, + shiny::uiOutput(outputId = ns("arms")), + shiny::textInput( + inputId = ns("filter"), + label = "Optional filter logic (e.g., ⁠[gender] = 'female')" + ) + ) + + params_ui <- + shiny::tagList( + shiny::tags$h4("Data import parameters"), + shiny::tags$div( + style = htmltools::css( + display = "grid", + gridTemplateColumns = "1fr 50px", + gridColumnGap = "10px" + ), + shiny::uiOutput(outputId = ns("fields")), + shiny::tags$div( + class = "shiny-input-container", + shiny::tags$label( + class = "control-label", + `for` = ns("dropdown_params"), + "...", + style = htmltools::css(visibility = "hidden") + ), + shinyWidgets::dropMenu( + shiny::actionButton( + inputId = ns("dropdown_params"), + label = shiny::icon("filter"), + width = "50px" + ), + filter_ui + ) + ) + ), + shiny::helpText("Select fields/variables to import and click the funnel to apply optional filters"), + shiny::tags$br(), + shiny::tags$br(), + shiny::uiOutput(outputId = ns("data_type")), + shiny::uiOutput(outputId = ns("fill")), + shiny::actionButton( + inputId = ns("data_import"), + label = "Import", + icon = shiny::icon("download", lib = "glyphicon"), + width = "100%", + disabled = TRUE + ), + shiny::tags$br(), + shiny::tags$br(), + tags$div( + id = ns("retrieved-placeholder"), + shinyWidgets::alert( + id = ns("retrieved-result"), + status = "info", + tags$p(phosphoricons::ph("info", weight = "bold"), "Please specify data to download, then press 'Import'.") + ), + dismissible = TRUE + ) + ) + + + shiny::fluidPage( + title = title, + server_ui, + # shiny::uiOutput(ns("params_ui")), + shiny::conditionalPanel( + condition = "output.connect_success == true", + params_ui, + ns = ns + ), + shiny::br() + ) +} + + +#' @rdname redcap_read_shiny_module +#' +#' @return shiny server module +#' @export +#' +m_redcap_readServer <- function(id) { + module <- function(input, output, session) { + ns <- session$ns + + data_rv <- shiny::reactiveValues( + dd_status = NULL, + data_status = NULL, + uri = NULL, + project_name = NULL, + info = NULL, + arms = NULL, + dd_list = NULL, + data = NULL, + rep_fields = NULL, + code = NULL + ) + + shiny::observeEvent(list(input$api, input$uri), { + shiny::req(input$api) + shiny::req(input$uri) + if (!is.null(input$uri)) { + uri <- paste0(ifelse(endsWith(input$uri, "/"), input$uri, paste0(input$uri, "/")), "api/") + } else { + uri <- input$uri + } + + if (is_valid_redcap_url(uri) & is_valid_token(input$api)) { + data_rv$uri <- uri + shiny::updateActionButton(inputId = "data_connect", disabled = FALSE) + } else { + shiny::updateActionButton(inputId = "data_connect", disabled = TRUE) + } + }) + + + tryCatch( + { + shiny::observeEvent( + list( + input$data_connect + ), + { + shiny::req(input$api) + shiny::req(data_rv$uri) + + parameters <- list( + redcap_uri = data_rv$uri, + token = input$api + ) + + # browser() + shiny::withProgress( + { + imported <- try(rlang::exec(REDCapR::redcap_metadata_read, !!!parameters), silent = TRUE) + }, + message = paste("Connecting to", data_rv$uri) + ) + + ## TODO: Simplify error messages + if (inherits(imported, "try-error") || NROW(imported) < 1 || ifelse(is.list(imported), !isTRUE(imported$success), FALSE)) { + if (ifelse(is.list(imported), !isTRUE(imported$success), FALSE)) { + mssg <- imported$raw_text + } else { + mssg <- attr(imported, "condition")$message + } + + datamods:::insert_error(mssg = mssg, selector = "connect") + data_rv$dd_status <- "error" + data_rv$dd_list <- NULL + } else if (isTRUE(imported$success)) { + data_rv$dd_status <- "success" + + data_rv$info <- REDCapR::redcap_project_info_read( + redcap_uri = data_rv$uri, + token = input$api + )$data + + datamods:::insert_alert( + selector = ns("connect"), + status = "success", + include_data_alert( + see_data_text = "Click to see data dictionary", + dataIdName = "see_dd", + extra = tags$p( + tags$b(phosphoricons::ph("check", weight = "bold"), "Connected to server!"), + glue::glue("The {data_rv$info$project_title} project is loaded.") + ), + btn_show_data = TRUE + ) + ) + + data_rv$dd_list <- imported + } + }, + ignoreInit = TRUE + ) + }, + warning = function(warn) { + showNotification(paste0(warn), type = "warning") + }, + error = function(err) { + showNotification(paste0(err), type = "err") + } + ) + + output$connect_success <- shiny::reactive(identical(data_rv$dd_status, "success")) + shiny::outputOptions(output, "connect_success", suspendWhenHidden = FALSE) + + + shiny::observeEvent(input$see_dd, { + show_data( + purrr::pluck(data_rv$dd_list, "data"), + title = "Data dictionary", + type = "modal", + show_classes = FALSE, + tags$b("Preview:") + ) + }) + + shiny::observeEvent(input$see_data, { + show_data( + # purrr::pluck(data_rv$dd_list, "data"), + data_rv$data, + title = "Imported data set", + type = "modal", + show_classes = FALSE, + tags$b("Preview:") + ) + }) + + arms <- shiny::reactive({ + shiny::req(input$api) + shiny::req(data_rv$uri) + + REDCapR::redcap_event_read( + redcap_uri = data_rv$uri, + token = input$api + )$data + }) + + output$fields <- shiny::renderUI({ + shiny::req(data_rv$dd_list) + shinyWidgets::virtualSelectInput( + inputId = ns("fields"), + label = "Select fields/variables to import:", + choices = purrr::pluck(data_rv$dd_list, "data") |> + dplyr::select(field_name, form_name) |> + (\(.x){ + split(.x$field_name, REDCapCAST::as_factor(.x$form_name)) + })(), + updateOn = "change", + multiple = TRUE, + search = TRUE, + showValueAsTags = TRUE, + width = "100%" + ) + }) + + output$data_type <- shiny::renderUI({ + shiny::req(data_rv$info) + if (isTRUE(data_rv$info$has_repeating_instruments_or_events)) { + vectorSelectInput( + inputId = ns("data_type"), + label = "Specify the data format", + choices = c( + "Wide data (One row for each subject)" = "wide", + "Long data for project with repeating instruments (default REDCap)" = "long" + ), + selected = "wide", + multiple = FALSE, + width = "100%" + ) + } + }) + + output$fill <- shiny::renderUI({ + shiny::req(data_rv$info) + shiny::req(input$data_type) + + ## Get repeated field + data_rv$rep_fields <- data_rv$dd_list$data$field_name[ + data_rv$dd_list$data$form_name %in% repeated_instruments( + uri = data_rv$uri, + token = input$api + ) + ] + + if (input$data_type == "long" && isTRUE(any(input$fields %in% data_rv$rep_fields))) { + vectorSelectInput( + inputId = ns("fill"), + label = "Fill missing values?", + choices = c( + "Yes, fill missing, non-repeated values" = "yes", + "No, leave the data as is" = "no" + ), + selected = "no", + multiple = FALSE, + width = "100%" + ) + } + }) + + shiny::observeEvent(input$fields, { + if (is.null(input$fields) | length(input$fields) == 0) { + shiny::updateActionButton(inputId = "data_import", disabled = TRUE) + } else { + shiny::updateActionButton(inputId = "data_import", disabled = FALSE) + } + }) + + output$arms <- shiny::renderUI({ + if (NROW(arms()) > 0) { + vectorSelectInput( + inputId = ns("arms"), + selected = NULL, + label = "Filter by events/arms", + choices = stats::setNames(arms()[[3]], arms()[[1]]), + multiple = TRUE, + width = "100%" + ) + } + }) + + shiny::observeEvent(input$data_import, { + shiny::req(input$fields) + + # browser() + record_id <- purrr::pluck(data_rv$dd_list, "data")[[1]][1] + + + parameters <- list( + uri = data_rv$uri, + token = input$api, + fields = unique(c(record_id, input$fields)), + events = input$arms, + raw_or_label = "both", + filter_logic = input$filter, + split_forms = ifelse( + input$data_type == "long" && !is.null(input$data_type), + "none", + "all" + ) + ) + + shiny::withProgress(message = "Downloading REDCap data. Hold on for a moment..", { + imported <- try(rlang::exec(REDCapCAST::read_redcap_tables, !!!parameters), silent = TRUE) + }) + + parameters_code <- parameters[c("uri", "fields", "events", "raw_or_label", "filter_logic")] + + code <- rlang::call2( + "easy_redcap", + !!!utils::modifyList( + parameters_code, + list( + data_format = ifelse( + input$data_type == "long" && !is.null(input$data_type), + "long", + "wide" + ), + project.name = simple_snake(data_rv$info$project_title) + ) + ), + .ns = "REDCapCAST" + ) + + if (inherits(imported, "try-error") || NROW(imported) < 1) { + data_rv$data_status <- "error" + data_rv$data_list <- NULL + data_rv$data_message <- imported$raw_text + } else { + data_rv$data_status <- "success" + data_rv$data_message <- "Requested data was retrieved!" + + ## The data management below should be separated to allow for changing + ## "wide"/"long" without re-importing data + + if (parameters$split_form == "all") { + # browser() + out <- imported |> + # redcap_wider() + REDCapCAST::redcap_wider() + } else { + if (input$fill == "yes") { + ## Repeated fields + + + ## Non-repeated fields in current dataset + inc_non_rep <- names(imported)[!names(imported) %in% data_rv$rep_fields] + + out <- imported |> + drop_empty_event() |> + dplyr::group_by(!!dplyr::sym(names(imported)[1])) |> + tidyr::fill(inc_non_rep) |> + dplyr::ungroup() + } else { + out <- imported |> + drop_empty_event() + } + } + + # browser() + in_data_check <- parameters$fields %in% names(out) | + sapply(names(out), \(.x) any(sapply(parameters$fields, \(.y) startsWith(.x, .y)))) + + if (!any(in_data_check[-1])) { + data_rv$data_status <- "warning" + data_rv$data_message <- "Data retrieved, but it looks like only the ID was retrieved from the server. Please check with your REDCap administrator that you have required permissions for data access." + } + + if (!all(in_data_check)) { + data_rv$data_status <- "warning" + data_rv$data_message <- "Data retrieved, but it looks like not all requested fields were retrieved from the server. Please check with your REDCap administrator that you have required permissions for data access." + } + + data_rv$code <- code + + data_rv$data <- out |> + dplyr::select(-dplyr::ends_with("_complete")) |> + # dplyr::select(-dplyr::any_of(record_id)) |> + REDCapCAST::suffix2label() + } + }) + + shiny::observeEvent( + data_rv$data_status, + { + # browser() + if (identical(data_rv$data_status, "error")) { + datamods:::insert_error(mssg = data_rv$data_message, selector = ns("retrieved")) + } else if (identical(data_rv$data_status, "success")) { + datamods:::insert_alert( + selector = ns("retrieved"), + status = data_rv$data_status, + # tags$p( + # tags$b(phosphoricons::ph("check", weight = "bold"), "Success!"), + # data_rv$data_message + # ), + include_data_alert( + see_data_text = "Click to see the imported data", + dataIdName = "see_data", + extra = tags$p( + tags$b(phosphoricons::ph("check", weight = "bold"), data_rv$data_message) + ), + btn_show_data = TRUE + ) + ) + } else { + datamods:::insert_alert( + selector = ns("retrieved"), + status = data_rv$data_status, + tags$p( + tags$b(phosphoricons::ph("warning", weight = "bold"), "Warning!"), + data_rv$data_message + ) + ) + } + } + ) + + return(list( + status = shiny::reactive(data_rv$data_status), + name = shiny::reactive(data_rv$info$project_title), + info = shiny::reactive(data_rv$info), + code = shiny::reactive(data_rv$code), + data = shiny::reactive(data_rv$data) + )) + } + + shiny::moduleServer( + id = id, + module = module + ) +} + +#' @importFrom htmltools tagList tags +#' @importFrom shiny icon getDefaultReactiveDomain +include_data_alert <- function(dataIdName = "see_data", + btn_show_data, + see_data_text = "Click to see data", + extra = NULL, + session = shiny::getDefaultReactiveDomain()) { + if (isTRUE(btn_show_data)) { + success_message <- tagList( + extra, + tags$br(), + shiny::actionLink( + inputId = session$ns(dataIdName), + label = tagList(phosphoricons::ph("book-open-text"), see_data_text) + ) + ) + } + return(success_message) +} + +# #' REDCap import teal data module +# #' +# #' @rdname redcap_read_shiny_module +# tdm_redcap_read <- teal::teal_data_module( +# ui <- function(id) { +# shiny::fluidPage( +# m_redcap_readUI(id) +# ) +# }, +# server = function(id) { +# m_redcap_readServer(id, output.format = "teal") +# } +# ) + + +#' Test if url is valid format for REDCap API +#' +#' @param url url +#' +#' @returns logical +#' @export +#' +#' @examples +#' url <- c( +#' "www.example.com", +#' "redcap.your.inst/api/", +#' "https://redcap.your.inst/api/", +#' "https://your.inst/redcap/api/", +#' "https://www.your.inst/redcap/api/" +#' ) +#' is_valid_redcap_url(url) +is_valid_redcap_url <- function(url) { + pattern <- "https://[^ /$.?#].[^\\s]*/api/$" + stringr::str_detect(url, pattern) +} + +#' Validate REDCap token +#' +#' @param token token +#' @param pattern_env pattern +#' +#' @returns logical +#' @export +#' +#' @examples +#' token <- paste(sample(c(1:9, LETTERS[1:6]), 32, TRUE), collapse = "") +#' is_valid_token(token) +is_valid_token <- function(token, pattern_env = NULL, nchar = 32) { + checkmate::assert_character(token, any.missing = TRUE, len = 1) + + if (!is.null(pattern_env)) { + checkmate::assert_character(pattern_env, + any.missing = FALSE, + len = 1 + ) + pattern <- pattern_env + } else { + pattern <- glue::glue("^([0-9A-Fa-f]{})(?:\\n)?$", + .open = "<", + .close = ">" + ) + } + + if (is.na(token)) { + out <- FALSE + } else if (is.null(token)) { + out <- FALSE + } else if (nchar(token) == 0L) { + out <- FALSE + } else if (!grepl(pattern, token, perl = TRUE)) { + out <- FALSE + } else { + out <- TRUE + } + out +} + +#' Get names of repeated instruments +#' +#' @param uri REDCap database uri +#' @param token database token +#' +#' @returns vector +#' @export +#' +repeated_instruments <- function(uri, token) { + instruments <- REDCapR::redcap_event_instruments(redcap_uri = uri, token = token) + unique(instruments$data$form[duplicated(instruments$data$form)]) +} + +#' Drop empty events from REDCap export +#' +#' @param data data +#' @param event "redcap_event_name", "redcap_repeat_instrument" or +#' "redcap_repeat_instance" +#' +#' @returns data.frame +#' @export +#' +drop_empty_event <- function(data, event = "redcap_event_name") { + generics <- c(names(data)[1], "redcap_event_name", "redcap_repeat_instrument", "redcap_repeat_instance") + + filt <- split(data, data[[event]]) |> + lapply(\(.x){ + dplyr::select(.x, -tidyselect::all_of(generics)) |> + REDCapCAST::all_na() + }) |> + unlist() + + data[data[[event]] %in% names(filt)[!filt], ] +} + + +#' Test app for the redcap_read_shiny_module +#' +#' @rdname redcap_read_shiny_module +#' +#' @examples +#' \dontrun{ +#' redcap_demo_app() +#' } +redcap_demo_app <- function() { + ui <- shiny::fluidPage( + m_redcap_readUI("data", url = NULL), + DT::DTOutput("data"), + shiny::tags$b("Code:"), + shiny::verbatimTextOutput(outputId = "code") + ) + server <- function(input, output, session) { + data_val <- m_redcap_readServer(id = "data") + + output$data <- DT::renderDataTable( + { + shiny::req(data_val$data) + data_val$data() + }, + options = list( + scrollX = TRUE, + pageLength = 5 + ), + ) + output$code <- shiny::renderPrint({ + shiny::req(data_val$code) + data_val$code() + }) + } + shiny::shinyApp(ui, server) +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//regression_model.R +######## + +#' Create a regression model programatically +#' +#' @param data data set +#' @param fun Name of function as character vector or function to use for model creation. +#' @param vars character vector of variables to include +#' @param outcome.str Name of outcome variable. Character vector. +#' @param auto.mode Make assumptions on function dependent on outcome data format. Overwrites other arguments. +#' @param formula.str Formula as string. Passed through 'glue::glue'. If given, 'outcome.str' and 'vars' are ignored. Optional. +#' @param args.list List of arguments passed to 'fun' with 'do.call'. +#' @param ... ignored for now +#' +#' @importFrom stats as.formula +#' +#' @return object of standard class for fun +#' @export +#' @rdname regression_model +#' +#' @examples +#' gtsummary::trial |> +#' regression_model(outcome.str = "age") +#' gtsummary::trial |> +#' regression_model( +#' outcome.str = "age", +#' auto.mode = FALSE, +#' fun = "stats::lm", +#' formula.str = "{outcome.str}~.", +#' args.list = NULL +#' ) +#' gtsummary::trial |> +#' default_parsing() |> +#' regression_model( +#' outcome.str = "trt", +#' auto.mode = FALSE, +#' fun = "stats::glm", +#' args.list = list(family = binomial(link = "logit")) +#' ) +#' m <- mtcars |> +#' default_parsing() |> +#' regression_model( +#' outcome.str = "mpg", +#' auto.mode = FALSE, +#' fun = "stats::lm", +#' formula.str = "{outcome.str}~{paste(vars,collapse='+')}", +#' args.list = NULL, +#' vars = c("mpg", "cyl") +#' ) +#' broom::tidy(m) +regression_model <- function(data, + outcome.str = NULL, + auto.mode = FALSE, + formula.str = NULL, + args.list = NULL, + fun = NULL, + vars = NULL, + ...) { + if (!is.null(formula.str)) { + if (formula.str == "") { + formula.str <- NULL + } + } + + ## This will handle if outcome is not in data for nicer shiny behavior + if (isTRUE(!outcome.str %in% names(data))) { + outcome.str <- names(data)[1] + print("Outcome variable is not in data, first column is used") + } + + if (!is.null(formula.str)) { + formula.glue <- glue::glue(formula.str) + outcome.str <- NULL + } else { + assertthat::assert_that(outcome.str %in% names(data), + msg = "Outcome variable is not present in the provided dataset" + ) + formula.glue <- glue::glue("{outcome.str}~{paste(vars,collapse='+')}") + } + + if (is.null(vars)) { + vars <- names(data)[!names(data) %in% outcome.str] + } else if (!is.null(outcome.str)) { + if (outcome.str %in% vars) { + vars <- vars[!vars %in% outcome.str] + } + data <- data |> dplyr::select(dplyr::all_of(c(vars, outcome.str))) + } + + # Formatting character variables as factor + # Improvement should add a missing vector to format as NA + data <- data |> + purrr::map(\(.x){ + if (is.character(.x)) { + suppressWarnings(REDCapCAST::as_factor(.x)) + } else { + .x + } + }) |> + dplyr::bind_cols(.name_repair = "unique_quiet") + + if (is.null(fun)) auto.mode <- TRUE + + if (isTRUE(auto.mode)) { + if (is.numeric(data[[outcome.str]])) { + fun <- "stats::lm" + } else if (is.factor(data[[outcome.str]])) { + if (length(levels(data[[outcome.str]])) == 2) { + fun <- "stats::glm" + args.list <- list(family = stats::binomial(link = "logit")) + } else if (length(levels(data[[outcome.str]])) > 2) { + fun <- "MASS::polr" + args.list <- list( + Hess = TRUE, + method = "logistic" + ) + } else { + stop("The provided output variable only has one level") + } + } else { + stop("Output variable should be either numeric or factor for auto.mode") + } + } + + assertthat::assert_that("character" %in% class(fun), + msg = "Please provide the function as a character vector." + ) + + out <- do.call( + getfun(fun), + c( + list( + data = data, + formula = as.formula(formula.glue) + ), + args.list + ) + ) + + # out <- REDCapCAST::set_attr(out,label = fun,attr = "fun.call") + + # Recreating the call + # out$call <- match.call(definition=eval(parse(text=fun)), call(fun, data = 'data',formula = as.formula(formula.str),args.list)) + + return(out) +} + +#' Create a regression model programatically +#' +#' @param data data set +#' @param fun Name of function as character vector or function to use for model creation. +#' @param vars character vector of variables to include +#' @param outcome.str Name of outcome variable. Character vector. +#' @param args.list List of arguments passed to 'fun' with 'do.call'. +#' @param ... ignored for now +#' +#' @importFrom stats as.formula +#' @rdname regression_model +#' +#' @return object of standard class for fun +#' @export +#' +#' @examples +#' \dontrun{ +#' gtsummary::trial |> +#' regression_model_uv(outcome.str = "age") +#' gtsummary::trial |> +#' regression_model_uv( +#' outcome.str = "age", +#' fun = "stats::lm", +#' args.list = NULL +#' ) +#' m <- gtsummary::trial |> regression_model_uv( +#' outcome.str = "trt", +#' fun = "stats::glm", +#' args.list = list(family = stats::binomial(link = "logit")) +#' ) +#' lapply(m, broom::tidy) |> dplyr::bind_rows() +#' } +regression_model_uv <- function(data, + outcome.str, + args.list = NULL, + fun = NULL, + vars = NULL, + ...) { + ## This will handle if outcome is not in data for nicer shiny behavior + if (!outcome.str %in% names(data)) { + outcome.str <- names(data)[1] + print("outcome is not in data, first column is used") + } + + if (!is.null(vars)) { + data <- data |> + dplyr::select(dplyr::all_of( + unique(c(outcome.str, vars)) + )) + } + + if (is.null(args.list)) { + args.list <- list() + } + + if (is.null(fun)) { + if (is.numeric(data[[outcome.str]])) { + fun <- "stats::lm" + } else if (is.factor(data[[outcome.str]])) { + if (length(levels(data[[outcome.str]])) == 2) { + fun <- "stats::glm" + args.list <- list(family = stats::binomial(link = "logit")) + } else if (length(levels(data[[outcome.str]])) > 2) { + fun <- "MASS::polr" + args.list <- list( + Hess = TRUE, + method = "logistic" + ) + } else { + stop("The provided output variable only has one level") + } + } else { + stop("Output variable should be either numeric or factor for auto.mode") + } + } + + assertthat::assert_that("character" %in% class(fun), + msg = "Please provide the function as a character vector." + ) + + out <- names(data)[!names(data) %in% outcome.str] |> + purrr::map(\(.var){ + do.call( + regression_model, + c( + list( + data = data[match(c(outcome.str, .var), names(data))], + outcome.str = outcome.str + ), + args.list + ) + ) + }) + + return(out) +} + + +### HELPERS + +#' Data type assessment. +#' +#' @description +#' These are more overall than the native typeof. This is used to assess a more +#' meaningful "clinical" data type. +#' +#' @param data vector or data.frame. if data frame, each column is evaluated. +#' +#' @returns outcome type +#' @export +#' +#' @examples +#' mtcars |> +#' default_parsing() |> +#' lapply(data_type) +#' mtcars |> +#' default_parsing() |> +#' data_type() +#' c(1, 2) |> data_type() +#' 1 |> data_type() +#' c(rep(NA, 10)) |> data_type() +#' sample(1:100, 50) |> data_type() +#' factor(letters[1:20]) |> data_type() +#' as.Date(1:20) |> data_type() +data_type <- function(data) { + if (is.data.frame(data)) { + sapply(data, data_type) + } else { + cl_d <- class(data) + l_unique <- length(unique(na.omit(data))) + if (all(is.na(data))) { + out <- "empty" + } else if (l_unique < 2) { + out <- "monotone" + } else if (any(c("factor", "logical") %in% cl_d) | l_unique == 2) { + if (identical("logical", cl_d) | l_unique == 2) { + out <- "dichotomous" + } else { + # if (is.ordered(data)) { + # out <- "ordinal" + # } else { + out <- "categorical" + # } + } + } else if (identical(cl_d, "character")) { + out <- "text" + } else if (any(c("hms", "Date", "POSIXct", "POSIXt") %in% cl_d)) { + out <- "datetime" + } else if (l_unique > 2) { + ## Previously had all thinkable classes + ## Now just assumes the class has not been defined above + ## any(c("numeric", "integer", "hms", "Date", "timediff") %in% cl_d) & + out <- "continuous" + } else { + out <- "unknown" + } + + out + } +} + +#' Recognised data types from data_type +#' +#' @returns vector +#' @export +#' +#' @examples +#' data_types() +data_types <- function() { + list( + "empty" = list(descr="Variable of all NAs",classes="Any class"), + "monotone" = list(descr="Variable with only one unique value",classes="Any class"), + "dichotomous" = list(descr="Variable with only two unique values",classes="Any class"), + "categorical"= list(descr="Factor variable",classes="factor (ordered or unordered)"), + "text"= list(descr="Character variable",classes="character"), + "datetime"= list(descr="Variable of time, date or datetime values",classes="hms, Date, POSIXct and POSIXt"), + "continuous"= list(descr="Numeric variable",classes="numeric, integer or double"), + "unknown"= list(descr="Anything not falling within the previous",classes="Any other class") + ) +} + + +#' Implemented functions +#' +#' @description +#' Library of supported functions. The list name and "descr" element should be +#' unique for each element on list. +#' +#' +#' @returns list +#' @export +#' +#' @examples +#' supported_functions() +supported_functions <- function() { + list( + lm = list( + descr = "Linear regression model", + design = "cross-sectional", + out.type = "continuous", + fun = "stats::lm", + args.list = NULL, + formula.str = "{outcome.str}~{paste(vars,collapse='+')}", + table.fun = "gtsummary::tbl_regression", + table.args.list = list(exponentiate = FALSE) + ), + glm = list( + descr = "Logistic regression model", + design = "cross-sectional", + out.type = "dichotomous", + fun = "stats::glm", + args.list = list(family = "binomial"), + formula.str = "{outcome.str}~{paste(vars,collapse='+')}", + table.fun = "gtsummary::tbl_regression", + table.args.list = list() + ), + polr = list( + descr = "Ordinal logistic regression model", + design = "cross-sectional", + out.type = c("categorical"), + fun = "MASS::polr", + args.list = list( + Hess = TRUE, + method = "logistic" + ), + formula.str = "{outcome.str}~{paste(vars,collapse='+')}", + table.fun = "gtsummary::tbl_regression", + table.args.list = list() + ) + ) +} + + +#' Get possible regression models +#' +#' @param data data +#' +#' @returns character vector +#' @export +#' +#' @examples +#' mtcars |> +#' default_parsing() |> +#' dplyr::pull("cyl") |> +#' possible_functions(design = "cross-sectional") +#' +#' mtcars |> +#' default_parsing() |> +#' dplyr::select("cyl") |> +#' possible_functions(design = "cross-sectional") +possible_functions <- function(data, design = c("cross-sectional")) { + # + # data <- if (is.reactive(data)) data() else data + if (is.data.frame(data)) { + data <- data[[1]] + } + + design <- match.arg(design) + type <- data_type(data) + + design_ls <- supported_functions() |> + lapply(\(.x){ + if (design %in% .x$design) { + .x + } + }) + + if (type == "unknown") { + out <- type + } else { + out <- design_ls |> + lapply(\(.x){ + if (type %in% .x$out.type) { + .x$descr + } + }) |> + unlist() + } + unname(out) +} + + +#' Get the function options based on the selected function description +#' +#' @param data vector +#' +#' @returns list +#' @export +#' +#' @examples +#' mtcars |> +#' default_parsing() |> +#' dplyr::pull(mpg) |> +#' possible_functions(design = "cross-sectional") |> +#' (\(.x){ +#' .x[[1]] +#' })() |> +#' get_fun_options() +get_fun_options <- function(data) { + descrs <- supported_functions() |> + lapply(\(.x){ + .x$descr + }) |> + unlist() + supported_functions() |> + (\(.x){ + .x[match(data, descrs)] + })() +} + + +#' Wrapper to create regression model based on supported models +#' +#' @description +#' Output is a concatenated list of model information and model +#' +#' +#' @param data data +#' @param outcome.str name of outcome variable +#' @param fun.descr Description of chosen function matching description in +#' "supported_functions()" +#' @param fun name of custom function. Default is NULL. +#' @param formula.str custom formula glue string. Default is NULL. +#' @param args.list custom character string to be converted using +#' argsstring2list() or list of arguments. Default is NULL. +#' @param ... ignored +#' +#' @returns list +#' @export +#' @rdname regression_model +#' +#' @examples +#' \dontrun{ +#' gtsummary::trial |> +#' regression_model( +#' outcome.str = "age", +#' fun = "stats::lm", +#' formula.str = "{outcome.str}~.", +#' args.list = NULL +#' ) +#' ls <- regression_model_list(data = default_parsing(mtcars), outcome.str = "cyl", fun.descr = "Ordinal logistic regression model") +#' summary(ls$model) +#' ls <- regression_model_list(data = default_parsing(mtcars), outcome.str = "mpg", fun.descr = "Linear regression model") +#' +#' ls <- regression_model_list(data = default_parsing(gtsummary::trial), outcome.str = "trt", fun.descr = "Logistic regression model") +#' tbl <- gtsummary::tbl_regression(ls$model, exponentiate = TRUE) +#' m <- gtsummary::trial |> +#' default_parsing() |> +#' regression_model( +#' outcome.str = "trt", +#' fun = "stats::glm", +#' formula.str = "{outcome.str}~.", +#' args.list = list(family = "binomial") +#' ) +#' tbl2 <- gtsummary::tbl_regression(m, exponentiate = TRUE) +#' broom::tidy(ls$model) +#' broom::tidy(m) +#' } +regression_model_list <- function(data, + outcome.str, + fun.descr, + fun = NULL, + formula.str = NULL, + args.list = NULL, + vars = NULL, + ...) { + options <- get_fun_options(fun.descr) |> + (\(.x){ + .x[[1]] + })() + + ## Custom, specific fun, args and formula options + + if (is.null(formula.str)) { + formula.str.c <- options$formula.str + } else { + formula.str.c <- formula.str + } + + if (is.null(fun)) { + fun.c <- options$fun + } else { + fun.c <- fun + } + + if (is.null(args.list)) { + args.list.c <- options$args.list + } else { + args.list.c <- args.list + } + + if (is.character(args.list.c)) args.list.c <- argsstring2list(args.list.c) + + ## Handling vars to print code + + if (is.null(vars)) { + vars <- names(data)[!names(data) %in% outcome.str] + } else { + if (outcome.str %in% vars) { + vars <- vars[!vars %in% outcome.str] + } + } + + parameters <- list( + data = data, + fun = fun.c, + formula.str = glue::glue(formula.str.c), + args.list = args.list.c + ) + + model <- do.call( + regression_model, + parameters + ) + + parameters_code <- Filter( + length, + modifyList(parameters, list( + data = as.symbol("df"), + formula.str = as.character(glue::glue(formula.str.c)), + outcome.str = NULL + # args.list = NULL, + )) + ) + + ## The easiest solution was to simple paste as a string + ## The rlang::call2 or rlang::expr functions would probably work as well + # code <- glue::glue("FreesearchR::regression_model({parameters_print}, args.list=list({list2str(args.list.c)}))", .null = "NULL") + code <- rlang::call2("regression_model", !!!parameters_code, .ns = "FreesearchR") + + list( + options = options, + model = model, + code = expression_string(code) + ) +} + +list2str <- function(data) { + out <- purrr::imap(data, \(.x, .i){ + if (is.logical(.x)) { + arg <- .x + } else { + arg <- glue::glue("'{.x}'") + } + glue::glue("{.i} = {arg}") + }) |> + unlist() |> + paste(collapse = (", ")) + + if (out == "") { + return(NULL) + } else { + out + } +} + + +#' @returns list +#' @export +#' @rdname regression_model +#' +#' @examples +#' \dontrun{ +#' gtsummary::trial |> +#' regression_model_uv( +#' outcome.str = "trt", +#' fun = "stats::glm", +#' args.list = list(family = stats::binomial(link = "logit")) +#' ) |> +#' lapply(broom::tidy) |> +#' dplyr::bind_rows() +#' ms <- regression_model_uv_list(data = default_parsing(mtcars), outcome.str = "mpg", fun.descr = "Linear regression model") +#' ms$code +#' ls <- regression_model_uv_list(data = default_parsing(mtcars), outcome.str = "am", fun.descr = "Logistic regression model") +#' ls$code +#' lapply(ms$model, broom::tidy) |> dplyr::bind_rows() +#' } +regression_model_uv_list <- function(data, + outcome.str, + fun.descr, + fun = NULL, + formula.str = NULL, + args.list = NULL, + vars = NULL, + ...) { + options <- get_fun_options(fun.descr) |> + (\(.x){ + .x[[1]] + })() + + ## Custom, specific fun, args and formula options + + if (is.null(formula.str)) { + formula.str.c <- options$formula.str + } else { + formula.str.c <- formula.str + } + + if (is.null(fun)) { + fun.c <- options$fun + } else { + fun.c <- fun + } + + if (is.null(args.list)) { + args.list.c <- options$args.list + } else { + args.list.c <- args.list + } + + if (is.character(args.list.c)) args.list.c <- argsstring2list(args.list.c) + + ## Handling vars to print code + + if (is.null(vars)) { + vars <- names(data)[!names(data) %in% outcome.str] + } else { + if (outcome.str %in% vars) { + vars <- vars[!vars %in% outcome.str] + } + } + + # assertthat::assert_that("character" %in% class(fun), + # msg = "Please provide the function as a character vector." + # ) + + # model <- do.call( + # regression_model, + # c( + # list(data = data), + # list(outcome.str = outcome.str), + # list(fun = fun.c), + # list(formula.str = formula.str.c), + # args.list.c + # ) + # ) + + model <- vars |> + lapply(\(.var){ + parameters <- + list( + fun = fun.c, + data = data[c(outcome.str, .var)], + formula.str = as.character(glue::glue(gsub("vars", ".var", formula.str.c))), + args.list = args.list.c + ) + + out <- do.call( + regression_model, + parameters + ) + + ## This is the very long version + ## Handles deeply nested glue string + # code <- glue::glue("FreesearchR::regression_model(data=df,{list2str(modifyList(parameters,list(data=NULL,args.list=list2str(args.list.c))))})") + code <- rlang::call2("regression_model", !!!modifyList(parameters, list(data = as.symbol("df"), args.list = args.list.c)), .ns = "FreesearchR") + REDCapCAST::set_attr(out, code, "code") + }) + + code <- model |> + lapply(\(.x)REDCapCAST::get_attr(.x, "code")) |> + lapply(expression_string) |> + pipe_string(collapse = ",\n") |> + (\(.x){ + paste0("list(\n", .x, ")") + })() + + + list( + options = options, + model = model, + code = code + ) +} + + +# regression_model(mtcars, fun = "stats::lm", formula.str = "mpg~cyl") + + +######## +#### Current file: /Users/au301842/FreesearchR/R//regression_plot.R +######## + +#' Regression coef plot from gtsummary. Slightly modified to pass on arguments +#' +#' @param x (`tbl_regression`, `tbl_uvregression`)\cr +#' A 'tbl_regression' or 'tbl_uvregression' object +#' @param plot_ref (scalar `logical`)\cr +#' plot reference values +#' @param remove_header_rows (scalar `logical`)\cr +#' logical indicating whether to remove header rows +#' for categorical variables. Default is `TRUE` +#' @param remove_reference_rows (scalar `logical`)\cr +#' logical indicating whether to remove reference rows +#' for categorical variables. Default is `FALSE`. +#' @param ... arguments passed to `ggstats::ggcoef_plot(...)` +#' +#' @returns ggplot object +#' @export +#' +#' @examples +#' \dontrun{ +#' mod <- lm(mpg ~ ., default_parsing(mtcars)) +#' p <- mod |> +#' gtsummary::tbl_regression() |> +#' plot(colour = "variable") +#' } +#' +plot.tbl_regression <- function(x, + plot_ref = TRUE, + remove_header_rows = TRUE, + remove_reference_rows = FALSE, + ...) { + # check_dots_empty() + gtsummary:::check_pkg_installed("ggstats") + gtsummary:::check_not_missing(x) + # gtsummary:::check_scalar_logical(remove_header_rows) + # gtsummary:::check_scalar_logical(remove_reference_rows) + + df_coefs <- x$table_body + + if (isTRUE(remove_header_rows)) { + df_coefs <- df_coefs |> dplyr::filter(!header_row %in% TRUE) + } + if (isTRUE(remove_reference_rows)) { + df_coefs <- df_coefs |> dplyr::filter(!reference_row %in% TRUE) + } + + # Removes redundant label + df_coefs$label[df_coefs$row_type == "label"] <- "" + # browser() + # Add estimate value to reference level + if (plot_ref == TRUE) { + df_coefs[df_coefs$var_type %in% c("categorical", "dichotomous") & df_coefs$reference_row & !is.na(df_coefs$reference_row), "estimate"] <- if (x$inputs$exponentiate) 1 else 0 + } + + p <- df_coefs |> + ggstats::ggcoef_plot(exponentiate = x$inputs$exponentiate, ...) + + if (x$inputs$exponentiate) { + p <- symmetrical_scale_x_log10(p) + } + p +} + + +#' Wrapper to pivot gtsummary table data to long for plotting +#' +#' @param list a custom regression models list +#' @param model.names names of models to include +#' +#' @returns list +#' @export +#' +merge_long <- function(list, model.names) { + l_subset <- list$tables[model.names] + + l_merged <- l_subset |> tbl_merge() + + df_body <- l_merged$table_body + + sel_list <- lapply(seq_along(l_subset), \(.i){ + endsWith(names(df_body), paste0("_", .i)) + }) |> + setNames(names(l_subset)) + + common <- !Reduce(`|`, sel_list) + + df_body_long <- sel_list |> + purrr::imap(\(.l, .i){ + d <- dplyr::bind_cols( + df_body[common], + df_body[.l], + model = .i + ) + setNames(d, gsub("_[0-9]{,}$", "", names(d))) + }) |> + dplyr::bind_rows() |> + dplyr::mutate(model = REDCapCAST::as_factor(model)) + + l_merged$table_body <- df_body_long + + l_merged$inputs$exponentiate <- !identical(class(list$models$Multivariable$model), "lm") + + l_merged +} + + +#' Easily round log scale limits for nice plots +#' +#' @param data data +#' @param fun rounding function (floor/ceiling) +#' @param ... ignored +#' +#' @returns numeric vector +#' @export +#' +#' @examples +#' limit_log(-.1, floor) +#' limit_log(.1, ceiling) +#' limit_log(-2.1, ceiling) +#' limit_log(2.1, ceiling) +limit_log <- function(data, fun, ...) { + fun(10^-floor(data) * 10^data) / 10^-floor(data) +} + +#' Create summetric log ticks +#' +#' @param data numeric vector +#' +#' @returns numeric vector +#' @export +#' +#' @examples +#' c(sample(seq(.1, 1, .1), 3), sample(1:10, 3)) |> create_log_tics() +create_log_tics <- function(data) { + sort(round(unique(c(1 / data, data, 1)), 2)) +} + +#' Ensure symmetrical plot around 1 on a logarithmic x scale for ratio plots +#' +#' @param plot ggplot2 plot +#' @param breaks breaks used and mirrored +#' @param ... ignored +#' +#' @returns ggplot2 object +#' @export +#' +symmetrical_scale_x_log10 <- function(plot, breaks = c(1, 2, 3, 5, 10), ...) { + rx <- ggplot2::layer_scales(plot)$x$get_limits() + + x_min <- floor(10 * rx[1]) / 10 + x_max <- ceiling(10 * rx[2]) / 10 + + rx_min <- limit_log(rx[1], floor) + rx_max <- limit_log(rx[2], ceiling) + + max_abs_x <- max(abs(c(x_min, x_max))) + + ticks <- log10(breaks) + (ceiling(max_abs_x) - 1) + + plot + ggplot2::scale_x_log10(limits = c(rx_min, rx_max), breaks = create_log_tics(10^ticks[ticks <= max_abs_x])) +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//regression_table.R +######## + +#' Create table of regression model +#' +#' @param x regression model +#' @param args.list list of arguments passed to 'fun'. +#' @param fun function to use for table creation. Default is "gtsummary::tbl_regression". +#' @param ... passed to methods +#' +#' @return object of standard class for fun +#' @export +#' @name regression_table +#' +#' @examples +#' \dontrun{ +#' tbl <- gtsummary::trial |> +#' regression_model( +#' outcome.str = "stage", +#' fun = "MASS::polr" +#' ) |> +#' regression_table(args.list = list("exponentiate" = TRUE)) +#' gtsummary::trial |> +#' regression_model( +#' outcome.str = "age", +#' fun = "stats::lm", +#' formula.str = "{outcome.str}~.", +#' args.list = NULL +#' ) |> +#' regression_table() |> +#' plot() +#' gtsummary::trial |> +#' regression_model( +#' outcome.str = "trt", +#' fun = "stats::glm", +#' args.list = list(family = binomial(link = "logit")) +#' ) |> +#' regression_table() +#' gtsummary::trial |> +#' regression_model_uv( +#' outcome.str = "trt", +#' fun = "stats::glm", +#' args.list = list(family = stats::binomial(link = "logit")) +#' ) |> +#' regression_table() +#' gtsummary::trial |> +#' regression_model_uv( +#' outcome.str = "stage", +#' args.list = list(family = stats::binomial(link = "logit")) +#' ) |> +#' regression_table() +#' mtcars|> +#' regression_model( +#' outcome.str = "mpg", +#' args.list = NULL) +#' ) |> +#' regression_table() +#' +#' +#' list( +#' "Univariable" = regression_model_uv, +#' "Multivariable" = regression_model +#' ) |> +#' lapply(\(.fun){ +#' do.call( +#' .fun, +#' c( +#' list(data = gtsummary::trial), +#' list(outcome.str = "stage") +#' ) +#' ) +#' }) |> +#' purrr::map(regression_table) |> +#' tbl_merge() +#' } +#' regression_table <- function(x, ...) { +#' UseMethod("regression_table") +#' } +#' +#' #' @rdname regression_table +#' #' @export +#' regression_table.list <- function(x, ...) { +#' x |> +#' purrr::map(\(.m){ +#' regression_table(x = .m, ...) |> +#' gtsummary::add_n() +#' }) |> +#' gtsummary::tbl_stack() +#' } +#' +#' #' @rdname regression_table +#' #' @export +#' regression_table.default <- function(x, ..., args.list = NULL, fun = "gtsummary::tbl_regression") { +#' # Stripping custom class +#' class(x) <- class(x)[class(x) != "freesearchr_model"] +#' +#' if (any(c(length(class(x)) != 1, class(x) != "lm"))) { +#' if (!"exponentiate" %in% names(args.list)) { +#' args.list <- c(args.list, list(exponentiate = TRUE)) +#' } +#' } +#' +#' out <- do.call(getfun(fun), c(list(x = x), args.list)) +#' out |> +#' gtsummary::add_glance_source_note() # |> +#' # gtsummary::bold_p() +#' } +regression_table <- function(x, ...) { + args <- list(...) + + if ("list" %in% class(x)) { + x |> + purrr::map(\(.m){ + regression_table_create(x = .m, args.list = args) |> + gtsummary::add_n() + }) |> + gtsummary::tbl_stack() + } else { + regression_table_create(x, args.list = args) + } +} + +#' Create regression summary table +#' +#' @param x (list of) regression model +#' @param ... ignored for now +#' @param args.list args.list for the summary function +#' @param fun table summary function. Default is "gtsummary::tbl_regression" +#' @param theme summary table theme +#' +#' @returns gtsummary list object +#' @export +#' +regression_table_create <- function(x, ..., args.list = NULL, fun = "gtsummary::tbl_regression", theme = c("jama", "lancet", "nejm", "qjecon")) { + # Stripping custom class + class(x) <- class(x)[class(x) != "freesearchr_model"] + + theme <- match.arg(theme) + + if (any(c(length(class(x)) != 1, class(x) != "lm"))) { + if (!"exponentiate" %in% names(args.list)) { + args.list <- c(args.list, list(exponentiate = TRUE, p.values = TRUE)) + } + } + + gtsummary::theme_gtsummary_journal(journal = theme) + if (inherits(x, "polr")) { + # browser() + out <- do.call(getfun(fun), c(list(x = x), args.list)) + # out <- do.call(getfun(fun), c(list(x = x, tidy_fun = list(residual_type = "normal")), args.list)) + # out <- do.call(what = getfun(fun), + # args = c( + # list( + # x = x, + # tidy_fun = list( + # conf.int = TRUE, + # conf.level = 0.95, + # residual_type = "normal")), + # args.list) + # ) + } else { + out <- do.call(getfun(fun), c(list(x = x), args.list)) + } + + out +} + + +#' A substitue to gtsummary::tbl_merge, that will use list names for the tab +#' spanner names. +#' +#' @param data gtsummary list object +#' +#' @return gt summary list object +#' @export +#' +tbl_merge <- function(data) { + if (is.null(names(data))) { + data |> gtsummary::tbl_merge() + } else { + data |> gtsummary::tbl_merge(tab_spanner = names(data)) + } +} + +# as_kable(tbl) |> write_lines(file=here::here("inst/apps/data_analysis_modules/www/_table1.md")) +# as_kable_extra(tbl)|> write_lines(file=here::here("inst/apps/data_analysis_modules/www/table1.md")) + + +######## +#### Current file: /Users/au301842/FreesearchR/R//regression-module.R +######## + +### On rewriting this module +### +### This module (and the plotting module) should be rewritten to allow for +### dynamically defining variable-selection for model evaluation. +### The principle of having a library of supported functions is fine, but should +### be expanded. +### +### + +# list( +# lm = list( +# descr = "Linear regression model", +# design = "cross-sectional", +# parameters=list( +# fun = "stats::lm", +# args.list = NULL +# ), +# variables = list( +# outcome.str = list( +# fun = "columnSelectInput", +# multiple = FALSE, +# label = "Select the dependent/outcome variable." +# ) +# ), +# out.type = "continuous", +# formula.str = "{outcome.str}~{paste(vars,collapse='+')}", +# table.fun = "gtsummary::tbl_regression", +# table.args.list = list(exponentiate = FALSE) +# )) +# +# Regarding the regression model, it really should be the design selection, +# that holds the input selection information, as this is what is deciding +# the number and type of primary inputs. +# +# Cross-sectional: outcome +# MMRM: outcome, random effect (id, time) +# Survival: time, status, strata(?) +# +# + + + +regression_ui <- function(id, ...) { + ns <- shiny::NS(id) + + shiny::tagList( + title = "", + sidebar = bslib::sidebar( + shiny::uiOutput(outputId = ns("data_info"), inline = TRUE), + bslib::accordion( + open = "acc_reg", + multiple = FALSE, + bslib::accordion_panel( + value = "acc_reg", + title = "Regression", + icon = bsicons::bs_icon("calculator"), + shiny::uiOutput(outputId = ns("outcome_var")), + # shiny::selectInput( + # inputId = "design", + # label = "Study design", + # selected = "no", + # inline = TRUE, + # choices = list( + # "Cross-sectional" = "cross-sectional" + # ) + # ), + shiny::uiOutput(outputId = ns("regression_type")), + shiny::radioButtons( + inputId = ns("all"), + label = "Specify covariables", + inline = TRUE, selected = 2, + choiceNames = c( + "Yes", + "No" + ), + choiceValues = c(1, 2) + ), + shiny::conditionalPanel( + condition = "input.all==1", + shiny::uiOutput(outputId = ns("regression_vars")), + shiny::helpText("If none are selected, all are included."), + shiny::tags$br(), + ns = ns + ), + bslib::input_task_button( + id = ns("load"), + label = "Analyse", + icon = bsicons::bs_icon("pencil"), + label_busy = "Working...", + icon_busy = fontawesome::fa_i("arrows-rotate", + class = "fa-spin", + "aria-hidden" = "true" + ), + type = "secondary", + auto_reset = TRUE + ), + shiny::helpText("Press 'Analyse' to create the regression model and after changing parameters."), + shiny::tags$br(), + shiny::radioButtons( + inputId = ns("add_regression_p"), + label = "Show p-value", + inline = TRUE, + selected = "yes", + choices = list( + "Yes" = "yes", + "No" = "no" + ) + ), + # shiny::tags$br(), + # shiny::radioButtons( + # inputId = ns("tbl_theme"), + # label = "Show p-value", + # inline = TRUE, + # selected = "jama", + # choices = list( + # "JAMA" = "jama", + # "Lancet" = "lancet", + # "NEJM" = "nejm" + # ) + # ), + shiny::tags$br() + ), + do.call( + bslib::accordion_panel, + c( + list( + value = "acc_plot", + title = "Coefficient plot", + icon = bsicons::bs_icon("bar-chart-steps"), + shiny::tags$br(), + shiny::uiOutput(outputId = ns("plot_model")) + ), + # plot_download_ui(ns("reg_plot_download")) + shiny::tagList( + shinyWidgets::noUiSliderInput( + inputId = ns("plot_height"), + label = "Plot height (mm)", + min = 50, + max = 300, + value = 100, + step = 1, + format = shinyWidgets::wNumbFormat(decimals = 0), + color = datamods:::get_primary_color() + ), + shinyWidgets::noUiSliderInput( + inputId = ns("plot_width"), + label = "Plot width (mm)", + min = 50, + max = 300, + value = 100, + step = 1, + format = shinyWidgets::wNumbFormat(decimals = 0), + color = datamods:::get_primary_color() + ), + shiny::selectInput( + inputId = ns("plot_type"), + label = "File format", + choices = list( + "png", + "tiff", + "eps", + "pdf", + "jpeg", + "svg" + ) + ), + shiny::br(), + # Button + shiny::downloadButton( + outputId = ns("download_plot"), + label = "Download plot", + icon = shiny::icon("download") + ) + ) + ) + ), + bslib::accordion_panel( + value = "acc_checks", + title = "Checks", + icon = bsicons::bs_icon("clipboard-check"), + shiny::uiOutput(outputId = ns("plot_checks")) + ) + ) + ), + bslib::nav_panel( + title = "Regression table", + gt::gt_output(outputId = ns("table2")) + ), + bslib::nav_panel( + title = "Coefficient plot", + shiny::plotOutput(outputId = ns("regression_plot"), height = "80vh") + ), + bslib::nav_panel( + title = "Model checks", + shiny::plotOutput(outputId = ns("check"), height = "90vh") + ) + ) +} + + +regression_server <- function(id, + data, + ...) { + shiny::moduleServer( + id = id, + module = function(input, output, session) { + ns <- session$ns + + rv <- shiny::reactiveValues( + data = NULL, + plot = NULL, + check = NULL, + list = list() + ) + + data_r <- shiny::reactive({ + if (shiny::is.reactive(data)) { + data() + } else { + data + } + }) + + output$data_info <- shiny::renderUI({ + shiny::req(regression_vars()) + shiny::req(data_r()) + data_description(data_r()[regression_vars()]) + }) + + ############################################################################## + ######### + ######### Input fields + ######### + ############################################################################## + + ## Keep these "old" selection options as a simple alternative to the modification pane + + + output$regression_vars <- shiny::renderUI({ + columnSelectInput( + inputId = ns("regression_vars"), + selected = NULL, + label = "Covariables to include", + data = data_r(), + multiple = TRUE + ) + }) + + output$outcome_var <- shiny::renderUI({ + columnSelectInput( + inputId = ns("outcome_var"), + selected = NULL, + label = "Select outcome variable", + data = data_r(), + multiple = FALSE + ) + }) + + output$regression_type <- shiny::renderUI({ + shiny::req(input$outcome_var) + shiny::selectizeInput( + inputId = ns("regression_type"), + label = "Choose regression analysis", + ## The below ifelse statement handles the case of loading a new dataset + choices = possible_functions( + data = dplyr::select( + data_r(), + ifelse(input$outcome_var %in% names(data_r()), + input$outcome_var, + names(data_r())[1] + ) + ), design = "cross-sectional" + ), + multiple = FALSE + ) + }) + + output$factor_vars <- shiny::renderUI({ + shiny::selectizeInput( + inputId = ns("factor_vars"), + selected = colnames(data_r())[sapply(data_r(), is.factor)], + label = "Covariables to format as categorical", + choices = colnames(data_r()), + multiple = TRUE + ) + }) + + ## Collected regression variables + regression_vars <- shiny::reactive({ + if (is.null(input$regression_vars)) { + out <- colnames(data_r()) + } else { + out <- unique(c(input$regression_vars, input$outcome_var)) + } + return(out) + }) + + output$strat_var <- shiny::renderUI({ + columnSelectInput( + inputId = ns("strat_var"), + selected = "none", + label = "Select variable to stratify baseline", + data = data_r(), + col_subset = c( + "none", + names(data_r())[unlist(lapply(data_r(), data_type)) %in% c("dichotomous", "categorical", "ordinal")] + ) + ) + }) + + + output$plot_model <- shiny::renderUI({ + shiny::req(rv$list$regression$tables) + shiny::selectInput( + inputId = ns("plot_model"), + selected = 1, + label = "Select models to plot", + choices = names(rv$list$regression$tables), + multiple = TRUE + ) + }) + + ############################################################################## + ######### + ######### Regression models + ######### + ############################################################################## + + shiny::observeEvent( + input$load, + { + shiny::req(input$outcome_var) + + rv$list$regression$models <- NULL + + tryCatch( + { + ## Which models to create should be decided by input + ## Could also include + ## imputed or + ## minimally adjusted + model_lists <- list( + "Univariable" = "regression_model_uv_list", + "Multivariable" = "regression_model_list" + ) |> + lapply(\(.fun){ + parameters <- list( + data = data_r()[regression_vars()], + outcome.str = input$outcome_var, + fun.descr = input$regression_type + ) + + do.call( + .fun, + parameters + ) + }) + + rv$list$regression$params <- get_fun_options(input$regression_type) |> + (\(.x){ + .x[[1]] + })() + + rv$list$regression$models <- model_lists + }, + error = function(err) { + showNotification(paste0("Creating regression models failed with the following error: ", err), type = "err") + } + ) + } + ) + + + + shiny::observeEvent( + list( + data_r(), + regression_vars() + ), + { + rv$list$regression$tables <- NULL + } + ) + + ############################################################################## + ######### + ######### Regression table + ######### + ############################################################################## + + ### Creating the regression table + shiny::observeEvent( + input$load, + { + shiny::req(rv$list$regression$models) + ## To avoid plotting old models on fail/error + rv$list$regression$tables <- NULL + + # browser() + tryCatch( + { + parameters <- list( + p.values = input$add_regression_p == "no" + ) + + out <- lapply(rv$list$regression$models, \(.x){ + .x$model + }) |> + purrr::map(\(.x){ + do.call( + regression_table, + append_list(.x, parameters, "x") + ) + }) + + rv$list$regression$models |> + purrr::imap(\(.x, .i){ + rv$list$regression$models[[.i]][["code_table"]] <- paste( + .x$code, + expression_string(rlang::call2(.fn = "regression_table", !!!parameters, .ns = "FreesearchR"), assign.str = NULL), + sep = "|>\n" + ) + }) + + rv$list$regression$tables <- out + rv$list$input <- input + }, + warning = function(warn) { + showNotification(paste0(warn), type = "warning") + }, + error = function(err) { + showNotification(paste0("Creating a regression table failed with the following error: ", err), type = "err") + } + ) + } + ) + + ## Consider creating merged table with theming and then passing object + ## to render. + + output$table2 <- gt::render_gt({ + ## Print checks if a regression table is present + if (!is.null(rv$list$regression$tables)) { + # gtsummary::theme_gtsummary_journal(journal = "jama") + merged <- rv$list$regression$tables |> + tbl_merge() + + if (input$add_regression_p == "no") { + merged <- merged |> + gtsummary::modify_column_hide(column = dplyr::starts_with("p.value")) + } + + out <- merged |> + gtsummary::as_gt() |> + gt::tab_header(gt::md(glue::glue("**Table 2: {rv$list$regression$params$descr}**"))) + + # rv$list$regression$table_merged <- out + + out + } else { + return(NULL) + } + }) + + ############################################################################## + ######### + ######### Coefficients plot + ######### + ############################################################################## + + shiny::observeEvent(list( + input$plot_model, + rv$list$regression + ), { + shiny::req(input$plot_model) + + tryCatch( + { + p <- merge_long( + rv$list$regression, + sort_by( + input$plot_model, + c("Univariable", "Minimal", "Multivariable"), + na.rm = TRUE + ) + ) |> + (\(.x){ + if (length(input$plot_model) > 1) { + plot.tbl_regression( + x = .x, + colour = "model", + dodged = TRUE + ) + + ggplot2::theme(legend.position = "bottom") + + ggplot2::guides(color = ggplot2::guide_legend(reverse = TRUE)) + } else { + plot.tbl_regression( + x = .x, + colour = "variable" + ) + + ggplot2::theme(legend.position = "none") + } + })() + + rv$plot <- p + + ggplot2::scale_y_discrete(labels = scales::label_wrap(15)) + + gg_theme_shiny() + }, + error = function(err) { + showNotification(paste0(err), type = "err") + } + ) + }) + + + output$regression_plot <- shiny::renderPlot( + { + shiny::req(input$plot_model) + + rv$plot + }, + alt = "Regression coefficient plot" + ) + + # plot_download_server( + # id = ns("reg_plot_download"), + # data = shiny::reactive(rv$plot) + # ) + + output$download_plot <- shiny::downloadHandler( + filename = paste0("regression_plot.", input$plot_type), + content = function(file) { + shiny::withProgress(message = "Saving the plot. Hold on for a moment..", { + ggplot2::ggsave( + filename = file, + plot = rv$plot, + width = input$plot_width, + height = input$plot_height, + dpi = 300, + units = "mm", scale = 2 + ) + }) + } + ) + + ############################################################################## + ######### + ######### Model checks + ######### + ############################################################################## + + shiny::observeEvent( + list( + rv$list$regression$models + ), + { + shiny::req(rv$list$regression$models) + tryCatch( + { + rv$check <- lapply(rv$list$regression$models, \(.x){ + .x$model + }) |> + purrr::pluck("Multivariable") |> + performance::check_model() + }, + # warning = function(warn) { + # showNotification(paste0(warn), type = "warning") + # }, + error = function(err) { + showNotification(paste0("Running model assumptions checks failed with the following error: ", err), type = "err") + } + ) + } + ) + + rv$check_plot <- shiny::reactive(plot(rv$check)) + + output$plot_checks <- shiny::renderUI({ + shiny::req(rv$list$regression$models) + shiny::req(rv$check_plot) + + ## Implement correct plotting + names <- sapply(rv$check_plot(), \(.i){ + # .i$labels$title + get_ggplot_label(.i, "title") + }) + + vectorSelectInput( + inputId = ns("plot_checks"), + selected = 1, + label = "Select checks to plot", + choices = names, + multiple = TRUE + ) + }) + + output$check <- shiny::renderPlot( + { + shiny::req(rv$check_plot) + shiny::req(input$plot_checks) + + ## Print checks if a regression table is present + if (!is.null(rv$list$regression$tables)) { + p <- rv$check_plot() + + # patchwork::wrap_plots() + + patchwork::plot_annotation(title = "Multivariable regression model checks") + + + layout <- sapply(seq_len(length(p)), \(.x){ + patchwork::area(.x, 1) + }) + + p_list <- p + patchwork::plot_layout(design = Reduce(c, layout)) + + index <- match( + input$plot_checks, + sapply(rv$check_plot(), \(.i){ + get_ggplot_label(.i, "title") + }) + ) + + ls <- list() + + for (i in index) { + p <- p_list[[i]] + + ggplot2::theme( + axis.text = ggplot2::element_text(size = 10), + axis.title = ggplot2::element_text(size = 12), + legend.text = ggplot2::element_text(size = 12), + plot.subtitle = ggplot2::element_text(size = 12), + plot.title = ggplot2::element_text(size = 18) + ) + ls <- c(ls, list(p)) + } + # browser() + tryCatch( + { + out <- patchwork::wrap_plots(ls, ncol = if (length(ls) == 1) 1 else 2) + }, + error = function(err) { + showNotification(err, type = "err") + } + ) + + out + } else { + return(NULL) + } + }, + alt = "Assumptions testing of the multivariable regression model" + ) + + ############################################################################## + ######### + ######### Output + ######### + ############################################################################## + + return(shiny::reactive({ + rv$list + })) + } + ) +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//report.R +######## + +#' Split vector by an index and embed addition +#' +#' @param data vector +#' @param index split index +#' @param add addition +#' +#' @return vector +#' @export +#' +index_embed <- function(data, index, add = NULL) { + start <- seq_len(index) + end <- seq_along(data)[-start] + c( + data[start], + add, + data[end] + ) +} + +#' Specify format arguments to include in qmd header/frontmatter +#' +#' @param data vector +#' @param fileformat format to include +#' +#' @return vector +#' @export +#' +specify_qmd_format <- function(data, fileformat = c("docx", "odt", "pdf", "all")) { + fileformat <- match.arg(fileformat) + args_list <- default_format_arguments() |> purrr::imap(format_writer) + + if (fileformat == "all") { + out <- data |> index_embed(index = 4, add = Reduce(c, args_list)) + } else { + out <- data |> index_embed(index = 4, add = args_list[[fileformat]]) + } + out +} + +#' Merges list of named arguments for qmd header generation +#' +#' @param data vector +#' @param name name +#' +#' @return vector +#' @export +#' +format_writer <- function(data, name) { + if (data == "default") { + glue::glue(" {name}: {data}") + } else { + warning("Not implemented") + } +} + +#' Defaults qmd formats +#' +#' @return list +#' @export +#' +default_format_arguments <- function() { + list( + docx = list("default"), + odt = list("default"), + pdf = list("default") + ) +} + +#' Wrapper to modify quarto file to render specific formats +#' +#' @param file filename +#' @param format desired output +#' +#' @return none +#' @export +#' +modify_qmd <- function(file, format) { + readLines(file) |> + specify_qmd_format(fileformat = "all") |> + writeLines(paste0(tools::file_path_sans_ext(file), "_format.", tools::file_ext(file))) +} + + + +######## +#### Current file: /Users/au301842/FreesearchR/R//syntax_highlight.R +######## + +## Inpiration: +## +## https://stackoverflow.com/questions/47445260/how-to-enable-syntax-highlighting-in-r-shiny-app-with-htmloutput + +prismCodeBlock <- function(code) { + tagList( + HTML(html_code_wrap(code)), + tags$script("Prism.highlightAll()") + ) +} + +prismDependencies <- tags$head( + tags$script(src = "https://cdnjs.cloudflare.com/ajax/libs/prism/1.8.4/prism.min.js"), + tags$link(rel = "stylesheet", type = "text/css", + href = "https://cdnjs.cloudflare.com/ajax/libs/prism/1.8.4/themes/prism.min.css") +) + +prismRDependency <- tags$head( + tags$script(src = "https://cdnjs.cloudflare.com/ajax/libs/prism/1.8.4/components/prism-r.min.js") +) + +html_code_wrap <- function(string,lang="r"){ + glue::glue("
{string}
+
") +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//theme.R +######## + +#' Custom theme based on unity +#' +#' @param ... everything passed on to bslib::bs_theme() +#' +#' @returns theme list +#' @export +custom_theme <- function(..., + version = 5, + primary = FreesearchR_colors("primary"), + secondary = FreesearchR_colors("secondary"), + bootswatch = "united", + base_font = bslib::font_google("Montserrat"), + heading_font = bslib::font_google("Public Sans", wght = "700"), + code_font = bslib::font_google("Open Sans"), + success = FreesearchR_colors("success"), + info = FreesearchR_colors("info"), + warning = FreesearchR_colors("warning"), + danger = FreesearchR_colors("danger") + # fg = "#000", + # bg="#fff", + # base_font = bslib::font_google("Alice"), + # heading_font = bslib::font_google("Jost", wght = "800"), + # heading_font = bslib::font_google("Noto Serif"), + # heading_font = bslib::font_google("Alice"), +) { + bslib::bs_theme( + ..., + "navbar-bg" = primary, + version = version, + primary = primary, + secondary = secondary, + bootswatch = bootswatch, + base_font = base_font, + heading_font = heading_font, + code_font = code_font, + success=success, + info=info, + warning=warning, + danger=danger + ) +} + +FreesearchR_colors <- function(choose = NULL) { + out <- c( + primary = "#1E4A8F", + secondary = "#FF6F61", + success = "#00C896", + warning = "#FFB100", + danger = "#CC2E25", + extra = "#8A4FFF", + info = "#11A0EC", + bg = "#FFFFFF", + dark = "#2D2D42", + fg = "#000000" + ) + if (!is.null(choose)) { + unname(out[choose]) + } else { + out + } +} + +#' Use the FreesearchR colors +#' +#' @param n number of colors +#' +#' @returns character vector +#' @export +#' +#' @examples +#' FreesearchR_palette(n=7) +FreesearchR_palette <- function(n){ + rep_len(FreesearchR_colors(),n) +} + + + +#' GGplot default theme for plotting in Shiny +#' +#' @param data ggplot object +#' +#' @returns ggplot object +#' @export +#' +gg_theme_shiny <- function() { + ggplot2::theme( + axis.title = ggplot2::element_text(size = 18), + axis.text = ggplot2::element_text(size = 14), + strip.text = ggplot2::element_text(size = 14), + legend.title = ggplot2::element_text(size = 18), + legend.text = ggplot2::element_text(size = 14), + plot.title = ggplot2::element_text(size = 24), + plot.subtitle = ggplot2::element_text(size = 18) + ) +} + + +#' GGplot default theme for plotting export objects +#' +#' @param data ggplot object +#' +#' @returns ggplot object +#' @export +#' +gg_theme_export <- function() { + ggplot2::theme( + axis.title = ggplot2::element_text(size = 18), + axis.text.x = ggplot2::element_text(size = 14), + legend.title = ggplot2::element_text(size = 18), + legend.text = ggplot2::element_text(size = 14), + plot.title = ggplot2::element_text(size = 24) + ) +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//update-factor-ext.R +######## + + +## Works, but not implemented +## +## These edits mainly allows for + + +#' @title Module to Reorder the Levels of a Factor Variable +#' +#' @description +#' This module contain an interface to reorder the levels of a factor variable. +#' +#' +#' @param id Module ID. +#' +#' @return A [shiny::reactive()] function returning the data. +#' @export +#' +#' @importFrom shiny NS fluidRow tagList column actionButton +#' @importFrom shinyWidgets virtualSelectInput prettyCheckbox +#' @importFrom toastui datagridOutput +#' @importFrom htmltools tags +#' +#' @name update-factor +#' +update_factor_ui <- function(id) { + ns <- NS(id) + tagList( + tags$style( + ".tui-grid-row-header-draggable span {width: 3px !important; height: 3px !important;}" + ), + fluidRow( + column( + width = 6, + shinyWidgets::virtualSelectInput( + inputId = ns("variable"), + label = i18n("Factor variable to reorder:"), + choices = NULL, + width = "100%", + zIndex = 50 + ) + ), + column( + width = 3, + class = "d-flex align-items-end", + actionButton( + inputId = ns("sort_levels"), + label = tagList( + phosphoricons::ph("sort-ascending"), + datamods:::i18n("Sort by levels") + ), + class = "btn-outline-primary mb-3", + width = "100%" + ) + ), + column( + width = 3, + class = "d-flex align-items-end", + actionButton( + inputId = ns("sort_occurrences"), + label = tagList( + phosphoricons::ph("sort-ascending"), + datamods:::i18n("Sort by count") + ), + class = "btn-outline-primary mb-3", + width = "100%" + ) + ) + ), + toastui::datagridOutput(ns("grid")), + tags$div( + class = "float-end", + shinyWidgets::prettyCheckbox( + inputId = ns("new_var"), + label = datamods:::i18n("Create a new variable (otherwise replaces the one selected)"), + value = FALSE, + status = "primary", + outline = TRUE, + inline = TRUE + ), + actionButton( + inputId = ns("create"), + label = tagList(phosphoricons::ph("arrow-clockwise"), datamods:::i18n("Update factor variable")), + class = "btn-outline-primary" + ) + ), + tags$div(class = "clearfix") + ) +} + + +#' @param data_r A [shiny::reactive()] function returning a `data.frame`. +#' +#' @export +#' +#' @importFrom shiny moduleServer observeEvent reactive reactiveValues req bindEvent isTruthy updateActionButton +#' @importFrom shinyWidgets updateVirtualSelect +#' @importFrom toastui renderDatagrid datagrid grid_columns grid_colorbar +#' +#' @rdname update-factor +update_factor_server <- function(id, data_r = reactive(NULL)) { + moduleServer( + id, + function(input, output, session) { + + rv <- reactiveValues(data = NULL, data_grid = NULL) + + bindEvent(observe({ + data <- data_r() + rv$data <- data + vars_factor <- vapply(data, is.factor, logical(1)) + vars_factor <- names(vars_factor)[vars_factor] + updateVirtualSelect( + inputId = "variable", + choices = vars_factor, + selected = if (isTruthy(input$variable)) input$variable else vars_factor[1] + ) + }), data_r(), input$hidden) + + observeEvent(input$variable, { + data <- req(data_r()) + variable <- req(input$variable) + grid <- as.data.frame(table(data[[variable]])) + rv$data_grid <- grid + }) + + observeEvent(input$sort_levels, { + if (input$sort_levels %% 2 == 1) { + decreasing <- FALSE + label <- tagList( + phosphoricons::ph("sort-descending"), + "Sort Levels" + ) + } else { + decreasing <- TRUE + label <- tagList( + phosphoricons::ph("sort-ascending"), + "Sort Levels" + ) + } + updateActionButton(inputId = "sort_levels", label = as.character(label)) + rv$data_grid <- rv$data_grid[order(rv$data_grid[[1]], decreasing = decreasing), ] + }) + + observeEvent(input$sort_occurrences, { + if (input$sort_occurrences %% 2 == 1) { + decreasing <- FALSE + label <- tagList( + phosphoricons::ph("sort-descending"), + datamods:::i18n("Sort count") + ) + } else { + decreasing <- TRUE + label <- tagList( + phosphoricons::ph("sort-ascending"), + datamods:::i18n("Sort count") + ) + } + updateActionButton(inputId = "sort_occurrences", label = as.character(label)) + rv$data_grid <- rv$data_grid[order(rv$data_grid[[2]], decreasing = decreasing), ] + }) + + + output$grid <- renderDatagrid({ + req(rv$data_grid) + gridTheme <- getOption("datagrid.theme") + if (length(gridTheme) < 1) { + datamods:::apply_grid_theme() + } + on.exit(toastui::reset_grid_theme()) + data <- rv$data_grid + data <- add_var_toset(data, "Var1", "New label") + + grid <- datagrid( + data = data, + draggable = TRUE, + sortable = FALSE, + data_as_input = TRUE + ) + grid <- grid_columns( + grid, + columns = c("Var1", "Var1_toset", "Freq"), + header = c(datamods:::i18n("Levels"), "New label", datamods:::i18n("Count")) + ) + grid <- grid_colorbar( + grid, + column = "Freq", + label_outside = TRUE, + label_width = "30px", + background = "#D8DEE9", + bar_bg = datamods:::get_primary_color(), + from = c(0, max(rv$data_grid$Freq) + 1) + ) + grid <- toastui::grid_style_column( + grid = grid, + column = "Var1_toset", + fontStyle = "italic" + ) + grid <- toastui::grid_editor( + grid = grid, + column = "Var1_toset", + type = "text" + ) + grid + }) + + data_updated_r <- reactive({ + data <- req(data_r()) + variable <- req(input$variable) + grid <- req(input$grid_data) + name_var <- if (isTRUE(input$new_var)) { + paste0(variable, "_updated") + } else { + variable + } + data[[name_var]] <- factor( + as.character(data[[variable]]), + levels = grid[["Var1"]] + ) + data[[name_var]] <- factor( + data[[variable]], + labels = ifelse(grid[["Var1_toset"]]=="New label",grid[["Var1"]],grid[["Var1_toset"]]) + ) + data + }) + + data_returned_r <- observeEvent(input$create, { + rv$data <- data_updated_r() + }) + return(reactive(rv$data)) + } + ) +} + + + +#' @inheritParams shiny::modalDialog +#' @export +#' +#' @importFrom shiny showModal modalDialog textInput +#' @importFrom htmltools tagList +#' +#' @rdname update-factor +modal_update_factor <- function(id, + title = i18n("Update levels of a factor"), + easyClose = TRUE, + size = "l", + footer = NULL) { + ns <- NS(id) + showModal(modalDialog( + title = tagList(title, datamods:::button_close_modal()), + update_factor_ui(id), + tags$div( + style = "display: none;", + textInput(inputId = ns("hidden"), label = NULL, value = datamods:::genId()) + ), + easyClose = easyClose, + size = size, + footer = footer + )) +} + + +#' @inheritParams shinyWidgets::WinBox +#' @export +#' +#' @importFrom shinyWidgets WinBox wbOptions wbControls +#' @importFrom htmltools tagList +#' @rdname update-factor +winbox_update_factor <- function(id, + title = i18n("Update levels of a factor"), + options = shinyWidgets::wbOptions(), + controls = shinyWidgets::wbControls()) { + ns <- NS(id) + WinBox( + title = title, + ui = tagList( + update_factor_ui(id), + tags$div( + style = "display: none;", + textInput(inputId = ns("hidden"), label = NULL, value = genId()) + ) + ), + options = modifyList( + shinyWidgets::wbOptions(height = "615px", modal = TRUE), + options + ), + controls = controls, + auto_height = FALSE + ) +} + + + +######## +#### Current file: /Users/au301842/FreesearchR/R//update-variables-ext.R +######## + +#' Select, rename and convert variables +#' +#' @param id Module id. See [shiny::moduleServer()]. +#' @param title Module's title, if `TRUE` use the default title, +#' use \code{NULL} for no title or a `shiny.tag` for a custom one. +#' +#' @return A [shiny::reactive()] function returning the updated data. +#' @export +#' +#' @name update-variables +#' +update_variables_ui <- function(id, title = "") { + ns <- NS(id) + if (isTRUE(title)) { + title <- htmltools::tags$h4( + i18n("Update & select variables"), + class = "datamods-title" + ) + } + htmltools::tags$div( + class = "datamods-update", + shinyWidgets::html_dependency_pretty(), + title, + htmltools::tags$div( + style = "min-height: 25px;", + htmltools::tags$div( + shiny::uiOutput(outputId = ns("data_info"), inline = TRUE), + shiny::tagAppendAttributes( + shinyWidgets::dropMenu( + placement = "bottom-end", + shiny::actionButton( + inputId = ns("settings"), + label = phosphoricons::ph("gear"), + class = "pull-right float-right" + ), + shinyWidgets::textInputIcon( + inputId = ns("format"), + label = i18n("Date format:"), + value = "%Y-%m-%d", + icon = list(phosphoricons::ph("clock")) + ), + shinyWidgets::textInputIcon( + inputId = ns("origin"), + label = i18n("Date to use as origin to convert date/datetime:"), + value = "1970-01-01", + icon = list(phosphoricons::ph("calendar")) + ), + shinyWidgets::textInputIcon( + inputId = ns("dec"), + label = i18n("Decimal separator:"), + value = ".", + icon = list("0.00") + ) + ), + style = "display: inline;" + ) + ), + htmltools::tags$br(), + toastui::datagridOutput(outputId = ns("table")) + ), + htmltools::tags$br(), + htmltools::tags$div( + id = ns("update-placeholder"), + shinyWidgets::alert( + id = ns("update-result"), + status = "info", + phosphoricons::ph("info"), + paste( + "Select variables to keep (if none selected, all are kept), rename", + "variables and labels, and convert variable type/class in the table", + "above. Apply changes by clicking the button below." + ) + ) + ), + shiny::actionButton( + inputId = ns("validate"), + label = htmltools::tagList( + phosphoricons::ph("arrow-circle-right", title = datamods::i18n("Apply changes")), + datamods::i18n("Apply changes") + ), + width = "100%" + ) + ) +} + +#' @export +#' +#' @param id Module's ID +#' @param data a \code{data.frame} or a \code{reactive} function returning a \code{data.frame}. +#' @param height Height for the table. +#' @param return_data_on_init Return initial data when module is called. +#' @param try_silent logical: should the report of error messages be suppressed? +#' +#' @rdname update-variables +#' +update_variables_server <- function(id, + data, + height = NULL, + return_data_on_init = FALSE, + try_silent = FALSE) { + shiny::moduleServer( + id = id, + module = function(input, output, session) { + ns <- session$ns + updated_data <- shiny::reactiveValues(x = NULL) + + data_r <- shiny::reactive({ + if (shiny::is.reactive(data)) { + data() + } else { + data + } + }) + + output$data_info <- shiny::renderUI({ + shiny::req(data_r()) + data_description(data_r()) + # sprintf(i18n("Data has %s observations and %s variables."), nrow(data), ncol(data)) + }) + + variables_r <- shiny::reactive({ + shiny::validate( + shiny::need(data(), i18n("No data to display.")) + ) + data <- data_r() + if (isTRUE(return_data_on_init)) { + updated_data$x <- data + } else { + updated_data$x <- NULL + } + summary_vars(data) + }) + + output$table <- toastui::renderDatagrid({ + shiny::req(variables_r()) + + variables <- variables_r() + + update_variables_datagrid( + variables, + height = height, + selectionId = ns("row_selected"), + buttonId = "validate" + ) + }) + + shiny::observeEvent(input$validate, + { + updated_data$list_rename <- NULL + updated_data$list_select <- NULL + updated_data$list_mutate <- NULL + updated_data$list_relabel <- NULL + # shiny::req(updated_data$x) + data <- data_r() + new_selections <- input$row_selected + if (length(new_selections) < 1) { + new_selections <- seq_along(data) + } + + data_inputs <- data.table::as.data.table(input$table_data) + data.table::setorderv(data_inputs, "rowKey") + + old_names <- data_inputs$name + new_names <- data_inputs$name_toset + new_names[new_names == "New name"] <- NA + new_names[is.na(new_names)] <- old_names[is.na(new_names)] + new_names[new_names == ""] <- old_names[new_names == ""] + + # browser() + + old_label <- data_inputs$label + new_label <- data_inputs$label_toset + + new_label[new_label == "New label"] <- old_label[new_label == "New label"] + + ## Later, "" will be interpreted as NA/empty and removed + new_label[is.na(new_label) | new_label %in% c('""',"''"," ")] <- "" + + # new_label[is.na(new_label)] <- old_label[is.na(new_label)] + new_label <- setNames(new_label, new_names) + + new_classes <- data_inputs$class_toset + new_classes[new_classes == "Select"] <- NA + + data_sv <- variables_r() + vars_to_change <- get_vars_to_convert(data_sv, setNames(as.list(new_classes), old_names)) + + res_update <- try( + { + # convert + if (nrow(vars_to_change) > 0) { + data <- convert_to( + data = data, + variable = vars_to_change$name, + new_class = vars_to_change$class_to_set, + origin = input$origin, + format = input$format, + dec = input$dec + ) + } + list_mutate <- attr(data, "code_03_convert") + + # rename + list_rename <- setNames( + as.list(old_names), + unlist(new_names, use.names = FALSE) + ) + list_rename <- list_rename[names(list_rename) != unlist(list_rename, use.names = FALSE)] + names(data) <- unlist(new_names, use.names = FALSE) + + # relabel + list_relabel <- as.list(new_label) + data <- set_column_label(data, list_relabel) + + # select + list_select <- setdiff(names(data), names(data)[new_selections]) + data <- data[, new_selections, drop = FALSE] + }, + silent = try_silent + ) + + if (inherits(res_update, "try-error")) { + datamods:::insert_error(selector = "update") + } else { + datamods:::insert_alert( + selector = ns("update"), + status = "success", + tags$b(phosphoricons::ph("check"), datamods::i18n("Data successfully updated!")) + ) + updated_data$x <- data + updated_data$list_rename <- list_rename + updated_data$list_select <- list_select + updated_data$list_mutate <- list_mutate + updated_data$list_relabel <- list_relabel + } + }, + ignoreNULL = TRUE, + ignoreInit = TRUE + ) + + # shiny::observeEvent(input$close, + # { + return(shiny::reactive({ + shiny::req(updated_data$x) + # browser() + data <- updated_data$x + code <- list() + if (!is.null(data) && shiny::isTruthy(updated_data$list_mutate) && length(updated_data$list_mutate) > 0) { + code <- c(code, list(rlang::call2("mutate", !!!updated_data$list_mutate,.ns="dplyr"))) + } + if (!is.null(data) && shiny::isTruthy(updated_data$list_rename) && length(updated_data$list_rename) > 0) { + code <- c(code, list(rlang::call2("rename", !!!updated_data$list_rename,.ns="dplyr"))) + } + if (!is.null(data) && shiny::isTruthy(updated_data$list_select) && length(updated_data$list_select) > 0) { + code <- c(code, list(rlang::expr(dplyr::select(-dplyr::any_of(c(!!!updated_data$list_select)))))) + } + if (!is.null(data) && shiny::isTruthy(updated_data$list_relabel) && length(updated_data$list_relabel) > 0) { + code <- c(code,list(rlang::call2("set_column_label",label=updated_data$list_relabel,.ns="FreesearchR"))) + } + if (length(code) > 0) { + attr(data, "code") <- Reduce( + f = function(x, y) rlang::expr(!!x %>% !!y), + x = code + ) + } + return(data) + })) + # }) + + # shiny::reactive({ + # data <- updated_data$x + # code <- list() + # if (!is.null(data) && shiny::isTruthy(updated_data$list_mutate) && length(updated_data$list_mutate) > 0) { + # code <- c(code, list(rlang::call2("mutate", !!!updated_data$list_mutate))) + # } + # if (!is.null(data) && shiny::isTruthy(updated_data$list_rename) && length(updated_data$list_rename) > 0) { + # code <- c(code, list(rlang::call2("rename", !!!updated_data$list_rename))) + # } + # if (!is.null(data) && shiny::isTruthy(updated_data$list_select) && length(updated_data$list_select) > 0) { + # code <- c(code, list(rlang::expr(select(-any_of(c(!!!updated_data$list_select)))))) + # } + # if (!is.null(data) && shiny::isTruthy(updated_data$list_relabel) && length(updated_data$list_relabel) > 0) { + # code <- c(code, list(rlang::call2("purrr::map2(list_relabel, + # function(.data,.label){ + # REDCapCAST::set_attr(.data,.label,attr = 'label') + # }) |> dplyr::bind_cols(.name_repair = 'unique_quiet')"))) + # } + # if (length(code) > 0) { + # attr(data, "code") <- Reduce( + # f = function(x, y) rlang::expr(!!x %>% !!y), + # x = code + # ) + # } + # updated_data$return_data <- data + # }) + + # shiny::observeEvent(input$close, + # { + # shiny::req(input$close) + # return(shiny::reactive({ + # data <- updated_data$return_data + # return(data) + # })) + # }) + } + ) +} + + +modal_update_variables <- function(id, + title = "Select, rename and reclass variables", + easyClose = TRUE, + size = "xl", + footer = NULL) { + ns <- NS(id) + showModal(modalDialog( + title = tagList(title, datamods:::button_close_modal()), + update_variables_ui(id), + # tags$div( + # style = "display: none;", + # textInput(inputId = ns("hidden"), label = NULL, value = datamods:::genId()) + # ), + easyClose = easyClose, + size = size, + footer = footer + )) +} + + + +# utils ------------------------------------------------------------------- + + +#' Get variables classes from a \code{data.frame} +#' +#' @param data a \code{data.frame} +#' +#' @return a \code{character} vector as same length as number of variables +#' @noRd +#' +#' @examples +#' +#' get_classes(mtcars) +get_classes <- function(data) { + classes <- lapply( + X = data, + FUN = function(x) { + paste(class(x), collapse = ", ") + } + ) + unlist(classes, use.names = FALSE) +} + + +#' Get count of unique values in variables of \code{data.frame} +#' +#' @param data a \code{data.frame} +#' +#' @return a \code{numeric} vector as same length as number of variables +#' @noRd +#' +#' +#' @examples +#' get_n_unique(mtcars) +get_n_unique <- function(data) { + u <- lapply(data, FUN = function(x) { + if (is.atomic(x)) { + data.table::uniqueN(x) + } else { + NA_integer_ + } + }) + unlist(u, use.names = FALSE) +} + + + +#' Add padding 0 to a vector +#' +#' @param x a \code{vector} +#' +#' @return a \code{character} vector +#' @noRd +#' +#' @examples +#' +#' pad0(1:10) +#' pad0(c(1, 15, 150, NA)) +pad0 <- function(x) { + NAs <- which(is.na(x)) + x <- formatC(x, width = max(nchar(as.character(x)), na.rm = TRUE), flag = "0") + x[NAs] <- NA + x +} + +#' Variables summary +#' +#' @param data a \code{data.frame} +#' +#' @return a \code{data.frame} +#' @noRd +#' +#' @examples +#' +#' summary_vars(iris) +#' summary_vars(mtcars) +summary_vars <- function(data) { + data <- as.data.frame(data) + datsum <- dplyr::tibble( + name = names(data), + label = lapply(data, \(.x) REDCapCAST::get_attr(.x, "label")) |> unlist(), + class = get_classes(data), + n_missing = unname(colSums(is.na(data))), + p_complete = 1 - n_missing / nrow(data), + n_unique = get_n_unique(data) + ) + + datsum +} + +add_var_toset <- function(data, var_name, default = "") { + datanames <- names(data) + datanames <- append( + x = datanames, + values = paste0(var_name, "_toset"), + after = which(datanames == var_name) + ) + data[[paste0(var_name, "_toset")]] <- default + data[, datanames] +} + +#' Modified from the datamods pacakge +#' +#' @param data data +#' +#' @param height height +#' @param selectionId selectionId +#' @param buttonId buttonId +#' +#' @examples +#' mtcars |> +#' summary_vars() |> +#' update_variables_datagrid() +#' +update_variables_datagrid <- function(data, height = NULL, selectionId = NULL, buttonId = NULL) { + # browser() + data <- add_var_toset(data, "name", "New name") + data <- add_var_toset(data, "class", "Select") + data <- add_var_toset(data, "label", "New label") + + gridTheme <- getOption("datagrid.theme") + if (length(gridTheme) < 1) { + datamods:::apply_grid_theme() + } + on.exit(toastui::reset_grid_theme()) + + col.names <- names(data) + + std_names <- c( + "name", "name_toset", "label", "label_toset", "class", "class_toset", "n_missing", "p_complete", "n_unique" + ) |> + setNames(c( + "Name", "New name", "Label", "New label", "Class", "New class", "Missing", "Complete", "Unique" + )) + + headers <- lapply(col.names, \(.x){ + if (.x %in% std_names) { + names(std_names)[match(.x, std_names)] + } else { + .x + } + }) |> unlist() + + grid <- toastui::datagrid( + data = data, + theme = "default", + colwidths = NULL + ) + grid <- toastui::grid_columns( + grid = grid, + columns = col.names, + header = headers, + minWidth = 100 + ) + + grid <- toastui::grid_format( + grid = grid, + "p_complete", + formatter = toastui::JS("function(obj) {return (obj.value*100).toFixed(0) + '%';}") + ) + grid <- toastui::grid_style_column( + grid = grid, + column = "name_toset", + fontStyle = "italic" + ) + grid <- toastui::grid_style_column( + grid = grid, + column = "label_toset", + fontStyle = "italic" + ) + grid <- toastui::grid_style_column( + grid = grid, + column = "class_toset", + fontStyle = "italic" + ) + + grid <- toastui::grid_filters( + grid = grid, + column = "name", + # columns = unname(std_names[std_names!="vals"]), + showApplyBtn = FALSE, + showClearBtn = TRUE, + type = "text" + ) + + # grid <- toastui::grid_columns( + # grid = grid, + # columns = "name_toset", + # editor = list(type = "text"), + # validation = toastui::validateOpts() + # ) + # + # grid <- toastui::grid_columns( + # grid = grid, + # columns = "label_toset", + # editor = list(type = "text"), + # validation = toastui::validateOpts() + # ) + # + # grid <- toastui::grid_columns( + # grid = grid, + # columns = "class_toset", + # editor = list( + # type = "radio", + # options = list( + # instantApply = TRUE, + # listItems = lapply( + # X = c("Select", "character", "factor", "numeric", "integer", "date", "datetime", "hms"), + # FUN = function(x) { + # list(text = x, value = x) + # } + # ) + # ) + # ), + # validation = toastui::validateOpts() + # ) + + grid <- toastui::grid_editor( + grid = grid, + column = "name_toset", + type = "text" + ) + grid <- toastui::grid_editor( + grid = grid, + column = "label_toset", + type = "text" + ) + grid <- toastui::grid_editor( + grid = grid, + column = "class_toset", + type = "select", + choices = c("Select", "character", "factor", "numeric", "integer", "date", "datetime", "hms") + ) + grid <- toastui::grid_editor_opts( + grid = grid, + editingEvent = "click", + actionButtonId = NULL, + session = NULL + ) + grid <- toastui::grid_selection_row( + grid = grid, + inputId = selectionId, + type = "checkbox", + return = "index" + ) + + return(grid) +} + + + +#' Convert a variable to specific new class +#' +#' @param data A \code{data.frame} +#' @param variable Name of the variable to convert +#' @param new_class Class to set +#' @param ... Other arguments passed on to methods. +#' +#' @return A \code{data.frame} +#' @noRd +#' +#' @importFrom utils type.convert +#' @importFrom rlang sym expr +#' +#' @examples +#' dat <- data.frame( +#' v1 = month.name, +#' v2 = month.abb, +#' v3 = 1:12, +#' v4 = as.numeric(Sys.Date() + 0:11), +#' v5 = as.character(Sys.Date() + 0:11), +#' v6 = as.factor(c("a", "a", "b", "a", "b", "a", "a", "b", "a", "b", "b", "a")), +#' v7 = as.character(11:22), +#' stringsAsFactors = FALSE +#' ) +#' +#' str(dat) +#' +#' str(convert_to(dat, "v3", "character")) +#' str(convert_to(dat, "v6", "character")) +#' str(convert_to(dat, "v7", "numeric")) +#' str(convert_to(dat, "v4", "date", origin = "1970-01-01")) +#' str(convert_to(dat, "v5", "date")) +#' +#' str(convert_to(dat, c("v1", "v3"), c("factor", "character"))) +#' +#' str(convert_to(dat, c("v1", "v3", "v4"), c("factor", "character", "date"), origin = "1970-01-01")) +#' +convert_to <- function(data, + variable, + new_class = c("character", "factor", "numeric", "integer", "date", "datetime", "hms"), + ...) { + new_class <- match.arg(new_class, several.ok = TRUE) + stopifnot(length(new_class) == length(variable)) + args <- list(...) + args$format <- clean_sep(args$format) + if (length(variable) > 1) { + for (i in seq_along(variable)) { + data <- convert_to(data, variable[i], new_class[i], ...) + } + return(data) + } + if (identical(new_class, "character")) { + data[[variable]] <- as.character(x = data[[variable]], ...) + attr(data, "code_03_convert") <- c( + attr(data, "code_03_convert"), + setNames(list(expr(as.character(!!sym(variable)))), variable) + ) + } else if (identical(new_class, "factor")) { + data[[variable]] <- REDCapCAST::as_factor(x = data[[variable]]) + attr(data, "code_03_convert") <- c( + attr(data, "code_03_convert"), + setNames(list(expr(REDCapCAST::as_factor(!!sym(variable)))), variable) + ) + } else if (identical(new_class, "numeric")) { + data[[variable]] <- as.numeric(data[[variable]], ...) + # This is the original, that would convert to character and then to numeric + # resulting in all NAs, setting as.is = FALSE would result in a numeric + # vector in order of appearance. Now it is acting like integer conversion + # data[[variable]] <- as.numeric(type.convert(data[[variable]], as.is = TRUE, ...)) + attr(data, "code_03_convert") <- c( + attr(data, "code_03_convert"), + setNames(list(expr(as.numeric(!!sym(variable)))), variable) + ) + } else if (identical(new_class, "integer")) { + data[[variable]] <- as.integer(x = data[[variable]], ...) + attr(data, "code_03_convert") <- c( + attr(data, "code_03_convert"), + setNames(list(expr(as.integer(!!sym(variable)))), variable) + ) + } else if (identical(new_class, "date")) { + data[[variable]] <- as.Date(x = clean_date(data[[variable]]), ...) + attr(data, "code_03_convert") <- c( + attr(data, "code_03_convert"), + setNames(list(expr(as.Date(clean_date(!!sym(variable)), origin = !!args$origin, format = clean_sep(!!args$format)))), variable) + ) + } else if (identical(new_class, "datetime")) { + data[[variable]] <- as.POSIXct(x = data[[variable]], ...) + attr(data, "code_03_convert") <- c( + attr(data, "code_03_convert"), + setNames(list(expr(as.POSIXct(!!sym(variable)))), variable) + ) + } else if (identical(new_class, "hms")) { + data[[variable]] <- hms::as_hms(x = data[[variable]]) + attr(data, "code_03_convert") <- c( + attr(data, "code_03_convert"), + setNames(list(expr(hms::as_hms(!!sym(variable)))), variable) + ) + } + return(data) +} + + + + + + + + +#' Get variable(s) to convert +#' +#' @param vars Output of [summary_vars()] +#' @param classes_input List of inputs containing new classes +#' +#' @return a `data.table`. +#' @noRd +#' +#' @importFrom data.table data.table as.data.table +#' +#' @examples +#' # 2 variables to convert +#' new_classes <- list( +#' "Sepal.Length" = "numeric", +#' "Sepal.Width" = "numeric", +#' "Petal.Length" = "character", +#' "Petal.Width" = "numeric", +#' "Species" = "character" +#' ) +#' get_vars_to_convert(summary_vars(iris), new_classes) +#' +#' +#' # No changes +#' new_classes <- list( +#' "Sepal.Length" = "numeric", +#' "Sepal.Width" = "numeric", +#' "Petal.Length" = "numeric", +#' "Petal.Width" = "numeric", +#' "Species" = "factor" +#' ) +#' get_vars_to_convert(summary_vars(iris), new_classes) +#' +#' # Not set = NA or "" +#' new_classes <- list( +#' "Sepal.Length" = NA, +#' "Sepal.Width" = NA, +#' "Petal.Length" = NA, +#' "Petal.Width" = NA, +#' "Species" = NA +#' ) +#' get_vars_to_convert(summary_vars(iris), new_classes) +#' +#' # Set for one var +#' new_classes <- list( +#' "Sepal.Length" = "", +#' "Sepal.Width" = "", +#' "Petal.Length" = "", +#' "Petal.Width" = "", +#' "Species" = "character" +#' ) +#' get_vars_to_convert(summary_vars(iris), new_classes) +#' +#' new_classes <- list( +#' "mpg" = "character", +#' "cyl" = "numeric", +#' "disp" = "character", +#' "hp" = "numeric", +#' "drat" = "character", +#' "wt" = "character", +#' "qsec" = "numeric", +#' "vs" = "character", +#' "am" = "numeric", +#' "gear" = "character", +#' "carb" = "integer" +#' ) +#' get_vars_to_convert(summary_vars(mtcars), new_classes) +get_vars_to_convert <- function(vars, classes_input) { + vars <- data.table::as.data.table(vars) + classes_input <- data.table::data.table( + name = names(classes_input), + class_to_set = unlist(classes_input, use.names = FALSE), + stringsAsFactors = FALSE + ) + classes_input <- classes_input[!is.na(class_to_set) & class_to_set != ""] + classes_df <- merge(x = vars, y = classes_input, by = "name") + classes_df <- classes_df[!is.na(class_to_set)] + classes_df[class != class_to_set] +} + + +#' gsub wrapper for piping with default values for separator substituting +#' +#' @param data character vector +#' @param old.sep old separator +#' @param new.sep new separator +#' +#' @returns character vector +#' @export +#' +clean_sep <- function(data, old.sep = "[-.,/]", new.sep = "-") { + gsub(old.sep, new.sep, data) +} + +#' Attempts at applying uniform date format +#' +#' @param data character string vector of possible dates +#' +#' @returns character string +#' @export +#' +clean_date <- function(data) { + data |> + clean_sep() |> + sapply(\(.x){ + if (is.na(.x)) { + .x + } else { + strsplit(.x, "-") |> + unlist() |> + lapply(\(.y){ + if (nchar(.y) == 1) paste0("0", .y) else .y + }) |> + paste(collapse = "-") + } + }) |> + unname() +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//visual_summary.R +######## + +#' Data correlations evaluation module +#' +#' @param id Module id +#' +#' @name data-missings +#' @returns Shiny ui module +#' @export +visual_summary_ui <- function(id) { + ns <- shiny::NS(id) + + shiny::tagList( + shiny::plotOutput(outputId = ns("visual_plot"), height = "70vh") + ) +} + +visual_summary_server <- function(id, + data_r=shiny::reactive(NULL), + ...) { + shiny::moduleServer( + id = id, + module = function(input, output, session) { + # ns <- session$ns + rv <- shiny::reactiveValues(data = NULL) + + shiny::bindEvent(shiny::observe({ + data <- data_r() + rv$data <- data + # vars_num <- vapply(data, \(.x){ + # is.numeric(.x) || is_datetime(.x) + # }, logical(1)) + # vars_num <- names(vars_num)[vars_num] + # shinyWidgets::updateVirtualSelect( + # inputId = "variable", + # choices = vars_num, + # selected = if (isTruthy(input$variable)) input$variable else vars_num[1] + # ) + }), data_r(), input$hidden) + + # datar <- if (is.reactive(data)) data else reactive(data) + + + # apexcharter::renderApexchart({ + # missings_apex_plot(datar(), ...) + # }) + output$visual_plot <- shiny::renderPlot(expr = { + visual_summary(data = rv$data,...) + }) + } + ) +} + +visual_summary_demo_app <- function() { + ui <- shiny::fluidPage( + shiny::actionButton( + inputId = "modal_missings", + label = "Visual summary", + width = "100%", + disabled = FALSE + ) + ) + server <- function(input, output, session) { + data_demo <- mtcars + data_demo[sample(1:32, 10), "cyl"] <- NA + data_demo[sample(1:32, 8), "vs"] <- NA + + visual_summary_server(id = "data", data = shiny::reactive(data_demo)) + + observeEvent(input$modal_missings, { + tryCatch( + { + modal_visual_summary(id = "data") + }, + error = function(err) { + showNotification(paste0("We encountered the following error browsing your data: ", err), type = "err") + } + ) + }) + } + shiny::shinyApp(ui, server) +} + +visual_summary_demo_app() + + +modal_visual_summary <- function(id, + title = "Visual overview of data classes and missing observations", + easyClose = TRUE, + size = "xl", + footer = NULL, + ...) { + showModal(modalDialog( + title = tagList(title, datamods:::button_close_modal()), + visual_summary_ui(id = id), + easyClose = easyClose, + size = size, + footer = footer + )) +} + + +## Slow with many observations... + +#' Plot missings and class with apexcharter +#' +#' @param data data frame +#' +#' @returns An [apexchart()] `htmlwidget` object. +#' @export +#' +#' @examples +#' data_demo <- mtcars +#' data_demo[2:4, "cyl"] <- NA +#' rbind(data_demo, data_demo, data_demo, data_demo) |> missings_apex_plot() +#' data_demo |> missings_apex_plot() +#' mtcars |> missings_apex_plot(animation = TRUE) +#' # dplyr::storms |> missings_apex_plot() +#' visdat::vis_dat(dplyr::storms) +missings_apex_plot <- function(data, animation = FALSE, ...) { + l <- data_summary_gather(data, ...) + + df_plot <- l$data + + out <- apexcharter::apex( + data = df_plot, + type = "heatmap", + mapping = apexcharter::aes(x = variable, y = rows, fill = valueType_num), + ... + ) |> + apexcharter::ax_stroke(width = NULL) |> + apexcharter::ax_plotOptions( + heatmap = apexcharter::heatmap_opts( + radius = 0, + enableShades = FALSE, + colorScale = list( + ranges = l$labels + ), + useFillColorAsStroke = TRUE + ) + ) |> + apexcharter::ax_dataLabels(enabled = FALSE) |> + apexcharter::ax_tooltip( + enabled = FALSE, + intersect = FALSE + ) + + if (!isTRUE(animation)) { + out <- out |> + apexcharter::ax_chart(animations = list(enabled = FALSE)) + } + + out +} + + + +#' Ggplot2 data summary visualisation based on visdat::vis_dat. +#' +#' @param data data +#' @param ... optional arguments passed to data_summary_gather() +#' +#' @returns ggplot2 object +#' @export +#' +#' @examples +#' data_demo <- mtcars +#' data_demo[sample(1:32, 10), "cyl"] <- NA +#' data_demo[sample(1:32, 8), "vs"] <- NA +#' visual_summary(data_demo) +#' visual_summary(data_demo, palette.fun = scales::hue_pal()) +#' visual_summary(dplyr::storms) +#' visual_summary(dplyr::storms, summary.fun = data_type) +visual_summary <- function(data, legend.title = "Data class", ...) { + l <- data_summary_gather(data, ...) + + df <- l$data + + df$valueType <- factor(df$valueType, levels = names(l$colors)) + df$variable <- factor(df$variable, levels = unique_short(names(data))) + + ggplot2::ggplot(data = df, ggplot2::aes(x = variable, y = rows)) + + ggplot2::geom_raster(ggplot2::aes(fill = valueType)) + + ggplot2::theme_minimal() + + ggplot2::theme(axis.text.x = ggplot2::element_text( + angle = 45, + vjust = 1, hjust = 1 + )) + + ggplot2::scale_fill_manual(values = l$colors) + + ggplot2::labs(x = "", y = "Observations") + + ggplot2::scale_y_reverse() + + ggplot2::theme(axis.text.x = ggplot2::element_text(hjust = 0.5)) + + ggplot2::guides(colour = "none") + + ggplot2::guides(fill = ggplot2::guide_legend(title = legend.title)) + + # change the limits etc. + ggplot2::guides(fill = ggplot2::guide_legend(title = "Type")) + + # add info about the axes + ggplot2::scale_x_discrete(position = "top") + + ggplot2::theme(axis.text.x = ggplot2::element_text(hjust = 0)) + + ggplot2::theme( + panel.grid.major = ggplot2::element_blank(), + panel.grid.minor = ggplot2::element_blank(), + text = ggplot2::element_text(size = 18), + plot.title = ggplot2::element_blank() + ) +} + +#' Data summary for printing visual summary +#' +#' @param data data.frame +#' @param fun summary function. Default is "class" +#' @param palette.fun optionally use specific palette functions. First argument +#' has to be the length. +#' +#' @returns data.frame +#' @export +#' +#' @examples +#' mtcars |> data_summary_gather() +data_summary_gather <- function(data, summary.fun = class, palette.fun = viridisLite::viridis) { + df_plot <- setNames(data, unique_short(names(data))) |> + purrr::map_df(\(x){ + ifelse(is.na(x), + yes = NA, + no = glue::glue_collapse(summary.fun(x), + sep = "\n" + ) + ) + }) |> + dplyr::mutate(rows = dplyr::row_number()) |> + tidyr::pivot_longer( + cols = -rows, + names_to = "variable", values_to = "valueType", values_transform = list(valueType = as.character) + ) |> + dplyr::arrange(rows, variable, valueType) + + + df_plot$valueType_num <- df_plot$valueType |> + forcats::as_factor() |> + as.numeric() + + df_plot$valueType[is.na(df_plot$valueType)] <- "NA" + df_plot$valueType_num[is.na(df_plot$valueType_num)] <- max(df_plot$valueType_num, na.rm = TRUE) + 1 + + labels <- setNames(unique(df_plot$valueType_num), unique(df_plot$valueType)) |> sort() + + if (any(df_plot$valueType == "NA")) { + colors <- setNames(c(palette.fun(length(labels) - 1), "#999999"), names(labels)) + } else { + colors <- setNames(palette.fun(length(labels)), names(labels)) + } + + + label_list <- labels |> + purrr::imap(\(.x, .i){ + list( + from = .x, + to = .x, + color = colors[[.i]], + name = .i + ) + }) |> + setNames(NULL) + + list(data = df_plot, colors = colors, labels = label_list) +} + + + +#' Create unique short names of character vector items based on index +#' +#' @description +#' The function will prefer original names, and only append index to long +#' strings. +#' +#' +#' @param data character vector +#' @param max maximum final name length +#' +#' @returns character vector +#' @export +#' +#' @examples +#' c("kahdleidnsallskdj", "hej") |> unique_short() +unique_short <- function(data, max = 15) { + purrr::imap(data, \(.x, .i){ + if (nchar(.x) > max) { + glue::glue("{substr(.x,1,(max-(nchar(.i)+1)))}_{.i}") + } else { + .x + } + }) |> unlist() +} + + +######## +#### Current file: /Users/au301842/FreesearchR/R//wide2long.R +######## + +#' Alternative pivoting method for easily pivoting based on name pattern +#' +#' @description +#' This function requires and assumes a systematic naming of variables. +#' For now only supports one level pivoting. Adding more levels would require +#' an added "ignore" string pattern or similarly. Example 2. +#' +#' +#' @param data data +#' @param pattern pattern(s) to match. Character vector of length 1 or more. +#' @param type type of match. can be one of "prefix","infix" or "suffix". +#' @param id.col ID column. Will fill ID for all. Column name or numeric index. +#' Default is "1", first column. +#' @param instance.name +#' +#' @returns data.frame +#' @export +#' +#' @examples +#' data.frame( +#' 1:20, sample(70:80, 20, TRUE), +#' sample(70:100, 20, TRUE), +#' sample(70:100, 20, TRUE), +#' sample(170:200, 20, TRUE) +#' ) |> +#' setNames(c("id", "age", "weight_0", "weight_1", "height_1")) |> +#' wide2long(pattern = c("_0", "_1"), type = "suffix") +#' data.frame( +#' 1:20, sample(70:80, 20, TRUE), +#' sample(70:100, 20, TRUE), +#' sample(70:100, 20, TRUE), +#' sample(170:200, 20, TRUE) +#' ) |> +#' setNames(c("id", "age", "weight_0", "weight_a_1", "height_b_1")) |> +#' wide2long(pattern = c("_0", "_1"), type = "suffix") +#' # Optional filling of missing values by last observation carried forward +#' # Needed for mmrm analyses +#' long_missings |> +#' # Fills record ID assuming none are missing +#' tidyr::fill(record_id) |> +#' # Grouping by ID for the last step +#' dplyr::group_by(record_id) |> +#' # Filling missing data by ID +#' tidyr::fill(names(long_missings)[!names(long_missings) %in% new_names]) |> +#' # Remove grouping +#' dplyr::ungroup() +wide2long <- function( + data, + pattern, + type = c("prefix", "infix", "suffix"), + id.col = 1, + instance.name = "instance") { + type <- match.arg(type) + + ## Give the unique suffix names to use for identifying repeated measures + # suffixes <- c("_0", "_1") + + ## If no ID column is present, one is added + if (id.col == "none" | is.null(id.col)) { + data <- stats::setNames( + data.frame(seq_len(nrow(data)), data), + make.names(c("id", names(data)), unique = TRUE) + ) + id.col <- 1 + } +# browser() + ## Relevant columns are determined based on suffixes + cols <- names(data)[grepl_fix(names(data), pattern = pattern, type = type)] + + ## New colnames are created by removing suffixes + new_names <- unique(gsub(paste(pattern, collapse = "|"), "", cols)) + + out <- split(data, seq_len(nrow(data))) |> # Splits dataset by row + # Starts data modifications for each subject + lapply(\(.x){ + ## Pivots data with repeated measures as determined by the defined suffixes + long_ls <- split.default( + # Subset only repeated data + .x[cols], + # ... and split by meassure + gsub(paste(new_names, collapse = "|"), "", cols) + ) |> + # Sort data by order of given suffixes to ensure chronology + sort_by(pattern) |> + # New colnames are applied + lapply(\(.y){ + setNames( + .y, + gsub(paste(pattern, collapse = "|"), "", names(.y)) + ) + }) + + # Subsets non-pivotted data (this is assumed to belong to same ) + single <- .x[-match(cols, names(.x))] + + # Extends with empty rows to get same dimensions as long data + single[(nrow(single) + 1):length(long_ls), ] <- NA + + # Fills ID col + single[id.col] <- single[1, id.col] + + # Everything is merged together + merged <- dplyr::bind_cols( + single, + # Instance names are defined as suffixes without leading non-characters + REDCapCAST::as_factor(data.frame(gsub( + "^[^[:alnum:]]+", "", + names(long_ls) + ))), + dplyr::bind_rows(long_ls) + ) + + # Ensure unique new names based on supplied + colnames(merged) <- make.names( + c( + names(single), + instance.name, + names(merged)[(NCOL(single) + 2):NCOL(merged)] + ), + unique = TRUE + ) + + merged + }) |> dplyr::bind_rows() + + rownames(out) <- NULL + + out +} + + +#' Matches pattern to vector based on match type +#' +#' @param data vector +#' @param pattern pattern(s) to match. Character vector of length 1 or more. +#' @param type type of match. can be one of "prefix","infix" or "suffix". +#' +#' @returns logical vector +#' @export +#' +#' @examples +#' c("id", "age", "weight_0", "weight_1") |> grepl_fix(pattern = c("_0", "_1"), type = "suffix") +grepl_fix <- function(data, pattern, type = c("prefix", "infix", "suffix")) { + type <- match.arg(type) + + if (type == "prefix") { + grepl(paste0("^(", paste(pattern, collapse = "|"), ")*"), data) + } else if (type == "suffix") { + grepl(paste0("*(", paste(pattern, collapse = "|"), ")$"), data) + } else if (type == "infix") { + grepl(paste0("*(", paste(pattern, collapse = "|"), ")*"), data) + } +} + + +######## +#### Current file: /Users/au301842/FreesearchR/dev/header_include.R +######## + +header_include <- function(){ + shiny::tags$head( + includeHTML("www/umami-app.html"), + tags$link(rel = "stylesheet", type = "text/css", href = "style.css")) +} + + +######## +#### Current file: /Users/au301842/FreesearchR/dev/dev_banner.R +######## + +dev_banner <- function(){ + NULL + } + + +######## +#### Current file: /Users/au301842/FreesearchR/app/ui.R +######## + +# ns <- NS(id) + + + +ui_elements <- list( + ############################################################################## + ######### + ######### Home panel + ######### + ############################################################################## + "home" = bslib::nav_panel( + title = "FreesearchR", + shiny::fluidRow( + ## On building the dev-version for shinyapps.io, the dev_banner() is redefined + ## Default just output "NULL" + ## This could probably be achieved more legantly, but this works. + dev_banner(), + shiny::column(width = 2), + shiny::column( + width = 8, + shiny::markdown(readLines("www/intro.md")), + shiny::column(width = 2) + ) + ), + icon = shiny::icon("home") + ), + ############################################################################## + ######### + ######### Import panel + ######### + ############################################################################## + "import" = bslib::nav_panel( + title = "Import", + shiny::fluidRow( + shiny::column(width = 2), + shiny::column( + width = 8, + shiny::h4("Choose your data source"), + shiny::br(), + # shiny::uiOutput(outputId = "source"), + shinyWidgets::radioGroupButtons( + inputId = "source", + selected = "file", + choices = c( + "File upload" = "file", + "REDCap server export" = "redcap", + "Local or sample data" = "env" + ), + size = "lg" + ), + shiny::tags$script('document.querySelector("#source div").style.width = "100%"'), + shiny::helpText("Upload a file from your device, get data directly from REDCap or select a sample data set for testing from the app."), + shiny::br(), + shiny::br(), + shiny::conditionalPanel( + condition = "input.source=='file'", + import_file_ui( + id = "file_import", + layout_params = "dropdown", + # title = "Choose a datafile to upload", + file_extensions = c(".csv", ".tsv", ".txt", ".xls", ".xlsx", ".rds", ".ods", ".dta") + ) + ), + shiny::conditionalPanel( + condition = "input.source=='redcap'", + shinyWidgets::alert( + id = "redcap-warning", + status = "info", + shiny::tags$h2(shiny::markdown("Careful with sensitive data")), + shiny::tags$p("The", shiny::tags$i(shiny::tags$b("FreesearchR")), "app only stores data for analyses, but please only use with sensitive data when running locally.", "", shiny::tags$a("Read more here", href = "https://agdamsbo.github.io/FreesearchR/#run-locally-on-your-own-machine"), "."), + dismissible = TRUE + ), + m_redcap_readUI( + id = "redcap_import", + title = "" + ) + ), + shiny::conditionalPanel( + condition = "input.source=='env'", + import_globalenv_ui(id = "env", title = NULL) + ), + # shiny::conditionalPanel( + # condition = "input.source=='redcap'", + # DT::DTOutput(outputId = "redcap_prev") + # ), + shiny::conditionalPanel( + condition = "output.data_loaded == true", + shiny::br(), + shiny::actionButton( + inputId = "modal_initial_view", + label = "Quick overview", + width = "100%", + icon = shiny::icon("binoculars"), + disabled = FALSE + ), + shiny::br(), + shiny::br(), + shiny::h5("Select variables for final import"), + shiny::fluidRow( + shiny::column( + width = 6, + shiny::p("Exclude incomplete variables:"), + shiny::br(), + shinyWidgets::noUiSliderInput( + inputId = "complete_cutoff", + label = NULL, + update_on = "end", + min = 0, + max = 100, + step = 5, + value = 30, + format = shinyWidgets::wNumbFormat(decimals = 0), + color = datamods:::get_primary_color() + ), + shiny::helpText("Only include variables missing less observations than the specified percentage."), + shiny::br() + ), + shiny::column( + width = 6, + shiny::p("Manual selection:"), + shiny::br(), + shiny::uiOutput(outputId = "import_var"), + shiny::br() + ) + ), + shiny::uiOutput(outputId = "data_info_import", inline = TRUE), + shiny::br(), + shiny::br(), + shiny::actionButton( + inputId = "act_start", + label = "Start", + width = "100%", + icon = shiny::icon("play"), + disabled = TRUE + ), + shiny::helpText('After importing, hit "Start" or navigate to the desired tab.'), + shiny::br(), + shiny::br() + ), + shiny::column(width = 2) + ), + shiny::br(), + shiny::br() + ) + ), + ############################################################################## + ######### + ######### Data overview panel + ######### + ############################################################################## + "overview" = + # bslib::nav_panel_hidden( + bslib::nav_panel( + # value = "overview", + title = "Data", + bslib::navset_bar( + fillable = TRUE, + bslib::nav_panel( + title = "Overview", + tags$h3("Overview and filtering"), + fluidRow( + shiny::column( + width = 9, + shiny::uiOutput(outputId = "data_info", inline = TRUE), + shiny::tags$p( + "Below is a short summary table, on the right you can click to visualise data classes or browse data and create different data filters." + ) + ), + shiny::column( + width = 3, + shiny::actionButton( + inputId = "modal_visual_overview", + label = "Visual overview", + width = "100%", + disabled = TRUE + ), + shiny::br(), + shiny::br(), + shiny::actionButton( + inputId = "modal_browse", + label = "Browse data", + width = "100%", + disabled = TRUE + ), + shiny::br(), + shiny::br() + ) + ), + fluidRow( + shiny::column( + width = 9, + data_summary_ui(id = "data_summary"), + shiny::br(), + shiny::br(), + shiny::br(), + shiny::br(), + shiny::br() + ), + shiny::column( + width = 3, + # shiny::actionButton( + # inputId = "modal_missings", + # label = "Visual overview", + # width = "100%", + # disabled = TRUE + # ), + # shiny::br(), + # shiny::br(), + # shiny::actionButton( + # inputId = "modal_browse", + # label = "Browse data", + # width = "100%", + # disabled = TRUE + # ), + # shiny::br(), + # shiny::br(), + shiny::tags$h6("Filter data types"), + shiny::uiOutput( + outputId = "column_filter" + ), + shiny::helpText("Read more on how ", tags$a( + "data types", + href = "https://agdamsbo.github.io/FreesearchR/articles/data-types.html", + target = "_blank", + rel = "noopener noreferrer" + ), " are defined."), + shiny::br(), + shiny::br(), + shiny::tags$h6("Filter observations"), + shiny::tags$p("Filter on observation level"), + IDEAFilter::IDEAFilter_ui("data_filter"), + shiny::br(), + shiny::br() + ) + ), + shiny::br(), + shiny::br(), + # shiny::br(), + # shiny::br(), + shiny::br() + ), + bslib::nav_panel( + title = "Modify", + tags$h3("Subset, rename and convert variables"), + fluidRow( + shiny::column( + width = 9, + shiny::tags$p( + shiny::markdown("Below, are several options for simple data manipulation like update variables by renaming, creating new labels (for nicer tables in the report) and changing variable classes (numeric, factor/categorical etc.)."), + shiny::markdown("There are more advanced options to modify factor/categorical variables as well as create new factor from a continous variable or new variables with *R* code. At the bottom you can restore the original data."), + shiny::markdown("Please note that data modifications are applied before any filtering.") + ) + ) + ), + # shiny::tags$br(), + update_variables_ui("modal_variables"), + shiny::tags$br(), + shiny::tags$br(), + shiny::tags$h4("Advanced data manipulation"), + shiny::tags$p("Below options allow more advanced varaible manipulations."), + shiny::tags$br(), + shiny::tags$br(), + shiny::fluidRow( + shiny::column( + width = 4, + shiny::actionButton( + inputId = "modal_update", + label = "Reorder factor levels", + width = "100%" + ), + shiny::tags$br(), + shiny::helpText("Reorder the levels of factor/categorical variables."), + shiny::tags$br(), + shiny::tags$br() + ), + shiny::column( + width = 4, + shiny::actionButton( + inputId = "modal_cut", + label = "New factor", + width = "100%" + ), + shiny::tags$br(), + shiny::helpText("Create factor/categorical variable from a continous variable (number/date/time)."), + shiny::tags$br(), + shiny::tags$br() + ), + shiny::column( + width = 4, + shiny::actionButton( + inputId = "modal_column", + label = "New variable", + width = "100%" + ), + shiny::tags$br(), + shiny::helpText(shiny::markdown("Create a new variable/column based on an *R*-expression.")), + shiny::tags$br(), + shiny::tags$br() + ) + ), + tags$h4("Compare modified data to original"), + shiny::tags$br(), + shiny::tags$p( + "Raw print of the original vs the modified data." + ), + shiny::tags$br(), + shiny::fluidRow( + shiny::column( + width = 6, + shiny::tags$b("Original data:"), + # verbatimTextOutput("original"), + shiny::verbatimTextOutput("original_str") + ), + shiny::column( + width = 6, + shiny::tags$b("Modified data:"), + # verbatimTextOutput("modified"), + shiny::verbatimTextOutput("modified_str") + ) + ), + shiny::tags$br(), + shiny::actionButton( + inputId = "data_reset", + label = "Restore original data", + width = "100%" + ), + shiny::tags$br(), + shiny::helpText("Reset to original imported dataset. Careful! There is no un-doing."), + shiny::tags$br() + ) + ) + ), + ############################################################################## + ######### + ######### Descriptive analyses panel + ######### + ############################################################################## + "describe" = + bslib::nav_panel( + title = "Evaluate", + id = "navdescribe", + bslib::navset_bar( + title = "", + sidebar = bslib::sidebar( + shiny::uiOutput(outputId = "data_info_nochar", inline = TRUE), + bslib::accordion( + open = "acc_chars", + multiple = FALSE, + bslib::accordion_panel( + value = "acc_chars", + title = "Characteristics", + icon = bsicons::bs_icon("table"), + shiny::uiOutput("strat_var"), + shiny::helpText("Only factor/categorical variables are available for stratification. Go back to the 'Data' tab to reclass a variable if it's not on the list."), + shiny::conditionalPanel( + condition = "input.strat_var!='none'", + shiny::radioButtons( + inputId = "add_p", + label = "Compare strata?", + selected = "no", + inline = TRUE, + choices = list( + "No" = "no", + "Yes" = "yes" + ) + ), + shiny::helpText("Option to perform statistical comparisons between strata in baseline table.") + ), + shiny::br(), + shiny::br(), + shiny::actionButton( + inputId = "act_eval", + label = "Evaluate", + width = "100%", + icon = shiny::icon("calculator"), + disabled = TRUE + ) + ), + bslib::accordion_panel( + vlaue = "acc_cor", + title = "Correlations", + icon = bsicons::bs_icon("bounding-box"), + shiny::uiOutput("outcome_var_cor"), + shiny::helpText("To avoid evaluating the correlation of the outcome variable, this can be excluded from the plot or select 'none'."), + shiny::br(), + shinyWidgets::noUiSliderInput( + inputId = "cor_cutoff", + label = "Correlation cut-off", + min = 0, + max = 1, + step = .01, + value = .8, + format = shinyWidgets::wNumbFormat(decimals = 2), + color = datamods:::get_primary_color() + ), + shiny::helpText("Set the cut-off for considered 'highly correlated'.") + ), + bslib::accordion_panel( + vlaue = "acc_mis", + title = "Missings", + icon = bsicons::bs_icon("x-circle"), + shiny::uiOutput("missings_var"), + shiny::helpText("To consider if daata is missing by random, choose the outcome/dependent variable, if it has any missings to evaluate if there is a significant difference across other variables depending on missing data or not.") + ) + ) + ), + bslib::nav_panel( + title = "Characteristics", + gt::gt_output(outputId = "table1") + ), + bslib::nav_panel( + title = "Correlations", + data_correlations_ui(id = "correlations", height = 600) + ), + bslib::nav_panel( + title = "Missings", + data_missings_ui(id = "missingness") + ) + ) + ), + ############################################################################## + ######### + ######### Download panel + ######### + ############################################################################## + "visuals" = bslib::nav_panel( + title = "Visuals", + id = "navvisuals", + do.call( + bslib::navset_bar, + c( + data_visuals_ui("visuals"), + shiny::tagList( + bslib::nav_spacer(), + bslib::nav_item( + # shiny::img(shiny::icon("book")), + shiny::tags$a( + href = "https://agdamsbo.github.io/FreesearchR/articles/visuals.html", + "Notes (external)", + target = "_blank", + rel = "noopener noreferrer" + ) + ) + ) + ) + ) + ), + ############################################################################## + ######### + ######### Regression analyses panel + ######### + ############################################################################## + "analyze" = + bslib::nav_panel( + title = "Regression", + id = "navanalyses", + do.call( + bslib::navset_bar, + regression_ui("regression") + ) + ), + ############################################################################## + ######### + ######### Download panel + ######### + ############################################################################## + "download" = + bslib::nav_panel( + title = "Download", + id = "navdownload", + shiny::fluidRow( + shiny::column(width = 2), + shiny::column( + width = 8, + shiny::fluidRow( + shiny::column( + width = 6, + shiny::h4("Report"), + shiny::helpText("Choose your favourite output file format for further work, and download, when the analyses are done."), + shiny::br(), + shiny::br(), + shiny::selectInput( + inputId = "output_type", + label = "Output format", + selected = NULL, + choices = list( + "MS Word" = "docx", + "LibreOffice" = "odt" + # , + # "PDF" = "pdf", + # "All the above" = "all" + ) + ), + shiny::br(), + # Button + shiny::downloadButton( + outputId = "report", + label = "Download report", + icon = shiny::icon("download") + ) + # shiny::helpText("If choosing to output to MS Word, please note, that when opening the document, two errors will pop-up. Choose to repair and choose not to update references. The issue is being worked on. You can always choose LibreOffice instead."), + ), + shiny::column( + width = 6, + shiny::h4("Data"), + shiny::helpText("Choose your favourite output data format to download the modified data."), + shiny::br(), + shiny::br(), + shiny::selectInput( + inputId = "data_type", + label = "Data format", + selected = NULL, + choices = list( + "R" = "rds", + "stata" = "dta", + "CSV" = "csv" + ) + ), + shiny::helpText("No metadata is saved when exporting to csv."), + shiny::br(), + shiny::br(), + # Button + shiny::downloadButton( + outputId = "data_modified", + label = "Download data", + icon = shiny::icon("download") + ) + ) + ), + shiny::br(), + shiny::br(), + shiny::h4("Code snippets"), + shiny::tags$p("Below are the code bits used to create the final data set and the main analyses."), + shiny::tags$p("This can be used as a starting point for learning to code and for reproducibility."), + shiny::tagList( + lapply( + paste0("code_", c( + "import", "format", "data", "variables", "filter", "table1", "univariable", "multivariable" + )), + \(.x)shiny::htmlOutput(outputId = .x) + ) + ), + shiny::tags$br(), + shiny::br() + ), + shiny::column(width = 2) + ) + ), + ############################################################################## + ######### + ######### Feedback link + ######### + ############################################################################## + "feedback" = bslib::nav_item( + # shiny::img(shiny::icon("book")), + shiny::tags$a( + href = "https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8", + "Feedback", shiny::icon("arrow-up-right-from-square"), + target = "_blank", + rel = "noopener noreferrer" + ) + ), + ############################################################################## + ######### + ######### Documentation link + ######### + ############################################################################## + "docs" = bslib::nav_item( + # shiny::img(shiny::icon("book")), + shiny::tags$a( + href = "https://agdamsbo.github.io/FreesearchR/", + "Docs", shiny::icon("arrow-up-right-from-square"), + target = "_blank", + rel = "noopener noreferrer" + ) + ) + # bslib::nav_panel( + # title = "Documentation", + # # shiny::tags$iframe("www/docs.html", height=600, width=535), + # shiny::htmlOutput("docs_file"), + # shiny::br() + # ) +) +# Initial attempt at creating light and dark versions +light <- custom_theme() +dark <- custom_theme( + bg = "#000", + fg = "#fff" +) + +# Fonts to consider: +# https://webdesignerdepot.com/17-open-source-fonts-youll-actually-love/ + +ui <- bslib::page_fixed( + prismDependencies, + prismRDependency, + header_include(), + ## This adds the actual favicon + ## png and ico versions are kept for compatibility + shiny::tags$head(tags$link(rel = "shortcut icon", href = "favicon.svg")), + title = "FreesearchR", + theme = light, + shiny::useBusyIndicators(), + shinyjs::useShinyjs(), + shiny::div( + id = "loading_page", + # shiny::h1("Loading the FreesearchR app..."), + shinybusy::add_busy_spinner(position = "full-page") + ), + shinyjs::hidden( + shiny::div( + id = "main_content", + bslib::page_navbar( + id = "main_panel", + ui_elements$home, + ui_elements$import, + ui_elements$overview, + ui_elements$describe, + ui_elements$visuals, + ui_elements$analyze, + ui_elements$download, + bslib::nav_spacer(), + ui_elements$feedback, + ui_elements$docs, + fillable = FALSE, + footer = shiny::tags$footer( + style = "background-color: #14131326; padding: 4px; text-align: center; bottom: 0; width: 100%;", + shiny::p( + style = "margin: 1", + "Data is only stored for analyses and deleted when the app is closed.", shiny::markdown("Consider [running ***FreesearchR*** locally](https://agdamsbo.github.io/FreesearchR/#run-locally-on-your-own-machine) if working with sensitive data.") + ), + shiny::p( + style = "margin: 1; color: #888;", + shiny::tags$a("Docs", href = "https://agdamsbo.github.io/FreesearchR/", target = "_blank", rel = "noopener noreferrer"), " | ", hosted_version(), " | ", shiny::tags$a("License: AGPLv3", href = "https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Source", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Share feedback", href = "https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8", target = "_blank", rel = "noopener noreferrer") + ), + ) + ) + ) + ) +) + + +######## +#### Current file: /Users/au301842/FreesearchR/app/server.R +######## + +data(mtcars) + +# trial <- gtsummary::trial +# starwars <- dplyr::starwars +# +# mtcars_na <- rbind(mtcars,NA,NA) + +# thematic::thematic_shiny() + +load_data <- function() { + Sys.sleep(1) + shinyjs::hide("loading_page") + shinyjs::show("main_content") +} + +# is_local = is.na(Sys.getenv('SHINY_SERVER_VERSION', NA)) + +server <- function(input, output, session) { + ## Listing files in www in session start to keep when ending and removing + ## everything else. + files.to.keep <- list.files("www/") + + load_data() + + ############################################################################## + ######### + ######### Night mode (just very popular, not really needed) + ######### + ############################################################################## + + # observeEvent(input$dark_mode,{ + # session$setCurrentTheme( + # if (isTRUE(input$dark_mode)) dark else light + # )}) + + # observe({ + # if(input$dark_mode==TRUE) + # session$setCurrentTheme(bs_theme_update(theme = custom_theme(version = 5))) + # if(input$dark_mode==FALSE) + # session$setCurrentTheme(bs_theme_update(theme = custom_theme(version = 5, bg = "#000",fg="#fff"))) + # }) + + + ############################################################################## + ######### + ######### Setting reactive values + ######### + ############################################################################## + + rv <- shiny::reactiveValues( + list = list(), + regression = NULL, + missings = NULL, + ds = NULL, + local_temp = NULL, + ready = NULL, + test = "no", + data_original = NULL, + data_temp = NULL, + data = NULL, + data_variables = NULL, + data_filtered = NULL, + models = NULL, + code = list() + ) + + ############################################################################## + ######### + ######### Data import section + ######### + ############################################################################## + + data_file <- import_file_server( + id = "file_import", + show_data_in = "popup", + trigger_return = "change", + return_class = "data.frame" + ) + + shiny::observeEvent(data_file$data(), { + shiny::req(data_file$data()) + rv$data_temp <- data_file$data() + rv$code <- modifyList(x = rv$code, list(import = data_file$code())) + }) + + from_redcap <- m_redcap_readServer( + id = "redcap_import" + ) + + shiny::observeEvent(from_redcap$data(), { + rv$data_temp <- from_redcap$data() + rv$code <- modifyList(x = rv$code, list(import = from_redcap$code())) + }) + + from_env <- datamods::import_globalenv_server( + id = "env", + trigger_return = "change", + btn_show_data = FALSE, + reset = reactive(input$hidden) + ) + + shiny::observeEvent(from_env$data(), { + shiny::req(from_env$data()) + + rv$data_temp <- from_env$data() + rv$code <- modifyList(x = rv$code, list(import = from_env$name())) + }) + + visual_summary_server( + id = "initial_summary", + data_r = shiny::reactive({ + shiny::req(rv$data_temp) + default_parsing(rv$data_temp) + }), + palette.fun = FreesearchR_palette + ) + + observeEvent(input$modal_initial_view, { + tryCatch( + { + modal_visual_summary( + id = "initial_summary", + footer = NULL, + size = "xl" + ) + }, + error = function(err) { + showNotification(paste0("We encountered the following error showing missingness: ", err), type = "err") + } + ) + }) + + output$import_var <- shiny::renderUI({ + shiny::req(rv$data_temp) + + preselect <- names(rv$data_temp)[sapply(rv$data_temp, missing_fraction) <= (input$complete_cutoff / 100)] + + shinyWidgets::virtualSelectInput( + inputId = "import_var", + label = "Select variables to include", + selected = preselect, + choices = names(rv$data_temp), + updateOn = "change", + multiple = TRUE, + search = TRUE, + showValueAsTags = TRUE + ) + }) + + output$data_loaded <- shiny::reactive({ + !is.null(rv$data_temp) + }) + + shiny::observeEvent(input$source, { + rv$data_temp <- NULL + }) + + shiny::outputOptions(output, "data_loaded", suspendWhenHidden = FALSE) + + shiny::observeEvent( + eventExpr = list( + input$import_var, + input$complete_cutoff, + rv$data_temp + ), + handlerExpr = { + shiny::req(rv$data_temp) + shiny::req(input$import_var) + # browser() + temp_data <- rv$data_temp + if (all(input$import_var %in% names(temp_data))) { + temp_data <- temp_data |> dplyr::select(input$import_var) + } + + rv$data_original <- temp_data |> + default_parsing() + + rv$code$import <- rv$code$import |> + expression_string(assign.str = "df <-") + + rv$code$format <- list( + "df", + rlang::expr(dplyr::select(dplyr::all_of(!!input$import_var))), + rlang::call2(.fn = "default_parsing", .ns = "FreesearchR") + ) |> + lapply(expression_string) |> + pipe_string() |> + expression_string(assign.str = "df <-") + + rv$code$filter <- NULL + rv$code$modify <- NULL + }, ignoreNULL = FALSE + ) + + output$data_info_import <- shiny::renderUI({ + shiny::req(rv$data_original) + data_description(rv$data_original) + }) + + ## Activating action buttons on data imported + shiny::observeEvent(rv$data_original, { + if (is.null(rv$data_original) | NROW(rv$data_original) == 0) { + shiny::updateActionButton(inputId = "act_start", disabled = TRUE) + shiny::updateActionButton(inputId = "modal_browse", disabled = TRUE) + shiny::updateActionButton(inputId = "modal_visual_overview", disabled = TRUE) + shiny::updateActionButton(inputId = "act_eval", disabled = TRUE) + } else { + shiny::updateActionButton(inputId = "act_start", disabled = FALSE) + shiny::updateActionButton(inputId = "modal_browse", disabled = FALSE) + shiny::updateActionButton(inputId = "modal_visual_overview", disabled = FALSE) + shiny::updateActionButton(inputId = "act_eval", disabled = FALSE) + } + }) + + ############################################################################## + ######### + ######### Data modification section + ######### + ############################################################################## + + shiny::observeEvent( + eventExpr = list( + rv$data_original + ), + handlerExpr = { + shiny::req(rv$data_original) + + rv$data <- rv$data_original + } + ) + + ## For now this solution work, but I would prefer to solve this with the above + shiny::observeEvent(input$reset_confirm, + { + if (isTRUE(input$reset_confirm)) { + shiny::req(rv$data_original) + rv$data <- rv$data_original + rv$code$filter <- NULL + rv$code$variables <- NULL + rv$code$modify <- NULL + } + }, + ignoreNULL = TRUE + ) + + + shiny::observeEvent(input$data_reset, { + shinyWidgets::ask_confirmation( + cancelOnDismiss = TRUE, + inputId = "reset_confirm", + title = "Please confirm data reset?", + type = "warning" + ) + }) + + ######### + ######### Modifications + ######### + + ## Using modified version of the datamods::cut_variable_server function + ## Further modifications are needed to have cut/bin options based on class of variable + ## Could be defined server-side + + output$data_info <- shiny::renderUI({ + shiny::req(data_filter()) + data_description(data_filter(), "The filtered data") + }) + + ######### Create factor + + shiny::observeEvent( + input$modal_cut, + modal_cut_variable("modal_cut", title = "Create new factor") + ) + + data_modal_cut <- cut_variable_server( + id = "modal_cut", + data_r = shiny::reactive(rv$data) + ) + + shiny::observeEvent(data_modal_cut(), { + rv$data <- data_modal_cut() + rv$code$modify[[length(rv$code$modify) + 1]] <- attr(rv$data, "code") + }) + + ######### Modify factor + + shiny::observeEvent( + input$modal_update, + datamods::modal_update_factor(id = "modal_update", title = "Reorder factor levels") + ) + + data_modal_update <- datamods::update_factor_server( + id = "modal_update", + data_r = reactive(rv$data) + ) + + shiny::observeEvent(data_modal_update(), { + shiny::removeModal() + rv$data <- data_modal_update() + rv$code$modify[[length(rv$code$modify) + 1]] <- attr(rv$data, "code") + }) + + ######### Create column + + shiny::observeEvent( + input$modal_column, + modal_create_column( + id = "modal_column", + footer = shiny::markdown("This window is aimed at advanced users and require some *R*-experience!"), + title = "Create new variables" + ) + ) + data_modal_r <- create_column_server( + id = "modal_column", + data_r = reactive(rv$data) + ) + shiny::observeEvent( + data_modal_r(), + { + rv$data <- data_modal_r() + rv$code$modify[[length(rv$code$modify) + 1]] <- attr(rv$data, "code") + } + ) + + ######### Subset, rename, reclass + + updated_data <- update_variables_server( + id = "modal_variables", + data = shiny::reactive(rv$data), + return_data_on_init = FALSE + ) + + shiny::observeEvent(updated_data(), { + rv$data <- updated_data() + rv$code$modify[[length(rv$code$modify) + 1]] <- attr(rv$data, "code") + }) + + ### Column filter + ### Completely implemented, but it takes a little considering where in the + ### data flow to implement, as it will act destructively on previous + ### manipulations + + output$column_filter <- shiny::renderUI({ + shiny::req(rv$data) + # c("dichotomous", "ordinal", "categorical", "datatime", "continuous") + shinyWidgets::virtualSelectInput( + inputId = "column_filter", + label = "Select data types to include", + selected = unique(data_type(rv$data)), + choices = unique(data_type(rv$data)), + updateOn = "change", + multiple = TRUE, + search = FALSE, + showValueAsTags = TRUE + ) + }) + + shiny::observe({ + # shiny::req(input$column_filter) + out <- data_type_filter(rv$data, input$column_filter) + rv$data_variables <- out + if (!is.null(input$column_filter)) { + rv$code$variables <- attr(out, "code") + } + # rv$code$modify[[length(rv$code$modify) + 1]] <- attr(rv$data, "code") + }) + + + ######### Data filter + # IDEAFilter has the least cluttered UI, but might have a License issue + # Consider using shinyDataFilter, though not on CRAN + data_filter <- IDEAFilter::IDEAFilter("data_filter", + data = shiny::reactive(rv$data_variables), + verbose = TRUE + ) + + shiny::observeEvent( + list( + shiny::reactive(rv$data_variables), + shiny::reactive(rv$data_original), + data_filter(), + # regression_vars(), + input$complete_cutoff + ), + { + ### Save filtered data + rv$data_filtered <- data_filter() + + ### Save filtered data + ### without empty factor levels + rv$list$data <- data_filter() |> + REDCapCAST::fct_drop() |> + (\(.x){ + .x[!sapply(.x, is.character)] + })() + + ## This looks messy!! But it works as intended for now + + out <- gsub( + "filter", "dplyr::filter", + gsub( + "\\s{2,}", " ", + paste0( + capture.output(attr(rv$data_filtered, "code")), + collapse = " " + ) + ) + ) + + out <- strsplit(out, "%>%") |> + unlist() |> + (\(.x){ + paste(c("df <- df", .x[-1], "REDCapCAST::fct_drop()"), + collapse = "|> \n " + ) + })() + + rv$code <- append_list(data = out, list = rv$code, index = "filter") + } + ) + + ######### Data preview + + ### Overview + + data_summary_server( + id = "data_summary", + data = shiny::reactive({ + rv$data_filtered + }), + color.main = "#2A004E", + color.sec = "#C62300", + pagination = 10 + ) + + observeEvent(input$modal_browse, { + tryCatch( + { + show_data(REDCapCAST::fct_drop(rv$data_filtered), title = "Uploaded data overview", type = "modal") + }, + error = function(err) { + showNotification(paste0("We encountered the following error browsing your data: ", err), type = "err") + } + ) + }) + + visual_summary_server( + id = "visual_overview", + data_r = shiny::reactive({ + shiny::req(rv$data_filtered) + REDCapCAST::fct_drop(rv$data_filtered) + }), + palette.fun = FreesearchR_palette + ) + + observeEvent(input$modal_visual_overview, { + tryCatch( + { + modal_visual_summary( + id = "visual_overview", + footer = "Here is an overview of how your data is interpreted, and where data is missing. Use this information to consider if data is missing at random or if some observations are missing systematically wich may be caused by an observation bias.", + size = "xl" + ) + }, + error = function(err) { + showNotification(paste0("We encountered the following error showing missingness: ", err), type = "err") + } + ) + }) + + output$original_str <- renderPrint({ + str(rv$data_original) + }) + + output$modified_str <- renderPrint({ + str(as.data.frame(rv$data_filtered) |> + REDCapCAST::set_attr( + label = NULL, + attr = "code" + )) + }) + + ## Evaluation table/plots reset on data change + ## This does not work (!?) + shiny::observeEvent( + list( + rv$data_filtered + ), + { + shiny::req(rv$data_filtered) + + rv$list$table1 <- NULL + } + ) + + + ############################################################################## + ######### + ######### Code export + ######### + ############################################################################## + + ## This really should be collapsed to only one call, but I'll leave it for now + ## as a working example of dynamically defining outputs and rendering. + + # output$code_import <- shiny::renderPrint({ + # shiny::req(rv$code$import) + # cat(c("#Data import\n", rv$code$import)) + # }) + + output$code_import <- shiny::renderUI({ + shiny::req(rv$code$import) + prismCodeBlock(paste0("#Data import\n", rv$code$import)) + }) + + output$code_format <- shiny::renderUI({ + shiny::req(rv$code$format) + prismCodeBlock(paste0("#Data import formatting\n", rv$code$format)) + }) + + output$code_data <- shiny::renderUI({ + shiny::req(rv$code$modify) + # browser() + ## This will create three lines for each modification + # ls <- rv$code$modify + ## This will remove all non-unique entries + # ls <- rv$code$modify |> unique() + ## This will only remove all non-repeating entries + ls <- rv$code$modify[!is_identical_to_previous(rv$code$modify)] + + out <- ls |> + lapply(expression_string) |> + pipe_string() |> + expression_string(assign.str = "df <- df |>\n") + + prismCodeBlock(paste0("#Data modifications\n", out)) + }) + + output$code_variables <- shiny::renderUI({ + shiny::req(rv$code$variables) + out <- expression_string(rv$code$variables, assign.str = "df <- df |>\n") + prismCodeBlock(paste0("#Variables filter\n", out)) + }) + + output$code_filter <- shiny::renderUI({ + shiny::req(rv$code$filter) + prismCodeBlock(paste0("#Data filter\n", rv$code$filter)) + }) + + output$code_table1 <- shiny::renderUI({ + shiny::req(rv$code$table1) + prismCodeBlock(paste0("#Data characteristics table\n", rv$code$table1)) + }) + + + ## Just a note to self + ## This is a very rewarding couple of lines marking new insights to dynamically rendering code + shiny::observe({ + shiny::req(rv$regression) + rv$regression()$regression$models |> purrr::imap(\(.x, .i){ + output[[paste0("code_", tolower(.i))]] <- shiny::renderUI({ + prismCodeBlock(paste0(paste("#", .i, "regression model\n"), .x$code_table)) + }) + }) + }) + + + ############################################################################## + ######### + ######### Data analyses Inputs + ######### + ############################################################################## + + output$strat_var <- shiny::renderUI({ + columnSelectInput( + inputId = "strat_var", + selected = "none", + label = "Select variable to stratify baseline", + data = shiny::reactive(rv$data_filtered)(), + col_subset = c( + "none", + names(rv$data_filtered)[unlist(lapply(rv$data_filtered, data_type)) %in% c("dichotomous", "categorical", "ordinal")] + ) + ) + }) + + ############################################################################## + ######### + ######### Descriptive evaluations + ######### + ############################################################################## + + + output$data_info_nochar <- shiny::renderUI({ + shiny::req(rv$list$data) + data_description(rv$list$data, data_text = "The dataset without text variables") + }) + + shiny::observeEvent( + list( + input$act_eval + ), + { + shiny::req(input$strat_var) + shiny::req(rv$list$data) + + parameters <- list( + by.var = input$strat_var, + add.p = input$add_p == "yes", + add.overall = TRUE + ) + + shiny::withProgress(message = "Creating the table. Hold on for a moment..", { + rv$list$table1 <- rlang::exec(create_baseline, !!!append_list(rv$list$data, parameters, "data")) + }) + + rv$code$table1 <- glue::glue("FreesearchR::create_baseline(df,{list2str(parameters)})") + } + ) + + output$table1 <- gt::render_gt({ + if (!is.null(rv$list$table1)) { + rv$list$table1 |> + gtsummary::as_gt() |> + gt::tab_header(gt::md("**Table 1: Baseline Characteristics**")) + } else { + return(NULL) + } + }) + + output$outcome_var_cor <- shiny::renderUI({ + columnSelectInput( + inputId = "outcome_var_cor", + selected = "none", + data = rv$list$data, + label = "Select outcome variable", + col_subset = c( + "none", + colnames(rv$list$data) + ), + multiple = FALSE + ) + }) + + data_correlations_server( + id = "correlations", + data = shiny::reactive({ + shiny::req(rv$list$data) + out <- rv$list$data + if (!is.null(input$outcome_var_cor) && input$outcome_var_cor != "none") { + out <- out[!names(out) %in% input$outcome_var_cor] + } + out + }), + cutoff = shiny::reactive(input$cor_cutoff) + ) + + output$missings_var <- shiny::renderUI({ + columnSelectInput( + inputId = "missings_var", + label = "Select variable to stratify analysis", + data = shiny::reactive({ + shiny::req(rv$data_filtered) + rv$data_filtered[apply(rv$data_filtered, 2, anyNA)] + })() + ) + }) + + rv$missings <- data_missings_server( + id = "missingness", + data = shiny::reactive(rv$data_filtered), + variable = shiny::reactive(input$missings_var) + ) + + + ############################################################################## + ######### + ######### Data visuals + ######### + ############################################################################## + + pl <- data_visuals_server("visuals", data = shiny::reactive(rv$list$data)) + + ############################################################################## + ######### + ######### Regression model analyses + ######### + ############################################################################## + + rv$regression <- regression_server("regression", data = shiny::reactive(rv$list$data)) + + ############################################################################## + ######### + ######### Page navigation + ######### + ############################################################################## + + shiny::observeEvent(input$act_start, { + bslib::nav_select(id = "main_panel", selected = "Data") + }) + + ############################################################################## + ######### + ######### Reactivity + ######### + ############################################################################## + + output$uploaded <- shiny::reactive({ + if (is.null(rv$ds)) { + "no" + } else { + "yes" + } + }) + + shiny::outputOptions(output, "uploaded", suspendWhenHidden = FALSE) + + output$ready <- shiny::reactive({ + if (is.null(rv$ready)) { + "no" + } else { + "yes" + } + }) + + shiny::outputOptions(output, "ready", suspendWhenHidden = FALSE) + + ############################################################################## + ######### + ######### Downloads + ######### + ############################################################################## + + # Could be rendered with other tables or should show progress + # Investigate quarto render problems + # On temp file handling: https://github.com/quarto-dev/quarto-cli/issues/3992 + output$report <- downloadHandler( + filename = shiny::reactive({ + paste0("report.", input$output_type) + }), + content = function(file, type = input$output_type) { + ## Notification is not progressing + ## Presumably due to missing + # Simplified for .rmd output attempt + format <- ifelse(type == "docx", "word_document", "odt_document") + + rv$list$regression <- rv$regression() + rv$list$missings <- rv$missings() + + shiny::withProgress(message = "Generating the report. Hold on for a moment..", { + tryCatch( + { + rv$list |> + write_rmd( + params.args = list( + regression.p = rv$list$regression$input$add_regression_p + ), + output_format = format, + input = file.path(getwd(), "www/report.rmd") + ) + }, + error = function(err) { + showNotification(paste0("We encountered the following error creating your report: ", err), type = "err") + } + ) + }) + file.rename(paste0("www/report.", type), file) + } + ) + + output$data_modified <- downloadHandler( + filename = shiny::reactive({ + paste0("modified_data.", input$data_type) + }), + content = function(file, type = input$data_type) { + if (type == "rds") { + readr::write_rds(rv$list$data, file = file) + } else if (type == "dta") { + haven::write_dta(as.data.frame(rv$list$data), path = file) + } else if (type == "csv") { + readr::write_csv(rv$list$data, file = file) + } + } + ) + + ############################################################################## + ######### + ######### Clearing the session on end + ######### + ############################################################################## + + session$onSessionEnded(function() { + cat("Session Ended\n") + files <- list.files("www/") + lapply(files[!files %in% files.to.keep], \(.x){ + unlink(paste0("www/", .x), recursive = FALSE) + print(paste(.x, "deleted")) + }) + }) +} + + +######## +#### Current file: /Users/au301842/FreesearchR/app/launch.R +######## + +shinyApp(ui, server) diff --git a/app_docker/www/FreesearchR-logo.png b/app_docker/www/FreesearchR-logo.png new file mode 100644 index 0000000000000000000000000000000000000000..e0f9f99ce3a8c12f5e079e7b0696b62e1bb28787 GIT binary patch literal 22712 zcmZ^~1z23ovMxNhLvVM`;O-KFI|O%!;Dfsb4el~X&=A~$ySoN=1`F;Emv8TL&p!Wo z?!V^g)wQbYt!mflNEIb%G-M)V004j{EAv_H-G6*{(TMQxZ;iD2t#=RBN?cJK0H}#W zc{YK2|E4gLQBwo}yy*adz;FMS4?F+>+}Hqszs3N7Kso?`?*wj96?&KbW}z)>si+9} z_)a4N;GnPoFz*!9`wsv`1o%hWI|Yz~BK~h$4T|BvWS{|na2o*Zf63^+`~N&L@9rPW 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+ + + + + + + + + + + + + + + + + + + + + + + diff --git a/app_docker/www/intro.md b/app_docker/www/intro.md new file mode 100644 index 00000000..0b644dcf --- /dev/null +++ b/app_docker/www/intro.md @@ -0,0 +1,31 @@ +# Welcome + +This is the ***FreesearchR*** data analysis tool. We intend ***FreesearchR*** to be a free tool for easy data evaluation and analysis. If you need more advanced tools, start with ***FreesearchR*** and then you'll probably be better off using *R* or similar directly. + +Here is a brief summary of the functions: + +1. **Import data** from a spreadsheet/file on your machine, direct export from a REDCap server, sample data or data from a your local environment if run locally. + +1. **Data inspection** and **modification** like modifying variables or creating new (categorical from numeric or time data, or completely new variables from the data) + +1. **Evaluate data** using descriptive analyses methods and inspect cross-correlations + +1. **Create and export simple, clean plots** for data overview and insights + +1. **Create regression simple models** for even more advanced data analyses + + - Linear, dichotomous or ordinal logistic regression will be used depending on specified outcome variable + + - Plot regression analysis coefficients + + - Evaluate model assumptions + +1. **Export results** + + - Descriptive and regression analyses results for MS Word or [LibreOffice](https://www.libreoffice.org/) + + - Modified data with preserved metadata + + - Code to recreate all steps locally + +The full [project documentation is here](https://agdamsbo.github.io/FreesearchR/) where you'll find detailed description of the app and link to the source code! If you want to [share feedback, please follow this link to a simple survey](https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8). diff --git a/app_docker/www/references.bib b/app_docker/www/references.bib new file mode 100644 index 00000000..ab4b8b80 --- /dev/null +++ b/app_docker/www/references.bib @@ -0,0 +1,11 @@ + +@book{andreasgammelgaarddamsbo2025, + title = {agdamsbo/FreesearchR: FreesearchR 25.4.3}, + author = {Damsbo, Andreas Gammelgaard}, + year = {2025}, + month = {04}, + date = {2025-04-24}, + publisher = {Zenodo}, + doi = {10.5281/ZENODO.14527429}, + url = {https://zenodo.org/doi/10.5281/zenodo.14527429} +} diff --git a/app_docker/www/report.rmd b/app_docker/www/report.rmd new file mode 100644 index 00000000..fcc6d4d3 --- /dev/null +++ b/app_docker/www/report.rmd @@ -0,0 +1,83 @@ +--- +title: "FreesearchR data report" +date: "Report generated `r gsub('(\\D)0', '\\1', format(Sys.time(), '%A, %d.%m.%Y'))`" +format: docx +author: FreesearchR data analysis tool +toc: false +params: + data.file: NA + version: NA + regression.p: NA +--- + +```{r setup, echo = FALSE} +knitr::opts_chunk$set(echo = FALSE, message = FALSE, warning = FALSE) +# glue::glue("{format(lubridate::today(),'%A')}, {lubridate::day(lubridate::today())}.{lubridate::month(lubridate::today())}.{lubridate::year(lubridate::today())}") +``` + +```{r} +web_data <- readr::read_rds(file = params$data.file) +# web_data <- readr::read_rds(file = "~/FreesearchR/inst/apps/FreesearchR/www/web_data.rds") +library(gtsummary) +library(gt) + +tbl_merge <- function(data) { + if (is.null(names(data))) { + data |> gtsummary::tbl_merge() + } else { + data |> gtsummary::tbl_merge(tab_spanner = names(data)) + } +} + +vec2sentence <- function(data, sep.word = "and") { + sep.word <- paste0(" ", gsub(" ", "", sep.word), " ") + if (length(data) < 2) { + out <- data + } else if (length(data) == 2) { + out <- paste(data, collapse = sep.word) + } else { + out <- paste(paste(data[-length(data)], collapse = ","), data[length(data)], sep = sep.word) + } + return(out) +} +``` + +## Introduction + +Research should be free and open with easy access for all. The *FreesearchR* tool attempts to help lower the bar to participate in research by making basic data exploration and analyses easily accessible. + +## Methods + +Analyses were conducted using the *FreesearchR* data analysis web-tool version `r params$version` based on *R* version 4.4.1. + +## Results + +Below are the baseline characteristics. + +```{r, results = 'asis'} +if ("table1" %in% names(web_data)) { + tbl <- gtsummary::as_gt(web_data$table1) + knitr::knit_print(tbl) +} +``` + +`r if (length(web_data$regression) > 0) glue::glue("Below are the results from the { tolower(vec2sentence(names(web_data$regression$regression$tables)))} {web_data$regression$regression$params$descr}.")` + +```{r, results = 'asis'} +if ("regression" %in% names(web_data) && length(web_data$regression) > 0) { + reg_tbl <- web_data$regression$regression$tables + + merged <- tbl_merge(reg_tbl) + + if (params$regression.p == "no") { + merged <- merged |> + gtsummary::modify_column_hide(column = dplyr::starts_with("p.value")) + } + + knitr::knit_print(merged) +} +``` + +## Discussion + +Good luck on your further work! diff --git a/app_docker/www/style.css b/app_docker/www/style.css new file mode 100644 index 00000000..fedcd1f7 --- /dev/null +++ b/app_docker/www/style.css @@ -0,0 +1,125 @@ + +/*! + * Copyright (c) 2025 FreesearchR + * + * FreesearchR, CSS styles + * https://github.com/agdamsbo/FreesearchR + * + * @version 0.0.1 + */ + +.container-fluid > .nav > li > + a[data-value='FreesearchR'] {font-size: 28px} + + +/* from datamods */ +.show-block { + display: block !important; +} +.show-inline { + display: inline !important; +} +.hidden { + display: none !important; +} +.invisible { + visibility: hidden; +} + +.container-rule { + position: relative; + text-align: center; + height: 25px; + margin-bottom: 5px; +} + +.horizontal-rule { + position: absolute; + top: 11px; + right: 0; + left: 0; + background-color: #d0cfcf; + height: 1px; + z-index: 100; + margin: 0; + border: none; +} + +.label-rule { + background: #FFF; + opacity: 1; + z-index: 101; + background-color: #FFF; + position: relative; + padding: 0 10px 0 10px; +} + +.datamods-table-container { + overflow: auto; + word-break: keep-all; + white-space: nowrap; +} + +.datamods-table-container > .table { + margin-bottom: 0 !important; +} + +.datamods-file-import { + display: grid; + grid-template-columns: auto 50px; + grid-column-gap: 10px; +} + +.datamods-dt-nowrap { + word-break: keep-all; + white-space: nowrap; +} + + + +/* validation */ +.datamods-validation-results { + display: grid; + grid-template-columns: repeat(3, 1fr); + grid-template-rows: 1fr; + height: 50px; + line-height: 50px; + font-size: large; +} + +.datamods-validation-summary { + font-weight: bold; + text-align: center; +} + +.datamods-validation-item { + font-size: larger; +} + + + +/* modified from esquisse for data types */ +.btn-column-categorical { + background-color: #00C896; + color: #FFFFFF; +} +.btn-column-continuous { + 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z1S!46$>{9-iTS1>PNjKjdCs1@v$n8mkv+8epRXIt?GMqZ=G@%|XURQQ5z44EmR9U~ z&+^>L%v?Q*&evxaR%hohq+sY&e|Cqb_cm+O3v*M`OS9IOv;3V#^VGsxW5xkz3sVc| zm9-oQIcr@Sov$yiqJ!x_(i#p~_cf;%rW&h@i?tQ2WBf$ZZuq%Lu7pc9(Kx6Qk$luO U?ua#hW$whv9Ei3=hWYXT4@bvznE(I) literal 0 HcmV?d00001 diff --git a/renv.lock b/renv.lock index 442e69c8..074b3f4f 100644 --- a/renv.lock +++ b/renv.lock @@ -8917,54 +8917,6 @@ "Author": "Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]", "Repository": "CRAN" }, - "visdat": { - "Package": "visdat", - "Version": "0.6.0", - "Source": "Repository", - "Title": "Preliminary Visualisation of Data", - "Authors@R": "c( person(\"Nicholas\", \"Tierney\", role = c(\"aut\", \"cre\"), email = \"nicholas.tierney@gmail.com\", comment = c(ORCID = \"https://orcid.org/0000-0003-1460-8722\")), person(\"Sean\", \"Hughes\", role = \"rev\", comment =c(ORCID = \"https://orcid.org/0000-0002-9409-9405\", \"Sean Hughes reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/87\")), person(\"Mara\", \"Averick\", role = \"rev\", comment = \"Mara Averick reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/87\"), person(\"Stuart\", \"Lee\", role = c(\"ctb\")), person(\"Earo\", \"Wang\", role = c(\"ctb\")), person(\"Nic\", \"Crane\", role = c(\"ctb\")), person(\"Christophe\", \"Regouby\", role=c(\"ctb\")) )", - "Description": "Create preliminary exploratory data visualisations of an entire dataset to identify problems or unexpected features using 'ggplot2'.", - "Depends": [ - "R (>= 3.2.2)" - ], - "License": "MIT + file LICENSE", - "LazyData": "true", - "RoxygenNote": "7.2.3", - "Imports": [ - "ggplot2", - "tidyr", - "dplyr", - "purrr", - "readr", - "magrittr", - "stats", - "tibble", - "glue", - "forcats", - "cli", - "scales" - ], - "URL": "https://docs.ropensci.org/visdat/, https://github.com/ropensci/visdat", - "BugReports": "https://github.com/ropensci/visdat/issues", - "Suggests": [ - "testthat (>= 3.0.0)", - "plotly (>= 4.5.6)", - "knitr", - "rmarkdown", - "vdiffr", - "spelling", - "covr", - "stringr" - ], - "VignetteBuilder": "knitr", - "Encoding": "UTF-8", - "Language": "en-US", - "Config/testthat/edition": "3", - "NeedsCompilation": "no", - "Author": "Nicholas Tierney [aut, cre] (), Sean Hughes [rev] (, Sean Hughes reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/87), Mara Averick [rev] (Mara Averick reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/87), Stuart Lee [ctb], Earo Wang [ctb], Nic Crane [ctb], Christophe Regouby [ctb]", - "Maintainer": "Nicholas Tierney ", - "Repository": "CRAN" - }, "vroom": { "Package": "vroom", "Version": "1.6.5", From 6b1a8af175176cd8d2b037ded40a5cf4de3d2596 Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Thu, 26 Jun 2025 10:42:26 +0200 Subject: [PATCH 7/7] new attempt --- .dockerignore | 6 + .github/workflows/docker-build.yml | 2 +- app_docker/Dockerfile | 4 +- app_docker/renv.lock | 7170 ++++++++++++++++++++++++++++ 4 files changed, 7179 insertions(+), 3 deletions(-) create mode 100644 .dockerignore create mode 100644 app_docker/renv.lock diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 00000000..aab0653a --- /dev/null +++ b/.dockerignore @@ -0,0 +1,6 @@ +.Rhistory +.git +.gitignore +manifest.json +rsconnect/ +.Rproj.user diff --git a/.github/workflows/docker-build.yml b/.github/workflows/docker-build.yml index 3cd45b8b..de40ad7c 100644 --- a/.github/workflows/docker-build.yml +++ b/.github/workflows/docker-build.yml @@ -41,7 +41,7 @@ jobs: - name: Build and push Docker image uses: docker/build-push-action@v4 with: - context: . + context: app_docker/ file: app_docker/Dockerfile push: true tags: | diff --git a/app_docker/Dockerfile b/app_docker/Dockerfile index 201620ab..47eaca46 100644 --- a/app_docker/Dockerfile +++ b/app_docker/Dockerfile @@ -1,9 +1,9 @@ FROM rocker/geospatial:4.4.1 -RUN apt-get update -y && apt-get install -y cmake make libcurl4-openssl-dev libicu-dev libssl-dev pandoc zlib1g-dev libsecret-1-dev libxml2-dev libx11-dev libcairo2-dev libfontconfig1-dev libfreetype6-dev libfribidi-dev libharfbuzz-dev libjpeg-dev libpng-dev libtiff-dev libfftw3-dev libsodium-dev && rm -rf /var/lib/apt/lists/* +RUN apt-get update -y && apt-get install -y make pandoc zlib1g-dev libicu-dev libcurl4-openssl-dev libsecret-1-dev libxml2-dev libssl-dev libx11-dev libfontconfig1-dev libfreetype6-dev git libsodium-dev && rm -rf /var/lib/apt/lists/* RUN mkdir -p /usr/local/lib/R/etc/ /usr/lib/R/etc/ RUN echo "options(renv.config.pak.enabled = FALSE, repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl', Ncpus = 4)" | tee /usr/local/lib/R/etc/Rprofile.site | tee /usr/lib/R/etc/Rprofile.site RUN R -e 'install.packages("remotes")' -RUN R -e 'remotes::install_version("renv", version = "1.1.4")' +RUN R -e 'remotes::install_version("renv", version = "1.0.3")' COPY renv.lock renv.lock RUN --mount=type=cache,id=renv-cache,target=/root/.cache/R/renv R -e 'renv::restore()' WORKDIR /srv/shiny-server/ diff --git a/app_docker/renv.lock b/app_docker/renv.lock new file mode 100644 index 00000000..be472d7e --- /dev/null +++ b/app_docker/renv.lock @@ -0,0 +1,7170 @@ +{ + "R": { + "Version": "4.4.1", + "Repositories": [ + { + "Name": "CRAN", + "URL": "https://cloud.r-project.org" + } + ] + }, + "Packages": { + "DT": { + "Package": "DT", + "Version": "0.33", + "Source": "Repository", + "Type": "Package", + "Title": "A Wrapper of the JavaScript Library 'DataTables'", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = \"aut\"), person(\"Joe\", \"Cheng\", email = \"joe@posit.co\", role = c(\"aut\", \"cre\")), person(\"Xianying\", \"Tan\", role = \"aut\"), person(\"JJ\", \"Allaire\", role = \"ctb\"), person(\"Maximilian\", \"Girlich\", role = \"ctb\"), person(\"Greg\", \"Freedman Ellis\", role = \"ctb\"), person(\"Johannes\", \"Rauh\", role = \"ctb\"), person(\"SpryMedia Limited\", role = c(\"ctb\", \"cph\"), comment = \"DataTables in htmlwidgets/lib\"), person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"), comment = \"selectize.js in htmlwidgets/lib\"), person(\"Leon\", \"Gersen\", role = c(\"ctb\", \"cph\"), comment = \"noUiSlider in htmlwidgets/lib\"), person(\"Bartek\", \"Szopka\", role = c(\"ctb\", \"cph\"), comment = \"jquery.highlight.js in htmlwidgets/lib\"), person(\"Alex\", \"Pickering\", role = c(\"ctb\")), person(\"William\", \"Holmes\", role = c(\"ctb\")), person(\"Mikko\", \"Marttila\", role = c(\"ctb\")), person(\"Andres\", \"Quintero\", role = c(\"ctb\")), person(\"Stéphane\", \"Laurent\", role = c(\"ctb\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Data objects in R can be rendered as HTML tables using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' library has been included in this R package. The package name 'DT' is an abbreviation of 'DataTables'.", + "URL": "https://github.com/rstudio/DT", + "BugReports": "https://github.com/rstudio/DT/issues", + "License": "GPL-3 | file LICENSE", + "Imports": [ + "htmltools (>= 0.3.6)", + "htmlwidgets (>= 1.3)", + "httpuv", + "jsonlite (>= 0.9.16)", + "magrittr", + "crosstalk", + "jquerylib", + "promises" + ], + "Suggests": [ + "knitr (>= 1.8)", + "rmarkdown", + "shiny (>= 1.6)", + "bslib", + "future", + "testit", + "tibble" + ], + "VignetteBuilder": "knitr", + "RoxygenNote": "7.3.1", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut], Joe Cheng [aut, cre], Xianying Tan [aut], JJ Allaire [ctb], Maximilian Girlich [ctb], Greg Freedman Ellis [ctb], Johannes Rauh [ctb], SpryMedia Limited [ctb, cph] (DataTables in htmlwidgets/lib), Brian Reavis [ctb, cph] (selectize.js in htmlwidgets/lib), Leon Gersen [ctb, cph] (noUiSlider in htmlwidgets/lib), Bartek Szopka [ctb, cph] (jquery.highlight.js in htmlwidgets/lib), Alex Pickering [ctb], William Holmes [ctb], Mikko Marttila [ctb], Andres Quintero [ctb], Stéphane Laurent [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Joe Cheng ", + "Repository": "CRAN" + }, + "Formula": { + "Package": "Formula", + "Version": "1.2-5", + "Source": "Repository", + "Date": "2023-02-23", + "Title": "Extended Model Formulas", + "Description": "Infrastructure for extended formulas with multiple parts on the right-hand side and/or multiple responses on the left-hand side (see ).", + "Authors@R": "c(person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = \"Yves\", family = \"Croissant\", role = \"aut\", email = \"Yves.Croissant@univ-reunion.fr\"))", + "Depends": [ + "R (>= 2.0.0)", + "stats" + ], + "License": "GPL-2 | GPL-3", + "NeedsCompilation": "no", + "Author": "Achim Zeileis [aut, cre] (), Yves Croissant [aut]", + "Maintainer": "Achim Zeileis ", + "Repository": "CRAN" + }, + "GenSA": { + "Package": "GenSA", + "Version": "1.1.14.1", + "Source": "Repository", + "Type": "Package", + "Title": "R Functions for Generalized Simulated Annealing", + "Date": "2024-01-22", + "Author": "Sylvain Gubian, Yang Xiang, Brian Suomela, Julia Hoeng, PMP SA.", + "Maintainer": "Sylvain Gubian ", + "Depends": [ + "R (>= 2.12.0)" + ], + "Description": "Performs search for global minimum of a very complex non-linear objective function with a very large number of optima.", + "License": "GPL-2", + "LazyLoad": "yes", + "NeedsCompilation": "yes", + "Repository": "CRAN", + "RoxygenNote": "7.2.3" + }, + "Hmisc": { + "Package": "Hmisc", + "Version": "5.2-3", + "Source": "Repository", + "Date": "2025-03-16", + "Title": "Harrell Miscellaneous", + "Authors@R": "c(person(given = \"Frank E\", family = \"Harrell Jr\", role = c(\"aut\", \"cre\"), email = \"fh@fharrell.com\", comment = c(ORCID = \"0000-0002-8271-5493\")), person(given = \"Charles\", family = \"Dupont\", role = \"ctb\", email = \"charles.dupont@vumc.org\", comment = \"contributed several functions and maintains latex functions\"))", + "Maintainer": "Frank E Harrell Jr ", + "Depends": [ + "R (>= 4.2.0)" + ], + "Imports": [ + "methods", + "ggplot2", + "cluster", + "rpart", + "nnet", + "foreign", + "gtable", + "grid", + "gridExtra", + "data.table", + "htmlTable (>= 1.11.0)", + "viridis", + "htmltools", + "base64enc", + "colorspace", + "rmarkdown", + "knitr", + "Formula" + ], + "Suggests": [ + "survival", + "qreport", + "acepack", + "chron", + "rms", + "mice", + "rstudioapi", + "tables", + "plotly (>= 4.5.6)", + "rlang", + "plyr", + "VGAM", + "leaps", + "pcaPP", + "digest", + "parallel", + "polspline", + "abind", + "kableExtra", + "rio", + "lattice", + "latticeExtra", + "gt", + "sparkline", + "jsonlite", + "htmlwidgets", + "qs", + "getPass", + "keyring", + "safer", + "htm2txt" + ], + "Description": "Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, simulation, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, recoding variables, caching, simplified parallel computing, encrypting and decrypting data using a safe workflow, general moving window statistical estimation, and assistance in interpreting principal component analysis.", + "License": "GPL (>= 2)", + "LazyLoad": "Yes", + "URL": "https://hbiostat.org/R/Hmisc/", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Frank E Harrell Jr [aut, cre] (), Charles Dupont [ctb] (contributed several functions and maintains latex functions)", + "Repository": "CRAN" + }, + "IDEAFilter": { + "Package": "IDEAFilter", + "Version": "0.2.0", + "Source": "Repository", + "Type": "Package", + "Title": "Agnostic, Idiomatic Data Filter Module for Shiny", + "Description": "When added to an existing shiny app, users may subset any developer-chosen R data.frame on the fly. That is, users are empowered to slice & dice data by applying multiple (order specific) filters using the AND (&) operator between each, and getting real-time updates on the number of rows effected/available along the way. Thus, any downstream processes that leverage this data source (like tables, plots, or statistical procedures) will re-render after new filters are applied. The shiny module’s user interface has a 'minimalist' aesthetic so that the focus can be on the data & other visuals. In addition to returning a reactive (filtered) data.frame, 'IDEAFilter' as also returns 'dplyr' filter statements used to actually slice the data.", + "Authors@R": "c( person( given = \"Aaron\", family = \"Clark\", email = \"clark.aaronchris@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-0123-0970\")), person( given = \"Jeff\", family = \"Thompson\", email = \"jeff.thompson51317@gmail.com\", role = \"aut\"), person( given = \"Doug\", family = \"Kelkhoff\", email = \"doug.kelkhoff@gmail.com\", role = c(\"ctb\", \"cph\"), comment = \"Author of shinyDataFilter\"), person( given = \"Maya\", family = \"Gans\", email = \"maya.gans@biogen.com\", role = \"ctb\"), person(family = \"SortableJS contributors\", role = \"ctb\", comment = \"SortableJS library\"), person(given = \"Biogen\", role = \"cph\"))", + "License": "MIT + file LICENSE", + "URL": "https://biogen-inc.github.io/IDEAFilter/, https://github.com/Biogen-Inc/IDEAFilter", + "BugReports": "https://github.com/Biogen-Inc/IDEAFilter/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Imports": [ + "crayon", + "ggplot2", + "pillar (>= 1.5.0)", + "purrr", + "RColorBrewer", + "shiny", + "shinyTime" + ], + "Suggests": [ + "dplyr", + "knitr", + "rmarkdown", + "shinytest", + "shinytest2", + "spelling", + "testthat" + ], + "Language": "en-US", + "VignetteBuilder": "knitr", + "Depends": [ + "R (>= 2.10)" + ], + "NeedsCompilation": "no", + "Author": "Aaron Clark [aut, cre] (), Jeff Thompson [aut], Doug Kelkhoff [ctb, cph] (Author of shinyDataFilter), Maya Gans [ctb], SortableJS contributors [ctb] (SortableJS library), Biogen [cph]", + "Maintainer": "Aaron Clark ", + "Repository": "CRAN" + }, + "KernSmooth": { + "Package": "KernSmooth", + "Version": "2.23-26", + "Source": "Repository", + "Priority": "recommended", + "Date": "2024-12-10", + "Title": "Functions for Kernel Smoothing Supporting Wand & Jones (1995)", + "Authors@R": "c(person(\"Matt\", \"Wand\", role = \"aut\", email = \"Matt.Wand@uts.edu.au\"), person(\"Cleve\", \"Moler\", role = \"ctb\", comment = \"LINPACK routines in src/d*\"), person(\"Brian\", \"Ripley\", role = c(\"trl\", \"cre\", \"ctb\"), email = \"Brian.Ripley@R-project.org\", comment = \"R port and updates\"))", + "Note": "Maintainers are not available to give advice on using a package they did not author.", + "Depends": [ + "R (>= 2.5.0)", + "stats" + ], + "Suggests": [ + "MASS", + "carData" + ], + "Description": "Functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) \"Kernel Smoothing\".", + "License": "Unlimited", + "ByteCompile": "yes", + "NeedsCompilation": "yes", + "Author": "Matt Wand [aut], Cleve Moler [ctb] (LINPACK routines in src/d*), Brian Ripley [trl, cre, ctb] (R port and updates)", + "Maintainer": "Brian Ripley ", + "Repository": "CRAN" + }, + "MASS": { + "Package": "MASS", + "Version": "7.3-65", + "Source": "Repository", + "Priority": "recommended", + "Date": "2025-02-19", + "Revision": "$Rev: 3681 $", + "Depends": [ + "R (>= 4.4.0)", + "grDevices", + "graphics", + "stats", + "utils" + ], + "Imports": [ + "methods" + ], + "Suggests": [ + "lattice", + "nlme", + "nnet", + "survival" + ], + "Authors@R": "c(person(\"Brian\", \"Ripley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Brian.Ripley@R-project.org\"), person(\"Bill\", \"Venables\", role = c(\"aut\", \"cph\")), person(c(\"Douglas\", \"M.\"), \"Bates\", role = \"ctb\"), person(\"Kurt\", \"Hornik\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"Albrecht\", \"Gebhardt\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"David\", \"Firth\", role = \"ctb\", comment = \"support functions for polr\"))", + "Description": "Functions and datasets to support Venables and Ripley, \"Modern Applied Statistics with S\" (4th edition, 2002).", + "Title": "Support Functions and Datasets for Venables and Ripley's MASS", + "LazyData": "yes", + "ByteCompile": "yes", + "License": "GPL-2 | GPL-3", + "URL": "http://www.stats.ox.ac.uk/pub/MASS4/", + "Contact": "", + "NeedsCompilation": "yes", + "Author": "Brian Ripley [aut, cre, cph], Bill Venables [aut, cph], Douglas M. Bates [ctb], Kurt Hornik [trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David Firth [ctb] (support functions for polr)", + "Maintainer": "Brian Ripley ", + "Repository": "CRAN" + }, + "Matrix": { + "Package": "Matrix", + "Version": "1.7-3", + "Source": "Repository", + "VersionNote": "do also bump src/version.h, inst/include/Matrix/version.h", + "Date": "2025-03-05", + "Priority": "recommended", + "Title": "Sparse and Dense Matrix Classes and Methods", + "Description": "A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. 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Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. 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Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the header files from the templated 'Armadillo' library. Thus users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. 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person(given = \"Hong\", family = \"Ooi\", role = \"ctb\", email = \"hongooi@microsoft.com\"), person(given = \"Henrik\", family = \"Bengtsson\", role = \"ctb\", email = \"henrikb@braju.com\"), person(given = \"Eduard\", family = \"Szocs\", role = \"ctb\", email = \"eduardszoecs@gmail.com\"), person(given = \"David\", family = \"Hugh-Jones\", role = \"ctb\", email = \"davidhughjones@gmail.com\"), person(given = \"Matthieu\", family = \"Stigler\", role = \"ctb\", email = \"Matthieu.Stigler@gmail.com\"), person(given = \"Hugo\", family = \"Tavares\", role = \"ctb\", email = \"hm533@cam.ac.uk\", comment = c(ORCID = \"0000-0001-9373-2726\")), person(given = \"R. Willem\", family = \"Vervoort\", role = \"ctb\", email = \"Willemvervoort@gmail.com\"), person(given = \"Brenton M.\", family = \"Wiernik\", role = \"ctb\", email = \"brenton@wiernik.org\"), person(given = \"Josh\", family = \"Yamamoto\", role = \"ctb\", email = \"joshuayamamoto5@gmail.com\"), person(given = \"Jasme\", family = \"Lee\", role = \"ctb\"), person(given = \"Taren\", family = \"Sanders\", role = \"ctb\", email = \"taren.sanders@acu.edu.au\", comment = c(ORCID = \"0000-0002-4504-6008\")), person(given = \"Ilaria\", family = \"Prosdocimi\", role = \"ctb\", email = \"prosdocimi.ilaria@gmail.com\", comment = c(ORCID = \"0000-0001-8565-094X\")), person(given = \"Daniel D.\", family = \"Sjoberg\", role = \"ctb\", email = \"danield.sjoberg@gmail.com\", comment = c(ORCID = \"0000-0003-0862-2018\")), person(given = \"Alex\", family = \"Reinhart\", role = \"ctb\", email = \"areinhar@stat.cmu.edu\", comment = c(ORCID = \"0000-0002-6658-514X\")))", + "Description": "Summarizes key information about statistical objects in tidy tibbles. This makes it easy to report results, create plots and consistently work with large numbers of models at once. Broom provides three verbs that each provide different types of information about a model. tidy() summarizes information about model components such as coefficients of a regression. glance() reports information about an entire model, such as goodness of fit measures like AIC and BIC. augment() adds information about individual observations to a dataset, such as fitted values or influence measures.", + "License": "MIT + file LICENSE", + "URL": "https://broom.tidymodels.org/, https://github.com/tidymodels/broom", + "BugReports": "https://github.com/tidymodels/broom/issues", + "Depends": [ + "R (>= 3.5)" + ], + "Imports": [ + "backports", + "cli", + "dplyr (>= 1.0.0)", + "generics (>= 0.0.2)", + "glue", + "lifecycle", + "purrr", + "rlang (>= 1.1.0)", + "stringr", + "tibble (>= 3.0.0)", + "tidyr (>= 1.0.0)" + ], + "Suggests": [ + "AER", + "AUC", + "bbmle", + "betareg (>= 3.2-1)", + "biglm", + "binGroup", + "boot", + "btergm (>= 1.10.6)", + "car (>= 3.1-2)", + "carData", + "caret", + 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[ctb], Ben Bolker [ctb], Francois Briatte [ctb], Jeffrey Arnold [ctb], Jonah Gabry [ctb], Luciano Selzer [ctb], Gavin Simpson [ctb], Jens Preussner [ctb], Jay Hesselberth [ctb], Hadley Wickham [ctb], Matthew Lincoln [ctb], Alessandro Gasparini [ctb], Lukasz Komsta [ctb], Frederick Novometsky [ctb], Wilson Freitas [ctb], Michelle Evans [ctb], Jason Cory Brunson [ctb], Simon Jackson [ctb], Ben Whalley [ctb], Karissa Whiting [ctb], Yves Rosseel [ctb], Michael Kuehn [ctb], Jorge Cimentada [ctb], Erle Holgersen [ctb], Karl Dunkle Werner [ctb] (), Ethan Christensen [ctb], Steven Pav [ctb], Paul PJ [ctb], Ben Schneider [ctb], Patrick Kennedy [ctb], Lily Medina [ctb], Brian Fannin [ctb], Jason Muhlenkamp [ctb], Matt Lehman [ctb], Bill Denney [ctb] (), Nic Crane [ctb], Andrew Bates [ctb], Vincent Arel-Bundock [ctb] (), Hideaki Hayashi [ctb], Luis Tobalina [ctb], Annie Wang [ctb], Wei Yang Tham [ctb], Clara Wang [ctb], Abby Smith [ctb] (), Jasper Cooper [ctb] (), E Auden Krauska [ctb] (), Alex Wang [ctb], Malcolm Barrett [ctb] (), Charles Gray [ctb] (), Jared Wilber [ctb], Vilmantas Gegzna [ctb] (), Eduard Szoecs [ctb], Frederik Aust [ctb] (), Angus Moore [ctb], Nick Williams [ctb], Marius Barth [ctb] (), Bruna Wundervald [ctb] (), Joyce Cahoon [ctb] (), Grant McDermott [ctb] (), Kevin Zarca [ctb], Shiro Kuriwaki [ctb] (), Lukas Wallrich [ctb] (), James Martherus [ctb] (), Chuliang Xiao [ctb] (), Joseph Larmarange [ctb], Max Kuhn [ctb], Michal Bojanowski [ctb], Hakon Malmedal [ctb], Clara Wang [ctb], Sergio Oller [ctb], Luke Sonnet [ctb], Jim Hester [ctb], Ben Schneider [ctb], Bernie Gray [ctb] (), Mara Averick [ctb], Aaron Jacobs [ctb], Andreas Bender [ctb], Sven Templer [ctb], Paul-Christian Buerkner [ctb], Matthew Kay [ctb], Erwan Le Pennec [ctb], Johan Junkka [ctb], Hao Zhu [ctb], Benjamin Soltoff [ctb], Zoe Wilkinson Saldana [ctb], Tyler Littlefield [ctb], Charles T. Gray [ctb], Shabbh E. Banks [ctb], Serina Robinson [ctb], Roger Bivand [ctb], Riinu Ots [ctb], Nicholas Williams [ctb], Nina Jakobsen [ctb], Michael Weylandt [ctb], Lisa Lendway [ctb], Karl Hailperin [ctb], Josue Rodriguez [ctb], Jenny Bryan [ctb], Chris Jarvis [ctb], Greg Macfarlane [ctb], Brian Mannakee [ctb], Drew Tyre [ctb], Shreyas Singh [ctb], Laurens Geffert [ctb], Hong Ooi [ctb], Henrik Bengtsson [ctb], Eduard Szocs [ctb], David Hugh-Jones [ctb], Matthieu Stigler [ctb], Hugo Tavares [ctb] (), R. Willem Vervoort [ctb], Brenton M. Wiernik [ctb], Josh Yamamoto [ctb], Jasme Lee [ctb], Taren Sanders [ctb] (), Ilaria Prosdocimi [ctb] (), Daniel D. Sjoberg [ctb] (), Alex Reinhart [ctb] ()", + "Maintainer": "Simon Couch ", + "Repository": "CRAN" + }, + "broom.helpers": { + "Package": "broom.helpers", + "Version": "1.21.0", + "Source": "Repository", + "Title": "Helpers for Model Coefficients Tibbles", + "Authors@R": "c( person(\"Joseph\", \"Larmarange\", , \"joseph@larmarange.net\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-7097-700X\")), person(\"Daniel D.\", \"Sjoberg\", , \"danield.sjoberg@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0003-0862-2018\")) )", + "Description": "Provides suite of functions to work with regression model 'broom::tidy()' tibbles. The suite includes functions to group regression model terms by variable, insert reference and header rows for categorical variables, add variable labels, and more.", + "License": "GPL (>= 3)", + "URL": "https://larmarange.github.io/broom.helpers/, https://github.com/larmarange/broom.helpers", + "BugReports": "https://github.com/larmarange/broom.helpers/issues", + "Depends": [ + "R (>= 4.1)" + ], + "Imports": [ + "broom (>= 0.8)", + "cards", + "cli", + "dplyr (>= 1.1.0)", + "labelled", + "lifecycle", + "purrr", + "rlang (>= 1.0.1)", + "stats", + "stringr", + "tibble", + "tidyr", + "tidyselect" + ], + "Suggests": [ + "betareg", + "biglm", + "brms (>= 2.13.0)", + "broom.mixed", + "cmprsk", + "covr", + "datasets", + "effects", + "emmeans", + "fixest (>= 0.10.0)", + "forcats", + "gam", + "gee", + "geepack", + "ggplot2", + "ggeffects (>= 1.3.2)", + "ggstats (>= 0.2.1)", + "glmmTMB", + "glmtoolbox", + "glue", + "gt", + "gtsummary (>= 2.0.0)", + "knitr", + "lavaan", + "lfe", + "lme4 (>= 1.1.28)", + "logitr (>= 0.8.0)", + "marginaleffects (>= 0.21.0)", + "margins", + "MASS", + "mgcv", + "mice", + "mmrm (>= 0.3.6)", + "multgee", + "nnet", + "ordinal", + "parameters", + "parsnip", + "patchwork", + "plm", + "pscl", + "rmarkdown", + "rstanarm", + "scales", + "spelling", + "survey", + "survival", + "testthat (>= 3.0.0)", + "tidycmprsk", + "VGAM", + "svyVGAM" + ], + "VignetteBuilder": "knitr", + "RdMacros": "lifecycle", + "Encoding": "UTF-8", + "Language": "en-US", + "LazyData": "true", + "RoxygenNote": "7.3.2", + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Author": "Joseph Larmarange [aut, cre] (), Daniel D. 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Developing Command Line Interfaces", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"gabor@posit.co\", role = c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", role = \"ctb\"), person(\"Kirill\", \"Müller\", role = \"ctb\"), person(\"Salim\", \"Brüggemann\", , \"salim-b@pm.me\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5329-5987\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A suite of tools to build attractive command line interfaces ('CLIs'), from semantic elements: headings, lists, alerts, paragraphs, etc. Supports custom themes via a 'CSS'-like language. It also contains a number of lower level 'CLI' elements: rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and text styles as well.", + "License": "MIT + file LICENSE", + "URL": "https://cli.r-lib.org, https://github.com/r-lib/cli", + "BugReports": "https://github.com/r-lib/cli/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ + "utils" + ], + "Suggests": [ + "callr", + "covr", + "crayon", + "digest", + "glue (>= 1.6.0)", + "grDevices", + "htmltools", + "htmlwidgets", + "knitr", + "methods", + "processx", + "ps (>= 1.3.4.9000)", + "rlang (>= 1.0.2.9003)", + "rmarkdown", + "rprojroot", + "rstudioapi", + "testthat (>= 3.2.0)", + "tibble", + "whoami", + "withr" + ], + "Config/Needs/website": "r-lib/asciicast, bench, brio, cpp11, decor, desc, fansi, prettyunits, sessioninfo, tidyverse/tidytemplate, usethis, vctrs", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Gábor Csárdi [aut, cre], Hadley Wickham [ctb], Kirill Müller [ctb], Salim Brüggemann [ctb] (), Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" + }, + "clipr": { + "Package": "clipr", + "Version": "0.8.0", + "Source": "Repository", + "Type": "Package", + "Title": "Read and Write from the System Clipboard", + "Authors@R": "c( person(\"Matthew\", \"Lincoln\", , \"matthew.d.lincoln@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4387-3384\")), person(\"Louis\", \"Maddox\", role = \"ctb\"), person(\"Steve\", \"Simpson\", role = \"ctb\"), person(\"Jennifer\", \"Bryan\", role = \"ctb\") )", + "Description": "Simple utility functions to read from and write to the Windows, OS X, and X11 clipboards.", + "License": "GPL-3", + "URL": "https://github.com/mdlincoln/clipr, http://matthewlincoln.net/clipr/", + "BugReports": "https://github.com/mdlincoln/clipr/issues", + "Imports": [ + "utils" + ], + "Suggests": [ + "covr", + "knitr", + "rmarkdown", + "rstudioapi (>= 0.5)", + "testthat (>= 2.0.0)" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.1.2", + "SystemRequirements": "xclip (https://github.com/astrand/xclip) or xsel (http://www.vergenet.net/~conrad/software/xsel/) for accessing the X11 clipboard, or wl-clipboard (https://github.com/bugaevc/wl-clipboard) for systems using Wayland.", + "NeedsCompilation": "no", + "Author": "Matthew Lincoln [aut, cre] (), Louis Maddox [ctb], Steve Simpson [ctb], Jennifer Bryan [ctb]", + "Maintainer": "Matthew Lincoln ", + "Repository": "CRAN" + }, + "cluster": { + "Package": "cluster", + "Version": "2.1.8.1", + "Source": "Repository", + "VersionNote": "Last CRAN: 2.1.8 on 2024-12-10; 2.1.7 on 2024-12-06; 2.1.6 on 2023-11-30; 2.1.5 on 2023-11-27", + "Date": "2025-03-11", + "Priority": "recommended", + "Title": "\"Finding Groups in Data\": Cluster Analysis Extended Rousseeuw et al.", + "Description": "Methods for Cluster analysis. Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".", + "Maintainer": "Martin Maechler ", + "Authors@R": "c(person(\"Martin\",\"Maechler\", role = c(\"aut\",\"cre\"), email=\"maechler@stat.math.ethz.ch\", comment = c(ORCID = \"0000-0002-8685-9910\")) ,person(\"Peter\", \"Rousseeuw\", role=\"aut\", email=\"peter.rousseeuw@kuleuven.be\", comment = c(\"Fortran original\", ORCID = \"0000-0002-3807-5353\")) ,person(\"Anja\", \"Struyf\", role=\"aut\", comment= \"S original\") ,person(\"Mia\", \"Hubert\", role=\"aut\", email= \"Mia.Hubert@uia.ua.ac.be\", comment = c(\"S original\", ORCID = \"0000-0001-6398-4850\")) ,person(\"Kurt\", \"Hornik\", role=c(\"trl\", \"ctb\"), email=\"Kurt.Hornik@R-project.org\", comment=c(\"port to R; maintenance(1999-2000)\", ORCID=\"0000-0003-4198-9911\")) ,person(\"Matthias\", \"Studer\", role=\"ctb\") ,person(\"Pierre\", \"Roudier\", role=\"ctb\") ,person(\"Juan\", \"Gonzalez\", role=\"ctb\") ,person(\"Kamil\", \"Kozlowski\", role=\"ctb\") ,person(\"Erich\", \"Schubert\", role=\"ctb\", comment = c(\"fastpam options for pam()\", ORCID = \"0000-0001-9143-4880\")) ,person(\"Keefe\", \"Murphy\", role=\"ctb\", comment = \"volume.ellipsoid({d >= 3})\") #not yet ,person(\"Fischer-Rasmussen\", \"Kasper\", role = \"ctb\", comment = \"Gower distance for CLARA\") )", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "graphics", + "grDevices", + "stats", + "utils" + ], + "Suggests": [ + "MASS", + "Matrix" + ], + "SuggestsNote": "MASS: two examples using cov.rob() and mvrnorm(); Matrix tools for testing", + "Enhances": [ + "mvoutlier", + "fpc", + "ellipse", + "sfsmisc" + ], + "EnhancesNote": "xref-ed in man/*.Rd", + "LazyLoad": "yes", + "LazyData": "yes", + "ByteCompile": "yes", + "BuildResaveData": "no", + "License": "GPL (>= 2)", + "URL": "https://svn.r-project.org/R-packages/trunk/cluster/", + "NeedsCompilation": "yes", + "Author": "Martin Maechler [aut, cre] (), Peter Rousseeuw [aut] (Fortran original, ), Anja Struyf [aut] (S original), Mia Hubert [aut] (S original, ), Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000), ), Matthias Studer [ctb], Pierre Roudier [ctb], Juan Gonzalez [ctb], Kamil Kozlowski [ctb], Erich Schubert [ctb] (fastpam options for pam(), ), Keefe Murphy [ctb] (volume.ellipsoid({d >= 3}))", + "Repository": "CRAN" + }, + "colorspace": { + "Package": "colorspace", + "Version": "2.1-1", + "Source": "Repository", + "Date": "2024-07-26", + "Title": "A Toolbox for Manipulating and Assessing Colors and Palettes", + "Authors@R": "c(person(given = \"Ross\", family = \"Ihaka\", role = \"aut\", email = \"ihaka@stat.auckland.ac.nz\"), person(given = \"Paul\", family = \"Murrell\", role = \"aut\", email = \"paul@stat.auckland.ac.nz\", comment = c(ORCID = \"0000-0002-3224-8858\")), person(given = \"Kurt\", family = \"Hornik\", role = \"aut\", email = \"Kurt.Hornik@R-project.org\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(given = c(\"Jason\", \"C.\"), family = \"Fisher\", role = \"aut\", email = \"jfisher@usgs.gov\", comment = c(ORCID = \"0000-0001-9032-8912\")), person(given = \"Reto\", family = \"Stauffer\", role = \"aut\", email = \"Reto.Stauffer@uibk.ac.at\", comment = c(ORCID = \"0000-0002-3798-5507\")), person(given = c(\"Claus\", \"O.\"), family = \"Wilke\", role = \"aut\", email = \"wilke@austin.utexas.edu\", comment = c(ORCID = \"0000-0002-7470-9261\")), person(given = c(\"Claire\", \"D.\"), family = \"McWhite\", role = \"aut\", email = \"claire.mcwhite@utmail.utexas.edu\", comment = c(ORCID = \"0000-0001-7346-3047\")), person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")))", + "Description": "Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided along with corresponding ggplot2 color scales. Color palette choice is aided by an interactive app (with either a Tcl/Tk or a shiny graphical user interface) and shiny apps with an HCL color picker and a color vision deficiency emulator. Plotting functions for displaying and assessing palettes include color swatches, visualizations of the HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation functions include: desaturation, lightening/darkening, mixing, and simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly). Details can be found on the project web page at and in the accompanying scientific paper: Zeileis et al. (2020, Journal of Statistical Software, ).", + "Depends": [ + "R (>= 3.0.0)", + "methods" + ], + "Imports": [ + "graphics", + "grDevices", + "stats" + ], + "Suggests": [ + "datasets", + "utils", + "KernSmooth", + "MASS", + "kernlab", + "mvtnorm", + "vcd", + "tcltk", + "shiny", + "shinyjs", + "ggplot2", + "dplyr", + "scales", + "grid", + "png", + "jpeg", + "knitr", + "rmarkdown", + "RColorBrewer", + "rcartocolor", + "scico", + "viridis", + "wesanderson" + ], + "VignetteBuilder": "knitr", + "License": "BSD_3_clause + file LICENSE", + "URL": "https://colorspace.R-Forge.R-project.org/, https://hclwizard.org/", + "BugReports": "https://colorspace.R-Forge.R-project.org/contact.html", + "LazyData": "yes", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "yes", + "Author": "Ross Ihaka [aut], Paul Murrell [aut] (), Kurt Hornik [aut] (), Jason C. Fisher [aut] (), Reto Stauffer [aut] (), Claus O. Wilke [aut] (), Claire D. McWhite [aut] (), Achim Zeileis [aut, cre] ()", + "Maintainer": "Achim Zeileis ", + "Repository": "CRAN" + }, + "commonmark": { + "Package": "commonmark", + "Version": "1.9.5", + "Source": "Repository", + "Type": "Package", + "Title": "High Performance CommonMark and Github Markdown Rendering in R", + "Authors@R": "c( person(\"Jeroen\", \"Ooms\", ,\"jeroenooms@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"John MacFarlane\", role = \"cph\", comment = \"Author of cmark\"))", + "Description": "The CommonMark specification defines a rationalized version of markdown syntax. This package uses the 'cmark' reference implementation for converting markdown text into various formats including html, latex and groff man. In addition it exposes the markdown parse tree in xml format. Also includes opt-in support for GFM extensions including tables, autolinks, and strikethrough text.", + "License": "BSD_2_clause + file LICENSE", + "URL": "https://docs.ropensci.org/commonmark/ https://ropensci.r-universe.dev/commonmark", + "BugReports": "https://github.com/r-lib/commonmark/issues", + "Suggests": [ + "curl", + "testthat", + "xml2" + ], + "RoxygenNote": "7.3.2", + "Language": "en-US", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (), John MacFarlane [cph] (Author of cmark)", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" + }, + "cpp11": { + "Package": "cpp11", + "Version": "0.5.2", + "Source": "Repository", + "Title": "A C++11 Interface for R's C Interface", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", email = \"davis@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4777-038X\")), person(\"Jim\",\"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Romain\", \"François\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Benjamin\", \"Kietzman\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides a header only, C++11 interface to R's C interface. Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.", + "License": "MIT + file LICENSE", + "URL": "https://cpp11.r-lib.org, https://github.com/r-lib/cpp11", + "BugReports": "https://github.com/r-lib/cpp11/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Suggests": [ + "bench", + "brio", + "callr", + "cli", + "covr", + "decor", + "desc", + "ggplot2", + "glue", + "knitr", + "lobstr", + "mockery", + "progress", + "rmarkdown", + "scales", + "Rcpp", + "testthat (>= 3.2.0)", + "tibble", + "utils", + "vctrs", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/Needs/cpp11/cpp_register": "brio, cli, decor, desc, glue, tibble, vctrs", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Davis Vaughan [aut, cre] (), Jim Hester [aut] (), Romain François [aut] (), Benjamin Kietzman [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" + }, + "crayon": { + "Package": "crayon", + "Version": "1.5.3", + "Source": "Repository", + "Title": "Colored Terminal Output", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Brodie\", \"Gaslam\", , \"brodie.gaslam@yahoo.com\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The crayon package is now superseded. Please use the 'cli' package for new projects. Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.", + "License": "MIT + file LICENSE", + "URL": "https://r-lib.github.io/crayon/, https://github.com/r-lib/crayon", + "BugReports": "https://github.com/r-lib/crayon/issues", + "Imports": [ + "grDevices", + "methods", + "utils" + ], + "Suggests": [ + "mockery", + "rstudioapi", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Collate": "'aaa-rstudio-detect.R' 'aaaa-rematch2.R' 'aab-num-ansi-colors.R' 'aac-num-ansi-colors.R' 'ansi-256.R' 'ansi-palette.R' 'combine.R' 'string.R' 'utils.R' 'crayon-package.R' 'disposable.R' 'enc-utils.R' 'has_ansi.R' 'has_color.R' 'link.R' 'styles.R' 'machinery.R' 'parts.R' 'print.R' 'style-var.R' 'show.R' 'string_operations.R'", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Brodie Gaslam [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" + }, + "crosstalk": { + "Package": "crosstalk", + "Version": "1.2.1", + "Source": "Repository", + "Type": "Package", + "Title": "Inter-Widget Interactivity for HTML Widgets", + "Authors@R": "c( person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@posit.co\"), person(\"Carson\", \"Sievert\", role = c(\"aut\", \"cre\"), email = \"carson@posit.co\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt\"), person(\"Mark\", \"Otto\", role = \"ctb\", comment = \"Bootstrap library\"), person(\"Jacob\", \"Thornton\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"), comment = \"selectize.js library\"), person(\"Kristopher Michael\", \"Kowal\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(family = \"es5-shim contributors\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(\"Denis\", \"Ineshin\", role = c(\"ctb\", \"cph\"), comment = \"ion.rangeSlider library\"), person(\"Sami\", \"Samhuri\", role = c(\"ctb\", \"cph\"), comment = \"Javascript strftime library\") )", + "Description": "Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). Currently supports linked brushing and filtering.", + "License": "MIT + file LICENSE", + "Imports": [ + "htmltools (>= 0.3.6)", + "jsonlite", + "lazyeval", + "R6" + ], + "Suggests": [ + "shiny", + "ggplot2", + "testthat (>= 2.1.0)", + "sass", + "bslib" + ], + "URL": "https://rstudio.github.io/crosstalk/, https://github.com/rstudio/crosstalk", + "BugReports": "https://github.com/rstudio/crosstalk/issues", + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Joe Cheng [aut], Carson Sievert [aut, cre] (), Posit Software, PBC [cph, fnd], jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Brian Reavis [ctb, cph] (selectize.js library), Kristopher Michael Kowal [ctb, cph] (es5-shim library), es5-shim contributors [ctb, cph] (es5-shim library), Denis Ineshin [ctb, cph] (ion.rangeSlider library), Sami Samhuri [ctb, cph] (Javascript strftime library)", + "Maintainer": "Carson Sievert ", + "Repository": "CRAN" + }, + "curl": { + "Package": "curl", + "Version": "6.2.2", + "Source": "Repository", + "Type": "Package", + "Title": "A Modern and Flexible Web Client for R", + "Authors@R": "c( person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Hadley\", \"Wickham\", role = \"ctb\"), person(\"Posit Software, PBC\", role = \"cph\"))", + "Description": "Bindings to 'libcurl' for performing fully configurable HTTP/FTP requests where responses can be processed in memory, on disk, or streaming via the callback or connection interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr2' package which builds on this package with http specific tools and logic.", + "License": "MIT + file LICENSE", + "SystemRequirements": "libcurl (>= 7.62): libcurl-devel (rpm) or libcurl4-openssl-dev (deb)", + "URL": "https://jeroen.r-universe.dev/curl", + "BugReports": "https://github.com/jeroen/curl/issues", + "Suggests": [ + "spelling", + "testthat (>= 1.0.0)", + "knitr", + "jsonlite", + "later", + "rmarkdown", + "httpuv (>= 1.4.4)", + "webutils" + ], + "VignetteBuilder": "knitr", + "Depends": [ + "R (>= 3.0.0)" + ], + "RoxygenNote": "7.3.2.9000", + "Encoding": "UTF-8", + "Language": "en-US", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (), Hadley Wickham [ctb], Posit Software, PBC [cph]", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" + }, + "data.table": { + "Package": "data.table", + "Version": "1.17.0", + "Source": "Repository", + "Title": "Extension of `data.frame`", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "methods" + ], + "Suggests": [ + "bit64 (>= 4.0.0)", + "bit (>= 4.0.4)", + "R.utils", + "xts", + "zoo (>= 1.8-1)", + "yaml", + "knitr", + "markdown" + ], + "Description": "Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.", + "License": "MPL-2.0 | file LICENSE", + "URL": "https://r-datatable.com, https://Rdatatable.gitlab.io/data.table, https://github.com/Rdatatable/data.table", + "BugReports": "https://github.com/Rdatatable/data.table/issues", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "ByteCompile": "TRUE", + "Authors@R": "c( person(\"Tyson\",\"Barrett\", role=c(\"aut\",\"cre\"), email=\"t.barrett88@gmail.com\", comment = c(ORCID=\"0000-0002-2137-1391\")), person(\"Matt\",\"Dowle\", role=\"aut\", email=\"mattjdowle@gmail.com\"), person(\"Arun\",\"Srinivasan\", role=\"aut\", email=\"asrini@pm.me\"), person(\"Jan\",\"Gorecki\", role=\"aut\"), person(\"Michael\",\"Chirico\", role=\"aut\", comment = c(ORCID=\"0000-0003-0787-087X\")), person(\"Toby\",\"Hocking\", role=\"aut\", comment = c(ORCID=\"0000-0002-3146-0865\")), person(\"Benjamin\",\"Schwendinger\",role=\"aut\", comment = c(ORCID=\"0000-0003-3315-8114\")), person(\"Ivan\", 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analysis workflow: (1) wrangling the raw data to get it in the needed form, (2) applying preprocessing steps and statistical transformations, and (3) compute statistical summaries of data properties and distributions. 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Ben-Shachar [aut] (), Brenton M. Wiernik [aut] (), Rémi Thériault [ctb] (), Thomas J. 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Further the package makes it easy to manipulate and combine 'gtable' objects so that complex compositions can be built up sequentially.", + "License": "MIT + file LICENSE", + "URL": "https://gtable.r-lib.org, https://github.com/r-lib/gtable", + "BugReports": "https://github.com/r-lib/gtable/issues", + "Depends": [ + "R (>= 4.0)" + ], + "Imports": [ + "cli", + "glue", + "grid", + "lifecycle", + "rlang (>= 1.1.0)", + "stats" + ], + "Suggests": [ + "covr", + "ggplot2", + "knitr", + "profvis", + "rmarkdown", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2024-10-25", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut], Thomas Lin Pedersen [aut, cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "CRAN" + }, + "gtsummary": { + "Package": "gtsummary", + "Version": "2.2.0", + "Source": "Repository", + "Title": "Presentation-Ready Data Summary and Analytic Result Tables", + "Authors@R": "c( person(\"Daniel D.\", \"Sjoberg\", , \"danield.sjoberg@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-0862-2018\")), person(\"Joseph\", \"Larmarange\", role = \"aut\", comment = c(ORCID = \"0000-0001-7097-700X\")), person(\"Michael\", \"Curry\", role = \"aut\", comment = c(ORCID = \"0000-0002-0261-4044\")), person(\"Emily\", \"de la Rua\", , role = \"aut\", comment = c(ORCID = \"0009-0000-8738-5561\")), person(\"Jessica\", \"Lavery\", role = \"aut\", comment = c(ORCID = \"0000-0002-2746-5647\")), person(\"Karissa\", \"Whiting\", role = \"aut\", comment = c(ORCID = \"0000-0002-4683-1868\")), person(\"Emily C.\", \"Zabor\", role = \"aut\", comment = c(ORCID = \"0000-0002-1402-4498\")), person(\"Xing\", \"Bai\", role = \"ctb\"), person(\"Esther\", \"Drill\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3315-4538\")), person(\"Jessica\", \"Flynn\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8310-6684\")), person(\"Margie\", \"Hannum\", role = \"ctb\", comment = c(ORCID = \"0000-0002-2953-0449\")), person(\"Stephanie\", \"Lobaugh\", role = \"ctb\"), person(\"Shannon\", \"Pileggi\", role = \"ctb\", comment = c(ORCID = \"0000-0002-7732-4164\")), person(\"Amy\", \"Tin\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8005-0694\")), person(\"Gustavo\", \"Zapata Wainberg\", role = \"ctb\", comment = c(ORCID = \"0000-0002-2524-3637\")) )", + "Description": "Creates presentation-ready tables summarizing data sets, regression models, and more. The code to create the tables is concise and highly customizable. Data frames can be summarized with any function, e.g. mean(), median(), even user-written functions. Regression models are summarized and include the reference rows for categorical variables. Common regression models, such as logistic regression and Cox proportional hazards regression, are automatically identified and the tables are pre-filled with appropriate column headers.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/ddsjoberg/gtsummary, https://www.danieldsjoberg.com/gtsummary/", + "BugReports": "https://github.com/ddsjoberg/gtsummary/issues", + "Depends": [ + "R (>= 4.2)" + ], + "Imports": [ + "cards (>= 0.6.0)", + "cli (>= 3.6.3)", + "dplyr (>= 1.1.3)", + "glue (>= 1.8.0)", + "gt (>= 0.11.1)", + "lifecycle (>= 1.0.3)", + "rlang (>= 1.1.1)", + "tidyr (>= 1.3.0)", + "vctrs (>= 0.6.4)" + ], + "Suggests": [ + "aod (>= 1.3.3)", + "broom (>= 1.0.5)", + "broom.helpers (>= 1.17.0)", + "broom.mixed (>= 0.2.9)", + "car (>= 3.0-11)", + "cardx (>= 0.2.4)", + "cmprsk", + "effectsize (>= 0.6.0)", + "emmeans (>= 1.7.3)", + "flextable (>= 0.8.1)", + "geepack (>= 1.3.10)", + "ggstats (>= 0.2.1)", + "huxtable (>= 5.4.0)", + "insight (>= 0.15.0)", + "kableExtra (>= 1.3.4)", + "knitr (>= 1.37)", + "lme4 (>= 1.1-31)", + "mice (>= 3.10.0)", + "nnet", + "officer", + "openxlsx", + "parameters (>= 0.20.2)", + "parsnip (>= 0.1.7)", + "rmarkdown", + "smd (>= 0.6.6)", + "spelling", + "survey (>= 4.2)", + "survival (>= 3.6-4)", + "testthat (>= 3.2.0)", + "withr (>= 2.5.0)", + "workflows (>= 0.2.4)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/check": "hms", + "Config/Needs/website": "forcats, sandwich, scales", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "Encoding": "UTF-8", + "Language": "en-US", + "LazyData": "true", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Daniel D. Sjoberg [aut, cre] (), Joseph Larmarange [aut] (), Michael Curry [aut] (), Emily de la Rua [aut] (), Jessica Lavery [aut] (), Karissa Whiting [aut] (), Emily C. Zabor [aut] (), Xing Bai [ctb], Esther Drill [ctb] (), Jessica Flynn [ctb] (), Margie Hannum [ctb] (), Stephanie Lobaugh [ctb], Shannon Pileggi [ctb] (), Amy Tin [ctb] (), Gustavo Zapata Wainberg [ctb] ()", + "Maintainer": "Daniel D. Sjoberg ", + "Repository": "CRAN" + }, + "haven": { + "Package": "haven", + "Version": "2.5.4", + "Source": "Repository", + "Title": "Import and Export 'SPSS', 'Stata' and 'SAS' Files", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Evan\", \"Miller\", role = c(\"aut\", \"cph\"), comment = \"Author of included ReadStat code\"), person(\"Danny\", \"Smith\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Import foreign statistical formats into R via the embedded 'ReadStat' C library, .", + "License": "MIT + file LICENSE", + "URL": "https://haven.tidyverse.org, https://github.com/tidyverse/haven, https://github.com/WizardMac/ReadStat", + "BugReports": "https://github.com/tidyverse/haven/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "cli (>= 3.0.0)", + "forcats (>= 0.2.0)", + "hms", + "lifecycle", + "methods", + "readr (>= 0.1.0)", + "rlang (>= 0.4.0)", + "tibble", + "tidyselect", + "vctrs (>= 0.3.0)" + ], + "Suggests": [ + "covr", + "crayon", + "fs", + "knitr", + "pillar (>= 1.4.0)", + "rmarkdown", + "testthat (>= 3.0.0)", + "utf8" + ], + "LinkingTo": [ + "cpp11" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "SystemRequirements": "GNU make, zlib: zlib1g-dev (deb), zlib-devel (rpm)", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre], Evan Miller [aut, cph] (Author of included ReadStat code), Danny Smith [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "here": { + "Package": "here", + "Version": "1.0.1", + "Source": "Repository", + "Title": "A Simpler Way to Find Your Files", + "Date": "2020-12-13", + "Authors@R": "c(person(given = \"Kirill\", family = \"M\\u00fcller\", role = c(\"aut\", \"cre\"), email = \"krlmlr+r@mailbox.org\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(given = \"Jennifer\", family = \"Bryan\", role = \"ctb\", email = \"jenny@rstudio.com\", comment = c(ORCID = \"0000-0002-6983-2759\")))", + "Description": "Constructs paths to your project's files. Declare the relative path of a file within your project with 'i_am()'. Use the 'here()' function as a drop-in replacement for 'file.path()', it will always locate the files relative to your project root.", + "License": "MIT + file LICENSE", + "URL": "https://here.r-lib.org/, https://github.com/r-lib/here", + "BugReports": "https://github.com/r-lib/here/issues", + "Imports": [ + "rprojroot (>= 2.0.2)" + ], + "Suggests": [ + "conflicted", + "covr", + "fs", + "knitr", + "palmerpenguins", + "plyr", + "readr", + "rlang", + "rmarkdown", + "testthat", + "uuid", + "withr" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.1.1.9000", + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Author": "Kirill Müller [aut, cre] (), Jennifer Bryan [ctb] ()", + "Maintainer": "Kirill Müller ", + "Repository": "CRAN" + }, + "highr": { + "Package": "highr", + "Version": "0.11", + "Source": "Repository", + "Type": "Package", + "Title": "Syntax Highlighting for R Source Code", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Yixuan\", \"Qiu\", role = \"aut\"), person(\"Christopher\", \"Gandrud\", role = \"ctb\"), person(\"Qiang\", \"Li\", role = \"ctb\") )", + "Description": "Provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package ().", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "xfun (>= 0.18)" + ], + "Suggests": [ + "knitr", + "markdown", + "testit" + ], + "License": "GPL", + "URL": "https://github.com/yihui/highr", + "BugReports": "https://github.com/yihui/highr/issues", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre] (), Yixuan Qiu [aut], Christopher Gandrud [ctb], Qiang Li [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" + }, + "hms": { + "Package": "hms", + "Version": "1.1.3", + "Source": "Repository", + "Title": "Pretty Time of Day", + "Date": "2023-03-21", + "Authors@R": "c( person(\"Kirill\", \"Müller\", role = c(\"aut\", \"cre\"), email = \"kirill@cynkra.com\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"R Consortium\", role = \"fnd\"), person(\"RStudio\", role = \"fnd\") )", + "Description": "Implements an S3 class for storing and formatting time-of-day values, based on the 'difftime' class.", + "Imports": [ + "lifecycle", + "methods", + "pkgconfig", + "rlang (>= 1.0.2)", + "vctrs (>= 0.3.8)" + ], + "Suggests": [ + "crayon", + "lubridate", + "pillar (>= 1.1.0)", + "testthat (>= 3.0.0)" + ], + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "URL": "https://hms.tidyverse.org/, https://github.com/tidyverse/hms", + "BugReports": "https://github.com/tidyverse/hms/issues", + "RoxygenNote": "7.2.3", + "Config/testthat/edition": "3", + "Config/autostyle/scope": "line_breaks", + "Config/autostyle/strict": "false", + "Config/Needs/website": "tidyverse/tidytemplate", + "NeedsCompilation": "no", + "Author": "Kirill Müller [aut, cre] (), R Consortium [fnd], RStudio [fnd]", + "Maintainer": "Kirill Müller ", + "Repository": "CRAN" + }, + "htmlTable": { + "Package": "htmlTable", + "Version": "2.4.3", + "Source": "Repository", + "Title": "Advanced Tables for Markdown/HTML", + "Authors@R": "c( person(\"Max\", \"Gordon\", email = \"max@gforge.se\", role = c(\"aut\", \"cre\")), person(\"Stephen\", \"Gragg\", role=c(\"aut\")), person(\"Peter\", \"Konings\", role=c(\"aut\")))", + "Maintainer": "Max Gordon ", + "Description": "Tables with state-of-the-art layout elements such as row spanners, column spanners, table spanners, zebra striping, and more. While allowing advanced layout, the underlying css-structure is simple in order to maximize compatibility with common word processors. The package also contains a few text formatting functions that help outputting text compatible with HTML/LaTeX.", + "License": "GPL (>= 3)", + "URL": "https://gforge.se/packages/", + "BugReports": "https://github.com/gforge/htmlTable/issues", + "Biarch": "yes", + "Depends": [ + "R (>= 4.1)" + ], + "Imports": [ + "stringr", + "knitr (>= 1.6)", + "magrittr (>= 1.5)", + "methods", + "checkmate", + "htmlwidgets", + "htmltools", + "rstudioapi (>= 0.6)" + ], + "Suggests": [ + "testthat", + "XML", + "xml2", + "Hmisc", + "rmarkdown", + "chron", + "lubridate", + "tibble", + "purrr", + "tidyselect", + "glue", + "rlang", + "tidyr (>= 0.7.2)", + "dplyr (>= 0.7.4)" + ], + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "VignetteBuilder": "knitr", + "RoxygenNote": "7.2.2", + "Author": "Max Gordon [aut, cre], Stephen Gragg [aut], Peter Konings [aut]", + "Repository": "CRAN" + }, + "htmltools": { + "Package": "htmltools", + "Version": "0.5.8.1", + "Source": "Repository", + "Type": "Package", + "Title": "Tools for HTML", + "Authors@R": "c( person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Barret\", \"Schloerke\", , \"barret@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0001-9986-114X\")), person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Yihui\", \"Xie\", , \"yihui@posit.co\", role = \"aut\"), person(\"Jeff\", \"Allen\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Tools for HTML generation and output.", + "License": "GPL (>= 2)", + "URL": "https://github.com/rstudio/htmltools, https://rstudio.github.io/htmltools/", + "BugReports": "https://github.com/rstudio/htmltools/issues", + "Depends": [ + "R (>= 2.14.1)" + ], + "Imports": [ + "base64enc", + "digest", + "fastmap (>= 1.1.0)", + "grDevices", + "rlang (>= 1.0.0)", + "utils" + ], + "Suggests": [ + "Cairo", + "markdown", + "ragg", + "shiny", + "testthat", + "withr" + ], + "Enhances": [ + "knitr" + ], + "Config/Needs/check": "knitr", + "Config/Needs/website": "rstudio/quillt, bench", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Collate": "'colors.R' 'fill.R' 'html_dependency.R' 'html_escape.R' 'html_print.R' 'htmltools-package.R' 'images.R' 'known_tags.R' 'selector.R' 'staticimports.R' 'tag_query.R' 'utils.R' 'tags.R' 'template.R'", + "NeedsCompilation": "yes", + "Author": "Joe Cheng [aut], Carson Sievert [aut, cre] (), Barret Schloerke [aut] (), Winston Chang [aut] (), Yihui Xie [aut], Jeff Allen [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Carson Sievert ", + "Repository": "CRAN" + }, + "htmlwidgets": { + "Package": "htmlwidgets", + "Version": "1.6.4", + "Source": "Repository", + "Type": "Package", + "Title": "HTML Widgets for R", + "Authors@R": "c( person(\"Ramnath\", \"Vaidyanathan\", role = c(\"aut\", \"cph\")), person(\"Yihui\", \"Xie\", role = \"aut\"), person(\"JJ\", \"Allaire\", role = \"aut\"), person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Kenton\", \"Russell\", role = c(\"aut\", \"cph\")), person(\"Ellis\", \"Hughes\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A framework for creating HTML widgets that render in various contexts including the R console, 'R Markdown' documents, and 'Shiny' web applications.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/ramnathv/htmlwidgets", + "BugReports": "https://github.com/ramnathv/htmlwidgets/issues", + "Imports": [ + "grDevices", + "htmltools (>= 0.5.7)", + "jsonlite (>= 0.9.16)", + "knitr (>= 1.8)", + "rmarkdown", + "yaml" + ], + "Suggests": [ + "testthat" + ], + "Enhances": [ + "shiny (>= 1.1)" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Ramnath Vaidyanathan [aut, cph], Yihui Xie [aut], JJ Allaire [aut], Joe Cheng [aut], Carson Sievert [aut, cre] (), Kenton Russell [aut, cph], Ellis Hughes [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Carson Sievert ", + "Repository": "CRAN" + }, + "httpuv": { + "Package": "httpuv", + "Version": "1.6.16", + "Source": "Repository", + "Type": "Package", + "Title": "HTTP and WebSocket Server Library", + "Authors@R": "c( person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit, PBC\", \"fnd\", role = \"cph\"), person(\"Hector\", \"Corrada Bravo\", role = \"ctb\"), person(\"Jeroen\", \"Ooms\", role = \"ctb\"), person(\"Andrzej\", \"Krzemienski\", role = \"cph\", comment = \"optional.hpp\"), person(\"libuv project contributors\", role = \"cph\", comment = \"libuv library, see src/libuv/AUTHORS file\"), person(\"Joyent, Inc. and other Node contributors\", role = \"cph\", comment = \"libuv library, see src/libuv/AUTHORS file; and http-parser library, see src/http-parser/AUTHORS file\"), person(\"Niels\", \"Provos\", role = \"cph\", comment = \"libuv subcomponent: tree.h\"), person(\"Internet Systems Consortium, Inc.\", role = \"cph\", comment = \"libuv subcomponent: inet_pton and inet_ntop, contained in src/libuv/src/inet.c\"), person(\"Alexander\", \"Chemeris\", role = \"cph\", comment = \"libuv subcomponent: stdint-msvc2008.h (from msinttypes)\"), person(\"Google, Inc.\", role = \"cph\", comment = \"libuv subcomponent: pthread-fixes.c\"), person(\"Sony Mobile Communcations AB\", role = \"cph\", comment = \"libuv subcomponent: pthread-fixes.c\"), person(\"Berkeley Software Design Inc.\", role = \"cph\", comment = \"libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c\"), person(\"Kenneth\", \"MacKay\", role = \"cph\", comment = \"libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c\"), person(\"Emergya (Cloud4all, FP7/2007-2013, grant agreement no 289016)\", role = \"cph\", comment = \"libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c\"), person(\"Steve\", \"Reid\", role = \"aut\", comment = \"SHA-1 implementation\"), person(\"James\", \"Brown\", role = \"aut\", comment = \"SHA-1 implementation\"), person(\"Bob\", \"Trower\", role = \"aut\", comment = \"base64 implementation\"), person(\"Alexander\", \"Peslyak\", role = \"aut\", comment = \"MD5 implementation\"), person(\"Trantor Standard Systems\", role = \"cph\", comment = \"base64 implementation\"), person(\"Igor\", \"Sysoev\", role = \"cph\", comment = \"http-parser\") )", + "Description": "Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)", + "License": "GPL (>= 2) | file LICENSE", + "URL": "https://github.com/rstudio/httpuv", + "BugReports": "https://github.com/rstudio/httpuv/issues", + "Depends": [ + "R (>= 2.15.1)" + ], + "Imports": [ + "later (>= 0.8.0)", + "promises", + "R6", + "Rcpp (>= 1.0.7)", + "utils" + ], + "Suggests": [ + "callr", + "curl", + "jsonlite", + "testthat", + "websocket" + ], + "LinkingTo": [ + "later", + "Rcpp" + ], + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "SystemRequirements": "GNU make, zlib", + "Collate": "'RcppExports.R' 'httpuv.R' 'random_port.R' 'server.R' 'staticServer.R' 'static_paths.R' 'utils.R'", + "NeedsCompilation": "yes", + "Author": "Joe Cheng [aut], Winston Chang [aut, cre], Posit, PBC fnd [cph], Hector Corrada Bravo [ctb], Jeroen Ooms [ctb], Andrzej Krzemienski [cph] (optional.hpp), libuv project contributors [cph] (libuv library, see src/libuv/AUTHORS file), Joyent, Inc. and other Node contributors [cph] (libuv library, see src/libuv/AUTHORS file; and http-parser library, see src/http-parser/AUTHORS file), Niels Provos [cph] (libuv subcomponent: tree.h), Internet Systems Consortium, Inc. [cph] (libuv subcomponent: inet_pton and inet_ntop, contained in src/libuv/src/inet.c), Alexander Chemeris [cph] (libuv subcomponent: stdint-msvc2008.h (from msinttypes)), Google, Inc. [cph] (libuv subcomponent: pthread-fixes.c), Sony Mobile Communcations AB [cph] (libuv subcomponent: pthread-fixes.c), Berkeley Software Design Inc. [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Kenneth MacKay [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Emergya (Cloud4all, FP7/2007-2013, grant agreement no 289016) [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Steve Reid [aut] (SHA-1 implementation), James Brown [aut] (SHA-1 implementation), Bob Trower [aut] (base64 implementation), Alexander Peslyak [aut] (MD5 implementation), Trantor Standard Systems [cph] (base64 implementation), Igor Sysoev [cph] (http-parser)", + "Maintainer": "Winston Chang ", + "Repository": "CRAN" + }, + "httr": { + "Package": "httr", + "Version": "1.4.7", + "Source": "Repository", + "Title": "Tools for Working with URLs and HTTP", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).", + "License": "MIT + file LICENSE", + "URL": "https://httr.r-lib.org/, https://github.com/r-lib/httr", + "BugReports": "https://github.com/r-lib/httr/issues", + "Depends": [ + "R (>= 3.5)" + ], + "Imports": [ + "curl (>= 5.0.2)", + "jsonlite", + "mime", + "openssl (>= 0.8)", + "R6" + ], + "Suggests": [ + "covr", + "httpuv", + "jpeg", + "knitr", + "png", + "readr", + "rmarkdown", + "testthat (>= 0.8.0)", + "xml2" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], Posit, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "insight": { + "Package": "insight", + "Version": "1.2.0", + "Source": "Repository", + "Type": "Package", + "Title": "Easy Access to Model Information for Various Model Objects", + "Authors@R": "c(person(given = \"Daniel\", family = \"Lüdecke\", role = c(\"aut\", \"cre\"), email = \"officialeasystats@gmail.com\", comment = c(ORCID = \"0000-0002-8895-3206\")), person(given = \"Dominique\", family = \"Makowski\", role = c(\"aut\", \"ctb\"), email = \"dom.makowski@gmail.com\", comment = c(ORCID = \"0000-0001-5375-9967\")), person(given = \"Indrajeet\", family = \"Patil\", role = c(\"aut\", \"ctb\"), email = \"patilindrajeet.science@gmail.com\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(given = \"Philip\", family = \"Waggoner\", role = c(\"aut\", \"ctb\"), email = \"philip.waggoner@gmail.com\", comment = c(ORCID = \"0000-0002-7825-7573\")), person(given = \"Mattan S.\", family = \"Ben-Shachar\", role = c(\"aut\", \"ctb\"), email = \"matanshm@post.bgu.ac.il\", comment = c(ORCID = \"0000-0002-4287-4801\")), person(given = \"Brenton M.\", family = \"Wiernik\", role = c(\"aut\", \"ctb\"), email = \"brenton@wiernik.org\", comment = c(ORCID = \"0000-0001-9560-6336\")), person(given = \"Vincent\", family = \"Arel-Bundock\", email = \"vincent.arel-bundock@umontreal.ca\", role = c(\"aut\", \"ctb\"), comment = c(ORCID = \"0000-0003-2042-7063\")), person(given = \"Etienne\", family = \"Bacher\", email = \"etienne.bacher@protonmail.com\", role = c(\"aut\", \"ctb\"), comment = c(ORCID = \"0000-0002-9271-5075\")), person(given = \"Alex\", family = \"Hayes\", role = c(\"rev\"), email = \"alexpghayes@gmail.com\", comment = c(ORCID = \"0000-0002-4985-5160\")), person(given = \"Grant\", family = \"McDermott\", role = c(\"ctb\"), email = \"grantmcd@uoregon.edu\", comment = c(ORCID = \"0000-0001-7883-8573\")), person(given = \"Rémi\", family = \"Thériault\", role = \"ctb\", email = \"remi.theriault@mail.mcgill.ca\", comment = c(ORCID = \"0000-0003-4315-6788\")), person(given = \"Alex\", family = \"Reinhart\", role = \"ctb\", email = \"areinhar@stat.cmu.edu\", comment = c(ORCID = \"0000-0002-6658-514X\")))", + "Maintainer": "Daniel Lüdecke ", + "Description": "A tool to provide an easy, intuitive and consistent access to information contained in various R models, like model formulas, model terms, information about random effects, data that was used to fit the model or data from response variables. 'insight' mainly revolves around two types of functions: Functions that find (the names of) information, starting with 'find_', and functions that get the underlying data, starting with 'get_'. The package has a consistent syntax and works with many different model objects, where otherwise functions to access these information are missing.", + "License": "GPL-3", + "URL": "https://easystats.github.io/insight/", + "BugReports": "https://github.com/easystats/insight/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "methods", + "stats", + "utils" + ], + "Suggests": [ + "AER", + "afex", + "aod", + "ape", + "BayesFactor", + "bayestestR", + "bbmle", + "bdsmatrix", + "betareg", + "bife", + "biglm", + "BH", + "blavaan (>= 0.5-5)", + "blme", + "boot", + "brms", + "broom", + "car", + "carData", + "censReg", + "cgam", + "clubSandwich", + "cobalt", + "coxme", + "cplm", + "crch", + "curl", + "datawizard", + "effectsize", + "emmeans", + "epiR", + "estimatr", + "feisr", + "fixest (>= 0.11.2)", + "fungible", + "fwb", + "gam", + "gamlss", + "gamlss.data", + "gamm4", + "gbm", + "gee", + "geepack", + "geoR", + "GLMMadaptive", + "glmmTMB (>= 1.1.10)", + "glmtoolbox", + "gmnl", + "grDevices", + "gt", + "httptest2", + "httr2", + "interp", + "ivreg", + "JM", + "knitr", + "lavaan", + "lavaSearch2", + "lfe", + "lme4", + "lmerTest", + "lmtest", + "logistf", + "logitr", + "marginaleffects (>= 0.25.0)", + "MASS", + "Matrix", + "mclogit", + "mclust", + "MCMCglmm", + "merTools", + "metaBMA", + "metadat", + "metafor", + "metaplus", + "mgcv", + "mice (>= 3.17.0)", + "mlogit", + "mmrm", + "modelbased (>= 0.9.0)", + "multgee", + "MuMIn", + "nestedLogit", + "nlme", + "nnet", + "nonnest2", + "ordinal", + "panelr", + "parameters", + "parsnip", + "pbkrtest", + "performance", + "phylolm", + "plm", + "poorman", + "PROreg (>= 1.3.0)", + "pscl", + "psych", + "quantreg", + "Rcpp", + "RcppEigen", + "rmarkdown", + "rms", + "robustbase", + "robustlmm", + "rpart", + "rstanarm (>= 2.21.1)", + "rstantools (>= 2.1.0)", + "rstudioapi", + "RWiener", + "sandwich", + "serp", + "speedglm", + "splines", + "statmod", + "survey", + "survival", + "svylme", + "testthat", + "tinytable (>= 0.8.0)", + "TMB", + "truncreg", + "tune", + "tweedie", + "VGAM", + "WeightIt", + "withr" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.2", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "Config/Needs/website": "easystats/easystatstemplate", + "Config/Needs/check": "stan-dev/cmdstanr", + "NeedsCompilation": "no", + "Author": "Daniel Lüdecke [aut, cre] (), Dominique Makowski [aut, ctb] (), Indrajeet Patil [aut, ctb] (), Philip Waggoner [aut, ctb] (), Mattan S. Ben-Shachar [aut, ctb] (), Brenton M. Wiernik [aut, ctb] (), Vincent Arel-Bundock [aut, ctb] (), Etienne Bacher [aut, ctb] (), Alex Hayes [rev] (), Grant McDermott [ctb] (), Rémi Thériault [ctb] (), Alex Reinhart [ctb] ()", + "Repository": "CRAN" + }, + "isoband": { + "Package": "isoband", + "Version": "0.2.7", + "Source": "Repository", + "Title": "Generate Isolines and Isobands from Regularly Spaced Elevation Grids", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Claus O.\", \"Wilke\", , \"wilke@austin.utexas.edu\", role = \"aut\", comment = c(\"Original author\", ORCID = \"0000-0002-7470-9261\")), person(\"Thomas Lin\", \"Pedersen\", , \"thomasp85@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-5147-4711\")) )", + "Description": "A fast C++ implementation to generate contour lines (isolines) and contour polygons (isobands) from regularly spaced grids containing elevation data.", + "License": "MIT + file LICENSE", + "URL": "https://isoband.r-lib.org", + "BugReports": "https://github.com/r-lib/isoband/issues", + "Imports": [ + "grid", + "utils" + ], + "Suggests": [ + "covr", + "ggplot2", + "knitr", + "magick", + "microbenchmark", + "rmarkdown", + "sf", + "testthat", + "xml2" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "SystemRequirements": "C++11", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre] (), Claus O. Wilke [aut] (Original author, ), Thomas Lin Pedersen [aut] ()", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "jquerylib": { + "Package": "jquerylib", + "Version": "0.1.4", + "Source": "Repository", + "Title": "Obtain 'jQuery' as an HTML Dependency Object", + "Authors@R": "c( person(\"Carson\", \"Sievert\", role = c(\"aut\", \"cre\"), email = \"carson@rstudio.com\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@rstudio.com\"), person(family = \"RStudio\", role = \"cph\"), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/lib/jquery-AUTHORS.txt\") )", + "Description": "Obtain any major version of 'jQuery' () and use it in any webpage generated by 'htmltools' (e.g. 'shiny', 'htmlwidgets', and 'rmarkdown'). Most R users don't need to use this package directly, but other R packages (e.g. 'shiny', 'rmarkdown', etc.) depend on this package to avoid bundling redundant copies of 'jQuery'.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Config/testthat/edition": "3", + "RoxygenNote": "7.0.2", + "Imports": [ + "htmltools" + ], + "Suggests": [ + "testthat" + ], + "NeedsCompilation": "no", + "Author": "Carson Sievert [aut, cre] (), Joe Cheng [aut], RStudio [cph], jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/lib/jquery-AUTHORS.txt)", + "Maintainer": "Carson Sievert ", + "Repository": "CRAN" + }, + "jsonlite": { + "Package": "jsonlite", + "Version": "2.0.0", + "Source": "Repository", + "Title": "A Simple and Robust JSON Parser and Generator for R", + "License": "MIT + file LICENSE", + "Depends": [ + "methods" + ], + "Authors@R": "c( person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Duncan\", \"Temple Lang\", role = \"ctb\"), person(\"Lloyd\", \"Hilaiel\", role = \"cph\", comment=\"author of bundled libyajl\"))", + "URL": "https://jeroen.r-universe.dev/jsonlite https://arxiv.org/abs/1403.2805", + "BugReports": "https://github.com/jeroen/jsonlite/issues", + "Maintainer": "Jeroen Ooms ", + "VignetteBuilder": "knitr, R.rsp", + "Description": "A reasonably fast JSON parser and generator, optimized for statistical data and the web. Offers simple, flexible tools for working with JSON in R, and is particularly powerful for building pipelines and interacting with a web API. The implementation is based on the mapping described in the vignette (Ooms, 2014). In addition to converting JSON data from/to R objects, 'jsonlite' contains functions to stream, validate, and prettify JSON data. The unit tests included with the package verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.", + "Suggests": [ + "httr", + "vctrs", + "testthat", + "knitr", + "rmarkdown", + "R.rsp", + "sf" + ], + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (), Duncan Temple Lang [ctb], Lloyd Hilaiel [cph] (author of bundled libyajl)", + "Repository": "CRAN" + }, + "juicyjuice": { + "Package": "juicyjuice", + "Version": "0.1.0", + "Source": "Repository", + "Title": "Inline CSS Properties into HTML Tags Using 'juice'", + "Authors@R": "c( person(\"Richard\", \"Iannone\", , \"riannone@me.com\", c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0003-3925-190X\")), person(\"Automattic\", role = c(\"cph\"), comment = \"juice library\"), person(\"juice contributors\", role = c(\"ctb\"), comment = \"juice library\") )", + "Description": "There are occasions where you need a piece of HTML with integrated styles. A prime example of this is HTML email. This transformation involves moving the CSS and associated formatting instructions from the style block in the head of your document into the body of the HTML. Many prominent email clients require integrated styles in HTML email; otherwise a received HTML email will be displayed without any styling. This package will quickly and precisely perform these CSS transformations when given HTML text and it does so by using the JavaScript 'juice' library.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/rich-iannone/juicyjuice", + "BugReports": "https://github.com/rich-iannone/juicyjuice/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.1", + "Imports": [ + "V8 (>= 4.2.0)" + ], + "Suggests": [ + "testthat (>= 3.0.0)" + ], + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Author": "Richard Iannone [aut, cre, cph] (), Automattic [cph] (juice library), juice contributors [ctb] (juice library)", + "Maintainer": "Richard Iannone ", + "Repository": "CRAN" + }, + "keyring": { + "Package": "keyring", + "Version": "1.3.2", + "Source": "Repository", + "Title": "Access the System Credential Store from R", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Alec\", \"Wong\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Platform independent 'API' to access the operating system's credential store. Currently supports: 'Keychain' on 'macOS', Credential Store on 'Windows', the Secret Service 'API' on 'Linux', and simple, platform independent stores implemented with environment variables or encrypted files. Additional storage back-ends can be added easily.", + "License": "MIT + file LICENSE", + "URL": "https://keyring.r-lib.org/, https://github.com/r-lib/keyring", + "BugReports": "https://github.com/r-lib/keyring/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "askpass", + "assertthat", + "filelock", + "openssl", + "R6", + "rappdirs", + "sodium", + "tools", + "utils", + "yaml" + ], + "Suggests": [ + "callr", + "covr", + "mockery", + "testthat (>= 3.0.0)", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "SystemRequirements": "Optional: libsecret on Linux (libsecret-1-dev on Debian/Ubuntu, libsecret-devel on Fedora/CentOS)", + "Collate": "'api.R' 'assertions.R' 'backend-class.R' 'backend-env.R' 'backend-file.R' 'backend-macos.R' 'backend-secret-service.R' 'backend-wincred.R' 'default_backend.R' 'keyring-package.R' 'package.R' 'pass.R' 'utils.R'", + "NeedsCompilation": "yes", + "Author": "Gábor Csárdi [aut, cre], Alec Wong [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" + }, + "knitr": { + "Package": "knitr", + "Version": "1.50", + "Source": "Repository", + "Type": "Package", + "Title": "A General-Purpose Package for Dynamic Report Generation in R", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\", URL = \"https://yihui.org\")), person(\"Abhraneel\", \"Sarma\", role = \"ctb\"), person(\"Adam\", \"Vogt\", role = \"ctb\"), person(\"Alastair\", \"Andrew\", role = \"ctb\"), person(\"Alex\", \"Zvoleff\", role = \"ctb\"), person(\"Amar\", \"Al-Zubaidi\", role = \"ctb\"), person(\"Andre\", \"Simon\", role = \"ctb\", comment = \"the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de\"), person(\"Aron\", \"Atkins\", role = \"ctb\"), person(\"Aaron\", \"Wolen\", role = \"ctb\"), 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Lattice is sufficient for typical graphics needs, and is also flexible enough to handle most nonstandard requirements. 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Some missing Markdown features in 'commonmark' are also supported, such as raw HTML or 'LaTeX' blocks, 'LaTeX' math, superscripts, subscripts, footnotes, element attributes, and appendices, but not all 'Pandoc' Markdown features are (or will be) supported. With additional JavaScript and CSS, you can also create HTML slides and articles. This package can be viewed as a trimmed-down version of R Markdown and 'knitr'. It does not aim at rich Markdown features or a large variety of output formats (the primary formats are HTML and 'LaTeX'). Book and website projects of multiple input documents are also supported.", + "Depends": [ + "R (>= 3.2.0)" + ], + "Imports": [ + "utils", + "commonmark (>= 1.9.5)", + "xfun (>= 0.52)" + ], + "Suggests": [ + "rbibutils", + "rstudioapi", + "tinytex" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/yihui/litedown", + "BugReports": "https://github.com/yihui/litedown/issues", + "VignetteBuilder": "litedown", + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre] (, https://yihui.org), Tim Taylor [ctb] ()", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" + }, + "lubridate": { + "Package": "lubridate", + "Version": "1.9.4", + "Source": "Repository", + "Type": "Package", + "Title": "Make Dealing with Dates a Little Easier", + "Authors@R": "c( person(\"Vitalie\", \"Spinu\", , \"spinuvit@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Garrett\", \"Grolemund\", role = \"aut\"), person(\"Hadley\", \"Wickham\", role = \"aut\"), person(\"Davis\", \"Vaughan\", role = \"ctb\"), person(\"Ian\", \"Lyttle\", role = \"ctb\"), person(\"Imanuel\", \"Costigan\", role = \"ctb\"), person(\"Jason\", \"Law\", role = \"ctb\"), person(\"Doug\", \"Mitarotonda\", role = \"ctb\"), person(\"Joseph\", \"Larmarange\", role = \"ctb\"), person(\"Jonathan\", \"Boiser\", role = \"ctb\"), person(\"Chel Hee\", \"Lee\", role = \"ctb\") )", + "Maintainer": "Vitalie Spinu ", + "Description": "Functions to work with date-times and time-spans: fast and user friendly parsing of date-time data, extraction and updating of components of a date-time (years, months, days, hours, minutes, and seconds), algebraic manipulation on date-time and time-span objects. The 'lubridate' package has a consistent and memorable syntax that makes working with dates easy and fun.", + "License": "GPL (>= 2)", + "URL": "https://lubridate.tidyverse.org, https://github.com/tidyverse/lubridate", + "BugReports": "https://github.com/tidyverse/lubridate/issues", + "Depends": [ + "methods", + "R (>= 3.2)" + ], + "Imports": [ + "generics", + "timechange (>= 0.3.0)" + ], + "Suggests": [ + "covr", + "knitr", + "rmarkdown", + "testthat (>= 2.1.0)", + "vctrs (>= 0.6.5)" + ], + "Enhances": [ + "chron", + "data.table", + "timeDate", + "tis", + "zoo" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.2.3", + "SystemRequirements": "C++11, A system with zoneinfo data (e.g. /usr/share/zoneinfo). 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Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.", + "License": "MIT + file LICENSE", + "URL": "https://jeroen.r-universe.dev/openssl", + "BugReports": "https://github.com/jeroen/openssl/issues", + "SystemRequirements": "OpenSSL >= 1.0.2", + "VignetteBuilder": "knitr", + "Imports": [ + "askpass" + ], + "Suggests": [ + "curl", + "testthat (>= 2.1.0)", + "digest", + "knitr", + "rmarkdown", + "jsonlite", + "jose", + "sodium" + ], + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (), Oliver Keyes [ctb]", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" + }, + "openxlsx2": { + "Package": "openxlsx2", + "Version": "1.15", + "Source": "Repository", + "Type": "Package", + "Title": "Read, Write and Edit 'xlsx' Files", + "Language": "en-US", + "Authors@R": "c( person(\"Jordan Mark\", \"Barbone\", email = \"jmbarbone@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0001-9788-3628\")), person(\"Jan Marvin\", \"Garbuszus\", email = \"jan.garbuszus@ruhr-uni-bochum.de\", role = c(\"aut\", \"cre\")), person(\"Olivier\", \"Roy\", role = \"ctb\"), person(family = \"openxlsx authors\", role = \"cph\", comment = \"openxlsx package\"), person(\"Arseny\", \"Kapoulkine\", role = c(\"ctb\", \"cph\"), comment = \"Author of included pugixml code\") )", + "Description": "Simplifies the creation of 'xlsx' files by providing a high level interface to writing, styling and editing worksheets.", + "License": "MIT + file LICENSE", + "URL": "https://janmarvin.github.io/openxlsx2/, https://github.com/JanMarvin/openxlsx2", + "BugReports": "https://github.com/JanMarvin/openxlsx2/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "R6", + "Rcpp", + "grDevices", + "magrittr", + "stringi", + "utils", + "zip" + ], + "LinkingTo": [ + "Rcpp" + ], + "Suggests": [ + "ggplot2", + "knitr", + "mschart (>= 0.4)", + "rmarkdown", + "rvg", + "testthat (>= 3.0.0)", + "waldo" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "NeedsCompilation": "yes", + "Author": "Jordan Mark Barbone [aut] (), Jan Marvin Garbuszus [aut, cre], Olivier Roy [ctb], openxlsx authors [cph] (openxlsx package), Arseny Kapoulkine [ctb, cph] (Author of included pugixml code)", + "Maintainer": "Jan Marvin Garbuszus ", + "Repository": "CRAN" + }, + "parameters": { + "Package": "parameters", + "Version": "0.24.2", + "Source": "Repository", + "Type": "Package", + "Title": "Processing of Model Parameters", + "Authors@R": "c(person(given = \"Daniel\", family = \"Lüdecke\", role = c(\"aut\", \"cre\"), email = \"d.luedecke@uke.de\", comment = c(ORCID = \"0000-0002-8895-3206\")), person(given = \"Dominique\", family = \"Makowski\", role = \"aut\", email = \"dom.makowski@gmail.com\", comment = c(ORCID = \"0000-0001-5375-9967\")), person(given = \"Mattan S.\", family = \"Ben-Shachar\", role = \"aut\", email = \"matanshm@post.bgu.ac.il\", comment = c(ORCID = \"0000-0002-4287-4801\")), person(given = \"Indrajeet\", family = \"Patil\", role = \"aut\", email = \"patilindrajeet.science@gmail.com\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(given = \"Søren\", family = \"Højsgaard\", role = \"aut\", email = \"sorenh@math.aau.dk\"), person(given = \"Brenton M.\", family = \"Wiernik\", role = \"aut\", email = \"brenton@wiernik.org\", comment = c(ORCID = \"0000-0001-9560-6336\")), person(given = \"Zen J.\", family = \"Lau\", role = \"ctb\", email = \"zenjuen.lau@ntu.edu.sg\"), person(given = \"Vincent\", family = \"Arel-Bundock\", role = \"ctb\", email = \"vincent.arel-bundock@umontreal.ca\", comment = c(ORCID = \"0000-0003-2042-7063\")), person(given = \"Jeffrey\", family = \"Girard\", role = \"ctb\", email = \"me@jmgirard.com\", comment = c(ORCID = \"0000-0002-7359-3746\")), person(given = \"Christina\", family = \"Maimone\", role = \"rev\", email = \"christina.maimone@northwestern.edu\"), person(given = \"Niels\", family = \"Ohlsen\", role = \"rev\"), person(given = \"Douglas Ezra\", family = \"Morrison\", role = \"ctb\", email = \"dmorrison01@ucla.edu\", comment = c(ORCID = \"0000-0002-7195-830X\")), person(given = \"Joseph\", family = \"Luchman\", role = \"ctb\", email = \"jluchman@gmail.com\", comment = c(ORCID = \"0000-0002-8886-9717\")))", + "Maintainer": "Daniel Lüdecke ", + "Description": "Utilities for processing the parameters of various statistical models. 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It is updated periodically to reflect changes made by political bodies to time zone boundaries, UTC offsets, and daylight saving time rules. Additionally, this package provides a C++ interface for working with the 'date' library. 'date' provides comprehensive support for working with dates and date-times, which this package exposes to make it easier for other R packages to utilize. 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Dahl [aut], David Scott [aut, cre], Charles Roosen [aut], Arni Magnusson [aut], Jonathan Swinton [aut], Ajay Shah [ctb], Arne Henningsen [ctb], Benno Puetz [ctb], Bernhard Pfaff [ctb], Claudio Agostinelli [ctb], Claudius Loehnert [ctb], David Mitchell [ctb], David Whiting [ctb], Fernando da Rosa [ctb], Guido Gay [ctb], Guido Schulz [ctb], Ian Fellows [ctb], Jeff Laake [ctb], John Walker [ctb], Jun Yan [ctb], Liviu Andronic [ctb], Markus Loecher [ctb], Martin Gubri [ctb], Matthieu Stigler [ctb], Robert Castelo [ctb], Seth Falcon [ctb], Stefan Edwards [ctb], Sven Garbade [ctb], Uwe Ligges [ctb]" + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.10", + "Source": "Repository", + "Type": "Package", + "Title": "Methods to Convert R Data to YAML and Back", + "Date": "2024-07-22", + "Suggests": [ + "RUnit" + ], + "Author": "Shawn P Garbett [aut], Jeremy Stephens [aut, cre], Kirill Simonov [aut], Yihui Xie [ctb], Zhuoer Dong [ctb], Hadley Wickham [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb], Brendan O'Connor [ctb], Gregory R. Warnes [ctb], Michael Quinn [ctb], Zhian N. Kamvar [ctb], Charlie Gao [ctb]", + "Maintainer": "Shawn Garbett ", + "License": "BSD_3_clause + file LICENSE", + "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter () for R.", + "URL": "https://github.com/vubiostat/r-yaml/", + "BugReports": "https://github.com/vubiostat/r-yaml/issues", + "NeedsCompilation": "yes", + "Repository": "CRAN" + }, + "zip": { + "Package": "zip", + "Version": "2.3.2", + "Source": "Repository", + "Title": "Cross-Platform 'zip' Compression", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Kuba\", \"Podgórski\", role = \"ctb\"), person(\"Rich\", \"Geldreich\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Cross-Platform 'zip' Compression Library. A replacement for the 'zip' function, that does not require any additional external tools on any platform.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/r-lib/zip, https://r-lib.github.io/zip/", + "BugReports": "https://github.com/r-lib/zip/issues", + "Suggests": [ + "covr", + "pillar", + "processx", + "R6", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Gábor Csárdi [aut, cre], Kuba Podgórski [ctb], Rich Geldreich [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" + } + } +}
+ + + + + + + + + + + + +

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