reverting and recovering from renv corruption

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()
 }

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,

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
       }