diff --git a/CITATION.cff b/CITATION.cff index 2a3ec2e..7581c53 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -9,7 +9,7 @@ type: software license: AGPL-3.0-or-later title: 'FreesearchR: A free and open-source browser based data analysis tool for researchers with publication ready output' -version: 25.6.4 +version: 25.7.1 doi: 10.5281/zenodo.14527429 identifiers: - type: url diff --git a/DESCRIPTION b/DESCRIPTION index d602b0a..44cba0a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: FreesearchR Title: A free and open-source browser based data analysis tool for researchers with publication ready output -Version: 25.6.4 +Version: 25.7.1 Authors@R: c( person("Andreas Gammelgaard", "Damsbo",email="agdamsbo@clin.au.dk", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7559-1154")), diff --git a/NAMESPACE b/NAMESPACE index 34c6092..de51a14 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -17,6 +17,7 @@ export(clean_common_axis) export(clean_date) export(clean_sep) export(columnSelectInput) +export(compare_missings) export(contrast_text) export(create_baseline) export(create_column_server) diff --git a/NEWS.md b/NEWS.md index fd59113..6f2aee4 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# FreesearchR 25.7.1 - DEV + +- *NEW* UI overhaul and navigation update. The interface is simplified to clearly show the relationship between panels and sub-items by abandoning multiple levels on panel to instead show a drop-down menu. This also results in simplified sidebar menus with room to add more controls in the future. + # FreesearchR 25.6.4 The app is now also published as a docker container. See the README for instructions. It is mainly to use for hosting the app. Work is ongoing to publish a true standalone app, preferably for both Windows and MacOS. diff --git a/R/app_version.R b/R/app_version.R index 151c116..e3d7b11 100644 --- a/R/app_version.R +++ b/R/app_version.R @@ -1 +1 @@ -app_version <- function()'25.6.4' +app_version <- function()'25.7.1' diff --git a/R/hosted_version.R b/R/hosted_version.R index 17d0c52..46b5b94 100644 --- a/R/hosted_version.R +++ b/R/hosted_version.R @@ -1 +1 @@ -hosted_version <- function()'v25.6.4-250627' +hosted_version <- function()'v25.7.1-250703' diff --git a/R/sysdata.rda b/R/sysdata.rda index ff32e16..35ebcff 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/SESSION.md b/SESSION.md index efcc1d9..7fbbf44 100644 --- a/SESSION.md +++ b/SESSION.md @@ -11,11 +11,11 @@ |collate |en_US.UTF-8 | |ctype |en_US.UTF-8 | |tz |Europe/Copenhagen | -|date |2025-06-27 | +|date |2025-07-03 | |rstudio |2025.05.0+496 Mariposa Orchid (desktop) | |pandoc |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) | |quarto |1.7.30 @ /usr/local/bin/quarto | -|FreesearchR |25.6.4.250627 | +|FreesearchR |25.7.1.250703 | -------------------------------------------------------------------------------- @@ -52,6 +52,7 @@ |colorspace |2.1-1 |2024-07-26 |CRAN (R 4.4.1) | |commonmark |1.9.5 |2025-03-17 |CRAN (R 4.4.1) | |crayon |1.5.3 |2024-06-20 |CRAN (R 4.4.1) | +|crosstalk |1.2.1 |2023-11-23 |CRAN (R 4.4.0) | |data.table |1.17.0 |2025-02-22 |CRAN (R 4.4.1) | |datamods |1.5.3 |2024-10-02 |CRAN (R 4.4.1) | |datawizard |1.0.2 |2025-03-24 |CRAN (R 4.4.1) | @@ -65,6 +66,7 @@ |DT |0.33 |2024-04-04 |CRAN (R 4.4.0) | |e1071 |1.7-16 |2024-09-16 |CRAN (R 4.4.1) | |easystats |0.7.4 |2025-02-06 |CRAN (R 4.4.1) | +|effectsize |1.0.0 |2024-12-10 |CRAN (R 4.4.1) | |ellipsis |0.3.2 |2021-04-29 |CRAN (R 4.4.1) | |emmeans |1.11.1 |2025-05-04 |CRAN (R 4.4.1) | |esquisse |2.1.0 |2025-02-21 |CRAN (R 4.4.1) | @@ -82,7 +84,7 @@ |foreach |1.5.2 |2022-02-02 |CRAN (R 4.4.0) | |foreign |0.8-90 |2025-03-31 |CRAN (R 4.4.1) | |Formula |1.2-5 |2023-02-24 |CRAN (R 4.4.1) | -|FreesearchR |25.6.4 |NA |NA | +|FreesearchR |25.7.1 |NA |NA | |fs |1.6.6 |2025-04-12 |CRAN (R 4.4.1) | |gdtools |0.4.2 |2025-03-27 |CRAN (R 4.4.1) | |generics |0.1.3 |2022-07-05 |CRAN (R 4.4.1) | @@ -114,15 +116,19 @@ |keyring |1.3.2 |2023-12-11 |CRAN (R 4.4.0) | |knitr |1.50 |2025-03-16 |CRAN (R 4.4.1) | |labeling |0.4.3 |2023-08-29 |CRAN (R 4.4.1) | +|labelled |2.14.0 |2025-01-08 |CRAN (R 4.4.1) | |later |1.4.2 |2025-04-08 |CRAN (R 4.4.1) | |lattice |0.22-7 |2025-04-02 |CRAN (R 4.4.1) | |lifecycle |1.0.4 |2023-11-07 |CRAN (R 4.4.1) | +|litedown |0.7 |2025-04-08 |CRAN (R 4.4.1) | |lme4 |1.1-37 |2025-03-26 |CRAN (R 4.4.1) | |lubridate |1.9.4 |2024-12-08 |CRAN (R 4.4.1) | |magrittr |2.0.3 |2022-03-30 |CRAN (R 4.4.1) | +|markdown |2.0 |2025-03-23 |CRAN (R 4.4.1) | |MASS |7.3-65 |2025-02-28 |CRAN (R 4.4.1) | |Matrix |1.7-3 |2025-03-11 |CRAN (R 4.4.1) | |memoise |2.0.1 |2021-11-26 |CRAN (R 4.4.0) | +|mgcv |1.9-3 |2025-04-04 |CRAN (R 4.4.1) | |mime |0.13 |2025-03-17 |CRAN (R 4.4.1) | |miniUI |0.1.2 |2025-04-17 |CRAN (R 4.4.1) | |minqa |1.2.8 |2024-08-17 |CRAN (R 4.4.1) | @@ -213,11 +219,8 @@ |tzdb |0.5.0 |2025-03-15 |CRAN (R 4.4.1) | |urlchecker |1.0.1 |2021-11-30 |CRAN (R 4.4.1) | |usethis |3.1.0 |2024-11-26 |CRAN (R 4.4.1) | -|utf8 |1.2.4 |2023-10-22 |CRAN (R 4.4.1) | |uuid |1.2-1 |2024-07-29 |CRAN (R 4.4.1) | |vctrs |0.6.5 |2023-12-01 |CRAN (R 4.4.0) | -|viridis |0.6.5 |2024-01-29 |CRAN (R 4.4.0) | -|viridisLite |0.4.2 |2023-05-02 |CRAN (R 4.4.1) | |vroom |1.6.5 |2023-12-05 |CRAN (R 4.4.0) | |withr |3.0.2 |2024-10-28 |CRAN (R 4.4.1) | |writexl |1.5.4 |2025-04-15 |CRAN (R 4.4.1) | diff --git a/app_docker/app.R b/app_docker/app.R index db2ebed..b3b5a1b 100644 --- a/app_docker/app.R +++ b/app_docker/app.R @@ -5,7 +5,7 @@ ######## library(shiny) -# library(shinyjs) +library(shinyjs) # library(methods) # library(readr) # library(MASS) @@ -49,7 +49,7 @@ library(rlang) #### Current file: /Users/au301842/FreesearchR/R//app_version.R ######## -app_version <- function()'25.6.3' +app_version <- function()'25.7.1' ######## @@ -1611,97 +1611,96 @@ plot_histogram <- function(data, column=NULL, bins = 30, breaks = NULL, color = 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$br(), - shiny::uiOutput(outputId = ns("type")), - shiny::uiOutput(outputId = ns("secondary")), - shiny::uiOutput(outputId = ns("tertiary")), - shiny::br(), - shiny::actionButton( - inputId = ns("act_plot"), - label = "Plot", - width = "100%", - icon = shiny::icon("palette"), - disabled = FALSE + bslib::layout_sidebar( + sidebar = bslib::sidebar( + bslib::accordion( + multiple = FALSE, + bslib::accordion_panel( + title = "Creating plot", + icon = bsicons::bs_icon("graph-up"), + shiny::uiOutput(outputId = ns("primary")), + shiny::helpText('Only non-text variables are available for plotting. Go the "Data" to reclass data to plot.'), + shiny::tags$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".') ), - 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" + 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") ) - ), - shiny::br(), - # Button - shiny::downloadButton( - outputId = ns("download_plot"), - label = "Download plot", - icon = shiny::icon("download") ) - ) - ) - ), - bslib::nav_panel( - title = tab_title, + ), + shiny::p("We have collected a few notes on visualising data and details on the options included in FreesearchR:", shiny::tags$a( + href = "https://agdamsbo.github.io/FreesearchR/articles/visuals.html", + "View notes in new tab", + target = "_blank", + rel = "noopener noreferrer" + )) + ), shiny::plotOutput(ns("plot"), height = "70vh"), shiny::tags$br(), shiny::tags$br(), shiny::htmlOutput(outputId = ns("code_plot")) ) ) + # ) } @@ -1937,7 +1936,14 @@ data_visuals_server <- function(id, ) shiny::withProgress(message = "Drawing the plot. Hold tight for a moment..", { - rv$plot <- rlang::exec(create_plot, !!!append_list(data(), parameters, "data")) + rv$plot <- rlang::exec( + create_plot, + !!!append_list( + data(), + parameters, + "data" + ) + ) }) rv$code <- glue::glue("FreesearchR::create_plot(df,{list2str(parameters)})") @@ -1993,13 +1999,12 @@ data_visuals_server <- function(id, paste0("plot.", input$plot_type) }), content = function(file) { - if (inherits(rv$plot,"patchwork")){ + if (inherits(rv$plot, "patchwork")) { plot <- rv$plot - } else if (inherits(rv$plot,"ggplot")){ + } else if (inherits(rv$plot, "ggplot")) { plot <- rv$plot - }else { + } else { plot <- rv$plot[[1]] - } # browser() shiny::withProgress(message = "Drawing the plot. Hold on for a moment..", { @@ -2259,12 +2264,12 @@ create_plot <- function(data, type, pri, sec, ter = NULL, ...) { out <- do.call( type, - modifyList(parameters,list(data=data)) + modifyList(parameters, list(data = data)) ) - code <- rlang::call2(type,!!!parameters,.ns = "FreesearchR") + code <- rlang::call2(type, !!!parameters, .ns = "FreesearchR") - attr(out,"code") <- code + attr(out, "code") <- code out } @@ -2319,6 +2324,7 @@ get_label <- function(data, var = NULL) { #' paste(sample(letters[1:10], 100, TRUE), collapse = "") |> line_break(force = TRUE) line_break <- function(data, lineLength = 20, force = FALSE) { if (isTRUE(force)) { + ## This eats some letters when splitting a sentence... ?? gsub(paste0("(.{1,", lineLength, "})(\\s|[[:alnum:]])"), "\\1\n", data) } else { paste(strwrap(data, lineLength), collapse = "\n") @@ -2331,11 +2337,17 @@ line_break <- function(data, lineLength = 20, force = FALSE) { #' #' @param data list of ggplot2 objects #' @param tag_levels passed to patchwork::plot_annotation if given. Default is NULL +#' @param title panel title +#' @param ... ignored for argument overflow #' #' @returns list of ggplot2 objects #' @export #' -wrap_plot_list <- function(data, tag_levels = NULL) { +wrap_plot_list <- function(data, + tag_levels = NULL, + title = NULL, + axis.font.family = NULL, + ...) { if (ggplot2::is_ggplot(data[[1]])) { if (length(data) > 1) { out <- data |> @@ -2349,17 +2361,35 @@ wrap_plot_list <- function(data, tag_levels = NULL) { } })() |> align_axes() |> - patchwork::wrap_plots(guides = "collect", axes = "collect", axis_titles = "collect") + patchwork::wrap_plots( + guides = "collect", + axes = "collect", + axis_titles = "collect" + ) if (!is.null(tag_levels)) { out <- out + patchwork::plot_annotation(tag_levels = tag_levels) } + if (!is.null(title)) { + out <- out + + patchwork::plot_annotation( + title = title, + theme = ggplot2::theme(plot.title = ggplot2::element_text(size = 25)) + ) + } } else { - out <- data + out <- data[[1]] } } else { cli::cli_abort("Can only wrap lists of {.cls ggplot} objects") } - out + + if (inherits(x = out, what = "patchwork")) { + out & + ggplot2::theme(axis.text = ggplot2::element_text(family = axis.font.family)) + } else { + out + + ggplot2::theme(axis.text = ggplot2::element_text(family = axis.font.family)) + } } @@ -3996,7 +4026,7 @@ simple_snake <- function(data){ #### Current file: /Users/au301842/FreesearchR/R//hosted_version.R ######## -hosted_version <- function()'v25.6.3-250626' +hosted_version <- function()'v25.7.1-250703' ######## @@ -4705,14 +4735,7 @@ data_missings_server <- function(id, 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) - } + out <- compare_missings(df_tbl,by_var) }, error = function(err) { showNotification(paste0("Error: ", err), type = "err") @@ -4790,13 +4813,25 @@ missing_demo_app <- function() { missing_demo_app() +#' Pairwise comparison of missings across covariables +#' +#' @param data data frame +#' @param by_var variable to stratify by missingness +#' +#' @returns gtsummary list object +#' @export +#' +compare_missings <- function(data,by_var){ + if (!is.null(by_var) && by_var != "" && by_var %in% names(data)) { + data[[by_var]] <- ifelse(is.na(data[[by_var]]), "Missing", "Non-missing") - - - - - - + out <- gtsummary::tbl_summary(data, by = by_var) |> + gtsummary::add_p() + } else { + out <- gtsummary::tbl_summary(data) + } + out +} ######## @@ -4805,17 +4840,27 @@ missing_demo_app() #' Beautiful box plot(s) #' +#' @param data data frame +#' @param pri primary variable +#' @param sec secondary variable +#' @param ter tertiary variable +#' @param ... passed on to wrap_plot_list +#' #' @returns ggplot2 object #' @export #' #' @name data-plots #' #' @examples -#' mtcars |> plot_box(pri = "mpg", sec = "cyl", ter = "gear") +#' mtcars |> plot_box(pri = "mpg", sec = "gear") +#' mtcars |> plot_box(pri = "mpg", sec="cyl") #' mtcars |> #' default_parsing() |> #' plot_box(pri = "mpg", sec = "cyl", ter = "gear") -plot_box <- function(data, pri, sec, ter = NULL) { +#' mtcars |> +#' default_parsing() |> +#' plot_box(pri = "mpg", sec = "cyl", ter = "gear",axis.font.family="mono") +plot_box <- function(data, pri, sec, ter = NULL,...) { if (!is.null(ter)) { ds <- split(data, data[ter]) } else { @@ -4830,7 +4875,7 @@ plot_box <- function(data, pri, sec, ter = NULL) { ) }) - wrap_plot_list(out) + wrap_plot_list(out,title=glue::glue("Grouped by {get_label(data,ter)}"),...) } @@ -4846,6 +4891,7 @@ plot_box <- function(data, pri, sec, ter = NULL) { #' @examples #' mtcars |> plot_box_single("mpg") #' mtcars |> plot_box_single("mpg","cyl") +#' gtsummary::trial |> plot_box_single("age","trt") plot_box_single <- function(data, pri, sec=NULL, seed = 2103) { set.seed(seed) @@ -4861,6 +4907,8 @@ plot_box_single <- function(data, pri, sec=NULL, seed = 2103) { 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::xlab(get_label(data,pri))+ + ggplot2::ylab(get_label(data,sec)) + ggplot2::coord_flip() + viridis::scale_fill_viridis(discrete = discrete, option = "D") + # ggplot2::theme_void() + @@ -4983,7 +5031,7 @@ plot_euler <- function(data, pri, sec, ter = NULL, seed = 2103) { }) # names(out) - wrap_plot_list(out) + wrap_plot_list(out,title=glue::glue("Grouped by {get_label(data,ter)}")) # patchwork::wrap_plots(out, guides = "collect") } @@ -5458,7 +5506,7 @@ plot_violin <- function(data, pri, sec, ter = NULL) { ) }) - wrap_plot_list(out) + wrap_plot_list(out,title=glue::glue("Grouped by {get_label(data,ter)}")) # patchwork::wrap_plots(out,guides = "collect") } @@ -7372,155 +7420,173 @@ 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"), + # title = "", + bslib::nav_panel( + title = "Regression table", + bslib::layout_sidebar( + 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::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", + shiny::radioButtons( + inputId = ns("add_regression_p"), + label = "Show p-value", + inline = TRUE, + selected = "yes", choices = list( - "png", - "tiff", - "eps", - "pdf", - "jpeg", - "svg" + "Yes" = "yes", + "No" = "no" ) ), - shiny::br(), - # Button - shiny::downloadButton( - outputId = ns("download_plot"), - label = "Download plot", - icon = shiny::icon("download") + # 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() + ) + ) + ), + gt::gt_output(outputId = ns("table2")) + ) + ), + bslib::nav_panel( + title = "Coefficient plot", + bslib::layout_sidebar( + sidebar = bslib::sidebar( + bslib::accordion( + open = "acc_reg", + multiple = FALSE, + 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")) - ) + shiny::plotOutput(outputId = ns("regression_plot"), height = "80vh") ) ), - 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") + bslib::layout_sidebar( + sidebar = bslib::sidebar( + bslib::accordion( + open = "acc_reg", + multiple = FALSE, + bslib::accordion_panel( + value = "acc_checks", + title = "Checks", + icon = bsicons::bs_icon("clipboard-check"), + shiny::uiOutput(outputId = ns("plot_checks")) + ) + ) + ), + shiny::plotOutput(outputId = ns("check"), height = "90vh") + ) ) ) } @@ -9831,6 +9897,8 @@ ui_elements <- list( ############################################################################## "home" = bslib::nav_panel( title = "FreesearchR", + # title = shiny::div(htmltools::img(src="FreesearchR-logo-white-nobg-h80.png")), + icon = shiny::icon("house"), shiny::fluidRow( ## On building the dev-version for shinyapps.io, the dev_banner() is redefined ## Default just output "NULL" @@ -9842,8 +9910,7 @@ ui_elements <- list( shiny::markdown(readLines("www/intro.md")), shiny::column(width = 2) ) - ), - icon = shiny::icon("home") + ) ), ############################################################################## ######### @@ -9851,7 +9918,8 @@ ui_elements <- list( ######### ############################################################################## "import" = bslib::nav_panel( - title = "Import", + title = "Get started", + icon = shiny::icon("upload"), shiny::fluidRow( shiny::column(width = 2), shiny::column( @@ -9907,13 +9975,13 @@ ui_elements <- list( 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::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"), @@ -9969,272 +10037,273 @@ ui_elements <- list( ######### Data overview panel ######### ############################################################################## - "overview" = - # bslib::nav_panel_hidden( + "prepare" = bslib::nav_menu( + title = "Prepare", + icon = shiny::icon("pen-to-square"), 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$p("Filter on observation level"), - IDEAFilter::IDEAFilter_ui("data_filter"), - shiny::br(), - shiny::br() - ) + title = "Overview", + icon = shiny::icon("eye"), + value = "nav_prepare_overview", + tags$h3("Overview and filtering"), + fluidRow( + shiny::column( + width = 9, + shiny::uiOutput(outputId = "data_info", inline = TRUE), + shiny::tags$p( + "Below is a short summary table, on the right you can click to visualise data classes or browse data and create different data filters." + ) + ), + shiny::column( + width = 3, + shiny::actionButton( + inputId = "modal_visual_overview", + label = "Visual overview", + width = "100%", + disabled = TRUE ), shiny::br(), shiny::br(), - # shiny::br(), - # shiny::br(), + shiny::actionButton( + inputId = "modal_browse", + label = "Browse data", + width = "100%", + disabled = TRUE + ), + shiny::br(), + shiny::br() + ) + ), + fluidRow( + shiny::column( + width = 9, + data_summary_ui(id = "data_summary"), + shiny::br(), + shiny::br(), + shiny::br(), + shiny::br(), shiny::br() ), - bslib::nav_panel( - title = "Modify", - tags$h3("Subset, rename and convert variables"), - fluidRow( - shiny::column( - width = 9, - shiny::tags$p( - shiny::markdown("Below, are several options for simple data manipulation like update variables by renaming, creating new labels (for nicer tables in the report) and changing variable classes (numeric, factor/categorical etc.)."), - shiny::markdown("There are more advanced options to modify factor/categorical variables as well as create new factor from a continous variable or new variables with *R* code. At the bottom you can restore the original data."), - shiny::markdown("Please note that data modifications are applied before any filtering.") - ) - ) + shiny::column( + width = 3, + shiny::tags$h6("Filter data types"), + shiny::uiOutput( + outputId = "column_filter" ), - # 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::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$p("Filter on observation level"), + IDEAFilter::IDEAFilter_ui("data_filter"), + shiny::br(), + shiny::br() + ) + ), + shiny::br(), + shiny::br(), + shiny::br() + ), + bslib::nav_panel( + title = "Modify", + icon = shiny::icon("file-pen"), + tags$h3("Subset, rename and convert variables"), + fluidRow( + shiny::column( + width = 9, 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$br(), + shiny::markdown("Below, are several options for simple data manipulation like update variables by renaming, creating new labels (for nicer tables in the report) and changing variable classes (numeric, factor/categorical etc.)."), + shiny::markdown("There are more advanced options to modify factor/categorical variables as well as create new factor from a continous variable or new variables with *R* code. At the bottom you can restore the original data."), + shiny::markdown("Please note that data modifications are applied before any filtering.") + ) + ) + ), + update_variables_ui("modal_variables"), + shiny::tags$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$br(), + shiny::fluidRow( + shiny::column( + width = 4, shiny::actionButton( - inputId = "data_reset", - label = "Restore original data", + inputId = "modal_update", + label = "Reorder factor levels", width = "100%" ), shiny::tags$br(), - shiny::helpText("Reset to original imported dataset. Careful! There is no un-doing."), + 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$b("Original data:"), + shiny::verbatimTextOutput("original_str") + ), + shiny::column( + width = 6, + shiny::tags$b("Modified data:"), + 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( + bslib::nav_menu( 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" - ) + icon = shiny::icon("magnifying-glass-chart"), + # id = "navdescribe", + # bslib::navset_bar( + # title = "", + bslib::nav_panel( + title = "Characteristics", + icon = bsicons::bs_icon("table"), + bslib::layout_sidebar( + sidebar = bslib::sidebar( + shiny::uiOutput(outputId = "data_info_nochar", inline = TRUE), + bslib::accordion( + open = "acc_chars", + multiple = FALSE, + bslib::accordion_panel( + open = TRUE, + value = "acc_chars", + title = "Settings", + icon = bsicons::bs_icon("table"), + shiny::uiOutput("strat_var"), + shiny::helpText("Only factor/categorical variables are available for stratification. Go back to the 'Prepare' 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::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 + 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", + ) + ), + bslib::nav_panel( + title = "Correlations", + icon = bsicons::bs_icon("bounding-box"), + bslib::layout_sidebar( + sidebar = bslib::sidebar( + shiny::uiOutput(outputId = "data_info_nochar", inline = TRUE), + bslib::accordion( + open = "acc_chars", + multiple = FALSE, + bslib::accordion_panel( + value = "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'.") + ) + ) + ), data_correlations_ui(id = "correlations", height = 600) - ), - bslib::nav_panel( - title = "Missings", + ) + ), + bslib::nav_panel( + title = "Missings", + icon = bsicons::bs_icon("x-circle"), + bslib::layout_sidebar( + sidebar = bslib::sidebar( + bslib::accordion( + open = "acc_chars", + multiple = FALSE, + bslib::accordion_panel( + vlaue = "acc_mis", + title = "Missings", + icon = bsicons::bs_icon("x-circle"), + shiny::uiOutput("missings_var"), + shiny::helpText("To consider if data 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.") + ) + ) + ), data_missings_ui(id = "missingness") ) ) @@ -10244,27 +10313,23 @@ ui_elements <- list( ######### 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" - ) - ) - ) - ) + "visuals" = do.call( + bslib::nav_panel, + c( + list( + title = "Visuals", + icon = shiny::icon("chart-line"), + id = "navvisuals" + ), + data_visuals_ui("visuals") ) + # do.call( + # bslib::navset_bar, + # data_visuals_ui("visuals")#, + # c( + + # ) + # ) ), ############################################################################## ######### @@ -10274,9 +10339,10 @@ ui_elements <- list( "analyze" = bslib::nav_panel( title = "Regression", + icon = shiny::icon("calculator"), id = "navanalyses", do.call( - bslib::navset_bar, + bslib::navset_card_tab, regression_ui("regression") ) ), @@ -10288,6 +10354,7 @@ ui_elements <- list( "download" = bslib::nav_panel( title = "Download", + icon = shiny::icon("download"), id = "navdownload", shiny::fluidRow( shiny::column(width = 2), @@ -10413,9 +10480,25 @@ dark <- custom_theme( # https://webdesignerdepot.com/17-open-source-fonts-youll-actually-love/ ui <- bslib::page_fixed( + ## Code formatting dependencies prismDependencies, prismRDependency, + ## Version dependent header header_include(), + ## Automatically close drop-downs on navigation + ## Thanks to claude.ai + tags$script(" + $(document).on('shown.bs.tab', '#main_panel', function(e) { + // Close dropdown in this specific navset only + $('#main_panel .dropdown-menu').removeClass('show'); + $('#main_panel .dropdown-toggle').removeClass('show').attr('aria-expanded', 'false'); + + // THE BELOW DOES NOT WORK + // Close navbar collapse (burger menu) + $('#main_panel .navbar-collapse collapse').removeClass('show'); + $('#main_panel .navbar-toggle').removeClass('collapsed').attr('aria-expanded', 'false'); + }); + "), ## This adds the actual favicon ## png and ico versions are kept for compatibility shiny::tags$head(tags$link(rel = "shortcut icon", href = "favicon.svg")), @@ -10435,14 +10518,14 @@ ui <- bslib::page_fixed( id = "main_panel", ui_elements$home, ui_elements$import, - ui_elements$overview, + ui_elements$prepare, ui_elements$describe, ui_elements$visuals, ui_elements$analyze, ui_elements$download, bslib::nav_spacer(), - ui_elements$feedback, - ui_elements$docs, + # ui_elements$feedback, + # ui_elements$docs, fillable = FALSE, footer = shiny::tags$footer( style = "background-color: #14131326; padding: 4px; text-align: center; bottom: 0; width: 100%;", @@ -10452,7 +10535,7 @@ ui <- bslib::page_fixed( ), 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") + shiny::tags$a("Documentation", href = "https://agdamsbo.github.io/FreesearchR/", target = "_blank", rel = "noopener noreferrer"), " | ", hosted_version(), " | ", shiny::tags$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") ), ) ) @@ -11164,7 +11247,7 @@ server <- function(input, output, session) { ############################################################################## shiny::observeEvent(input$act_start, { - bslib::nav_select(id = "main_panel", selected = "Data") + bslib::nav_select(id = "main_panel", selected = "nav_prepare_overview") }) ############################################################################## diff --git a/app_docker/www/FreesearchR-logo-black-nobg.png b/app_docker/www/FreesearchR-logo-black-nobg.png new file mode 100644 index 0000000..2b92707 Binary files /dev/null and b/app_docker/www/FreesearchR-logo-black-nobg.png differ diff --git a/app_docker/www/FreesearchR-logo-blue-nobg.png b/app_docker/www/FreesearchR-logo-blue-nobg.png new file mode 100644 index 0000000..0a0e572 Binary files /dev/null and b/app_docker/www/FreesearchR-logo-blue-nobg.png differ diff --git a/app_docker/www/FreesearchR-logo-white-nobg-h80.png b/app_docker/www/FreesearchR-logo-white-nobg-h80.png new file mode 100644 index 0000000..2423010 Binary files /dev/null and b/app_docker/www/FreesearchR-logo-white-nobg-h80.png differ diff --git a/app_docker/www/FreesearchR-logo-white-nobg.png b/app_docker/www/FreesearchR-logo-white-nobg.png new file mode 100644 index 0000000..d9a6883 Binary files /dev/null and b/app_docker/www/FreesearchR-logo-white-nobg.png differ diff --git a/inst/apps/FreesearchR/www/FreesearchR-logo-black-nobg.png b/inst/apps/FreesearchR/www/FreesearchR-logo-black-nobg.png new file mode 100644 index 0000000..2b92707 Binary files /dev/null and b/inst/apps/FreesearchR/www/FreesearchR-logo-black-nobg.png differ diff --git a/inst/apps/FreesearchR/www/FreesearchR-logo-blue-nobg.png b/inst/apps/FreesearchR/www/FreesearchR-logo-blue-nobg.png new file mode 100644 index 0000000..0a0e572 Binary files /dev/null and b/inst/apps/FreesearchR/www/FreesearchR-logo-blue-nobg.png differ diff --git a/inst/apps/FreesearchR/www/FreesearchR-logo-white-nobg-h80.png b/inst/apps/FreesearchR/www/FreesearchR-logo-white-nobg-h80.png new file mode 100644 index 0000000..2423010 Binary files /dev/null and b/inst/apps/FreesearchR/www/FreesearchR-logo-white-nobg-h80.png differ diff --git a/inst/apps/FreesearchR/www/FreesearchR-logo-white-nobg.png b/inst/apps/FreesearchR/www/FreesearchR-logo-white-nobg.png new file mode 100644 index 0000000..d9a6883 Binary files /dev/null and b/inst/apps/FreesearchR/www/FreesearchR-logo-white-nobg.png differ diff --git a/man/compare_missings.Rd b/man/compare_missings.Rd new file mode 100644 index 0000000..8950200 --- /dev/null +++ b/man/compare_missings.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/missings-module.R +\name{compare_missings} +\alias{compare_missings} +\title{Pairwise comparison of missings across covariables} +\usage{ +compare_missings(data, by_var) +} +\arguments{ +\item{data}{data frame} + +\item{by_var}{variable to stratify by missingness} +} +\value{ +gtsummary list object +} +\description{ +Pairwise comparison of missings across covariables +}