NAMESPACE

@@ -42,7 +42,6 @@ export(getfun)
 export(gg_theme_export)
 export(gg_theme_shiny)
 export(grepl_fix)
-export(if_not_missing)
 export(import_delim)
 export(import_dta)
 export(import_file_server)

NEWS.md

@@ -1,7 +1,3 @@
-# FreesearchR 25.4.12
-
-Polished and simplified data import module including a much improved REDCap import module.
-
 # FreesearchR 25.4.1
 
 Focus is on polish and improved ui/ux.

R/app_version.R

@@ -1 +1 @@
-app_version <- function()'Version: 25.4.1.250403_1409'
+app_version <- function()'250402_1131'

R/correlations-module.R

@@ -128,7 +128,7 @@ sentence_paste <- function(data, and.str = "and") {
   } else if (length(data) == 2) {
     paste(data, collapse = glue::glue(" {and.str} "))
   } else if (length(data) > 2) {
-    paste(paste(data[-length(data)], collapse = ", "), data[length(data)], sep = glue::glue(" {and.str} "))
+    paste(paste(data[-length(data)], collapse = ", "), data[length(data)], collapse = glue::glue(" {and.str} "))
   }
 }
 

R/helpers.R

@@ -335,7 +335,7 @@ data_description <- function(data) {
   p_complete <- n_complete/n
 
   sprintf(
-    i18n("Data has %s observations and %s variables, with %s (%s%%) complete cases."),
+    i18n("Data has %s observations and %s variables, with %s (%s%%) complete cases"),
     n,
     n_var,
     n_complete,
@@ -369,26 +369,3 @@ get_ggplot_label <- function(data,label){
   assertthat::assert_that(ggplot2::is.ggplot(data))
   data$labels[[label]]
 }
-
-
-#' Return if available
-#'
-#' @param data vector
-#' @param default assigned value for missings
-#'
-#' @returns vector
-#' @export
-#'
-#' @examples
-#' NULL |> if_not_missing("new")
-#' c(2,"a",NA) |> if_not_missing()
-#' "See" |> if_not_missing()
-if_not_missing <- function(data,default=NULL){
-  if (length(data)>1){
-    Reduce(c,lapply(data,if_not_missing))
-  } else if (is.na(data) || is.null(data)){
-    return(default)
-  } else {
-    return(data)
-  }
-}

R/redcap_read_shiny_module.R

@@ -7,7 +7,7 @@
 #'
 #' @return shiny ui element
 #' @export
-m_redcap_readUI <- function(id, title = TRUE, url = NULL) {
+m_redcap_readUI <- function(id, title = TRUE) {
   ns <- shiny::NS(id)
 
   if (isTRUE(title)) {
@@ -23,7 +23,7 @@ m_redcap_readUI <- function(id, title = TRUE, url = NULL) {
     shiny::textInput(
       inputId = ns("uri"),
       label = "Web address",
-      value = if_not_missing(url, "https://redcap.your.institution/")
+      value = "https://redcap.your.institution/"
     ),
     shiny::helpText("Format should be either 'https://redcap.your.institution/' or 'https://your.institution/redcap/'"),
     shiny::textInput(
@@ -32,13 +32,11 @@ m_redcap_readUI <- function(id, title = TRUE, url = NULL) {
       value = ""
     ),
     shiny::helpText("The token is a string of 32 numbers and letters."),
-    shiny::br(),
-    shiny::br(),
     shiny::actionButton(
       inputId = ns("data_connect"),
       label = "Connect",
       icon = shiny::icon("link", lib = "glyphicon"),
-      width = "100%",
+      # width = NULL,
       disabled = TRUE
     ),
     shiny::br(),
@@ -55,15 +53,6 @@ m_redcap_readUI <- function(id, title = TRUE, url = NULL) {
     shiny::br()
   )
 
-  filter_ui <-
-    shiny::tagList(
-      # width = 6,
-      shiny::uiOutput(outputId = ns("arms")),
-      shiny::textInput(
-        inputId = ns("filter"),
-        label = "Optional filter logic (e.g., ⁠[gender] = 'female')"
-      )
-    )
 
   params_ui <-
     shiny::tagList(
@@ -71,28 +60,41 @@ m_redcap_readUI <- function(id, title = TRUE, url = NULL) {
       shiny::tags$h4("Data import parameters"),
       shiny::helpText("Options here will show, when API and uri are typed"),
       shiny::uiOutput(outputId = ns("fields")),
-      shiny::tags$div(
-        class = "shiny-input-container",
-        shiny::tags$label(
-          class = "control-label",
-          `for` = ns("dropdown_params"),
-          "...",
-          style = htmltools::css(visibility = "hidden")
-        ),
-        shinyWidgets::dropMenu(
-          shiny::actionButton(
-            inputId = ns("dropdown_params"),
-            label = "Add data filters",
-            icon = shiny::icon("filter"),
-            width = "100%",
-            class = "px-1"
-          ),
-          filter_ui
-        ),
-        shiny::helpText("Optionally filter project arms if logitudinal or apply server side data filters")
-      ),
       shiny::uiOutput(outputId = ns("data_type")),
       shiny::uiOutput(outputId = ns("fill")),
+      shinyWidgets::switchInput(
+        inputId = "do_filter",
+        label = "Apply filter?",
+        value = FALSE,
+        inline = FALSE,
+        onLabel = "YES",
+        offLabel = "NO"
+      ),
+      shiny::conditionalPanel(
+        condition = "input.do_filter",
+        shiny::uiOutput(outputId = ns("arms")),
+        shiny::textInput(
+          inputId = ns("filter"),
+          label = "Optional filter logic (e.g., ⁠[gender] = 'female')"
+        )
+      )
+    )
+
+
+  shiny::fluidPage(
+    title=title,
+    bslib::layout_columns(
+      server_ui,
+      params_ui,
+      col_widths = bslib::breakpoints(
+        sm = c(12, 12),
+        md = c(12, 12)
+      )
+    ),
+    shiny::column(
+      width = 12,
+      # shiny::actionButton(inputId = ns("import"), label = "Import"),
+      ## TODO: Use busy indicator like on download to have button activate/deactivate
       shiny::actionButton(
         inputId = ns("data_import"),
         label = "Import",
@@ -100,18 +102,6 @@ m_redcap_readUI <- function(id, title = TRUE, url = NULL) {
         width = "100%",
         disabled = TRUE
       ),
-      shiny::tags$br(),
-      shiny::tags$br(),
-      tags$div(
-        id = ns("retrieved-placeholder"),
-        shinyWidgets::alert(
-          id = ns("retrieved-result"),
-          status = "info",
-          tags$p(phosphoricons::ph("info", weight = "bold"), "Please specify data to download, then press 'Import'.")
-        ),
-        dismissible = TRUE
-      )#,
-      ## TODO: Use busy indicator like on download to have button activate/deactivate
       # bslib::input_task_button(
       #   id = ns("data_import"),
       #   label = "Import",
@@ -124,21 +114,13 @@ m_redcap_readUI <- function(id, title = TRUE, url = NULL) {
       #   type = "primary",
       #   auto_reset = TRUE#,state="busy"
       # ),
-      # shiny::br(),
+      shiny::br(),
-      # shiny::helpText("Press 'Import' to get data from the REDCap server. Check the preview below before proceeding.")
+      shiny::br(),
-    )
+      shiny::helpText("Press 'Import' to get data from the REDCap server. Check the preview below before proceeding."),
-
+      shiny::br(),
-
-  shiny::fluidPage(
-    title = title,
-    server_ui,
-    shiny::conditionalPanel(
-      condition = "output.connect_success == true",
-      params_ui,
-      ns = ns
-    ),
       shiny::br()
     )
+  )
 }
 
 
@@ -222,11 +204,9 @@ m_redcap_readServer <- function(id) {
               datamods:::insert_alert(
                 selector = ns("connect"),
                 status = "success",
-                include_data_alert(
+                include_data_alert(see_data_text = "Click to see data dictionary",
-                  see_data_text = "Click to see data dictionary",
                   dataIdName = "see_data",
-                  extra = tags$p(tags$b(phosphoricons::ph("check", weight = "bold"), "Connected to server!"),
+                  extra = tags$p(tags$b(phosphoricons::ph("check", weight = "bold"), "Connected to server!"), tags$p(paste0(data_rv$info$project_title, " loaded."))),
-                                 glue::glue("The {data_rv$info$project_title} project is loaded.")),
                   btn_show_data = TRUE
                 )
               )
@@ -245,9 +225,6 @@ 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$see_data, {
       datamods::show_data(
         purrr::pluck(data_rv$dd_list, "data"),
@@ -336,7 +313,6 @@ m_redcap_readServer <- function(id) {
     })
 
     output$arms <- shiny::renderUI({
-      if (NROW(arms()) > 0) {
       vectorSelectInput(
         inputId = ns("arms"),
         selected = NULL,
@@ -344,13 +320,10 @@ m_redcap_readServer <- function(id) {
         choices = stats::setNames(arms()[[3]], arms()[[1]]),
         multiple = TRUE
       )
-      }
     })
 
     shiny::observeEvent(input$data_import, {
       shiny::req(input$fields)
-
-      # browser()
       record_id <- purrr::pluck(data_rv$dd_list, "data")[[1]][1]
 
 
@@ -361,11 +334,7 @@ m_redcap_readServer <- function(id) {
         events = input$arms,
         raw_or_label = "both",
         filter_logic = input$filter,
-        split_forms = ifelse(
+        split_forms = if (input$data_type == "long") "none" else "all"
-          input$data_type == "long" && !is.null(input$data_type),
-          "none",
-          "all"
-        )
       )
 
       shiny::withProgress(message = "Downloading REDCap data. Hold on for a moment..", {
@@ -373,24 +342,19 @@ m_redcap_readServer <- function(id) {
       })
 
       code <- rlang::call2("read_redcap_tables",
-        !!!utils::modifyList(parameters, list(token = "PERSONAL_API_TOKEN")), ,
+                           !!!utils::modifyList(parameters,list(token="PERSONAL_API_TOKEN")),
-        .ns = "REDCapCAST"
+                           , .ns = "REDCapCAST")
-      )
 
-      # browser()
 
       if (inherits(imported, "try-error") || NROW(imported) < 1) {
         data_rv$data_status <- "error"
         data_rv$data_list <- NULL
-        data_rv$data_message <- imported$raw_text
       } else {
         data_rv$data_status <- "success"
-        data_rv$data_message <- "Requested data was retrieved!"
 
         ## The data management below should be separated to allow for changing
         ## "wide"/"long" without re-importing data
-
+        if (input$data_type != "long") {
-        if (parameters$split_form == "all") {
           # browser()
           out <- imported |>
             # redcap_wider()
@@ -414,20 +378,6 @@ m_redcap_readServer <- function(id) {
           }
         }
 
-        # browser()
-        in_data_check <- parameters$fields %in% names(out) |
-          sapply(names(out), \(.x) any(sapply(parameters$fields, \(.y) startsWith(.x, .y))))
-
-        if (!any(in_data_check[-1])) {
-          data_rv$data_status <- "warning"
-          data_rv$data_message <- "Data retrieved, but it looks like only the ID was retrieved from the server. Please check with your REDCap administrator that you have required permissions for data access."
-        }
-
-        if (!all(in_data_check)) {
-          data_rv$data_status <- "warning"
-          data_rv$data_message <- "Data retrieved, but it looks like not all requested fields were retrieved from the server. Please check with your REDCap administrator that you have required permissions for data access."
-        }
-
         data_rv$code <- code
 
         data_rv$data <- out |>
@@ -437,33 +387,13 @@ m_redcap_readServer <- function(id) {
       }
     })
 
-    shiny::observeEvent(
+    # shiny::observe({
-      data_rv$data_status,
+    #   shiny::req(data_rv$imported)
-      {
+    #
-        # browser()
+    #   imported <- data_rv$imported
-        if (identical(data_rv$data_status, "error")) {
+    #
-          datamods:::insert_error(mssg = data_rv$data_message, selector = ns("retrieved"))
+    #
-        } else if (identical(data_rv$data_status, "success")) {
+    # })
-          datamods:::insert_alert(
-            selector = ns("retrieved"),
-            status = data_rv$data_status,
-            tags$p(
-              tags$b(phosphoricons::ph("check", weight = "bold"), "Success!"),
-              data_rv$data_message
-            )
-          )
-        } else {
-          datamods:::insert_alert(
-            selector = ns("retrieved"),
-            status = data_rv$data_status,
-            tags$p(
-              tags$b(phosphoricons::ph("warning", weight = "bold"), "Warning!"),
-              data_rv$data_message
-            )
-          )
-        }
-      }
-    )
 
     return(list(
       status = shiny::reactive(data_rv$data_status),
@@ -623,12 +553,13 @@ drop_empty_event <- function(data, event = "redcap_event_name") {
 #' }
 redcap_demo_app <- function() {
   ui <- shiny::fluidPage(
-    m_redcap_readUI("data", url = NULL),
+    m_redcap_readUI("data"),
     DT::DTOutput("data"),
     shiny::tags$b("Code:"),
     shiny::verbatimTextOutput(outputId = "code")
   )
   server <- function(input, output, session) {
+
     data_val <- m_redcap_readServer(id = "data")
 
     output$data <- DT::renderDataTable(

R/regression_plot.R

@@ -2,14 +2,12 @@
 #'
 #' @param x (`tbl_regression`, `tbl_uvregression`)\cr
 #'   A 'tbl_regression' or 'tbl_uvregression' object
-#' @param plot_ref (scalar `logical`)\cr
+##  #' @param remove_header_rows (scalar `logical`)\cr
-#'   plot reference values
+##  #'   logical indicating whether to remove header rows
-#' @param remove_header_rows (scalar `logical`)\cr
+##  #'   for categorical variables. Default is `TRUE`
-#'   logical indicating whether to remove header rows
+##  #' @param remove_reference_rows (scalar `logical`)\cr
-#'   for categorical variables. Default is `TRUE`
+##  #'   logical indicating whether to remove reference rows
-#' @param remove_reference_rows (scalar `logical`)\cr
+##  #'   for categorical variables. Default is `FALSE`.
-#'   logical indicating whether to remove reference rows
-#'   for categorical variables. Default is `FALSE`.
 #' @param ... arguments passed to `ggstats::ggcoef_plot(...)`
 #'
 #' @returns ggplot object

R/update-variables-ext.R

@@ -118,8 +118,8 @@ update_variables_server <- function(id,
 
       output$data_info <- shiny::renderUI({
         shiny::req(data_r())
-        data_description(data_r())
+        data <- data_r()
-        # sprintf(i18n("Data has %s observations and %s variables."), nrow(data), ncol(data))
+        sprintf(i18n("Data has %s observations and %s variables."), nrow(data), ncol(data))
       })
 
       variables_r <- shiny::reactive({
@@ -645,10 +645,10 @@ convert_to <- function(data,
       setNames(list(expr(as.character(!!sym(variable)))), variable)
     )
   } else if (identical(new_class, "factor")) {
-    data[[variable]] <- REDCapCAST::as_factor(x = data[[variable]])
+    data[[variable]] <- as.factor(x = data[[variable]])
     attr(data, "code_03_convert") <- c(
       attr(data, "code_03_convert"),
-      setNames(list(expr(REDCapCAST::as_factor(!!sym(variable)))), variable)
+      setNames(list(expr(as.factor(!!sym(variable)))), variable)
     )
   } else if (identical(new_class, "numeric")) {
     data[[variable]] <- as.numeric(data[[variable]], ...)

inst/apps/FreesearchR/app.R

@@ -10,7 +10,7 @@
 #### Current file: /Users/au301842/FreesearchR/R//app_version.R 
 ########
 
-app_version <- function()'Version: 25.4.1.250403_1409'
+app_version <- function()'250402_1131'
 
 
 ########
@@ -287,7 +287,7 @@ sentence_paste <- function(data, and.str = "and") {
   } else if (length(data) == 2) {
     paste(data, collapse = glue::glue(" {and.str} "))
   } else if (length(data) > 2) {
-    paste(paste(data[-length(data)], collapse = ", "), data[length(data)], sep = glue::glue(" {and.str} "))
+    paste(paste(data[-length(data)], collapse = ", "), data[length(data)], collapse = glue::glue(" {and.str} "))
   }
 }
 
@@ -2808,7 +2808,7 @@ data_description <- function(data) {
   p_complete <- n_complete/n
 
   sprintf(
-    i18n("Data has %s observations and %s variables, with %s (%s%%) complete cases."),
+    i18n("Data has %s observations and %s variables, with %s (%s%%) complete cases"),
     n,
     n_var,
     n_complete,
@@ -2844,29 +2844,6 @@ get_ggplot_label <- function(data,label){
 }
 
 
-#' Return if available
-#'
-#' @param data vector
-#' @param default assigned value for missings
-#'
-#' @returns vector
-#' @export
-#'
-#' @examples
-#' NULL |> if_not_missing("new")
-#' c(2,"a",NA) |> if_not_missing()
-#' "See" |> if_not_missing()
-if_not_missing <- function(data,default=NULL){
-  if (length(data)>1){
-    Reduce(c,lapply(data,if_not_missing))
-  } else if (is.na(data) || is.null(data)){
-    return(default)
-  } else {
-    return(data)
-  }
-}
-
-
 ########
 #### Current file: /Users/au301842/FreesearchR/R//import-file-ext.R 
 ########
@@ -4191,7 +4168,7 @@ plot_download_server <- function(id,
 #'
 #' @return shiny ui element
 #' @export
-m_redcap_readUI <- function(id, title = TRUE, url = NULL) {
+m_redcap_readUI <- function(id, title = TRUE) {
   ns <- shiny::NS(id)
 
   if (isTRUE(title)) {
@@ -4207,7 +4184,7 @@ m_redcap_readUI <- function(id, title = TRUE, url = NULL) {
     shiny::textInput(
       inputId = ns("uri"),
       label = "Web address",
-      value = if_not_missing(url, "https://redcap.your.institution/")
+      value = "https://redcap.your.institution/"
     ),
     shiny::helpText("Format should be either 'https://redcap.your.institution/' or 'https://your.institution/redcap/'"),
     shiny::textInput(
@@ -4216,13 +4193,11 @@ m_redcap_readUI <- function(id, title = TRUE, url = NULL) {
       value = ""
     ),
     shiny::helpText("The token is a string of 32 numbers and letters."),
-    shiny::br(),
-    shiny::br(),
     shiny::actionButton(
       inputId = ns("data_connect"),
       label = "Connect",
       icon = shiny::icon("link", lib = "glyphicon"),
-      width = "100%",
+      # width = NULL,
       disabled = TRUE
     ),
     shiny::br(),
@@ -4239,15 +4214,6 @@ m_redcap_readUI <- function(id, title = TRUE, url = NULL) {
     shiny::br()
   )
 
-  filter_ui <-
-    shiny::tagList(
-      # width = 6,
-      shiny::uiOutput(outputId = ns("arms")),
-      shiny::textInput(
-        inputId = ns("filter"),
-        label = "Optional filter logic (e.g., ⁠[gender] = 'female')"
-      )
-    )
 
   params_ui <-
     shiny::tagList(
@@ -4255,28 +4221,41 @@ m_redcap_readUI <- function(id, title = TRUE, url = NULL) {
       shiny::tags$h4("Data import parameters"),
       shiny::helpText("Options here will show, when API and uri are typed"),
       shiny::uiOutput(outputId = ns("fields")),
-      shiny::tags$div(
-        class = "shiny-input-container",
-        shiny::tags$label(
-          class = "control-label",
-          `for` = ns("dropdown_params"),
-          "...",
-          style = htmltools::css(visibility = "hidden")
-        ),
-        shinyWidgets::dropMenu(
-          shiny::actionButton(
-            inputId = ns("dropdown_params"),
-            label = "Add data filters",
-            icon = shiny::icon("filter"),
-            width = "100%",
-            class = "px-1"
-          ),
-          filter_ui
-        ),
-        shiny::helpText("Optionally filter project arms if logitudinal or apply server side data filters")
-      ),
       shiny::uiOutput(outputId = ns("data_type")),
       shiny::uiOutput(outputId = ns("fill")),
+      shinyWidgets::switchInput(
+        inputId = "do_filter",
+        label = "Apply filter?",
+        value = FALSE,
+        inline = FALSE,
+        onLabel = "YES",
+        offLabel = "NO"
+      ),
+      shiny::conditionalPanel(
+        condition = "input.do_filter",
+        shiny::uiOutput(outputId = ns("arms")),
+        shiny::textInput(
+          inputId = ns("filter"),
+          label = "Optional filter logic (e.g., ⁠[gender] = 'female')"
+        )
+      )
+    )
+
+
+  shiny::fluidPage(
+    title=title,
+    bslib::layout_columns(
+      server_ui,
+      params_ui,
+      col_widths = bslib::breakpoints(
+        sm = c(12, 12),
+        md = c(12, 12)
+      )
+    ),
+    shiny::column(
+      width = 12,
+      # shiny::actionButton(inputId = ns("import"), label = "Import"),
+      ## TODO: Use busy indicator like on download to have button activate/deactivate
       shiny::actionButton(
         inputId = ns("data_import"),
         label = "Import",
@@ -4284,18 +4263,6 @@ m_redcap_readUI <- function(id, title = TRUE, url = NULL) {
         width = "100%",
         disabled = TRUE
       ),
-      shiny::tags$br(),
-      shiny::tags$br(),
-      tags$div(
-        id = ns("retrieved-placeholder"),
-        shinyWidgets::alert(
-          id = ns("retrieved-result"),
-          status = "info",
-          tags$p(phosphoricons::ph("info", weight = "bold"), "Please specify data to download, then press 'Import'.")
-        ),
-        dismissible = TRUE
-      )#,
-      ## TODO: Use busy indicator like on download to have button activate/deactivate
       # bslib::input_task_button(
       #   id = ns("data_import"),
       #   label = "Import",
@@ -4308,21 +4275,13 @@ m_redcap_readUI <- function(id, title = TRUE, url = NULL) {
       #   type = "primary",
       #   auto_reset = TRUE#,state="busy"
       # ),
-      # shiny::br(),
+      shiny::br(),
-      # shiny::helpText("Press 'Import' to get data from the REDCap server. Check the preview below before proceeding.")
+      shiny::br(),
-    )
+      shiny::helpText("Press 'Import' to get data from the REDCap server. Check the preview below before proceeding."),
-
+      shiny::br(),
-
-  shiny::fluidPage(
-    title = title,
-    server_ui,
-    shiny::conditionalPanel(
-      condition = "output.connect_success == true",
-      params_ui,
-      ns = ns
-    ),
       shiny::br()
     )
+  )
 }
 
 
@@ -4406,11 +4365,9 @@ m_redcap_readServer <- function(id) {
               datamods:::insert_alert(
                 selector = ns("connect"),
                 status = "success",
-                include_data_alert(
+                include_data_alert(see_data_text = "Click to see data dictionary",
-                  see_data_text = "Click to see data dictionary",
                   dataIdName = "see_data",
-                  extra = tags$p(tags$b(phosphoricons::ph("check", weight = "bold"), "Connected to server!"),
+                  extra = tags$p(tags$b(phosphoricons::ph("check", weight = "bold"), "Connected to server!"), tags$p(paste0(data_rv$info$project_title, " loaded."))),
-                                 glue::glue("The {data_rv$info$project_title} project is loaded.")),
                   btn_show_data = TRUE
                 )
               )
@@ -4429,9 +4386,6 @@ 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$see_data, {
       datamods::show_data(
         purrr::pluck(data_rv$dd_list, "data"),
@@ -4520,7 +4474,6 @@ m_redcap_readServer <- function(id) {
     })
 
     output$arms <- shiny::renderUI({
-      if (NROW(arms()) > 0) {
       vectorSelectInput(
         inputId = ns("arms"),
         selected = NULL,
@@ -4528,13 +4481,10 @@ m_redcap_readServer <- function(id) {
         choices = stats::setNames(arms()[[3]], arms()[[1]]),
         multiple = TRUE
       )
-      }
     })
 
     shiny::observeEvent(input$data_import, {
       shiny::req(input$fields)
-
-      # browser()
       record_id <- purrr::pluck(data_rv$dd_list, "data")[[1]][1]
 
 
@@ -4545,11 +4495,7 @@ m_redcap_readServer <- function(id) {
         events = input$arms,
         raw_or_label = "both",
         filter_logic = input$filter,
-        split_forms = ifelse(
+        split_forms = if (input$data_type == "long") "none" else "all"
-          input$data_type == "long" && !is.null(input$data_type),
-          "none",
-          "all"
-        )
       )
 
       shiny::withProgress(message = "Downloading REDCap data. Hold on for a moment..", {
@@ -4557,24 +4503,19 @@ m_redcap_readServer <- function(id) {
       })
 
       code <- rlang::call2("read_redcap_tables",
-        !!!utils::modifyList(parameters, list(token = "PERSONAL_API_TOKEN")), ,
+                           !!!utils::modifyList(parameters,list(token="PERSONAL_API_TOKEN")),
-        .ns = "REDCapCAST"
+                           , .ns = "REDCapCAST")
-      )
 
-      # browser()
 
       if (inherits(imported, "try-error") || NROW(imported) < 1) {
         data_rv$data_status <- "error"
         data_rv$data_list <- NULL
-        data_rv$data_message <- imported$raw_text
       } else {
         data_rv$data_status <- "success"
-        data_rv$data_message <- "Requested data was retrieved!"
 
         ## The data management below should be separated to allow for changing
         ## "wide"/"long" without re-importing data
-
+        if (input$data_type != "long") {
-        if (parameters$split_form == "all") {
           # browser()
           out <- imported |>
             # redcap_wider()
@@ -4598,20 +4539,6 @@ m_redcap_readServer <- function(id) {
           }
         }
 
-        # browser()
-        in_data_check <- parameters$fields %in% names(out) |
-          sapply(names(out), \(.x) any(sapply(parameters$fields, \(.y) startsWith(.x, .y))))
-
-        if (!any(in_data_check[-1])) {
-          data_rv$data_status <- "warning"
-          data_rv$data_message <- "Data retrieved, but it looks like only the ID was retrieved from the server. Please check with your REDCap administrator that you have required permissions for data access."
-        }
-
-        if (!all(in_data_check)) {
-          data_rv$data_status <- "warning"
-          data_rv$data_message <- "Data retrieved, but it looks like not all requested fields were retrieved from the server. Please check with your REDCap administrator that you have required permissions for data access."
-        }
-
         data_rv$code <- code
 
         data_rv$data <- out |>
@@ -4621,33 +4548,13 @@ m_redcap_readServer <- function(id) {
       }
     })
 
-    shiny::observeEvent(
+    # shiny::observe({
-      data_rv$data_status,
+    #   shiny::req(data_rv$imported)
-      {
+    #
-        # browser()
+    #   imported <- data_rv$imported
-        if (identical(data_rv$data_status, "error")) {
+    #
-          datamods:::insert_error(mssg = data_rv$data_message, selector = ns("retrieved"))
+    #
-        } else if (identical(data_rv$data_status, "success")) {
+    # })
-          datamods:::insert_alert(
-            selector = ns("retrieved"),
-            status = data_rv$data_status,
-            tags$p(
-              tags$b(phosphoricons::ph("check", weight = "bold"), "Success!"),
-              data_rv$data_message
-            )
-          )
-        } else {
-          datamods:::insert_alert(
-            selector = ns("retrieved"),
-            status = data_rv$data_status,
-            tags$p(
-              tags$b(phosphoricons::ph("warning", weight = "bold"), "Warning!"),
-              data_rv$data_message
-            )
-          )
-        }
-      }
-    )
 
     return(list(
       status = shiny::reactive(data_rv$data_status),
@@ -4807,12 +4714,13 @@ drop_empty_event <- function(data, event = "redcap_event_name") {
 #' }
 redcap_demo_app <- function() {
   ui <- shiny::fluidPage(
-    m_redcap_readUI("data", url = NULL),
+    m_redcap_readUI("data"),
     DT::DTOutput("data"),
     shiny::tags$b("Code:"),
     shiny::verbatimTextOutput(outputId = "code")
   )
   server <- function(input, output, session) {
+
     data_val <- m_redcap_readServer(id = "data")
 
     output$data <- DT::renderDataTable(
@@ -5514,14 +5422,12 @@ regression_model_uv_list <- function(data,
 #'
 #' @param x (`tbl_regression`, `tbl_uvregression`)\cr
 #'   A 'tbl_regression' or 'tbl_uvregression' object
-#' @param plot_ref (scalar `logical`)\cr
+##  #' @param remove_header_rows (scalar `logical`)\cr
-#'   plot reference values
+##  #'   logical indicating whether to remove header rows
-#' @param remove_header_rows (scalar `logical`)\cr
+##  #'   for categorical variables. Default is `TRUE`
-#'   logical indicating whether to remove header rows
+##  #' @param remove_reference_rows (scalar `logical`)\cr
-#'   for categorical variables. Default is `TRUE`
+##  #'   logical indicating whether to remove reference rows
-#' @param remove_reference_rows (scalar `logical`)\cr
+##  #'   for categorical variables. Default is `FALSE`.
-#'   logical indicating whether to remove reference rows
-#'   for categorical variables. Default is `FALSE`.
 #' @param ... arguments passed to `ggstats::ggcoef_plot(...)`
 #'
 #' @returns ggplot object
@@ -7005,8 +6911,8 @@ update_variables_server <- function(id,
 
       output$data_info <- shiny::renderUI({
         shiny::req(data_r())
-        data_description(data_r())
+        data <- data_r()
-        # sprintf(i18n("Data has %s observations and %s variables."), nrow(data), ncol(data))
+        sprintf(i18n("Data has %s observations and %s variables."), nrow(data), ncol(data))
       })
 
       variables_r <- shiny::reactive({
@@ -7532,10 +7438,10 @@ convert_to <- function(data,
       setNames(list(expr(as.character(!!sym(variable)))), variable)
     )
   } else if (identical(new_class, "factor")) {
-    data[[variable]] <- REDCapCAST::as_factor(x = data[[variable]])
+    data[[variable]] <- as.factor(x = data[[variable]])
     attr(data, "code_03_convert") <- c(
       attr(data, "code_03_convert"),
-      setNames(list(expr(REDCapCAST::as_factor(!!sym(variable)))), variable)
+      setNames(list(expr(as.factor(!!sym(variable)))), variable)
     )
   } else if (identical(new_class, "numeric")) {
     data[[variable]] <- as.numeric(data[[variable]], ...)
@@ -7934,8 +7840,6 @@ ui_elements <- list(
           condition = "input.source=='redcap'",
           DT::DTOutput(outputId = "redcap_prev")
         ),
-        shiny::conditionalPanel(
-          condition = "output.data_loaded == true",
         shiny::br(),
         shiny::br(),
         shiny::h5("Specify variables to include"),
@@ -7952,7 +7856,7 @@ ui_elements <- list(
             shinyWidgets::noUiSliderInput(
               inputId = "complete_cutoff",
               label = NULL,
-              update_on = "end",
+              update_on = "change",
               min = 0,
               max = 100,
               step = 5,
@@ -7960,13 +7864,12 @@ ui_elements <- list(
               format = shinyWidgets::wNumbFormat(decimals = 0),
               color = datamods:::get_primary_color()
             ),
-            shiny::helpText("Exclude variables with completeness below the specified percentage."),
+            shiny::helpText("Filter variables with completeness above the specified percentage."),
             shiny::br(),
             shiny::br(),
             shiny::uiOutput(outputId = "import_var"),
             shiny::uiOutput(outputId = "data_info_import", inline = TRUE)
           )
-        )
         ),
         shiny::br(),
         shiny::br(),
@@ -8049,20 +7952,36 @@ ui_elements <- list(
           fluidRow(
             shiny::column(
               width = 9,
-              shiny::tags$p(shiny::markdown("Below, are several options for simple data manipulation like update variables by renaming, creating new labels (for nicer tables in the report) and changing variable classes (numeric, factor/categorical etc.)."),
+              shiny::tags$p(shiny::markdown("Below, are several options to update variables (rename, set new labels (for nicer tables in the report) and change variable classes (numeric, factor/categorical etc.).), modify factor/categorical variables as well as create new factor from a continous variable or new variables with *R* code."))
-                            shiny::tags$p("There are also more advanced options to modify factor/categorical variables as well as create new factor from a continous variable or new variables with *R* code. At the bottom you can restore the original data."))
             )
           ),
-          # shiny::tags$br(),
+          shiny::tags$br(),
+          shiny::tags$br(),
           update_variables_ui("modal_variables"),
           shiny::tags$br(),
           shiny::tags$br(),
+          fluidRow(
+            shiny::column(
+              width = 2
+            ),
+            shiny::column(
+              width = 8,
               tags$h4("Advanced data manipulation"),
               shiny::tags$br(),
-          shiny::tags$br(),
+              fluidRow(
-          shiny::fluidRow(
                 shiny::column(
-              width = 4,
+                  width = 6,
+                  # tags$h4("Update or modify variables"),
+                  # shiny::tags$br(),
+                  # shiny::actionButton(
+                  #   inputId = "modal_variables",
+                  #   label = "Subset, rename and change class/type",
+                  #   width = "100%"
+                  # ),
+                  # shiny::tags$br(),
+                  # shiny::helpText("Subset variables, rename variables and labels, and apply new class to variables"),
+                  # shiny::tags$br(),
+                  # shiny::tags$br(),
                   shiny::actionButton(
                     inputId = "modal_update",
                     label = "Reorder factor levels",
@@ -8070,50 +7989,7 @@ ui_elements <- list(
                   ),
                   shiny::tags$br(),
                   shiny::helpText("Reorder the levels of factor/categorical variables."),
-            ),
-            shiny::column(
-              width = 4,
-              shiny::actionButton(
-                inputId = "modal_cut",
-                label = "New factor",
-                width = "100%"
-              ),
                   shiny::tags$br(),
-              shiny::helpText("Create factor/categorical variable from a continous variable (number/date/time).")
-            ),
-            shiny::column(
-              width = 4,
-              shiny::actionButton(
-                inputId = "modal_column",
-                label = "New variable",
-                width = "100%"
-              ),
-              shiny::tags$br(),
-              shiny::helpText(shiny::markdown("Create a new variable/column based on an *R*-expression."))
-            )
-          ),
-          shiny::tags$br(),
-          shiny::tags$br(),
-          tags$h4("Compare modified data to original"),
-          shiny::tags$br(),
-          shiny::tags$p(
-            "Raw print of the original vs the modified data."
-          ),
-          shiny::tags$br(),
-          shiny::fluidRow(
-            shiny::column(
-              width = 6,
-              shiny::tags$b("Original data:"),
-              # verbatimTextOutput("original"),
-              shiny::verbatimTextOutput("original_str")
-            ),
-            shiny::column(
-              width = 6,
-              shiny::tags$b("Modified data:"),
-              # verbatimTextOutput("modified"),
-              shiny::verbatimTextOutput("modified_str")
-            )
-          ),
                   shiny::tags$br(),
                   shiny::actionButton(
                     inputId = "data_reset",
@@ -8122,7 +7998,69 @@ ui_elements <- list(
                   ),
                   shiny::tags$br(),
                   shiny::helpText("Reset to original imported dataset. Careful! There is no un-doing."),
+                  shiny::tags$br(),
                   shiny::tags$br()
+                ),
+                shiny::column(
+                  width = 6,
+                  # tags$h4("Create new variables"),
+                  # shiny::tags$br(),
+                  shiny::actionButton(
+                    inputId = "modal_cut",
+                    label = "New factor",
+                    width = "100%"
+                  ),
+                  shiny::tags$br(),
+                  shiny::helpText("Create factor/categorical variable from a continous variable (number/date/time)."),
+                  shiny::tags$br(),
+                  shiny::tags$br(),
+                  shiny::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("Restore"),
+              # shiny::actionButton(
+              #   inputId = "data_reset",
+              #   label = "Restore original data",
+              #   width = "100%"
+              # ),
+              # shiny::tags$br(),
+              # shiny::helpText("Reset to original imported dataset. Careful! There is no un-doing.")
+            ),
+            shiny::column(
+              width = 2
+            )
+          ),
+          shiny::tags$br(),
+          shiny::tags$br(),
+          tags$h4("Compare modified data to original"),
+          shiny::tags$br(),
+          shiny::tags$p(
+            "Here is a overview of the original vs the modified data."
+          ),
+          shiny::tags$br(),
+          shiny::tags$br(),
+          fluidRow(
+            column(
+              width = 6,
+              tags$b("Original data:"),
+              # verbatimTextOutput("original"),
+              verbatimTextOutput("original_str")
+            ),
+            column(
+              width = 6,
+              tags$b("Modified data:"),
+              # verbatimTextOutput("modified"),
+              verbatimTextOutput("modified_str")
+            )
+          )
         )
       )
     ),
@@ -8665,34 +8603,19 @@ server <- function(input, output, session) {
     )
   })
 
-  output$data_loaded <- shiny::reactive({
-    !is.null(rv$data_temp)
-    })
-
-  shiny::observeEvent(input$source,{
-    rv$data_temp <- NULL
-    })
-
-  shiny::outputOptions(output, "data_loaded", suspendWhenHidden = FALSE)
 
   shiny::observeEvent(
     eventExpr = list(
       input$import_var,
-      input$complete_cutoff,
+      input$complete_cutoff
-      rv$data_temp
     ),
     handlerExpr = {
       shiny::req(rv$data_temp)
       # browser()
-      temp_data <- rv$data_temp
+      rv$data_original <- rv$data_temp |>
-      if (all(input$import_var %in% names(temp_data))){
+        dplyr::select(input$import_var) |>
-        temp_data <- temp_data |> dplyr::select(input$import_var)
-      }
-
-      rv$data_original <- temp_data |>
         default_parsing()
 
-
       rv$code$import <- rv$code$import |>
         deparse() |>
         paste(collapse = "") |>
@@ -8705,7 +8628,7 @@ server <- function(input, output, session) {
 
       rv$code$filter <- NULL
       rv$code$modify <- NULL
-    },ignoreNULL = FALSE
+    }
   )
 
   output$data_info_import <- shiny::renderUI({
@@ -8730,7 +8653,8 @@ server <- function(input, output, session) {
 
   shiny::observeEvent(
     eventExpr = list(
-      rv$data_original
+      rv$data_original,
+      input$complete_cutoff
     ),
     handlerExpr = {
       shiny::req(rv$data_original)

inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf

@@ -5,6 +5,6 @@ account: agdamsbo
 server: shinyapps.io
 hostUrl: https://api.shinyapps.io/v1
 appId: 13611288
-bundleId: 10049531
+bundleId: 10042980
 url: https://agdamsbo.shinyapps.io/freesearcheR/
 version: 1

inst/apps/FreesearchR/server.R

@@ -158,34 +158,19 @@ server <- function(input, output, session) {
     )
   })
 
-  output$data_loaded <- shiny::reactive({
-    !is.null(rv$data_temp)
-    })
-
-  shiny::observeEvent(input$source,{
-    rv$data_temp <- NULL
-    })
-
-  shiny::outputOptions(output, "data_loaded", suspendWhenHidden = FALSE)
 
   shiny::observeEvent(
     eventExpr = list(
       input$import_var,
-      input$complete_cutoff,
+      input$complete_cutoff
-      rv$data_temp
     ),
     handlerExpr = {
       shiny::req(rv$data_temp)
       # browser()
-      temp_data <- rv$data_temp
+      rv$data_original <- rv$data_temp |>
-      if (all(input$import_var %in% names(temp_data))){
+        dplyr::select(input$import_var) |>
-        temp_data <- temp_data |> dplyr::select(input$import_var)
-      }
-
-      rv$data_original <- temp_data |>
         default_parsing()
 
-
       rv$code$import <- rv$code$import |>
         deparse() |>
         paste(collapse = "") |>
@@ -198,7 +183,7 @@ server <- function(input, output, session) {
 
       rv$code$filter <- NULL
       rv$code$modify <- NULL
-    },ignoreNULL = FALSE
+    }
   )
 
   output$data_info_import <- shiny::renderUI({
@@ -223,7 +208,8 @@ server <- function(input, output, session) {
 
   shiny::observeEvent(
     eventExpr = list(
-      rv$data_original
+      rv$data_original,
+      input$complete_cutoff
     ),
     handlerExpr = {
       shiny::req(rv$data_original)

inst/apps/FreesearchR/ui.R

@@ -68,8 +68,6 @@ ui_elements <- list(
           condition = "input.source=='redcap'",
           DT::DTOutput(outputId = "redcap_prev")
         ),
-        shiny::conditionalPanel(
-          condition = "output.data_loaded == true",
         shiny::br(),
         shiny::br(),
         shiny::h5("Specify variables to include"),
@@ -86,7 +84,7 @@ ui_elements <- list(
             shinyWidgets::noUiSliderInput(
               inputId = "complete_cutoff",
               label = NULL,
-              update_on = "end",
+              update_on = "change",
               min = 0,
               max = 100,
               step = 5,
@@ -94,13 +92,12 @@ ui_elements <- list(
               format = shinyWidgets::wNumbFormat(decimals = 0),
               color = datamods:::get_primary_color()
             ),
-            shiny::helpText("Exclude variables with completeness below the specified percentage."),
+            shiny::helpText("Filter variables with completeness above the specified percentage."),
             shiny::br(),
             shiny::br(),
             shiny::uiOutput(outputId = "import_var"),
             shiny::uiOutput(outputId = "data_info_import", inline = TRUE)
           )
-        )
         ),
         shiny::br(),
         shiny::br(),
@@ -183,20 +180,36 @@ ui_elements <- list(
           fluidRow(
             shiny::column(
               width = 9,
-              shiny::tags$p(shiny::markdown("Below, are several options for simple data manipulation like update variables by renaming, creating new labels (for nicer tables in the report) and changing variable classes (numeric, factor/categorical etc.)."),
+              shiny::tags$p(shiny::markdown("Below, are several options to update variables (rename, set new labels (for nicer tables in the report) and change variable classes (numeric, factor/categorical etc.).), modify factor/categorical variables as well as create new factor from a continous variable or new variables with *R* code."))
-                            shiny::tags$p("There are also more advanced options to modify factor/categorical variables as well as create new factor from a continous variable or new variables with *R* code. At the bottom you can restore the original data."))
             )
           ),
-          # shiny::tags$br(),
+          shiny::tags$br(),
+          shiny::tags$br(),
           update_variables_ui("modal_variables"),
           shiny::tags$br(),
           shiny::tags$br(),
+          fluidRow(
+            shiny::column(
+              width = 2
+            ),
+            shiny::column(
+              width = 8,
               tags$h4("Advanced data manipulation"),
               shiny::tags$br(),
-          shiny::tags$br(),
+              fluidRow(
-          shiny::fluidRow(
                 shiny::column(
-              width = 4,
+                  width = 6,
+                  # tags$h4("Update or modify variables"),
+                  # shiny::tags$br(),
+                  # shiny::actionButton(
+                  #   inputId = "modal_variables",
+                  #   label = "Subset, rename and change class/type",
+                  #   width = "100%"
+                  # ),
+                  # shiny::tags$br(),
+                  # shiny::helpText("Subset variables, rename variables and labels, and apply new class to variables"),
+                  # shiny::tags$br(),
+                  # shiny::tags$br(),
                   shiny::actionButton(
                     inputId = "modal_update",
                     label = "Reorder factor levels",
@@ -204,50 +217,7 @@ ui_elements <- list(
                   ),
                   shiny::tags$br(),
                   shiny::helpText("Reorder the levels of factor/categorical variables."),
-            ),
-            shiny::column(
-              width = 4,
-              shiny::actionButton(
-                inputId = "modal_cut",
-                label = "New factor",
-                width = "100%"
-              ),
                   shiny::tags$br(),
-              shiny::helpText("Create factor/categorical variable from a continous variable (number/date/time).")
-            ),
-            shiny::column(
-              width = 4,
-              shiny::actionButton(
-                inputId = "modal_column",
-                label = "New variable",
-                width = "100%"
-              ),
-              shiny::tags$br(),
-              shiny::helpText(shiny::markdown("Create a new variable/column based on an *R*-expression."))
-            )
-          ),
-          shiny::tags$br(),
-          shiny::tags$br(),
-          tags$h4("Compare modified data to original"),
-          shiny::tags$br(),
-          shiny::tags$p(
-            "Raw print of the original vs the modified data."
-          ),
-          shiny::tags$br(),
-          shiny::fluidRow(
-            shiny::column(
-              width = 6,
-              shiny::tags$b("Original data:"),
-              # verbatimTextOutput("original"),
-              shiny::verbatimTextOutput("original_str")
-            ),
-            shiny::column(
-              width = 6,
-              shiny::tags$b("Modified data:"),
-              # verbatimTextOutput("modified"),
-              shiny::verbatimTextOutput("modified_str")
-            )
-          ),
                   shiny::tags$br(),
                   shiny::actionButton(
                     inputId = "data_reset",
@@ -256,7 +226,69 @@ ui_elements <- list(
                   ),
                   shiny::tags$br(),
                   shiny::helpText("Reset to original imported dataset. Careful! There is no un-doing."),
+                  shiny::tags$br(),
                   shiny::tags$br()
+                ),
+                shiny::column(
+                  width = 6,
+                  # tags$h4("Create new variables"),
+                  # shiny::tags$br(),
+                  shiny::actionButton(
+                    inputId = "modal_cut",
+                    label = "New factor",
+                    width = "100%"
+                  ),
+                  shiny::tags$br(),
+                  shiny::helpText("Create factor/categorical variable from a continous variable (number/date/time)."),
+                  shiny::tags$br(),
+                  shiny::tags$br(),
+                  shiny::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("Restore"),
+              # shiny::actionButton(
+              #   inputId = "data_reset",
+              #   label = "Restore original data",
+              #   width = "100%"
+              # ),
+              # shiny::tags$br(),
+              # shiny::helpText("Reset to original imported dataset. Careful! There is no un-doing.")
+            ),
+            shiny::column(
+              width = 2
+            )
+          ),
+          shiny::tags$br(),
+          shiny::tags$br(),
+          tags$h4("Compare modified data to original"),
+          shiny::tags$br(),
+          shiny::tags$p(
+            "Here is a overview of the original vs the modified data."
+          ),
+          shiny::tags$br(),
+          shiny::tags$br(),
+          fluidRow(
+            column(
+              width = 6,
+              tags$b("Original data:"),
+              # verbatimTextOutput("original"),
+              verbatimTextOutput("original_str")
+            ),
+            column(
+              width = 6,
+              tags$b("Modified data:"),
+              # verbatimTextOutput("modified"),
+              verbatimTextOutput("modified_str")
+            )
+          )
         )
       )
     ),

man/if_not_missing.Rd

@@ -1,24 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/helpers.R
-\name{if_not_missing}
-\alias{if_not_missing}
-\title{Return if available}
-\usage{
-if_not_missing(data, default = NULL)
-}
-\arguments{
-\item{data}{vector}
-
-\item{default}{assigned value for missings}
-}
-\value{
-vector
-}
-\description{
-Return if available
-}
-\examples{
-NULL |> if_not_missing("new")
-c(2,"a",NA) |> if_not_missing()
-"See" |> if_not_missing()
-}

man/plot.tbl_regression.Rd

@@ -16,17 +16,6 @@
 \item{x}{(\code{tbl_regression}, \code{tbl_uvregression})\cr
 A 'tbl_regression' or 'tbl_uvregression' object}
 
-\item{plot_ref}{(scalar \code{logical})\cr
-plot reference values}
-
-\item{remove_header_rows}{(scalar \code{logical})\cr
-logical indicating whether to remove header rows
-for categorical variables. Default is \code{TRUE}}
-
-\item{remove_reference_rows}{(scalar \code{logical})\cr
-logical indicating whether to remove reference rows
-for categorical variables. Default is \code{FALSE}.}
-
 \item{...}{arguments passed to \code{ggstats::ggcoef_plot(...)}}
 }
 \value{

man/redcap_read_shiny_module.Rd

@@ -6,7 +6,7 @@
 \alias{redcap_demo_app}
 \title{Shiny module to browser and export REDCap data}
 \usage{
-m_redcap_readUI(id, title = TRUE, url = NULL)
+m_redcap_readUI(id, title = TRUE)
 
 m_redcap_readServer(id)
 

vignettes/FreesearchR.Rmd

@@ -9,7 +9,6 @@ vignette: >
 
 ```{r setup, include=FALSE}
 knitr::opts_chunk$set(echo = TRUE,eval = FALSE)
-source(here::here("functions.R"))
 ```
 
 # Getting started with ***FreesearchR***
@@ -58,25 +57,7 @@ Currently several data file formats are supported for easy import (csv, txt, xls
 
 ## Visualise
 
-Below are the available plot types listed.
+- Would be nice to have a table of possible plots, their description and data options
-
-```{r echo = FALSE, eval = TRUE}
-c("continuous", "dichotomous", "ordinal", "categorical") |> 
-  lapply(\(.x){
-    dplyr::bind_cols(
-      dplyr::tibble("Data type"=.x),
-      supported_plots() |> 
-      lapply(\(.y){
-        if (.x %in% .y$primary.type){
-          .y[c("descr","note")]|> dplyr::bind_cols()
-        }
-})|> 
-  dplyr::bind_rows() |> 
-  setNames(c("Plot type","Description")))
-  }) |> 
-  dplyr::bind_rows() |> 
-  toastui::datagrid(filters=TRUE,theme="striped")
-```
 
 
 ## Regression