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2a39655e96
...
1613386096
29 changed files with 208 additions and 323 deletions
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@ -9,7 +9,7 @@ type: software
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license: AGPL-3.0-or-later
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title: 'FreesearchR: A free and open-source browser based data analysis tool for researchers
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with publication ready output'
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version: 25.5.4
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version: 25.5.2
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doi: 10.5281/zenodo.14527429
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identifiers:
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- type: url
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@ -1,6 +1,6 @@
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Package: FreesearchR
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Title: A free and open-source browser based data analysis tool for researchers with publication ready output
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Version: 25.5.4
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Version: 25.5.2
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Authors@R: c(
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person("Andreas Gammelgaard", "Damsbo",email="agdamsbo@clin.au.dk", role = c("aut", "cre"),
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comment = c(ORCID = "0000-0002-7559-1154")),
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@ -108,7 +108,6 @@ export(sankey_ready)
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export(selectInputIcon)
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export(set_column_label)
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export(show_data)
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export(simple_snake)
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export(sort_by)
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export(specify_qmd_format)
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export(subset_types)
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@ -131,6 +130,7 @@ export(write_quarto)
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importFrom(classInt,classIntervals)
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importFrom(data.table,as.data.table)
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importFrom(data.table,data.table)
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importFrom(grDevices,col2rgb)
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importFrom(graphics,abline)
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importFrom(graphics,axis)
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importFrom(graphics,hist)
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@ -141,6 +141,7 @@ importFrom(htmltools,css)
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importFrom(htmltools,tagList)
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importFrom(htmltools,tags)
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importFrom(htmltools,validateCssUnit)
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importFrom(phosphoricons,ph)
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importFrom(rlang,"%||%")
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importFrom(rlang,call2)
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importFrom(rlang,expr)
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@ -159,20 +160,25 @@ importFrom(shiny,isTruthy)
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importFrom(shiny,modalDialog)
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importFrom(shiny,moduleServer)
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importFrom(shiny,numericInput)
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importFrom(shiny,observe)
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importFrom(shiny,observeEvent)
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importFrom(shiny,plotOutput)
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importFrom(shiny,reactive)
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importFrom(shiny,reactiveValues)
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importFrom(shiny,renderPlot)
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importFrom(shiny,renderUI)
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importFrom(shiny,req)
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importFrom(shiny,restoreInput)
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importFrom(shiny,selectizeInput)
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importFrom(shiny,showModal)
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importFrom(shiny,tagList)
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importFrom(shiny,textAreaInput)
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importFrom(shiny,textInput)
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importFrom(shiny,uiOutput)
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importFrom(shiny,updateActionButton)
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importFrom(shiny,updateTextAreaInput)
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importFrom(shinyWidgets,WinBox)
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importFrom(shinyWidgets,alert)
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importFrom(shinyWidgets,noUiSliderInput)
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importFrom(shinyWidgets,prettyCheckbox)
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importFrom(shinyWidgets,updateVirtualSelect)
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18
NEWS.md
18
NEWS.md
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@ -1,21 +1,3 @@
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# FreesearchR 25.5.4
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- *FIX* correctly omit NAs in `data_type()` call
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- *FIX* omit NAs when plotting Euler diagrams.
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- *FIX* print correct labels in horizontal stacked bars.
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- *FIX* initial app load should feel faster.
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# FreesearchR 25.5.3
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- *FIX* a little polish on the data import
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- *FIX* polished REDCap import and new code to reference the `REDCapCAST::easy_redcap()` function.
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- *FIX* updated documentation to reflect new private hosting on a Hetzner server in Germany.
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# FreesearchR 25.5.2
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- *FIX*: correct export of plots. The solution in the last version broke more than it solved.
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@ -1 +1 @@
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app_version <- function()'25.5.4'
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app_version <- function()'25.5.2'
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@ -25,6 +25,7 @@
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#' contrast_text(c("#F2F2F2", "blue"), method="relative")
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#' @export
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#'
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#' @importFrom grDevices col2rgb
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#'
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contrast_text <- function(background,
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light_text = 'white',
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@ -17,17 +17,20 @@
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#' @export
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#'
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#' @importFrom htmltools tagList tags css
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#' @importFrom shiny NS textInput textAreaInput uiOutput actionButton
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#' @importFrom phosphoricons ph
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#' @importFrom shinyWidgets virtualSelectInput
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#'
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#' @name create-column
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#'
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#' @example examples/create_column_module_demo.R
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create_column_ui <- function(id) {
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ns <- NS(id)
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htmltools::tagList(
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tagList(
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# datamods:::html_dependency_datamods(),
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# html_dependency_FreesearchR(),
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shiny::tags$head(
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shiny::tags$link(rel = "stylesheet", type = "text/css", href = "FreesearchR/inst/assets/css/FreesearchR.css")
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tags$head(
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tags$link(rel = "stylesheet", type = "text/css", href = "FreesearchR/inst/assets/css/FreesearchR.css")
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),
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# tags$head(
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# # Note the wrapping of the string in HTML()
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@ -81,7 +84,7 @@ create_column_ui <- function(id) {
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)
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)
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),
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shiny::textAreaInput(
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textAreaInput(
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inputId = ns("expression"),
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label = i18n("Enter an expression to define new column:"),
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value = "",
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@ -129,6 +132,9 @@ create_column_ui <- function(id) {
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#'
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#' @rdname create-column
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#'
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#' @importFrom shiny moduleServer reactiveValues observeEvent renderUI req
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#' updateTextAreaInput reactive bindEvent observe
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#' @importFrom shinyWidgets alert updateVirtualSelect
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create_column_server <- function(id,
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data_r = reactive(NULL),
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allowed_operations = list_allowed_operations()) {
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@ -1,3 +1,9 @@
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library(datamods)
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library(toastui)
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library(phosphoricons)
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library(rlang)
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library(shiny)
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#' Extended cutting function with fall-back to the native base::cut
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#'
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#' @param x an object inheriting from class "hms"
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@ -206,9 +212,9 @@ cut_variable_ui <- function(id) {
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shiny::fluidRow(
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column(
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width = 3,
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shinyWidgets::virtualSelectInput(
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virtualSelectInput(
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inputId = ns("variable"),
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label = datamods:::i18n("Variable to cut:"),
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label = i18n("Variable to cut:"),
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choices = NULL,
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width = "100%"
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)
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@ -221,7 +227,7 @@ cut_variable_ui <- function(id) {
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width = 3,
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numericInput(
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inputId = ns("n_breaks"),
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label = datamods:::i18n("Number of breaks:"),
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label = i18n("Number of breaks:"),
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value = 3,
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min = 2,
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max = 12,
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@ -232,12 +238,12 @@ cut_variable_ui <- function(id) {
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width = 3,
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checkboxInput(
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inputId = ns("right"),
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label = datamods:::i18n("Close intervals on the right"),
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label = i18n("Close intervals on the right"),
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value = TRUE
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),
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checkboxInput(
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inputId = ns("include_lowest"),
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label = datamods:::i18n("Include lowest value"),
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label = i18n("Include lowest value"),
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value = TRUE
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)
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)
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|
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@ -248,10 +254,10 @@ cut_variable_ui <- function(id) {
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uiOutput(outputId = ns("slider_fixed"))
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),
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plotOutput(outputId = ns("plot"), width = "100%", height = "270px"),
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toastui::datagridOutput2(outputId = ns("count")),
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datagridOutput2(outputId = ns("count")),
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actionButton(
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inputId = ns("create"),
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label = tagList(phosphoricons::ph("scissors"), datamods:::i18n("Create factor variable")),
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label = tagList(ph("scissors"), i18n("Create factor variable")),
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class = "btn-outline-primary float-end"
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),
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tags$div(class = "clearfix")
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|
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@ -282,7 +288,7 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
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is.numeric(.x) || is_datetime(.x)
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}, logical(1))
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vars_num <- names(vars_num)[vars_num]
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shinyWidgets::updateVirtualSelect(
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updateVirtualSelect(
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inputId = "variable",
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choices = vars_num,
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selected = if (isTruthy(input$variable)) input$variable else vars_num[1]
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|
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@ -319,9 +325,9 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
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}
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|
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shinyWidgets::noUiSliderInput(
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noUiSliderInput(
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inputId = session$ns("fixed_brks"),
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label = datamods:::i18n("Fixed breaks:"),
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label = i18n("Fixed breaks:"),
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min = lower,
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max = upper,
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value = brks,
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|
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@ -376,7 +382,7 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
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|||
|
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shinyWidgets::virtualSelectInput(
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inputId = session$ns("method"),
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||||
label = datamods:::i18n("Method:"),
|
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label = i18n("Method:"),
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choices = choices,
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selected = NULL,
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width = "100%"
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@ -519,7 +525,7 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
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data
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})
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||||
output$count <- toastui::renderDatagrid2({
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output$count <- renderDatagrid2({
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# shiny::req(rv$new_var_name)
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data <- req(data_cutted_r())
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# variable <- req(input$variable)
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@ -535,14 +541,14 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
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datamods:::apply_grid_theme()
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}
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on.exit(toastui::reset_grid_theme())
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grid <- toastui::datagrid(
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grid <- datagrid(
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data = count_data,
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colwidths = "guess",
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theme = "default",
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bodyHeight = "auto"
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||||
)
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||||
grid <- toastui::grid_columns(grid, className = "font-monospace")
|
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toastui::grid_colorbar(
|
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grid_colorbar(
|
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grid,
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||||
column = "count",
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label_outside = TRUE,
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|
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@ -570,7 +576,7 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
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#'
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#' @rdname cut-variable
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modal_cut_variable <- function(id,
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title = datamods:::i18n("Convert Numeric to Factor"),
|
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title = i18n("Convert Numeric to Factor"),
|
||||
easyClose = TRUE,
|
||||
size = "l",
|
||||
footer = NULL) {
|
||||
|
|
|
|||
|
|
@ -681,7 +681,6 @@ create_plot <- function(data, type, pri, sec, ter = NULL, ...) {
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#' mtcars |> get_label()
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#' mtcars$mpg |> get_label()
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#' gtsummary::trial |> get_label(var = "trt")
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#' gtsummary::trial$trt |> get_label()
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#' 1:10 |> get_label()
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get_label <- function(data, var = NULL) {
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# data <- if (is.reactive(data)) data() else data
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|
|
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|
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@ -35,7 +35,7 @@ show_data <- function(data,
|
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if (is.null(options))
|
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options <- list()
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|
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options$height <- 500
|
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options$height <- 550
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options$minBodyHeight <- 400
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options$data <- data
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options$theme <- "default"
|
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|
|
|
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14
R/helpers.R
14
R/helpers.R
|
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@ -652,17 +652,3 @@ is_identical_to_previous <- function(data, no.name = TRUE) {
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}
|
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}, FUN.VALUE = logical(1))
|
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}
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|
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#' Simplified version of the snakecase packages to_snake_case
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#'
|
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#' @param data character string vector
|
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#'
|
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#' @returns vector
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#' @export
|
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#'
|
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#' @examples
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#' c("foo bar", "fooBar21", "!!Foo'B'a-r", "foo_bar", "F OO bar") |> simple_snake()
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simple_snake <- function(data){
|
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gsub("[\\s+]","_",gsub("[^\\w\\s:-]", "", tolower(data), perl=TRUE), perl=TRUE)
|
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}
|
||||
|
|
|
|||
|
|
@ -1 +1 @@
|
|||
hosted_version <- function()'v25.5.4-250510'
|
||||
hosted_version <- function()'v25.5.2-250508'
|
||||
|
|
|
|||
|
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@ -87,11 +87,10 @@ plot_euler <- function(data, pri, sec, ter = NULL, seed = 2103) {
|
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out <- lapply(ds, \(.x){
|
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.x[c(pri, sec)] |>
|
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as.data.frame() |>
|
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na.omit() |>
|
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plot_euler_single()
|
||||
})
|
||||
|
||||
# names(out)
|
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# names(out)
|
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wrap_plot_list(out)
|
||||
# patchwork::wrap_plots(out, guides = "collect")
|
||||
}
|
||||
|
|
|
|||
|
|
@ -62,8 +62,9 @@ vertical_stacked_bars <- function(data,
|
|||
contrast_cut <-
|
||||
sum(contrast_text(colors, threshold = .3) == "white")
|
||||
|
||||
score_label <- data |> get_label(var = score)
|
||||
group_label <- data |> get_label(var = group)
|
||||
score_label <- ifelse(is.na(REDCapCAST::get_attr(data$score, "label")), score, REDCapCAST::get_attr(data$score, "label"))
|
||||
group_label <- ifelse(is.na(REDCapCAST::get_attr(data$group, "label")), group, REDCapCAST::get_attr(data$group, "label"))
|
||||
|
||||
|
||||
p |>
|
||||
(\(.x){
|
||||
|
|
|
|||
|
|
@ -119,6 +119,7 @@ plot_sankey <- function(data, pri, sec, ter = NULL, color.group = "pri", colors
|
|||
#' plot_sankey_single("first", "last", color.group = "pri")
|
||||
#' mtcars |>
|
||||
#' default_parsing() |>
|
||||
#' str()
|
||||
#' 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)
|
||||
|
|
@ -131,6 +132,8 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
|
|||
|
||||
data <- data |> sankey_ready(pri = pri, sec = sec, ...)
|
||||
|
||||
library(ggalluvial)
|
||||
|
||||
na.color <- "#2986cc"
|
||||
box.color <- "#1E4B66"
|
||||
|
||||
|
|
@ -194,8 +197,6 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
|
|||
)
|
||||
}
|
||||
|
||||
## Will fail to use stat="stratum" if library is not loaded.
|
||||
library(ggalluvial)
|
||||
p +
|
||||
ggplot2::geom_text(
|
||||
stat = "stratum",
|
||||
|
|
|
|||
0
R/redcap.R
Normal file
0
R/redcap.R
Normal file
|
|
@ -200,12 +200,9 @@ m_redcap_readServer <- function(id) {
|
|||
)
|
||||
|
||||
# browser()
|
||||
shiny::withProgress(
|
||||
{
|
||||
imported <- try(rlang::exec(REDCapR::redcap_metadata_read, !!!parameters), silent = TRUE)
|
||||
},
|
||||
message = paste("Connecting to", data_rv$uri)
|
||||
)
|
||||
shiny::withProgress({
|
||||
imported <- try(rlang::exec(REDCapR::redcap_metadata_read, !!!parameters), silent = TRUE)
|
||||
},message = paste("Connecting to",data_rv$uri))
|
||||
|
||||
## TODO: Simplify error messages
|
||||
if (inherits(imported, "try-error") || NROW(imported) < 1 || ifelse(is.list(imported), !isTRUE(imported$success), FALSE)) {
|
||||
|
|
@ -231,7 +228,7 @@ m_redcap_readServer <- function(id) {
|
|||
status = "success",
|
||||
include_data_alert(
|
||||
see_data_text = "Click to see data dictionary",
|
||||
dataIdName = "see_dd",
|
||||
dataIdName = "see_data",
|
||||
extra = tags$p(
|
||||
tags$b(phosphoricons::ph("check", weight = "bold"), "Connected to server!"),
|
||||
glue::glue("The {data_rv$info$project_title} project is loaded.")
|
||||
|
|
@ -257,8 +254,8 @@ m_redcap_readServer <- function(id) {
|
|||
output$connect_success <- shiny::reactive(identical(data_rv$dd_status, "success"))
|
||||
shiny::outputOptions(output, "connect_success", suspendWhenHidden = FALSE)
|
||||
|
||||
shiny::observeEvent(input$see_dd, {
|
||||
show_data(
|
||||
shiny::observeEvent(input$see_data, {
|
||||
datamods::show_data(
|
||||
purrr::pluck(data_rv$dd_list, "data"),
|
||||
title = "Data dictionary",
|
||||
type = "modal",
|
||||
|
|
@ -267,17 +264,6 @@ m_redcap_readServer <- function(id) {
|
|||
)
|
||||
})
|
||||
|
||||
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)
|
||||
|
|
@ -392,24 +378,13 @@ m_redcap_readServer <- function(id) {
|
|||
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)
|
||||
)
|
||||
),
|
||||
code <- rlang::call2("read_redcap_tables",
|
||||
!!!utils::modifyList(parameters, list(token = "PERSONAL_API_TOKEN")), ,
|
||||
.ns = "REDCapCAST"
|
||||
)
|
||||
|
||||
# browser()
|
||||
|
||||
if (inherits(imported, "try-error") || NROW(imported) < 1) {
|
||||
data_rv$data_status <- "error"
|
||||
data_rv$data_list <- NULL
|
||||
|
|
@ -478,17 +453,9 @@ m_redcap_readServer <- function(id) {
|
|||
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$data_message)
|
||||
),
|
||||
btn_show_data = TRUE
|
||||
tags$p(
|
||||
tags$b(phosphoricons::ph("check", weight = "bold"), "Success!"),
|
||||
data_rv$data_message
|
||||
)
|
||||
)
|
||||
} else {
|
||||
|
|
|
|||
|
|
@ -271,13 +271,12 @@ data_type <- function(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) {
|
||||
} else if (length(unique(data)) < 2) {
|
||||
out <- "monotone"
|
||||
} else if (any(c("factor", "logical") %in% cl_d) | l_unique == 2) {
|
||||
if (identical("logical", cl_d) | l_unique == 2) {
|
||||
} else if (any(c("factor", "logical") %in% cl_d) | length(unique(data)) == 2) {
|
||||
if (identical("logical", cl_d) | length(unique(data)) == 2) {
|
||||
out <- "dichotomous"
|
||||
} else {
|
||||
# if (is.ordered(data)) {
|
||||
|
|
@ -290,7 +289,7 @@ data_type <- function(data) {
|
|||
out <- "text"
|
||||
} else if (any(c("hms", "Date", "POSIXct", "POSIXt") %in% cl_d)) {
|
||||
out <- "datetime"
|
||||
} else if (l_unique > 2) {
|
||||
} else if (!length(unique(data)) == 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) &
|
||||
|
|
|
|||
BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
|
|
@ -31,7 +31,7 @@ update_factor_ui <- function(id) {
|
|||
fluidRow(
|
||||
column(
|
||||
width = 6,
|
||||
shinyWidgets::virtualSelectInput(
|
||||
virtualSelectInput(
|
||||
inputId = ns("variable"),
|
||||
label = i18n("Factor variable to reorder:"),
|
||||
choices = NULL,
|
||||
|
|
@ -66,10 +66,10 @@ update_factor_ui <- function(id) {
|
|||
)
|
||||
)
|
||||
),
|
||||
toastui::datagridOutput(ns("grid")),
|
||||
datagridOutput(ns("grid")),
|
||||
tags$div(
|
||||
class = "float-end",
|
||||
shinyWidgets::prettyCheckbox(
|
||||
prettyCheckbox(
|
||||
inputId = ns("new_var"),
|
||||
label = i18n("Create a new variable (otherwise replaces the one selected)"),
|
||||
value = FALSE,
|
||||
|
|
|
|||
|
|
@ -1,3 +1,7 @@
|
|||
library(data.table)
|
||||
library(rlang)
|
||||
|
||||
|
||||
#' Select, rename and convert variables
|
||||
#'
|
||||
#' @param id Module id. See [shiny::moduleServer()].
|
||||
|
|
|
|||
|
|
@ -7,9 +7,9 @@
|
|||
[](https://agdamsbo.shinyapps.io/FreesearchR/)
|
||||
<!-- badges: end -->
|
||||
|
||||
The [***FreesearchR***](https://app.freesearchr.org) is a simple, clinical health data exploration and analysis tool to democratise clinical research by assisting any researcher to easily evaluate and analyse data and export publication ready results.
|
||||
The [***FreesearchR***](https://agdamsbo.shinyapps.io/FreesearchR/) is a simple, clinical health data exploration and analysis tool to democratise clinical research by assisting any researcher to easily evaluate and analyse data and export publication ready results.
|
||||
|
||||
[***FreesearchR***](https://app.freesearchr.org) is free and open-source, and is [accessible in your web browser through this link](https://app.freesearchr.org). The app can also run locally, please [see below](#run-locally-on-your-own-machine-sec-run-locally).
|
||||
[***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!
|
||||
|
||||
|
|
|
|||
25
SESSION.md
25
SESSION.md
|
|
@ -11,11 +11,11 @@
|
|||
|collate |en_US.UTF-8 |
|
||||
|ctype |en_US.UTF-8 |
|
||||
|tz |Europe/Copenhagen |
|
||||
|date |2025-05-10 |
|
||||
|date |2025-05-08 |
|
||||
|rstudio |2024.12.1+563 Kousa Dogwood (desktop) |
|
||||
|pandoc |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) |
|
||||
|quarto |1.7.30 @ /usr/local/bin/quarto |
|
||||
|FreesearchR |25.5.4.250510 |
|
||||
|quarto |1.6.40 @ /usr/local/bin/quarto |
|
||||
|FreesearchR |25.5.2.250508 |
|
||||
|
||||
|
||||
--------------------------------------------------------------------------------
|
||||
|
|
@ -44,6 +44,7 @@
|
|||
|commonmark |1.9.5 |2025-03-17 |CRAN (R 4.4.1) |
|
||||
|correlation |0.8.7 |2025-03-03 |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) |
|
||||
|curl |6.2.2 |2025-03-24 |CRAN (R 4.4.1) |
|
||||
|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) |
|
||||
|
|
@ -58,7 +59,6 @@
|
|||
|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) |
|
||||
|eulerr |7.0.2 |2024-03-28 |CRAN (R 4.4.0) |
|
||||
|evaluate |1.0.3 |2025-01-10 |CRAN (R 4.4.1) |
|
||||
|farver |2.1.2 |2024-05-13 |CRAN (R 4.4.1) |
|
||||
|fastmap |1.2.0 |2024-05-15 |CRAN (R 4.4.1) |
|
||||
|
|
@ -66,11 +66,8 @@
|
|||
|forcats |1.0.0 |2023-01-29 |CRAN (R 4.4.0) |
|
||||
|fs |1.6.6 |2025-04-12 |CRAN (R 4.4.1) |
|
||||
|generics |0.1.3 |2022-07-05 |CRAN (R 4.4.1) |
|
||||
|ggalluvial |0.12.5 |2023-02-22 |CRAN (R 4.4.0) |
|
||||
|ggforce |0.4.2 |2024-02-19 |CRAN (R 4.4.0) |
|
||||
|ggplot2 |3.5.2 |2025-04-09 |CRAN (R 4.4.1) |
|
||||
|glue |1.8.0 |2024-09-30 |CRAN (R 4.4.1) |
|
||||
|gridExtra |2.3 |2017-09-09 |CRAN (R 4.4.1) |
|
||||
|gt |1.0.0 |2025-04-05 |CRAN (R 4.4.1) |
|
||||
|gtable |0.3.6 |2024-10-25 |CRAN (R 4.4.1) |
|
||||
|gtsummary |2.2.0 |2025-04-14 |CRAN (R 4.4.1) |
|
||||
|
|
@ -88,7 +85,6 @@
|
|||
|KernSmooth |2.23-26 |2025-01-01 |CRAN (R 4.4.1) |
|
||||
|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) |
|
||||
|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) |
|
||||
|
|
@ -105,6 +101,7 @@
|
|||
|nloptr |2.2.1 |2025-03-17 |CRAN (R 4.4.1) |
|
||||
|openssl |2.3.2 |2025-02-03 |CRAN (R 4.4.1) |
|
||||
|openxlsx2 |1.15 |2025-04-25 |CRAN (R 4.4.1) |
|
||||
|pak |0.8.0.2 |2025-04-08 |CRAN (R 4.4.1) |
|
||||
|parameters |0.24.2 |2025-03-04 |CRAN (R 4.4.1) |
|
||||
|patchwork |1.3.0 |2024-09-16 |CRAN (R 4.4.1) |
|
||||
|performance |0.13.0 |2025-01-15 |CRAN (R 4.4.1) |
|
||||
|
|
@ -113,8 +110,6 @@
|
|||
|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) |
|
||||
|polyclip |1.10-7 |2024-07-23 |CRAN (R 4.4.1) |
|
||||
|polylabelr |0.3.0 |2024-11-19 |CRAN (R 4.4.1) |
|
||||
|processx |3.8.6 |2025-02-21 |CRAN (R 4.4.1) |
|
||||
|profvis |0.4.0 |2024-09-20 |CRAN (R 4.4.1) |
|
||||
|promises |1.3.2 |2024-11-28 |CRAN (R 4.4.1) |
|
||||
|
|
@ -127,8 +122,6 @@
|
|||
|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) |
|
||||
|ragg |1.4.0 |2025-04-10 |CRAN (R 4.4.1) |
|
||||
|rankinPlot |1.1.0 |2023-01-30 |CRAN (R 4.4.0) |
|
||||
|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) |
|
||||
|
|
@ -146,7 +139,6 @@
|
|||
|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) |
|
||||
|roxygen2 |7.3.2 |2024-06-28 |CRAN (R 4.4.0) |
|
||||
|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) |
|
||||
|
|
@ -160,23 +152,16 @@
|
|||
|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) |
|
||||
|stringr |1.5.1 |2023-11-14 |CRAN (R 4.4.0) |
|
||||
|styler |1.10.3 |2024-04-07 |CRAN (R 4.4.0) |
|
||||
|systemfonts |1.2.2 |2025-04-04 |CRAN (R 4.4.1) |
|
||||
|textshaping |1.0.0 |2025-01-20 |CRAN (R 4.4.1) |
|
||||
|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) |
|
||||
|tweenr |2.0.3 |2024-02-26 |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) |
|
||||
|utf8 |1.2.4 |2023-10-22 |CRAN (R 4.4.1) |
|
||||
|V8 |6.0.3 |2025-03-26 |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) |
|
||||
|
|
|
|||
|
|
@ -11,7 +11,7 @@ template:
|
|||
# Adding the switch destroys the theme colors
|
||||
light-switch: false
|
||||
includes:
|
||||
in_header: <script defer src="https://stats.freesearchr.org/script.js" data-website-id="85bfd1e8-2cbe-4a4a-aa34-1dfb2960905b"></script>
|
||||
in_header: <script defer src="https://analytics.gdamsbo.dk/script.js" data-website-id="1f3baf18-29aa-4612-931b-58ea35922ae4"></script>
|
||||
|
||||
navbar:
|
||||
bg: primary
|
||||
|
|
|
|||
|
|
@ -1,44 +1,5 @@
|
|||
|
||||
|
||||
########
|
||||
#### Current file: /Users/au301842/FreesearchR/app/libs.R
|
||||
########
|
||||
|
||||
library(shiny)
|
||||
# library(shinyjs)
|
||||
# library(methods)
|
||||
# library(readr)
|
||||
# library(MASS)
|
||||
# library(stats)
|
||||
# library(gt)
|
||||
# library(openxlsx2)
|
||||
# library(haven)
|
||||
# library(readODS)
|
||||
# library(bslib)
|
||||
# library(assertthat)
|
||||
# library(dplyr)
|
||||
# library(quarto)
|
||||
# library(here)
|
||||
# library(broom)
|
||||
# library(broom.helpers)
|
||||
# library(easystats)
|
||||
# library(patchwork)
|
||||
# library(DHARMa)
|
||||
# library(apexcharter)
|
||||
library(toastui)
|
||||
# library(datamods)
|
||||
# library(IDEAFilter)
|
||||
library(shinyWidgets)
|
||||
# library(DT)
|
||||
# library(data.table)
|
||||
# library(gtsummary)
|
||||
library(bsicons)
|
||||
library(rlang)
|
||||
# library(datamods)
|
||||
# library(toastui)
|
||||
# library(phosphoricons)
|
||||
|
||||
|
||||
########
|
||||
#### Current file: /Users/au301842/FreesearchR/app/functions.R
|
||||
########
|
||||
|
|
@ -49,7 +10,7 @@ library(rlang)
|
|||
#### Current file: /Users/au301842/FreesearchR/R//app_version.R
|
||||
########
|
||||
|
||||
app_version <- function()'25.5.3'
|
||||
app_version <- function()'25.5.2'
|
||||
|
||||
|
||||
########
|
||||
|
|
@ -168,6 +129,7 @@ create_baseline <- function(data, ..., by.var, add.p = FALSE, add.overall = FALS
|
|||
#' contrast_text(c("#F2F2F2", "blue"), method="relative")
|
||||
#' @export
|
||||
#'
|
||||
#' @importFrom grDevices col2rgb
|
||||
#'
|
||||
contrast_text <- function(background,
|
||||
light_text = 'white',
|
||||
|
|
@ -361,17 +323,20 @@ sentence_paste <- function(data, and.str = "and") {
|
|||
#' @export
|
||||
#'
|
||||
#' @importFrom htmltools tagList tags css
|
||||
#' @importFrom shiny NS textInput textAreaInput uiOutput actionButton
|
||||
#' @importFrom phosphoricons ph
|
||||
#' @importFrom shinyWidgets virtualSelectInput
|
||||
#'
|
||||
#' @name create-column
|
||||
#'
|
||||
#' @example examples/create_column_module_demo.R
|
||||
create_column_ui <- function(id) {
|
||||
ns <- NS(id)
|
||||
htmltools::tagList(
|
||||
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(
|
||||
tags$link(rel = "stylesheet", type = "text/css", href = "FreesearchR/inst/assets/css/FreesearchR.css")
|
||||
),
|
||||
# tags$head(
|
||||
# # Note the wrapping of the string in HTML()
|
||||
|
|
@ -425,7 +390,7 @@ create_column_ui <- function(id) {
|
|||
)
|
||||
)
|
||||
),
|
||||
shiny::textAreaInput(
|
||||
textAreaInput(
|
||||
inputId = ns("expression"),
|
||||
label = i18n("Enter an expression to define new column:"),
|
||||
value = "",
|
||||
|
|
@ -473,6 +438,9 @@ create_column_ui <- function(id) {
|
|||
#'
|
||||
#' @rdname create-column
|
||||
#'
|
||||
#' @importFrom shiny moduleServer reactiveValues observeEvent renderUI req
|
||||
#' updateTextAreaInput reactive bindEvent observe
|
||||
#' @importFrom shinyWidgets alert updateVirtualSelect
|
||||
create_column_server <- function(id,
|
||||
data_r = reactive(NULL),
|
||||
allowed_operations = list_allowed_operations()) {
|
||||
|
|
@ -979,6 +947,12 @@ vectorSelectInput <- function(inputId,
|
|||
#### Current file: /Users/au301842/FreesearchR/R//cut-variable-dates.R
|
||||
########
|
||||
|
||||
library(datamods)
|
||||
library(toastui)
|
||||
library(phosphoricons)
|
||||
library(rlang)
|
||||
library(shiny)
|
||||
|
||||
#' Extended cutting function with fall-back to the native base::cut
|
||||
#'
|
||||
#' @param x an object inheriting from class "hms"
|
||||
|
|
@ -1187,9 +1161,9 @@ cut_variable_ui <- function(id) {
|
|||
shiny::fluidRow(
|
||||
column(
|
||||
width = 3,
|
||||
shinyWidgets::virtualSelectInput(
|
||||
virtualSelectInput(
|
||||
inputId = ns("variable"),
|
||||
label = datamods:::i18n("Variable to cut:"),
|
||||
label = i18n("Variable to cut:"),
|
||||
choices = NULL,
|
||||
width = "100%"
|
||||
)
|
||||
|
|
@ -1202,7 +1176,7 @@ cut_variable_ui <- function(id) {
|
|||
width = 3,
|
||||
numericInput(
|
||||
inputId = ns("n_breaks"),
|
||||
label = datamods:::i18n("Number of breaks:"),
|
||||
label = i18n("Number of breaks:"),
|
||||
value = 3,
|
||||
min = 2,
|
||||
max = 12,
|
||||
|
|
@ -1213,12 +1187,12 @@ cut_variable_ui <- function(id) {
|
|||
width = 3,
|
||||
checkboxInput(
|
||||
inputId = ns("right"),
|
||||
label = datamods:::i18n("Close intervals on the right"),
|
||||
label = i18n("Close intervals on the right"),
|
||||
value = TRUE
|
||||
),
|
||||
checkboxInput(
|
||||
inputId = ns("include_lowest"),
|
||||
label = datamods:::i18n("Include lowest value"),
|
||||
label = i18n("Include lowest value"),
|
||||
value = TRUE
|
||||
)
|
||||
)
|
||||
|
|
@ -1229,10 +1203,10 @@ cut_variable_ui <- function(id) {
|
|||
uiOutput(outputId = ns("slider_fixed"))
|
||||
),
|
||||
plotOutput(outputId = ns("plot"), width = "100%", height = "270px"),
|
||||
toastui::datagridOutput2(outputId = ns("count")),
|
||||
datagridOutput2(outputId = ns("count")),
|
||||
actionButton(
|
||||
inputId = ns("create"),
|
||||
label = tagList(phosphoricons::ph("scissors"), datamods:::i18n("Create factor variable")),
|
||||
label = tagList(ph("scissors"), i18n("Create factor variable")),
|
||||
class = "btn-outline-primary float-end"
|
||||
),
|
||||
tags$div(class = "clearfix")
|
||||
|
|
@ -1263,7 +1237,7 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
|
|||
is.numeric(.x) || is_datetime(.x)
|
||||
}, logical(1))
|
||||
vars_num <- names(vars_num)[vars_num]
|
||||
shinyWidgets::updateVirtualSelect(
|
||||
updateVirtualSelect(
|
||||
inputId = "variable",
|
||||
choices = vars_num,
|
||||
selected = if (isTruthy(input$variable)) input$variable else vars_num[1]
|
||||
|
|
@ -1300,9 +1274,9 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
|
|||
}
|
||||
|
||||
|
||||
shinyWidgets::noUiSliderInput(
|
||||
noUiSliderInput(
|
||||
inputId = session$ns("fixed_brks"),
|
||||
label = datamods:::i18n("Fixed breaks:"),
|
||||
label = i18n("Fixed breaks:"),
|
||||
min = lower,
|
||||
max = upper,
|
||||
value = brks,
|
||||
|
|
@ -1357,7 +1331,7 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
|
|||
|
||||
shinyWidgets::virtualSelectInput(
|
||||
inputId = session$ns("method"),
|
||||
label = datamods:::i18n("Method:"),
|
||||
label = i18n("Method:"),
|
||||
choices = choices,
|
||||
selected = NULL,
|
||||
width = "100%"
|
||||
|
|
@ -1500,7 +1474,7 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
|
|||
data
|
||||
})
|
||||
|
||||
output$count <- toastui::renderDatagrid2({
|
||||
output$count <- renderDatagrid2({
|
||||
# shiny::req(rv$new_var_name)
|
||||
data <- req(data_cutted_r())
|
||||
# variable <- req(input$variable)
|
||||
|
|
@ -1516,14 +1490,14 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
|
|||
datamods:::apply_grid_theme()
|
||||
}
|
||||
on.exit(toastui::reset_grid_theme())
|
||||
grid <- toastui::datagrid(
|
||||
grid <- datagrid(
|
||||
data = count_data,
|
||||
colwidths = "guess",
|
||||
theme = "default",
|
||||
bodyHeight = "auto"
|
||||
)
|
||||
grid <- toastui::grid_columns(grid, className = "font-monospace")
|
||||
toastui::grid_colorbar(
|
||||
grid_colorbar(
|
||||
grid,
|
||||
column = "count",
|
||||
label_outside = TRUE,
|
||||
|
|
@ -1551,7 +1525,7 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
|
|||
#'
|
||||
#' @rdname cut-variable
|
||||
modal_cut_variable <- function(id,
|
||||
title = datamods:::i18n("Convert Numeric to Factor"),
|
||||
title = i18n("Convert Numeric to Factor"),
|
||||
easyClose = TRUE,
|
||||
size = "l",
|
||||
footer = NULL) {
|
||||
|
|
@ -2281,7 +2255,6 @@ create_plot <- function(data, type, pri, sec, ter = NULL, ...) {
|
|||
#' mtcars |> get_label()
|
||||
#' mtcars$mpg |> get_label()
|
||||
#' gtsummary::trial |> get_label(var = "trt")
|
||||
#' gtsummary::trial$trt |> get_label()
|
||||
#' 1:10 |> get_label()
|
||||
get_label <- function(data, var = NULL) {
|
||||
# data <- if (is.reactive(data)) data() else data
|
||||
|
|
@ -3010,7 +2983,7 @@ show_data <- function(data,
|
|||
if (is.null(options))
|
||||
options <- list()
|
||||
|
||||
options$height <- 500
|
||||
options$height <- 550
|
||||
options$minBodyHeight <- 400
|
||||
options$data <- data
|
||||
options$theme <- "default"
|
||||
|
|
@ -3978,25 +3951,11 @@ is_identical_to_previous <- function(data, no.name = TRUE) {
|
|||
}
|
||||
|
||||
|
||||
#' 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()'v25.5.3-250510'
|
||||
hosted_version <- function()'v25.5.2-250508'
|
||||
|
||||
|
||||
########
|
||||
|
|
@ -4834,11 +4793,10 @@ plot_euler <- function(data, pri, sec, ter = NULL, seed = 2103) {
|
|||
out <- lapply(ds, \(.x){
|
||||
.x[c(pri, sec)] |>
|
||||
as.data.frame() |>
|
||||
na.omit() |>
|
||||
plot_euler_single()
|
||||
})
|
||||
|
||||
# names(out)
|
||||
# names(out)
|
||||
wrap_plot_list(out)
|
||||
# patchwork::wrap_plots(out, guides = "collect")
|
||||
}
|
||||
|
|
@ -4950,8 +4908,9 @@ vertical_stacked_bars <- function(data,
|
|||
contrast_cut <-
|
||||
sum(contrast_text(colors, threshold = .3) == "white")
|
||||
|
||||
score_label <- data |> get_label(var = score)
|
||||
group_label <- data |> get_label(var = group)
|
||||
score_label <- ifelse(is.na(REDCapCAST::get_attr(data$score, "label")), score, REDCapCAST::get_attr(data$score, "label"))
|
||||
group_label <- ifelse(is.na(REDCapCAST::get_attr(data$group, "label")), group, REDCapCAST::get_attr(data$group, "label"))
|
||||
|
||||
|
||||
p |>
|
||||
(\(.x){
|
||||
|
|
@ -5141,6 +5100,7 @@ plot_sankey <- function(data, pri, sec, ter = NULL, color.group = "pri", colors
|
|||
#' plot_sankey_single("first", "last", color.group = "pri")
|
||||
#' mtcars |>
|
||||
#' default_parsing() |>
|
||||
#' str()
|
||||
#' 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)
|
||||
|
|
@ -5153,6 +5113,8 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
|
|||
|
||||
data <- data |> sankey_ready(pri = pri, sec = sec, ...)
|
||||
|
||||
library(ggalluvial)
|
||||
|
||||
na.color <- "#2986cc"
|
||||
box.color <- "#1E4B66"
|
||||
|
||||
|
|
@ -5216,8 +5178,6 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
|
|||
)
|
||||
}
|
||||
|
||||
## Will fail to use stat="stratum" if library is not loaded.
|
||||
library(ggalluvial)
|
||||
p +
|
||||
ggplot2::geom_text(
|
||||
stat = "stratum",
|
||||
|
|
@ -5606,12 +5566,9 @@ m_redcap_readServer <- function(id) {
|
|||
)
|
||||
|
||||
# browser()
|
||||
shiny::withProgress(
|
||||
{
|
||||
imported <- try(rlang::exec(REDCapR::redcap_metadata_read, !!!parameters), silent = TRUE)
|
||||
},
|
||||
message = paste("Connecting to", data_rv$uri)
|
||||
)
|
||||
shiny::withProgress({
|
||||
imported <- try(rlang::exec(REDCapR::redcap_metadata_read, !!!parameters), silent = TRUE)
|
||||
},message = paste("Connecting to",data_rv$uri))
|
||||
|
||||
## TODO: Simplify error messages
|
||||
if (inherits(imported, "try-error") || NROW(imported) < 1 || ifelse(is.list(imported), !isTRUE(imported$success), FALSE)) {
|
||||
|
|
@ -5637,7 +5594,7 @@ m_redcap_readServer <- function(id) {
|
|||
status = "success",
|
||||
include_data_alert(
|
||||
see_data_text = "Click to see data dictionary",
|
||||
dataIdName = "see_dd",
|
||||
dataIdName = "see_data",
|
||||
extra = tags$p(
|
||||
tags$b(phosphoricons::ph("check", weight = "bold"), "Connected to server!"),
|
||||
glue::glue("The {data_rv$info$project_title} project is loaded.")
|
||||
|
|
@ -5663,8 +5620,8 @@ m_redcap_readServer <- function(id) {
|
|||
output$connect_success <- shiny::reactive(identical(data_rv$dd_status, "success"))
|
||||
shiny::outputOptions(output, "connect_success", suspendWhenHidden = FALSE)
|
||||
|
||||
shiny::observeEvent(input$see_dd, {
|
||||
show_data(
|
||||
shiny::observeEvent(input$see_data, {
|
||||
datamods::show_data(
|
||||
purrr::pluck(data_rv$dd_list, "data"),
|
||||
title = "Data dictionary",
|
||||
type = "modal",
|
||||
|
|
@ -5673,17 +5630,6 @@ m_redcap_readServer <- function(id) {
|
|||
)
|
||||
})
|
||||
|
||||
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)
|
||||
|
|
@ -5798,24 +5744,13 @@ m_redcap_readServer <- function(id) {
|
|||
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)
|
||||
)
|
||||
),
|
||||
code <- rlang::call2("read_redcap_tables",
|
||||
!!!utils::modifyList(parameters, list(token = "PERSONAL_API_TOKEN")), ,
|
||||
.ns = "REDCapCAST"
|
||||
)
|
||||
|
||||
# browser()
|
||||
|
||||
if (inherits(imported, "try-error") || NROW(imported) < 1) {
|
||||
data_rv$data_status <- "error"
|
||||
data_rv$data_list <- NULL
|
||||
|
|
@ -5884,17 +5819,9 @@ m_redcap_readServer <- function(id) {
|
|||
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$data_message)
|
||||
),
|
||||
btn_show_data = TRUE
|
||||
tags$p(
|
||||
tags$b(phosphoricons::ph("check", weight = "bold"), "Success!"),
|
||||
data_rv$data_message
|
||||
)
|
||||
)
|
||||
} else {
|
||||
|
|
@ -6095,6 +6022,13 @@ redcap_demo_app <- function() {
|
|||
}
|
||||
|
||||
|
||||
########
|
||||
#### Current file: /Users/au301842/FreesearchR/R//redcap.R
|
||||
########
|
||||
|
||||
|
||||
|
||||
|
||||
########
|
||||
#### Current file: /Users/au301842/FreesearchR/R//regression_model.R
|
||||
########
|
||||
|
|
@ -6372,13 +6306,12 @@ data_type <- function(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) {
|
||||
} else if (length(unique(data)) < 2) {
|
||||
out <- "monotone"
|
||||
} else if (any(c("factor", "logical") %in% cl_d) | l_unique == 2) {
|
||||
if (identical("logical", cl_d) | l_unique == 2) {
|
||||
} else if (any(c("factor", "logical") %in% cl_d) | length(unique(data)) == 2) {
|
||||
if (identical("logical", cl_d) | length(unique(data)) == 2) {
|
||||
out <- "dichotomous"
|
||||
} else {
|
||||
# if (is.ordered(data)) {
|
||||
|
|
@ -6391,7 +6324,7 @@ data_type <- function(data) {
|
|||
out <- "text"
|
||||
} else if (any(c("hms", "Date", "POSIXct", "POSIXt") %in% cl_d)) {
|
||||
out <- "datetime"
|
||||
} else if (l_unique > 2) {
|
||||
} else if (!length(unique(data)) == 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) &
|
||||
|
|
@ -8066,7 +7999,7 @@ update_factor_ui <- function(id) {
|
|||
fluidRow(
|
||||
column(
|
||||
width = 6,
|
||||
shinyWidgets::virtualSelectInput(
|
||||
virtualSelectInput(
|
||||
inputId = ns("variable"),
|
||||
label = i18n("Factor variable to reorder:"),
|
||||
choices = NULL,
|
||||
|
|
@ -8101,10 +8034,10 @@ update_factor_ui <- function(id) {
|
|||
)
|
||||
)
|
||||
),
|
||||
toastui::datagridOutput(ns("grid")),
|
||||
datagridOutput(ns("grid")),
|
||||
tags$div(
|
||||
class = "float-end",
|
||||
shinyWidgets::prettyCheckbox(
|
||||
prettyCheckbox(
|
||||
inputId = ns("new_var"),
|
||||
label = i18n("Create a new variable (otherwise replaces the one selected)"),
|
||||
value = FALSE,
|
||||
|
|
@ -8330,6 +8263,10 @@ winbox_update_factor <- function(id,
|
|||
#### Current file: /Users/au301842/FreesearchR/R//update-variables-ext.R
|
||||
########
|
||||
|
||||
library(data.table)
|
||||
library(rlang)
|
||||
|
||||
|
||||
#' Select, rename and convert variables
|
||||
#'
|
||||
#' @param id Module id. See [shiny::moduleServer()].
|
||||
|
|
@ -9380,10 +9317,10 @@ ui_elements <- list(
|
|||
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 = "input.source=='redcap'",
|
||||
DT::DTOutput(outputId = "redcap_prev")
|
||||
),
|
||||
shiny::conditionalPanel(
|
||||
condition = "output.data_loaded == true",
|
||||
shiny::br(),
|
||||
|
|
@ -9392,8 +9329,13 @@ ui_elements <- list(
|
|||
shiny::fluidRow(
|
||||
shiny::column(
|
||||
width = 6,
|
||||
shiny::p("Filter by completeness threshold:"),
|
||||
shiny::br(),
|
||||
shiny::p("Filter by completeness threshold and manual selection:"),
|
||||
shiny::br(),
|
||||
shiny::br()
|
||||
),
|
||||
shiny::column(
|
||||
width = 6,
|
||||
shinyWidgets::noUiSliderInput(
|
||||
inputId = "complete_cutoff",
|
||||
label = NULL,
|
||||
|
|
@ -9406,17 +9348,12 @@ ui_elements <- list(
|
|||
color = datamods:::get_primary_color()
|
||||
),
|
||||
shiny::helpText("Exclude variables with completeness below the specified percentage."),
|
||||
shiny::br()
|
||||
),
|
||||
shiny::column(
|
||||
width = 6,
|
||||
shiny::p("Specify manually:"),
|
||||
shiny::br(),
|
||||
shiny::br(),
|
||||
shiny::uiOutput(outputId = "import_var"),
|
||||
shiny::br()
|
||||
shiny::uiOutput(outputId = "data_info_import", inline = TRUE)
|
||||
)
|
||||
),
|
||||
shiny::uiOutput(outputId = "data_info_import", inline = TRUE)
|
||||
)
|
||||
),
|
||||
shiny::br(),
|
||||
shiny::br(),
|
||||
|
|
@ -9893,7 +9830,33 @@ ui <- bslib::page_fixed(
|
|||
#### Current file: /Users/au301842/FreesearchR/app/server.R
|
||||
########
|
||||
|
||||
|
||||
library(readr)
|
||||
library(MASS)
|
||||
library(stats)
|
||||
library(gt)
|
||||
# library(openxlsx2)
|
||||
library(haven)
|
||||
library(readODS)
|
||||
require(shiny)
|
||||
library(bslib)
|
||||
library(assertthat)
|
||||
library(dplyr)
|
||||
library(quarto)
|
||||
library(here)
|
||||
library(broom)
|
||||
library(broom.helpers)
|
||||
library(easystats)
|
||||
library(patchwork)
|
||||
library(DHARMa)
|
||||
library(apexcharter)
|
||||
library(toastui)
|
||||
library(datamods)
|
||||
library(IDEAFilter)
|
||||
library(shinyWidgets)
|
||||
library(DT)
|
||||
library(data.table)
|
||||
library(gtsummary)
|
||||
library(shinyjs)
|
||||
|
||||
data(starwars)
|
||||
data(mtcars)
|
||||
|
|
@ -9901,8 +9864,8 @@ data(trial)
|
|||
|
||||
load_data <- function() {
|
||||
Sys.sleep(1)
|
||||
shinyjs::hide("loading_page")
|
||||
shinyjs::show("main_content")
|
||||
hide("loading_page")
|
||||
show("main_content")
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -9983,14 +9946,14 @@ server <- function(input, output, session) {
|
|||
})
|
||||
|
||||
## This is used to ensure the reactive data is retrieved
|
||||
# output$redcap_prev <- DT::renderDT(
|
||||
# {
|
||||
# DT::datatable(head(from_redcap$data(), 5),
|
||||
# caption = "First 5 observations"
|
||||
# )
|
||||
# },
|
||||
# server = TRUE
|
||||
# )
|
||||
output$redcap_prev <- DT::renderDT(
|
||||
{
|
||||
DT::datatable(head(from_redcap$data(), 5),
|
||||
caption = "First 5 observations"
|
||||
)
|
||||
},
|
||||
server = TRUE
|
||||
)
|
||||
|
||||
from_env <- datamods::import_globalenv_server(
|
||||
id = "env",
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@ cut_variable_server(id, data_r = reactive(NULL))
|
|||
|
||||
modal_cut_variable(
|
||||
id,
|
||||
title = datamods:::i18n("Convert Numeric to Factor"),
|
||||
title = i18n("Convert Numeric to Factor"),
|
||||
easyClose = TRUE,
|
||||
size = "l",
|
||||
footer = NULL
|
||||
|
|
|
|||
|
|
@ -22,6 +22,5 @@ mtcars |> get_label(var = "mpg")
|
|||
mtcars |> get_label()
|
||||
mtcars$mpg |> get_label()
|
||||
gtsummary::trial |> get_label(var = "trt")
|
||||
gtsummary::trial$trt |> get_label()
|
||||
1:10 |> get_label()
|
||||
}
|
||||
|
|
|
|||
|
|
@ -39,5 +39,6 @@ data.frame(
|
|||
plot_sankey_single("first", "last", color.group = "pri")
|
||||
mtcars |>
|
||||
default_parsing() |>
|
||||
str()
|
||||
plot_sankey_single("cyl", "vs", color.group = "pri")
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,20 +0,0 @@
|
|||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/helpers.R
|
||||
\name{simple_snake}
|
||||
\alias{simple_snake}
|
||||
\title{Simplified version of the snakecase packages to_snake_case}
|
||||
\usage{
|
||||
simple_snake(data)
|
||||
}
|
||||
\arguments{
|
||||
\item{data}{character string vector}
|
||||
}
|
||||
\value{
|
||||
vector
|
||||
}
|
||||
\description{
|
||||
Simplified version of the snakecase packages to_snake_case
|
||||
}
|
||||
\examples{
|
||||
c("foo bar", "fooBar21", "!!Foo'B'a-r", "foo_bar", "F OO bar") |> simple_snake()
|
||||
}
|
||||
Loading…
Add table
Reference in a new issue