From 2ad36d6dde02d9f56e145a42ad67adac01e24d83 Mon Sep 17 00:00:00 2001
From: Andreas Gammelgaard Damsbo <andreas@gdamsbo.dk>
Date: Thu, 19 Dec 2024 21:21:29 +0100
Subject: [PATCH] reverting and recovering from renv corruption

---
 DESCRIPTION                                   |  9 ++-
 NAMESPACE                                     |  6 --
 R/helpers.R                                   | 31 +++----
 R/redcap_read_shiny_module.R                  |  7 +-
 R/regression_model.R                          |  3 +-
 inst/apps/data_analysis/server.R              | 13 +--
 inst/apps/data_analysis_modules/app.R         | 81 +++++++------------
 .../shinyapps.io/agdamsbo/freesearcheR.dcf    |  2 +-
 inst/apps/data_analysis_modules/server.R      | 13 +--
 inst/apps/data_analysis_modules/ui.R          |  4 +-
 man/default_parsing.Rd                        |  6 +-
 renv.lock                                     | 31 ++++---
 12 files changed, 78 insertions(+), 128 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index c2d3250..76cfb3c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -45,13 +45,18 @@ Imports:
     lubridate,
     bsicons,
     thematic,
-    reshape2
+    reshape2,
+    shinyWidgets,
+    classInt,
+    htmltools,
+    rlang
 Suggests: 
     styler,
     devtools,
     rhub,
     usethis,
     roxygen2,
-    pak
+    pak,
+    rsconnect
 URL: https://github.com/agdamsbo/freesearcheR
 BugReports: https://github.com/agdamsbo/freesearcheR/issues
diff --git a/NAMESPACE b/NAMESPACE
index 800bc03..513c28e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -28,12 +28,6 @@ export(specify_qmd_format)
 export(tbl_merge)
 export(winbox_cut_variable)
 export(write_quarto)
-importFrom(REDCapCAST,as_factor)
-importFrom(REDCapCAST,numchar2fct)
-importFrom(REDCapCAST,parse_data)
-importFrom(REDCapCAST,read_redcap_tables)
-importFrom(REDCapCAST,redcap_wider)
-importFrom(REDCapCAST,suffix2label)
 importFrom(classInt,classIntervals)
 importFrom(graphics,abline)
 importFrom(graphics,axis)
diff --git a/R/helpers.R b/R/helpers.R
index a99f382..95e21b2 100644
--- a/R/helpers.R
+++ b/R/helpers.R
@@ -98,7 +98,6 @@ argsstring2list <- function(string) {
 #' @param vars variables to force factorize
 #'
 #' @return data.frame
-#' @importFrom REDCapCAST as_factor
 #' @export
 factorize <- function(data, vars) {
   if (!is.null(vars)) {
@@ -106,7 +105,7 @@ factorize <- function(data, vars) {
       dplyr::mutate(
         dplyr::across(
           dplyr::all_of(vars),
-          as_factor
+          REDCapCAST::as_factor
         )
       )
   } else {
@@ -138,7 +137,6 @@ dummy_Imports <- function() {
 #'
 #' @returns data
 #' @export
-#' @importFrom REDCapCAST as_factor parse_data numchar2fct
 #'
 file_export <- function(data, output.format = c("df", "teal", "list"), filename, ...) {
   output.format <- match.arg(output.format)
@@ -151,9 +149,7 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
       {
         assign(name, value |>
           dplyr::bind_cols() |>
-          parse_data() |>
-          as_factor() |>
-          numchar2fct())
+          default_parsing())
       },
       value = data,
       name = filename
@@ -161,17 +157,15 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
 
     datanames(out) <- filename
   } else if (output.format == "df") {
-    out <- data|>
-      parse_data() |>
-      as_factor() |>
-      numchar2fct()
+    out <- data |>
+      default_parsing()
   } else if (output.format == "list") {
     out <- list(
       data = data,
       name = filename
     )
 
-    out <- c(out,...)
+    out <- c(out, ...)
   }
 
   out
@@ -180,18 +174,19 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
 
 #' Default data parsing
 #'
-#' @param data
+#' @param data data
 #'
 #' @returns data.frame or tibble
 #' @export
-#' @importFrom REDCapCAST as_factor parse_data numchar2fct
 #'
 #' @examples
 #' mtcars |> str()
-#' mtcars |> default_parsing() |> str()
-default_parsing <- function(data){
+#' mtcars |>
+#'   default_parsing() |>
+#'   str()
+default_parsing <- function(data) {
   data |>
-    parse_data() |>
-    as_factor() |>
-    numchar2fct()
+    REDCapCAST::parse_data() |>
+    REDCapCAST::as_factor() |>
+    REDCapCAST::numchar2fct()
 }
diff --git a/R/redcap_read_shiny_module.R b/R/redcap_read_shiny_module.R
index b486498..061a6e7 100644
--- a/R/redcap_read_shiny_module.R
+++ b/R/redcap_read_shiny_module.R
@@ -100,7 +100,6 @@ m_redcap_readUI <- function(id, include_title = TRUE) {
 #'
 #' @return shiny server module
 #' @export
-#' @importFrom REDCapCAST read_redcap_tables redcap_wider suffix2label
 #'
 m_redcap_readServer <- function(id, output.format = c("df", "teal", "list")) {
   output.format <- match.arg(output.format)
@@ -227,7 +226,7 @@ m_redcap_readServer <- function(id, output.format = c("df", "teal", "list")) {
       shiny::req(input$fields)
       record_id <- dd()[[1]][1]
 
-      redcap_data <- read_redcap_tables(
+      redcap_data <- REDCapCAST::read_redcap_tables(
         uri = input$uri,
         token = input$api,
         fields = unique(c(record_id, input$fields)),
@@ -236,10 +235,10 @@ m_redcap_readServer <- function(id, output.format = c("df", "teal", "list")) {
         raw_or_label = "both",
         filter_logic = input$filter
       ) |>
-        redcap_wider() |>
+        REDCapCAST::redcap_wider() |>
         dplyr::select(-dplyr::ends_with("_complete")) |>
         dplyr::select(-dplyr::any_of(record_id)) |>
-        suffix2label()
+        REDCapCAST::suffix2label()
 
       out_object <- file_export(redcap_data,
                                 output.format = output.format,
diff --git a/R/regression_model.R b/R/regression_model.R
index 8d6f188..d9d4529 100644
--- a/R/regression_model.R
+++ b/R/regression_model.R
@@ -10,7 +10,6 @@
 #' @param ... ignored for now
 #'
 #' @importFrom stats as.formula
-#' @importFrom REDCapCAST as_factor
 #'
 #' @return object of standard class for fun
 #' @export
@@ -67,7 +66,7 @@ regression_model <- function(data,
   data <- data |>
     purrr::map(\(.x){
       if (is.character(.x)) {
-        suppressWarnings(as_factor(.x))
+        suppressWarnings(REDCapCAST::as_factor(.x))
       } else {
         .x
       }
diff --git a/inst/apps/data_analysis/server.R b/inst/apps/data_analysis/server.R
index 45361d1..431e337 100644
--- a/inst/apps/data_analysis/server.R
+++ b/inst/apps/data_analysis/server.R
@@ -28,17 +28,6 @@ if (file.exists(here::here("functions.R"))) {
   source(here::here("functions.R"))
 }
 
-#' freesearcheR server
-#'
-#' @param input input
-#' @param output output
-#' @param session session
-#'
-#' @returns server
-#' @export
-#' @importFrom REDCapCAST numchar2fct
-#'
-#' @examples
 server <- function(input, output, session) {
   ## Listing files in www in session start to keep when ending and removing
   ## everything else.
@@ -75,7 +64,7 @@ server <- function(input, output, session) {
       out <- out |>
         (\(.x){
           suppressWarnings(
-            numchar2fct(.x)
+            REDCapCAST::numchar2fct(.x)
           )
         })()
     }
diff --git a/inst/apps/data_analysis_modules/app.R b/inst/apps/data_analysis_modules/app.R
index 5acd7c6..eb6b180 100644
--- a/inst/apps/data_analysis_modules/app.R
+++ b/inst/apps/data_analysis_modules/app.R
@@ -1,13 +1,13 @@
 
 
 ########
-#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/functions.R 
+#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/functions.R
 ########
 
 
 
 ########
-#### Current file: R//baseline_table.R 
+#### Current file: R//baseline_table.R
 ########
 
 
@@ -35,7 +35,7 @@ baseline_table <- function(data, fun.args = NULL, fun = gtsummary::tbl_summary,
 
 
 ########
-#### Current file: R//cut-variable-dates.R 
+#### Current file: R//cut-variable-dates.R
 ########
 
 library(datamods)
@@ -677,7 +677,7 @@ plot_histogram <- function(data, column, bins = 30, breaks = NULL, color = "#112
 
 
 ########
-#### Current file: R//file-import-module.R 
+#### Current file: R//file-import-module.R
 ########
 
 
@@ -808,7 +808,7 @@ plot_histogram <- function(data, column, bins = 30, breaks = NULL, color = "#112
 
 
 ########
-#### Current file: R//helpers.R 
+#### Current file: R//helpers.R
 ########
 
 
@@ -912,14 +912,13 @@ argsstring2list <- function(string) {
 
 
 
-
 factorize <- function(data, vars) {
   if (!is.null(vars)) {
     data |>
       dplyr::mutate(
         dplyr::across(
           dplyr::all_of(vars),
-          as_factor
+          REDCapCAST::as_factor
         )
       )
   } else {
@@ -952,8 +951,6 @@ dummy_Imports <- function() {
 
 
 
-
-
 file_export <- function(data, output.format = c("df", "teal", "list"), filename, ...) {
   output.format <- match.arg(output.format)
 
@@ -965,9 +962,7 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
       {
         assign(name, value |>
           dplyr::bind_cols() |>
-          parse_data() |>
-          as_factor() |>
-          numchar2fct())
+          default_parsing())
       },
       value = data,
       name = filename
@@ -975,17 +970,15 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
 
     datanames(out) <- filename
   } else if (output.format == "df") {
-    out <- data|>
-      parse_data() |>
-      as_factor() |>
-      numchar2fct()
+    out <- data |>
+      default_parsing()
   } else if (output.format == "list") {
     out <- list(
       data = data,
       name = filename
     )
 
-    out <- c(out,...)
+    out <- c(out, ...)
   }
 
   out
@@ -1003,16 +996,17 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
 
 
 
-default_parsing <- function(data){
+
+default_parsing <- function(data) {
   data |>
-    parse_data() |>
-    as_factor() |>
-    numchar2fct()
+    REDCapCAST::parse_data() |>
+    REDCapCAST::as_factor() |>
+    REDCapCAST::numchar2fct()
 }
 
 
 ########
-#### Current file: R//redcap_read_shiny_module.R 
+#### Current file: R//redcap_read_shiny_module.R
 ########
 
 
@@ -1118,7 +1112,6 @@ m_redcap_readUI <- function(id, include_title = TRUE) {
 
 
 
-
 m_redcap_readServer <- function(id, output.format = c("df", "teal", "list")) {
   output.format <- match.arg(output.format)
 
@@ -1244,7 +1237,7 @@ m_redcap_readServer <- function(id, output.format = c("df", "teal", "list")) {
       shiny::req(input$fields)
       record_id <- dd()[[1]][1]
 
-      redcap_data <- read_redcap_tables(
+      redcap_data <- REDCapCAST::read_redcap_tables(
         uri = input$uri,
         token = input$api,
         fields = unique(c(record_id, input$fields)),
@@ -1253,10 +1246,10 @@ m_redcap_readServer <- function(id, output.format = c("df", "teal", "list")) {
         raw_or_label = "both",
         filter_logic = input$filter
       ) |>
-        redcap_wider() |>
+        REDCapCAST::redcap_wider() |>
         dplyr::select(-dplyr::ends_with("_complete")) |>
         dplyr::select(-dplyr::any_of(record_id)) |>
-        suffix2label()
+        REDCapCAST::suffix2label()
 
       out_object <- file_export(redcap_data,
                                 output.format = output.format,
@@ -1383,7 +1376,7 @@ redcap_app <- function() {
 
 
 ########
-#### Current file: R//regression_model.R 
+#### Current file: R//regression_model.R
 ########
 
 
@@ -1417,7 +1410,6 @@ redcap_app <- function() {
 
 
 
-
 
 
 regression_model <- function(data,
@@ -1455,7 +1447,7 @@ regression_model <- function(data,
   data <- data |>
     purrr::map(\(.x){
       if (is.character(.x)) {
-        suppressWarnings(as_factor(.x))
+        suppressWarnings(REDCapCAST::as_factor(.x))
       } else {
         .x
       }
@@ -1594,7 +1586,7 @@ regression_model_uv <- function(data,
 
 
 ########
-#### Current file: R//regression_table.R 
+#### Current file: R//regression_table.R
 ########
 
 
@@ -1742,7 +1734,7 @@ tbl_merge <- function(data) {
 
 
 ########
-#### Current file: R//report.R 
+#### Current file: R//report.R
 ########
 
 
@@ -1829,7 +1821,7 @@ modify_qmd <- function(file, format) {
 
 
 ########
-#### Current file: R//shiny_freesearcheR.R 
+#### Current file: R//shiny_freesearcheR.R
 ########
 
 
@@ -1860,7 +1852,7 @@ shiny_freesearcheR <- function(...) {
 
 
 ########
-#### Current file: R//theme.R 
+#### Current file: R//theme.R
 ########
 
 
@@ -1901,7 +1893,7 @@ custom_theme <- function(...,
 
 
 ########
-#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/ui.R 
+#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/ui.R
 ########
 
 # ns <- NS(id)
@@ -2213,7 +2205,7 @@ ui <- bslib::page_fluid(
   title = "freesearcheR",
   theme = light,
   shiny::useBusyIndicators(),
-  bslib::page_navbar(
+  bslib::page_navbar(title = "freesearcheR",
     id = "main_panel",
     # header = shiny::tags$header(shiny::p("Data is only stored temporarily for analysis and deleted immediately afterwards.")),
     ui_elements$import,
@@ -2221,7 +2213,7 @@ ui <- bslib::page_fluid(
     ui_elements$analyze,
     ui_elements$docs,
     # bslib::nav_spacer(),
-    # bslib::nav_item(shinyWidgets::materialSwitch(inputId = "mode", label = icon("moon"), right=TRUE,status = "success")),
+    # bslib::nav_item(shinyWidgets::circleButton(inputId = "mode", icon = icon("moon"),status = "primary")),
     fillable = TRUE,
     footer = shiny::tags$footer(
       style = "background-color: #14131326; padding: 4px; text-align: center; bottom: 0; width: 100%;",
@@ -2238,7 +2230,7 @@ ui <- bslib::page_fluid(
 
 
 ########
-#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/server.R 
+#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/server.R
 ########
 
 library(readr)
@@ -2277,17 +2269,6 @@ library(DT)
 # dark <- custom_theme(bg = "#000",fg="#fff")
 
 
-#' freesearcheR server
-#'
-#' @param input input
-#' @param output output
-#' @param session session
-#'
-#' @returns server
-#' @export
-#' @importFrom REDCapCAST fct_drop.data.frame
-#'
-#' @examples
 server <- function(input, output, session) {
   ## Listing files in www in session start to keep when ending and removing
   ## everything else.
@@ -2579,7 +2560,7 @@ server <- function(input, output, session) {
         {
           data <- data_filter() |>
             dplyr::mutate(dplyr::across(dplyr::where(is.character), as.factor)) |>
-            fct_drop.data.frame() |>
+            REDCapCAST::fct_drop.data.frame() |>
             factorize(vars = input$factor_vars)
 
           if (input$strat_var == "none") {
@@ -2799,7 +2780,7 @@ server <- function(input, output, session) {
 
 
 ########
-#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/launch.R 
+#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/launch.R
 ########
 
 shinyApp(ui, server)
diff --git a/inst/apps/data_analysis_modules/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf b/inst/apps/data_analysis_modules/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf
index 8d0b399..07d9f7c 100644
--- a/inst/apps/data_analysis_modules/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf
+++ b/inst/apps/data_analysis_modules/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf
@@ -5,6 +5,6 @@ account: agdamsbo
 server: shinyapps.io
 hostUrl: https://api.shinyapps.io/v1
 appId: 13611288
-bundleId:
+bundleId: 9546880
 url: https://agdamsbo.shinyapps.io/freesearcheR/
 version: 1
diff --git a/inst/apps/data_analysis_modules/server.R b/inst/apps/data_analysis_modules/server.R
index 719a763..43a14bc 100644
--- a/inst/apps/data_analysis_modules/server.R
+++ b/inst/apps/data_analysis_modules/server.R
@@ -34,17 +34,6 @@ library(DT)
 # dark <- custom_theme(bg = "#000",fg="#fff")
 
 
-#' freesearcheR server
-#'
-#' @param input input
-#' @param output output
-#' @param session session
-#'
-#' @returns server
-#' @export
-#' @importFrom REDCapCAST fct_drop.data.frame
-#'
-#' @examples
 server <- function(input, output, session) {
   ## Listing files in www in session start to keep when ending and removing
   ## everything else.
@@ -336,7 +325,7 @@ server <- function(input, output, session) {
         {
           data <- data_filter() |>
             dplyr::mutate(dplyr::across(dplyr::where(is.character), as.factor)) |>
-            fct_drop.data.frame() |>
+            REDCapCAST::fct_drop.data.frame() |>
             factorize(vars = input$factor_vars)
 
           if (input$strat_var == "none") {
diff --git a/inst/apps/data_analysis_modules/ui.R b/inst/apps/data_analysis_modules/ui.R
index f16edd6..7471e72 100644
--- a/inst/apps/data_analysis_modules/ui.R
+++ b/inst/apps/data_analysis_modules/ui.R
@@ -307,7 +307,7 @@ ui <- bslib::page_fluid(
   title = "freesearcheR",
   theme = light,
   shiny::useBusyIndicators(),
-  bslib::page_navbar(
+  bslib::page_navbar(title = "freesearcheR",
     id = "main_panel",
     # header = shiny::tags$header(shiny::p("Data is only stored temporarily for analysis and deleted immediately afterwards.")),
     ui_elements$import,
@@ -315,7 +315,7 @@ ui <- bslib::page_fluid(
     ui_elements$analyze,
     ui_elements$docs,
     # bslib::nav_spacer(),
-    # bslib::nav_item(shinyWidgets::materialSwitch(inputId = "mode", label = icon("moon"), right=TRUE,status = "success")),
+    # bslib::nav_item(shinyWidgets::circleButton(inputId = "mode", icon = icon("moon"),status = "primary")),
     fillable = TRUE,
     footer = shiny::tags$footer(
       style = "background-color: #14131326; padding: 4px; text-align: center; bottom: 0; width: 100%;",
diff --git a/man/default_parsing.Rd b/man/default_parsing.Rd
index b1ad21d..d7237c2 100644
--- a/man/default_parsing.Rd
+++ b/man/default_parsing.Rd
@@ -7,7 +7,7 @@
 default_parsing(data)
 }
 \arguments{
-\item{data}{}
+\item{data}{data}
 }
 \value{
 data.frame or tibble
@@ -17,5 +17,7 @@ Default data parsing
 }
 \examples{
 mtcars |> str()
-mtcars |> default_parsing() |> str()
+mtcars |>
+  default_parsing() |>
+  str()
 }
diff --git a/renv.lock b/renv.lock
index 0868c9d..15e502d 100644
--- a/renv.lock
+++ b/renv.lock
@@ -193,13 +193,9 @@
     },
     "REDCapCAST": {
       "Package": "REDCapCAST",
-      "Version": "24.11.3",
-      "Source": "GitHub",
-      "RemoteType": "github",
-      "RemoteHost": "api.github.com",
-      "RemoteRepo": "REDCapCAST",
-      "RemoteUsername": "agdamsbo",
-      "RemoteSha": "45315080c596d3c1ea5f2e815ef27d2a50230326",
+      "Version": "24.12.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
         "REDCapR",
@@ -209,6 +205,7 @@
         "forcats",
         "glue",
         "gt",
+        "gtsummary",
         "haven",
         "here",
         "keyring",
@@ -223,7 +220,7 @@
         "vctrs",
         "zip"
       ],
-      "Hash": "9a9744292f30f1fb7fad55c2dd2e9baf"
+      "Hash": "d0925e579ddfbedeb536c5cbf65fc42f"
     },
     "REDCapR": {
       "Package": "REDCapR",
@@ -555,9 +552,9 @@
     },
     "cardx": {
       "Package": "cardx",
-      "Version": "0.2.1",
+      "Version": "0.2.2",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
         "cards",
@@ -568,7 +565,7 @@
         "rlang",
         "tidyr"
       ],
-      "Hash": "e5458dd65b0602136b16aed802d3bd50"
+      "Hash": "21f5ce5381d529b08783dca434af3003"
     },
     "cellranger": {
       "Package": "cellranger",
@@ -1593,7 +1590,7 @@
     },
     "lubridate": {
       "Package": "lubridate",
-      "Version": "1.9.3",
+      "Version": "1.9.4",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1602,7 +1599,7 @@
         "methods",
         "timechange"
       ],
-      "Hash": "680ad542fbcf801442c83a6ac5a2126c"
+      "Hash": "be38bc740fc51783a78edb5a157e4104"
     },
     "magrittr": {
       "Package": "magrittr",
@@ -1790,7 +1787,7 @@
     },
     "openxlsx2": {
       "Package": "openxlsx2",
-      "Version": "1.11",
+      "Version": "1.12",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1803,7 +1800,7 @@
         "utils",
         "zip"
       ],
-      "Hash": "c519244e5080a630292e1fdc36717f0d"
+      "Hash": "be241f0f1a58220243d69141407a97ac"
     },
     "parameters": {
       "Package": "parameters",
@@ -2547,10 +2544,10 @@
     },
     "sodium": {
       "Package": "sodium",
-      "Version": "1.3.2",
+      "Version": "1.4.0",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "869b09ca565ecaa9efc62534ebfa3efd"
+      "Hash": "ae00d33a499e429a04409bc1167c4995"
     },
     "sourcetools": {
       "Package": "sourcetools",