From 39c948e12cda33375556ea1cb6ac379045069939 Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Mon, 28 Apr 2025 08:31:23 +0200 Subject: [PATCH] updated docs --- DESCRIPTION | 4 +- R/app_version.R | 2 +- R/create-column-mod.R | 2 +- R/datagrid-infos-mod.R | 5 - R/plot_box.R | 2 +- R/sysdata.rda | Bin 2097 -> 1208 bytes README.md | 6 +- SESSION.md | 236 ++++++------------ inst/apps/FreesearchR/app.R | 11 +- .../shinyapps.io/agdamsbo/FreesearchR.dcf | 2 +- man/create-column.Rd | 71 ++++++ man/custom_theme.Rd | 10 +- 12 files changed, 166 insertions(+), 185 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index b3a0612..24d87ee 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,10 +1,10 @@ Package: FreesearchR -Title: Browser Based Data Analysis +Title: Clinical Health Data Analysis Version: 25.4.3 Authors@R: person("Andreas Gammelgaard", "Damsbo", , "agdamsbo@clin.au.dk", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7559-1154")) -Description: Free and open source browser based data exploration and analysis with publication ready output. +Description: Free and open source browser based clinical health data exploration and analysis with publication ready output. License: AGPL (>= 3) Encoding: UTF-8 Roxygen: list(markdown = TRUE) diff --git a/R/app_version.R b/R/app_version.R index c99b806..1ff412a 100644 --- a/R/app_version.R +++ b/R/app_version.R @@ -1 +1 @@ -app_version <- function()'v25.4.3.250424' +app_version <- function()'v25.4.3.250428' diff --git a/R/create-column-mod.R b/R/create-column-mod.R index f25dbdd..9bb71c4 100644 --- a/R/create-column-mod.R +++ b/R/create-column-mod.R @@ -23,7 +23,7 @@ #' #' @name create-column #' -#' @example example/create_column_module_demo.R +#' @example examples/create_column_module_demo.R create_column_ui <- function(id) { ns <- NS(id) tagList( diff --git a/R/datagrid-infos-mod.R b/R/datagrid-infos-mod.R index 6958e6b..1a250d7 100644 --- a/R/datagrid-infos-mod.R +++ b/R/datagrid-infos-mod.R @@ -16,11 +16,6 @@ #' @return No value. #' @export #' -#' @importFrom htmltools tags tagList css -#' @importFrom shiny showModal modalDialog -#' @importFrom utils modifyList packageVersion -#' -#' @example examples/show_data.R show_data <- function(data, title = NULL, options = NULL, diff --git a/R/plot_box.R b/R/plot_box.R index d0165dd..b516bc3 100644 --- a/R/plot_box.R +++ b/R/plot_box.R @@ -55,7 +55,7 @@ plot_box_single <- function(data, pri, sec=NULL, seed = 2103) { 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 = .5) + + 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() + diff --git a/R/sysdata.rda b/R/sysdata.rda index 51dd6d0980b3ba31b0d5d615ddd3926f286af25c..c5013e2e719fc3d12af52c4ce019d44a294ca3b1 100644 GIT binary patch literal 1208 zcmV;p1V{TqT4*^jL0KkKS+5xFtpErj|HS|QXaz!V|KM*aoCdWzzLu*i6TuQ zJk<=14^RLA00ThK00vAYoQc9H*i4NS-t?m8fFN)EZdpaOh-dI<-05^Pj<9QQX5Zd4 z3Aq%`D~W*N#Q*JDd!i*sPvdXF&v6VBlNH%&Rqdv$Lepv-s7|)5I$q=CXs7 zOxbPfz4^d);0o#m0E&W0FeD@(fP{#Z1yw%qMcareZcL+J=7REl$JY+nJZOq?`CWY; z%rV^IK^IP)dJTCZk}#4CibxVd6Rf9U8vq28v`LwT5ym2zCF~;QLrMjln5tko0W^^+ zCRo_kS4k!{+Q_q%+ir9fZwL`hx*SMx3UX+yPzMqlmF{>)kxC}9YXh9&fU>Y+OgR>2 z-G&%MpytR%X)8fR$eCgULaS8-x@PHA%?eamNd`r}5Y#`slh)|CtJquw}?f-FJWf|Z!4$QbQjim(G~6>AW*iDNO0SXD5LBP6Q!z{GAr z2uTw~Qpt%+!OyKBB)KSsUl4_;sO5-Z=t13p?!-%%V;K;U5=2hEdptNg_8GC&)kbzK z0}T>FLQJbWX#+fQ#@ODkYqAmyk|czXZVJ>f5oS9yVG^+*kP3kT34tNxEhvBn9M0<6W4r^s{A?dg-B|m zz6>p2*45DzOpIy93M4OR0A*vIAJe)+1Vw;1n8eI)l*PgJgfk~B5l~S|mY0yi%=5e~ z8Tu>Dj}_6Q7M|xq)-I>v$gss(rHIi)6&mw6S(*5mLZ4KUB3ZZi!TCP1@T-N>N0o1>1wSs%RH#vea{Y8QUfIn890ZOVRqRGw?R5CO?oX0yVa>wxa74{XMFZ%Y;@S$ WH;us6+_`YM{}*yaI8czU811dYtS0-4FCWDWB>pFGyo*hNQ8-+n1-5YWCy4K0004?00GS! 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All feedback is welcome and can be shared as a GitHub issue. Any suggestions on collaboration is much welcomed. Please reach out! +[***FreesearchR***](https://agdamsbo.shinyapps.io/FreesearchR/) is free and open-source, and is directly accessible here: [link to the app freely hosted on shinyapps.io](https://agdamsbo.shinyapps.io/FreesearchR/). The app can also run locally, please see below. + +All feedback is welcome and can be shared as a GitHub issue. Any suggestions on collaboration is much welcomed. Please reach out! ## Motivation diff --git a/SESSION.md b/SESSION.md index 8620ab6..02a62e5 100644 --- a/SESSION.md +++ b/SESSION.md @@ -1,169 +1,83 @@ -------------------------------------------------------------------------------- -------------------------------- R environment --------------------------------- -------------------------------------------------------------------------------- -|setting |value | -|:-----------|:------------------------------------------| -|version |R version 4.4.1 (2024-06-14) | -|os |macOS 15.3.1 | -|system |aarch64, darwin20 | -|ui |RStudio | -|language |(EN) | -|collate |en_US.UTF-8 | -|ctype |en_US.UTF-8 | -|tz |Europe/Copenhagen | -|date |2025-04-24 | -|rstudio |2024.12.1+563 Kousa Dogwood (desktop) | -|pandoc |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) | -|quarto |1.6.40 @ /usr/local/bin/quarto | -|FreesearchR |25.4.3.250424 | +|setting |value | +|:-----------|:-------------------------------------| +|version |R version 4.4.1 (2024-06-14) | +|os |macOS 15.3.1 | +|system |aarch64, darwin20 | +|ui |RStudio | +|language |(EN) | +|collate |en_US.UTF-8 | +|ctype |en_US.UTF-8 | +|tz |Europe/Copenhagen | +|date |2025-04-28 | +|rstudio |2024.12.1+563 Kousa Dogwood (desktop) | +|pandoc |3.6.4 @ /opt/homebrew/bin/pandoc | +|quarto |1.6.40 @ /usr/local/bin/quarto | +|FreesearchR |25.4.3.250428 | -------------------------------------------------------------------------------- ----------------------------------- packages ----------------------------------- -------------------------------------------------------------------------------- -|package |loadedversion |date |source | -|:-------------|:-------------|:----------|:--------------| -|apexcharter |0.4.4 |2024-09-06 |CRAN (R 4.4.1) | -|askpass |1.2.1 |2024-10-04 |CRAN (R 4.4.1) | -|assertthat |0.2.1 |2019-03-21 |CRAN (R 4.4.1) | -|backports |1.5.0 |2024-05-23 |CRAN (R 4.4.1) | -|bayestestR |0.15.2 |2025-02-07 |CRAN (R 4.4.1) | -|bit |4.6.0 |2025-03-06 |CRAN (R 4.4.1) | -|bit64 |4.6.0-1 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| -|purrr |1.0.4 |2025-02-05 |CRAN (R 4.4.1) | -|quarto |1.4.4 |2024-07-20 |CRAN (R 4.4.0) | -|R.cache |0.16.0 |2022-07-21 |CRAN (R 4.4.0) | -|R.methodsS3 |1.8.2 |2022-06-13 |CRAN (R 4.4.1) | -|R.oo |1.27.0 |2024-11-01 |CRAN (R 4.4.1) | -|R.utils |2.13.0 |2025-02-24 |CRAN (R 4.4.1) | -|R6 |2.6.1 |2025-02-15 |CRAN (R 4.4.1) | -|rbibutils |2.3 |2024-10-04 |CRAN (R 4.4.1) | -|RColorBrewer |1.1-3 |2022-04-03 |CRAN (R 4.4.1) | -|Rcpp |1.0.14 |2025-01-12 |CRAN (R 4.4.1) | -|Rdpack |2.6.4 |2025-04-09 |CRAN (R 4.4.1) | -|reactable |0.4.4 |2023-03-12 |CRAN (R 4.4.0) | -|readODS |2.3.2 |2025-01-13 |CRAN (R 4.4.1) | -|readr |2.1.5 |2024-01-10 |CRAN (R 4.4.0) | -|readxl |1.4.5 |2025-03-07 |CRAN (R 4.4.1) | -|REDCapCAST |25.3.2 |2025-03-10 |CRAN (R 4.4.1) | -|REDCapR |1.4.0 |2025-01-11 |CRAN (R 4.4.1) | -|reformulas |0.4.0 |2024-11-03 |CRAN (R 4.4.1) | -|remotes |2.5.0 |2024-03-17 |CRAN (R 4.4.1) | -|renv |1.1.4 |2025-03-20 |CRAN (R 4.4.1) | -|report |0.6.1 |2025-02-07 |CRAN (R 4.4.1) | -|rio |1.2.3 |2024-09-25 |CRAN (R 4.4.1) | -|rlang |1.1.6 |2025-04-11 |CRAN (R 4.4.1) | -|rmarkdown |2.29 |2024-11-04 |CRAN (R 4.4.1) | -|rprojroot |2.0.4 |2023-11-05 |CRAN (R 4.4.1) | -|rsconnect |1.3.4 |2025-01-22 |CRAN (R 4.4.1) | -|rstudioapi |0.17.1 |2024-10-22 |CRAN (R 4.4.1) | -|sass |0.4.10 |2025-04-11 |CRAN (R 4.4.1) | -|scales |1.3.0 |2023-11-28 |CRAN (R 4.4.0) | -|see |0.11.0 |2025-03-11 |CRAN (R 4.4.1) | -|sessioninfo |1.2.3 |2025-02-05 |CRAN (R 4.4.1) | -|shiny |1.10.0 |2024-12-14 |CRAN (R 4.4.1) | -|shinybusy |0.3.3 |2024-03-09 |CRAN (R 4.4.0) | -|shinyTime |1.0.3 |2022-08-19 |CRAN (R 4.4.0) | -|shinyWidgets |0.9.0 |2025-02-21 |CRAN (R 4.4.1) | -|stringi |1.8.7 |2025-03-27 |CRAN (R 4.4.1) | -|styler |1.10.3 |2024-04-07 |CRAN (R 4.4.0) | -|tibble |3.2.1 |2023-03-20 |CRAN (R 4.4.0) | -|tidyr |1.3.1 |2024-01-24 |CRAN (R 4.4.1) | -|tidyselect |1.2.1 |2024-03-11 |CRAN (R 4.4.0) | -|toastui |0.4.0 |2025-04-03 |CRAN (R 4.4.1) | -|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) | -|vctrs |0.6.5 |2023-12-01 |CRAN (R 4.4.0) | -|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) | -|xfun |0.52 |2025-04-02 |CRAN (R 4.4.1) | -|xml2 |1.3.8 |2025-03-14 |CRAN (R 4.4.1) | -|xtable |1.8-4 |2019-04-21 |CRAN (R 4.4.1) | -|yaml |2.3.10 |2024-07-26 |CRAN (R 4.4.1) | -|zip |2.3.2 |2025-02-01 |CRAN (R 4.4.1) | +|package |loadedversion |date |source | +|:-----------|:-------------|:----------|:--------------| +|bit |4.6.0 |2025-03-06 |CRAN (R 4.4.1) | +|bit64 |4.6.0-1 |2025-01-16 |CRAN (R 4.4.1) | +|cachem |1.1.0 |2024-05-16 |CRAN (R 4.4.1) | +|cli |3.6.5 |2025-04-23 |CRAN (R 4.4.1) | +|colorspace |2.1-1 |2024-07-26 |CRAN (R 4.4.1) | +|crayon |1.5.3 |2024-06-20 |CRAN (R 4.4.1) | +|desc |1.4.3 |2023-12-10 |CRAN (R 4.4.1) | +|devtools |2.4.5 |2022-10-11 |CRAN (R 4.4.0) | +|digest |0.6.37 |2024-08-19 |CRAN (R 4.4.1) | +|dplyr |1.1.4 |2023-11-17 |CRAN (R 4.4.0) | +|ellipsis |0.3.2 |2021-04-29 |CRAN (R 4.4.1) | +|fastmap |1.2.0 |2024-05-15 |CRAN (R 4.4.1) | +|fs |1.6.6 |2025-04-12 |CRAN (R 4.4.1) | +|generics |0.1.3 |2022-07-05 |CRAN (R 4.4.1) | +|ggplot2 |3.5.2 |2025-04-09 |CRAN (R 4.4.1) | +|ggstats |0.9.0 |2025-03-10 |CRAN (R 4.4.1) | +|glue |1.8.0 |2024-09-30 |CRAN (R 4.4.1) | +|gtable |0.3.6 |2024-10-25 |CRAN (R 4.4.1) | +|here |1.0.1 |2020-12-13 |CRAN (R 4.4.1) | +|hms |1.1.3 |2023-03-21 |CRAN (R 4.4.0) | +|htmltools |0.5.8.1 |2024-04-04 |CRAN (R 4.4.1) | +|htmlwidgets |1.6.4 |2023-12-06 |CRAN (R 4.4.0) | +|httpuv |1.6.16 |2025-04-16 |CRAN (R 4.4.1) | +|later |1.4.2 |2025-04-08 |CRAN (R 4.4.1) | +|lifecycle |1.0.4 |2023-11-07 |CRAN (R 4.4.1) | +|magrittr |2.0.3 |2022-03-30 |CRAN (R 4.4.1) | +|memoise |2.0.1 |2021-11-26 |CRAN (R 4.4.0) | +|mime |0.13 |2025-03-17 |CRAN (R 4.4.1) | +|miniUI |0.1.2 |2025-04-17 |CRAN (R 4.4.1) | +|munsell |0.5.1 |2024-04-01 |CRAN (R 4.4.1) | +|pillar |1.10.2 |2025-04-05 |CRAN (R 4.4.1) | +|pkgbuild |1.4.7 |2025-03-24 |CRAN (R 4.4.1) | +|pkgconfig |2.0.3 |2019-09-22 |CRAN (R 4.4.1) | +|pkgload |1.4.0 |2024-06-28 |CRAN (R 4.4.0) | +|profvis |0.4.0 |2024-09-20 |CRAN (R 4.4.1) | +|promises |1.3.2 |2024-11-28 |CRAN (R 4.4.1) | +|purrr |1.0.4 |2025-02-05 |CRAN (R 4.4.1) | +|R6 |2.6.1 |2025-02-15 |CRAN (R 4.4.1) | +|Rcpp |1.0.14 |2025-01-12 |CRAN (R 4.4.1) | +|readr |2.1.5 |2024-01-10 |CRAN (R 4.4.0) | +|remotes |2.5.0 |2024-03-17 |CRAN (R 4.4.1) | +|renv |1.1.4 |2025-03-20 |CRAN (R 4.4.1) | +|rlang |1.1.6 |2025-04-11 |CRAN (R 4.4.1) | +|rprojroot |2.0.4 |2023-11-05 |CRAN (R 4.4.1) | +|rsconnect |1.3.4 |2025-01-22 |CRAN (R 4.4.1) | +|rstudioapi |0.17.1 |2024-10-22 |CRAN (R 4.4.1) | +|scales |1.3.0 |2023-11-28 |CRAN (R 4.4.0) | +|sessioninfo |1.2.3 |2025-02-05 |CRAN (R 4.4.1) | +|shiny |1.10.0 |2024-12-14 |CRAN (R 4.4.1) | +|tibble |3.2.1 |2023-03-20 |CRAN (R 4.4.0) | +|tidyselect |1.2.1 |2024-03-11 |CRAN (R 4.4.0) | +|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) | +|vctrs |0.6.5 |2023-12-01 |CRAN (R 4.4.0) | +|vroom |1.6.5 |2023-12-05 |CRAN (R 4.4.0) | +|withr |3.0.2 |2024-10-28 |CRAN (R 4.4.1) | +|xtable |1.8-4 |2019-04-21 |CRAN (R 4.4.1) | diff --git a/inst/apps/FreesearchR/app.R b/inst/apps/FreesearchR/app.R index b041778..585c587 100644 --- a/inst/apps/FreesearchR/app.R +++ b/inst/apps/FreesearchR/app.R @@ -10,7 +10,7 @@ #### Current file: /Users/au301842/FreesearchR/R//app_version.R ######## -app_version <- function()'v25.4.3.250424' +app_version <- function()'v25.4.3.250428' ######## @@ -329,7 +329,7 @@ sentence_paste <- function(data, and.str = "and") { #' #' @name create-column #' -#' @example example/create_column_module_demo.R +#' @example examples/create_column_module_demo.R create_column_ui <- function(id) { ns <- NS(id) tagList( @@ -2924,11 +2924,6 @@ get_var_icon <- function(data,class.type=c("class","type")){ #' @return No value. #' @export #' -#' @importFrom htmltools tags tagList css -#' @importFrom shiny showModal modalDialog -#' @importFrom utils modifyList packageVersion -#' -#' @example examples/show_data.R show_data <- function(data, title = NULL, options = NULL, @@ -4632,7 +4627,7 @@ plot_box_single <- function(data, pri, sec=NULL, seed = 2103) { 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 = .5) + + 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() + diff --git a/inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/FreesearchR.dcf b/inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/FreesearchR.dcf index 7d73d94..bacb1fc 100644 --- a/inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/FreesearchR.dcf +++ b/inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/FreesearchR.dcf @@ -5,6 +5,6 @@ account: agdamsbo server: shinyapps.io hostUrl: https://api.shinyapps.io/v1 appId: 14600805 -bundleId: 10170173 +bundleId: 10170345 url: https://agdamsbo.shinyapps.io/FreesearchR/ version: 1 diff --git a/man/create-column.Rd b/man/create-column.Rd index 452cb3d..45a0e0f 100644 --- a/man/create-column.Rd +++ b/man/create-column.Rd @@ -74,3 +74,74 @@ You can add more operations using the \code{allowed_operations} argument, for e \if{html}{\out{
}}\preformatted{c(list_allowed_operations(), getNamespaceExports("lubridate")) }\if{html}{\out{
}} } +\examples{ + +library(shiny) +library(reactable) + +ui <- fluidPage( + theme = bslib::bs_theme(version = 5L, preset = "bootstrap"), + shinyWidgets::html_dependency_winbox(), + tags$h2("Create new column"), + fluidRow( + column( + width = 4, + create_column_ui("inline"), + actionButton("modal", "Or click here to open a modal to create a column"), + tags$br(), tags$br(), + actionButton("winbox", "Or click here to open a WinBox to create a column") + ), + column( + width = 8, + reactableOutput(outputId = "table"), + verbatimTextOutput("code") + ) + ) +) + +server <- function(input, output, session) { + + rv <- reactiveValues(data = MASS::Cars93[, c(1, 3, 4, 5, 6, 10)]) + + # inline mode + data_inline_r <- create_column_server( + id = "inline", + data_r = reactive(rv$data) + ) + observeEvent(data_inline_r(), rv$data <- data_inline_r()) + + # modal window mode + observeEvent(input$modal, modal_create_column("modal")) + data_modal_r <- create_column_server( + id = "modal", + data_r = reactive(rv$data) + ) + observeEvent(data_modal_r(), rv$data <- data_modal_r()) + + # WinBox window mode + observeEvent(input$winbox, winbox_create_column("winbox")) + data_winbox_r <- create_column_server( + id = "winbox", + data_r = reactive(rv$data) + ) + observeEvent(data_winbox_r(), rv$data <- data_winbox_r()) + + # Show result + output$table <- renderReactable({ + data <- req(rv$data) + reactable( + data = data, + bordered = TRUE, + compact = TRUE, + striped = TRUE + ) + }) + + output$code <- renderPrint({ + attr(rv$data, "code") + }) +} + +if (interactive()) + shinyApp(ui, server) +} diff --git a/man/custom_theme.Rd b/man/custom_theme.Rd index 963a51f..9480411 100644 --- a/man/custom_theme.Rd +++ b/man/custom_theme.Rd @@ -7,12 +7,16 @@ custom_theme( ..., version = 5, - primary = "#1E4A8F", - secondary = "#FF6F61", + 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") + code_font = bslib::font_google("Open Sans"), + success = FreesearchR_colors("success"), + info = FreesearchR_colors("info"), + warning = FreesearchR_colors("warning"), + danger = FreesearchR_colors("danger") ) } \arguments{