adjusting

DESCRIPTION

@@ -71,6 +71,7 @@ Collate:
     'ds2dd_detailed.R'
     'easy_redcap.R'
     'export_redcap_instrument.R'
+    'fct_drop.R'
     'html_styling.R'
     'mtcars_redcap.R'
     'read_redcap_instrument.R'

NAMESPACE

@@ -1,17 +1,21 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(as_factor,character)
+S3method(as_factor,data.frame)
 S3method(as_factor,factor)
 S3method(as_factor,haven_labelled)
 S3method(as_factor,labelled)
 S3method(as_factor,logical)
 S3method(as_factor,numeric)
+S3method(as_factor,redcapcast_labelled)
 S3method(process_user_input,character)
 S3method(process_user_input,data.frame)
 S3method(process_user_input,default)
 S3method(process_user_input,response)
 export(REDCap_split)
 export(all_na)
+export(apply_factor_labels)
+export(apply_field_label)
 export(as_factor)
 export(case_match_regex_list)
 export(cast_data_overview)
@@ -30,6 +34,8 @@ export(ds2dd_detailed)
 export(easy_redcap)
 export(export_redcap_instrument)
 export(fct2num)
+export(fct_drop)
+export(fct_drop.data.frame)
 export(file_extension)
 export(focused_metadata)
 export(format_subheader)
@@ -39,6 +45,7 @@ export(guess_time_only)
 export(guess_time_only_filter)
 export(haven_all_levels)
 export(html_tag_wrap)
+export(is.labelled)
 export(is_repeated_longitudinal)
 export(match_fields_to_form)
 export(named_levels)
@@ -49,9 +56,7 @@ export(possibly_roman)
 export(process_user_input)
 export(read_input)
 export(read_redcap_instrument)
-export(read_redcap_labelled)
 export(read_redcap_tables)
-export(redcap_meta_default)
 export(redcap_wider)
 export(sanitize_split)
 export(set_attr)
@@ -64,6 +69,7 @@ importFrom(REDCapR,redcap_event_instruments)
 importFrom(REDCapR,redcap_metadata_read)
 importFrom(REDCapR,redcap_read)
 importFrom(forcats,as_factor)
+importFrom(forcats,fct_drop)
 importFrom(keyring,key_get)
 importFrom(keyring,key_list)
 importFrom(keyring,key_set)

NEWS.md

@@ -2,7 +2,11 @@
 
 The hosting on shinyapps.io has given a lot of trouble recently. Modyfied package structure a little around the `shiny_cast()`, to accommodate an alternative hosting approach with all package functions included in a script instead of requiring the package.
 
-* read_readcap_labelled(): 
+* NEW: A new option to `raw_or_label` in `read_readcap_tables()` has been added: "both". Get raw values with REDCap labels applied as labels. Use `as_factor()` to format factors with original labels and use the `gtsummary` package to easily get beautiful tables with original labels from REDCap. Use `fct_drop()` to drop empty levels.
+
+* NEW: fct_drop() has been added with an extension to `forcats::fct_drop()`, that works across data.frames. Use as `fct_drop()`.
+
+* CHANGE: the default data export method of `easy_redcap()` has been changed to use the new labelled data export with `read_readcap_tables()`.
 
 # REDCapCAST 24.11.3
 

R/ds2dd_detailed.R

@@ -99,26 +99,6 @@ hms2character <- function(data) {
 }
 
 
-#' Default column names of a REDCap data dictionary
-#'
-#' @param ... ignored for now
-#'
-#' @return character vector
-#' @export
-#'
-#' @examples
-#' dput(redcap_meta_default())
-redcap_meta_default <- function(...) {
-  c(
-    "field_name", "form_name", "section_header", "field_type",
-    "field_label", "select_choices_or_calculations", "field_note",
-    "text_validation_type_or_show_slider_number", "text_validation_min",
-    "text_validation_max", "identifier", "branching_logic", "required_field",
-    "custom_alignment", "question_number", "matrix_group_name", "matrix_ranking",
-    "field_annotation"
-  )
-}
-
 #' (DEPRECATED) Data set to data dictionary function
 #'
 #' @description
@@ -141,7 +121,7 @@ redcap_meta_default <- function(...) {
 #' @param include.column.names Flag to give detailed output including new
 #' column names for original data set for upload.
 #' @param metadata Metadata column names. Default is the included
-#' REDCapCAST::redcap_meta_default.
+#' names(REDCapCAST::redcapcast_meta).
 #'
 #' @return data.frame or list of data.frame and vector
 #' @export
@@ -157,7 +137,7 @@ ds2dd <-
            field.type = "text",
            field.label = NULL,
            include.column.names = FALSE,
-           metadata = REDCapCAST::redcap_meta_default()
+           metadata = names(REDCapCAST::redcapcast_meta)
            ) {
     dd <- data.frame(matrix(ncol = length(metadata), nrow = ncol(ds)))
     colnames(dd) <- metadata
@@ -244,7 +224,7 @@ ds2dd <-
 #' or attribute `factor.labels.attr` for haven_labelled data set (imported .dta
 #' file with `haven::read_dta()`).
 #' @param metadata redcap metadata headings. Default is
-#' REDCapCAST::redcap_meta_default().
+#' names(REDCapCAST::redcapcast_meta).
 #' @param convert.logicals convert logicals to factor. Default is TRUE.
 #'
 #' @return list of length 2
@@ -286,7 +266,7 @@ ds2dd_detailed <- function(data,
                            field.label = NULL,
                            field.label.attr = "label",
                            field.validation = NULL,
-                           metadata = REDCapCAST::redcap_meta_default(),
+                           metadata = names(REDCapCAST::redcapcast_meta),
                            convert.logicals = TRUE) {
 
   if (convert.logicals) {

data-raw/metadata_names.R

@@ -7,9 +7,9 @@
 #   "matrix_ranking", "field_annotation"
 # )
 
-# metadata_names <- REDCapR::redcap_metadata_read(
+metadata_names <- REDCapR::redcap_metadata_read(
-#   redcap_uri = keyring::key_get("DB_URI"),
+  redcap_uri = keyring::key_get("DB_URI"),
-#   token = keyring::key_get("cast_api")
+  token = keyring::key_get("cast_api")
-# )$data |> names()
+)$data |> names()
-#
+
-# usethis::use_data(metadata_names, overwrite = TRUE, internal = TRUE)
+usethis::use_data(metadata_names, overwrite = TRUE, internal = TRUE)

man/ds2dd_detailed.Rd

@@ -15,7 +15,7 @@ ds2dd_detailed(
   field.label = NULL,
   field.label.attr = "label",
   field.validation = NULL,
-  metadata = REDCapCAST::redcap_meta_default(),
+  metadata = names(REDCapCAST::redcapcast_meta),
   convert.logicals = TRUE
 )
 }
@@ -55,7 +55,7 @@ or attribute `factor.labels.attr` for haven_labelled data set (imported .dta
 file with `haven::read_dta()`).}
 
 \item{metadata}{redcap metadata headings. Default is
-REDCapCAST::redcap_meta_default().}
+names(REDCapCAST::redcapcast_meta).}
 
 \item{convert.logicals}{convert logicals to factor. Default is TRUE.}
 }