latest dev version

CITATION.cff

@@ -9,7 +9,7 @@ type: software
 license: AGPL-3.0-or-later
 title: 'FreesearchR: A free and open-source browser based data analysis tool for researchers
   with publication ready output'
-version: 25.6.1
+version: 25.6.2
 doi: 10.5281/zenodo.14527429
 identifiers:
 - type: url

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: FreesearchR
 Title: A free and open-source browser based data analysis tool for researchers with publication ready output
-Version: 25.6.1
+Version: 25.6.3
 Authors@R: c(
     person("Andreas Gammelgaard", "Damsbo",email="agdamsbo@clin.au.dk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7559-1154")),
@@ -64,7 +64,8 @@ Imports:
     RcppArmadillo,
     ggcorrplot,
     shinyjs,
-    emmeans
+    emmeans,
+    visdat
 Suggests: 
     styler,
     devtools,

NAMESPACE

@@ -30,6 +30,8 @@ export(cut_variable_ui)
 export(data_correlations_server)
 export(data_correlations_ui)
 export(data_description)
+export(data_missings_server)
+export(data_missings_ui)
 export(data_summary_server)
 export(data_summary_ui)
 export(data_type)

NEWS.md

@@ -1,3 +1,17 @@
+# FreesearchR 25.6.3
+
+- *NEW* First go at introducing more options to evaluate missings. Also reworded the text on the initial filter to only include variables missings less than the given threshold.
+
+# FreesearchR 25.6.2
+
+- *FIX* Added warning about only using REDCap with sensitive data running locally. THis applies to all data actually. Considering taking REDCap out in hosted version. Standalone app is in the works.
+
+- *FIX* Reworded the completeness filter to be on missingness, as this is a more commonly used concept.
+
+- *FIX* Improved layout around data filters to improve usage.
+
+- *FIX* Regression table in report respects inclusion of p-values or not.
+
 # FreesearchR 25.6.1
 
 - *FIX* big not allowing to browse data

R/app_version.R

@@ -1 +1 @@
-app_version <- function()'25.6.1'
+app_version <- function()'25.6.3'

R/helpers.R

@@ -50,7 +50,7 @@ write_quarto <- function(data, ...) {
   )
 }
 
-write_rmd <- function(data, ...) {
+write_rmd <- function(data, ..., params.args=NULL) {
   # Exports data to temporary location
   #
   # I assume this is more secure than putting it in the www folder and deleting
@@ -65,7 +65,7 @@ write_rmd <- function(data, ...) {
   ## Ref: https://github.com/quarto-dev/quarto-cli/discussions/4041
   ## Outputs to the same as the .qmd file
   rmarkdown::render(
-    params = list(data.file = "web_data.rds",version=app_version()),
+    params = modifyList(list(data.file = "web_data.rds",version=app_version()),params.args),
     # execute_params = list(data.file = temp),
     ...
   )

R/hosted_version.R

@@ -1 +1 @@
-hosted_version <- function()'v25.6.1-250604'
+hosted_version <- function()'v25.6.3-250620'

R/missings-module.R

@@ -0,0 +1,113 @@
+#' Data correlations evaluation module
+#'
+#' @param id Module id
+#'
+#' @name data-missings
+#' @returns Shiny ui module
+#' @export
+data_missings_ui <- function(id) {
+  ns <- shiny::NS(id)
+
+  shiny::tagList(
+    gt::gt_output(outputId = ns("missings_table")),
+    shiny::plotOutput(outputId = ns("missings_plot"))
+  )
+}
+
+
+#'
+#' @param data data
+#' @param output.format output format
+#'
+#' @name data-missings
+#' @returns shiny server module
+#' @export
+data_missings_server <- function(id,
+                                 data,
+                                 ...) {
+  shiny::moduleServer(
+    id = id,
+    module = function(input, output, session) {
+      # ns <- session$ns
+
+      rv <- shiny::reactiveValues(
+        data = NULL
+      )
+
+      rv$data <- if (is.reactive(data)) data else reactive(data)
+
+      output$missings_plot <- shiny::renderPlot({
+        visdat::vis_dat(rv$data(),palette = "cb_safe")
+      })
+    }
+  )
+}
+
+
+missing_demo_app <- function() {
+  ui <- shiny::fluidPage(
+    shiny::actionButton(
+      inputId = "modal_missings",
+      label = "Browse data",
+      width = "100%",
+      disabled = FALSE
+    )#,
+    # data_missings_ui("data")
+  )
+  server <- function(input, output, session) {
+    data_demo <- mtcars
+    data_demo[2:4, "cyl"] <- NA
+
+    observeEvent(input$modal_missings, {
+      tryCatch(
+        {
+          modal_data_missings(data = data_demo, id = "modal_missings")
+        },
+        error = function(err) {
+          showNotification(paste0("We encountered the following error browsing your data: ", err), type = "err")
+        }
+      )
+    })
+  }
+  shiny::shinyApp(ui, server)
+}
+
+missing_demo_app()
+
+
+modal_data_missings <- function(data,
+                                title = "Show missing pattern",
+                                easyClose = TRUE,
+                                size = "xl",
+                                footer = NULL,
+                                ...) {
+
+  datar <- if (is.reactive(data)) data else reactive(data)
+
+  showModal(modalDialog(
+    title = tagList(title, datamods:::button_close_modal()),
+    tags$div(
+      shiny::renderPlot({
+        visdat::vis_dat(datar())+
+          ggplot2::guides(fill = ggplot2::guide_legend(title = "Data class")) +
+          # ggplot2::theme_void() +
+          ggplot2::theme(
+            # legend.position = "none",
+            panel.grid.major = ggplot2::element_blank(),
+            panel.grid.minor = ggplot2::element_blank(),
+            # axis.text.y = element_blank(),
+            # axis.title.y = element_blank(),
+            text = ggplot2::element_text(size = 15),
+            # axis.text = ggplot2::element_blank(),
+            # panel.background = ggplot2::element_rect(fill = "white"),
+            # plot.background = ggplot2::element_rect(fill = "white"),
+            # panel.border = ggplot2::element_blank()
+            plot.title = ggplot2::element_blank()
+          )
+      })
+    ),
+    easyClose = easyClose,
+    size = size,
+    footer = footer
+  ))
+}

SESSION.md

@@ -11,11 +11,11 @@
 |collate     |en_US.UTF-8                                |
 |ctype       |en_US.UTF-8                                |
 |tz          |Europe/Copenhagen                          |
-|date        |2025-06-04                                 |
+|date        |2025-06-06                                 |
 |rstudio     |2025.05.0+496 Mariposa Orchid (desktop)    |
 |pandoc      |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) |
 |quarto      |1.7.30 @ /usr/local/bin/quarto             |
-|FreesearchR |25.6.1.250604                              |
+|FreesearchR |25.6.2.250606                              |
                                                                                 
                                                                                 
 --------------------------------------------------------------------------------
@@ -76,7 +76,6 @@
 |farver            |2.1.2         |2024-05-13 |CRAN (R 4.4.1) |
 |fastmap           |1.2.0         |2024-05-15 |CRAN (R 4.4.1) |
 |flextable         |0.9.7         |2024-10-27 |CRAN (R 4.4.1) |
-|fontawesome       |0.5.3         |2024-11-16 |CRAN (R 4.4.1) |
 |fontBitstreamVera |0.1.1         |2017-02-01 |CRAN (R 4.4.1) |
 |fontLiberation    |0.1.0         |2016-10-15 |CRAN (R 4.4.1) |
 |fontquiver        |0.2.1         |2017-02-01 |CRAN (R 4.4.0) |
@@ -84,7 +83,7 @@
 |foreach           |1.5.2         |2022-02-02 |CRAN (R 4.4.0) |
 |foreign           |0.8-90        |2025-03-31 |CRAN (R 4.4.1) |
 |Formula           |1.2-5         |2023-02-24 |CRAN (R 4.4.1) |
-|FreesearchR       |25.6.1        |NA         |NA             |
+|FreesearchR       |25.6.2        |NA         |NA             |
 |fs                |1.6.6         |2025-04-12 |CRAN (R 4.4.1) |
 |gdtools           |0.4.2         |2025-03-27 |CRAN (R 4.4.1) |
 |generics          |0.1.3         |2022-07-05 |CRAN (R 4.4.1) |
@@ -160,6 +159,7 @@
 |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) |
+|rappdirs          |0.3.3         |2021-01-31 |CRAN (R 4.4.1) |
 |rbibutils         |2.3           |2024-10-04 |CRAN (R 4.4.1) |
 |RColorBrewer      |1.1-3         |2022-04-03 |CRAN (R 4.4.1) |
 |Rcpp              |1.0.14        |2025-01-12 |CRAN (R 4.4.1) |

inst/apps/FreesearchR/app.R

@@ -16,7 +16,7 @@ library(shiny)
 # library(readODS)
 # library(bslib)
 # library(assertthat)
-# library(dplyr)
+library(dplyr)
 # library(quarto)
 # library(here)
 # library(broom)
@@ -31,7 +31,7 @@ library(datamods)
 library(shinyWidgets)
 # library(DT)
 # library(data.table)
-# library(gtsummary)
+library(gtsummary)
 library(bsicons)
 library(rlang)
 # library(datamods)
@@ -49,7 +49,7 @@ library(rlang)
 #### Current file: /Users/au301842/FreesearchR/R//app_version.R 
 ########
 
-app_version <- function()'25.6.1'
+app_version <- function()'25.6.3'
 
 
 ########
@@ -3374,7 +3374,7 @@ write_quarto <- function(data, ...) {
   )
 }
 
-write_rmd <- function(data, ...) {
+write_rmd <- function(data, ..., params.args=NULL) {
   # Exports data to temporary location
   #
   # I assume this is more secure than putting it in the www folder and deleting
@@ -3389,7 +3389,7 @@ write_rmd <- function(data, ...) {
   ## Ref: https://github.com/quarto-dev/quarto-cli/discussions/4041
   ## Outputs to the same as the .qmd file
   rmarkdown::render(
-    params = list(data.file = "web_data.rds",version=app_version()),
+    params = modifyList(list(data.file = "web_data.rds",version=app_version()),params.args),
     # execute_params = list(data.file = temp),
     ...
   )
@@ -3996,7 +3996,7 @@ simple_snake <- function(data){
 #### Current file: /Users/au301842/FreesearchR/R//hosted_version.R 
 ########
 
-hosted_version <- function()'v25.6.1-250604'
+hosted_version <- function()'v25.6.3-250620'
 
 
 ########
@@ -4655,6 +4655,125 @@ launch_FreesearchR <- function(...){
 
 
 
+########
+#### Current file: /Users/au301842/FreesearchR/R//missings-module.R 
+########
+
+#' Data correlations evaluation module
+#'
+#' @param id Module id
+#'
+#' @name data-missings
+#' @returns Shiny ui module
+#' @export
+data_missings_ui <- function(id) {
+  ns <- shiny::NS(id)
+
+  shiny::tagList(
+    gt::gt_output(outputId = ns("missings_table")),
+    shiny::plotOutput(outputId = ns("missings_plot"))
+  )
+}
+
+
+#'
+#' @param data data
+#' @param output.format output format
+#'
+#' @name data-missings
+#' @returns shiny server module
+#' @export
+data_missings_server <- function(id,
+                                 data,
+                                 ...) {
+  shiny::moduleServer(
+    id = id,
+    module = function(input, output, session) {
+      # ns <- session$ns
+
+      rv <- shiny::reactiveValues(
+        data = NULL
+      )
+
+      rv$data <- if (is.reactive(data)) data else reactive(data)
+
+      output$missings_plot <- shiny::renderPlot({
+        visdat::vis_dat(rv$data(),palette = "cb_safe")
+      })
+    }
+  )
+}
+
+
+missing_demo_app <- function() {
+  ui <- shiny::fluidPage(
+    shiny::actionButton(
+      inputId = "modal_missings",
+      label = "Browse data",
+      width = "100%",
+      disabled = FALSE
+    )#,
+    # data_missings_ui("data")
+  )
+  server <- function(input, output, session) {
+    data_demo <- mtcars
+    data_demo[2:4, "cyl"] <- NA
+
+    observeEvent(input$modal_missings, {
+      tryCatch(
+        {
+          modal_data_missings(data = data_demo, id = "modal_missings")
+        },
+        error = function(err) {
+          showNotification(paste0("We encountered the following error browsing your data: ", err), type = "err")
+        }
+      )
+    })
+  }
+  shiny::shinyApp(ui, server)
+}
+
+missing_demo_app()
+
+
+modal_data_missings <- function(data,
+                                title = "Show missing pattern",
+                                easyClose = TRUE,
+                                size = "xl",
+                                footer = NULL,
+                                ...) {
+
+  datar <- if (is.reactive(data)) data else reactive(data)
+
+  showModal(modalDialog(
+    title = tagList(title, datamods:::button_close_modal()),
+    tags$div(
+      shiny::renderPlot({
+        visdat::vis_dat(datar())+
+          ggplot2::guides(fill = ggplot2::guide_legend(title = "Data class")) +
+          # ggplot2::theme_void() +
+          ggplot2::theme(
+            # legend.position = "none",
+            panel.grid.major = ggplot2::element_blank(),
+            panel.grid.minor = ggplot2::element_blank(),
+            # axis.text.y = element_blank(),
+            # axis.title.y = element_blank(),
+            text = ggplot2::element_text(size = 15),
+            # axis.text = ggplot2::element_blank(),
+            # panel.background = ggplot2::element_rect(fill = "white"),
+            # plot.background = ggplot2::element_rect(fill = "white"),
+            # panel.border = ggplot2::element_blank()
+            plot.title = ggplot2::element_blank()
+          )
+      })
+    ),
+    easyClose = easyClose,
+    size = size,
+    footer = footer
+  ))
+}
+
+
 ########
 #### Current file: /Users/au301842/FreesearchR/R//plot_box.R 
 ########
@@ -9404,6 +9523,7 @@ ui_elements <- list(
         width = 8,
         shiny::h4("Choose your data source"),
         shiny::br(),
+        # shiny::uiOutput(outputId = "source"),
         shinyWidgets::radioGroupButtons(
           inputId = "source",
           selected = "file",
@@ -9429,6 +9549,13 @@ ui_elements <- list(
         ),
         shiny::conditionalPanel(
           condition = "input.source=='redcap'",
+          shinyWidgets::alert(
+            id = "redcap-warning",
+            status = "info",
+            shiny::tags$h2(shiny::markdown("Careful with sensitive data")),
+            shiny::tags$p("The", shiny::tags$i(shiny::tags$b("FreesearchR")), "app only stores data for analyses, but please only use with sensitive data when running locally.", "", shiny::tags$a("Read more here", href = "https://agdamsbo.github.io/FreesearchR/#run-locally-on-your-own-machine"),"."),
+            dismissible = TRUE
+          ),
           m_redcap_readUI(
             id = "redcap_import",
             title = ""
@@ -9446,11 +9573,11 @@ ui_elements <- list(
           condition = "output.data_loaded == true",
           shiny::br(),
           shiny::br(),
-          shiny::h5("Specify variables to include"),
+          shiny::h5("Select variables for final import"),
           shiny::fluidRow(
             shiny::column(
               width = 6,
-              shiny::p("Filter by completeness threshold:"),
+              shiny::p("Exclude incomplete variables:"),
               shiny::br(),
               shinyWidgets::noUiSliderInput(
                 inputId = "complete_cutoff",
@@ -9459,16 +9586,16 @@ ui_elements <- list(
                 min = 0,
                 max = 100,
                 step = 5,
-                value = 70,
+                value = 30,
                 format = shinyWidgets::wNumbFormat(decimals = 0),
                 color = datamods:::get_primary_color()
               ),
-              shiny::helpText("Exclude variables with completeness below the specified percentage."),
+              shiny::helpText("Only include variables with missingness below the specified percentage."),
               shiny::br()
             ),
             shiny::column(
               width = 6,
-              shiny::p("Specify manually:"),
+              shiny::p("Manual selection:"),
               shiny::br(),
               shiny::uiOutput(outputId = "import_var"),
               shiny::br()
@@ -9528,34 +9655,45 @@ ui_elements <- list(
             ),
             shiny::column(
               width = 3,
+              shiny::actionButton(
+                inputId = "modal_missings",
+                label = "Visual overview",
+                width = "100%",
+                disabled = TRUE
+              ),
+              shiny::br(),
+              shiny::br(),
               shiny::actionButton(
                 inputId = "modal_browse",
                 label = "Browse data",
                 width = "100%",
                 disabled = TRUE
               ),
-              shiny::tags$br(),
-              shiny::tags$br(),
-              shiny::uiOutput(outputId = "column_filter"),
-              shiny::helpText("Variable ", tags$a(
-                "data type",
+              shiny::br(),
+              shiny::br(),
+              shiny::tags$h6("Filter data types"),
+              shiny::uiOutput(
+                outputId = "column_filter"),
+              shiny::helpText("Read more on how ", tags$a(
+                "data types",
                 href = "https://agdamsbo.github.io/FreesearchR/articles/data-types.html",
                 target = "_blank",
                 rel = "noopener noreferrer"
-              ), " filtering."),
-              shiny::tags$br(),
-              shiny::tags$br(),
+              ), " are defined."),
+              shiny::br(),
+              shiny::br(),
+              shiny::tags$h6("Create data filters"),
+              shiny::tags$p("Filter on observation level"),
               IDEAFilter::IDEAFilter_ui("data_filter"),
-              shiny::helpText("Observations level filtering."),
-              shiny::tags$br(),
-              shiny::tags$br()
+              shiny::br(),
+              shiny::br()
             )
           ),
-          shiny::tags$br(),
-          shiny::tags$br(),
-          shiny::tags$br(),
-          shiny::tags$br(),
-          shiny::tags$br()
+          shiny::br(),
+          shiny::br(),
+          # shiny::br(),
+          # shiny::br(),
+          shiny::br()
         ),
         bslib::nav_panel(
           title = "Modify",
@@ -9953,9 +10091,15 @@ ui <- bslib::page_fixed(
 
 
 
-data(starwars)
+
 data(mtcars)
-data(trial)
+
+# trial <- gtsummary::trial
+# starwars <- dplyr::starwars
+#
+# mtcars_na <- rbind(mtcars,NA,NA)
+
+# thematic::thematic_shiny()
 
 load_data <- function() {
   Sys.sleep(1)
@@ -9963,6 +10107,7 @@ load_data <- function() {
   shinyjs::show("main_content")
 }
 
+# is_local = is.na(Sys.getenv('SHINY_SERVER_VERSION', NA))
 
 server <- function(input, output, session) {
   ## Listing files in www in session start to keep when ending and removing
@@ -10018,6 +10163,28 @@ server <- function(input, output, session) {
   #########
   ##############################################################################
 
+  ## This does not render correctly apparently due to css and load order
+  # output$source <- shiny::renderUI({
+  #
+  #   choices <- c(
+  #     "File upload" = "file",
+  #     "REDCap server export" = "redcap",
+  #     "Local or sample data" = "env"
+  #   )
+  #
+  #   if (isTRUE(is_local)){
+  #     choices <- choices[c(1,3)]
+  #   }
+  #
+  #   shinyWidgets::radioGroupButtons(
+  #     inputId = "source",
+  #     selected = "file",
+  #     choices = choices,
+  #     size = "lg"
+  #   )
+  # })
+
+
   data_file <- import_file_server(
     id = "file_import",
     show_data_in = "popup",
@@ -10067,7 +10234,7 @@ server <- function(input, output, session) {
   output$import_var <- shiny::renderUI({
     shiny::req(rv$data_temp)
 
-    preselect <- names(rv$data_temp)[sapply(rv$data_temp, missing_fraction) <= input$complete_cutoff / 100]
+    preselect <- names(rv$data_temp)[sapply(rv$data_temp, missing_fraction) <= (input$complete_cutoff / 100)]
 
     shinyWidgets::virtualSelectInput(
       inputId = "import_var",
@@ -10136,10 +10303,12 @@ server <- function(input, output, session) {
     if (is.null(rv$data_original) | NROW(rv$data_original) == 0) {
       shiny::updateActionButton(inputId = "act_start", disabled = TRUE)
       shiny::updateActionButton(inputId = "modal_browse", disabled = TRUE)
+      shiny::updateActionButton(inputId = "modal_missings", disabled = TRUE)
       shiny::updateActionButton(inputId = "act_eval", disabled = TRUE)
     } else {
       shiny::updateActionButton(inputId = "act_start", disabled = FALSE)
       shiny::updateActionButton(inputId = "modal_browse", disabled = FALSE)
+      shiny::updateActionButton(inputId = "modal_missings", disabled = FALSE)
       shiny::updateActionButton(inputId = "act_eval", disabled = FALSE)
     }
   })
@@ -10279,7 +10448,7 @@ server <- function(input, output, session) {
     # c("dichotomous", "ordinal", "categorical", "datatime", "continuous")
     shinyWidgets::virtualSelectInput(
       inputId = "column_filter",
-      label = "Select variable types to include",
+      label = "Select data types to include",
       selected = unique(data_type(rv$data)),
       choices = unique(data_type(rv$data)),
       updateOn = "change",
@@ -10378,6 +10547,19 @@ server <- function(input, output, session) {
     )
   })
 
+  observeEvent(input$modal_missings, {
+    tryCatch(
+      {
+        modal_data_missings(data = REDCapCAST::fct_drop(rv$data_filtered),
+                            footer = "This pop-up gives you an overview of how your data is interpreted, and where data is missing. Use this information to consider if data is missing at random or if some observations are missing systematically wich may be caused by an observation bias.")
+      },
+      error = function(err) {
+        showNotification(paste0("We encountered the following error showing missingness: ", err), type = "err")
+      }
+    )
+  })
+
+
   output$original_str <- renderPrint({
     str(rv$data_original)
   })
@@ -10660,6 +10842,9 @@ server <- function(input, output, session) {
           {
             rv$list |>
               write_rmd(
+                params.args = list(
+                  regression.p=rv$list$regression$input$add_regression_p
+                  ),
                 output_format = format,
                 input = file.path(getwd(), "www/report.rmd")
               )

inst/apps/FreesearchR/www/report.rmd

@@ -7,6 +7,7 @@ toc: false
 params:
   data.file: NA
   version: NA
+  regression.p: NA
 ---
 
 ```{r setup, echo = FALSE}
@@ -65,7 +66,15 @@ if ("table1" %in% names(web_data)) {
 ```{r, results = 'asis'}
 if ("regression" %in% names(web_data) && length(web_data$regression) > 0) {
   reg_tbl <- web_data$regression$regression$tables
-  knitr::knit_print(tbl_merge(reg_tbl))
+  
+  merged <- tbl_merge(reg_tbl)
+  
+  if (params$regression.p == "no") {
+            merged <- merged |>
+              gtsummary::modify_column_hide(column = dplyr::starts_with("p.value"))
+          }
+  
+  knitr::knit_print(merged)
 }
 ```
 

inst/apps/FreesearchR/www/umami-app.html

@@ -0,0 +1 @@
+<script defer src="https://stats.freesearchr.org/script.js" data-website-id="349608b9-78f8-47ee-9185-0d3716095fd5"></script>

man/data-missings.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/missings-module.R
+\name{data-missings}
+\alias{data-missings}
+\alias{data_missings_ui}
+\alias{data_missings_server}
+\title{Data correlations evaluation module}
+\usage{
+data_missings_ui(id)
+
+data_missings_server(id, data, ...)
+}
+\arguments{
+\item{id}{Module id}
+
+\item{data}{data}
+
+\item{output.format}{output format}
+}
+\value{
+Shiny ui module
+
+shiny server module
+}
+\description{
+Data correlations evaluation module
+}