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

@@ -89,6 +89,7 @@ modal_data_missings <- function(data,
     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",

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

@@ -4750,6 +4750,7 @@ modal_data_missings <- function(data,
     tags$div(
       shiny::renderPlot({
         visdat::vis_dat(datar())+
+          ggplot2::guides(fill = ggplot2::guide_legend(title = "Data class")) +
           # ggplot2::theme_void() +
           ggplot2::theme(
             # legend.position = "none",
@@ -10549,7 +10550,8 @@ server <- function(input, output, session) {
   observeEvent(input$modal_missings, {
     tryCatch(
       {
-        modal_data_missings(data = REDCapCAST::fct_drop(rv$data_filtered))
+        modal_data_missings(data = REDCapCAST::fct_drop(rv$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")

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>