minor adjustments and bug fixing

NAMESPACE

@@ -11,6 +11,7 @@ S3method(process_user_input,data.frame)
 S3method(process_user_input,default)
 S3method(process_user_input,response)
 export(REDCap_split)
+export(all_na)
 export(as_factor)
 export(case_match_regex_list)
 export(cast_data_overview)
@@ -18,6 +19,7 @@ export(cast_meta_overview)
 export(char2choice)
 export(char2cond)
 export(clean_redcap_name)
+export(compact_vec)
 export(create_html_table)
 export(create_instrument_meta)
 export(d2w)
@@ -42,6 +44,7 @@ export(named_levels)
 export(nav_bar_page)
 export(numchar2fct)
 export(parse_data)
+export(possibly_roman)
 export(process_user_input)
 export(read_input)
 export(read_redcap_instrument)
@@ -53,6 +56,7 @@ export(shiny_cast)
 export(split_non_repeating_forms)
 export(strsplitx)
 export(var2fct)
+export(vec2choice)
 importFrom(REDCapR,redcap_event_instruments)
 importFrom(REDCapR,redcap_metadata_read)
 importFrom(REDCapR,redcap_read)

R/as_factor.R

@@ -56,13 +56,14 @@ as_factor.numeric <- function(x, ...) {
 #' @export
 as_factor.character <- function(x, ...) {
   labels <- get_attr(x)
-  if (is.roman(x)){
+  if (possibly_roman(x)){
     x <- factor(x)
   } else {
   x <- structure(
     forcats::fct_inorder(x),
     label = attr(x, "label", exact = TRUE)
-  )}
+  )
+  }
   set_attr(x, labels, overwrite = FALSE)
 }
 
@@ -201,11 +202,19 @@ named_levels <- function(data, label = "labels", na.label = NULL, na.value = 99)
     )
   }
 
+  # Handle empty factors
+  if (all_na(data)){
+    d <- data.frame(
+      name = levels(data),
+      value = seq_along(levels(data))
+    )
+  } else {
     d <- data.frame(
       name = levels(data)[data],
       value = as.numeric(data)
     ) |>
       unique()
+  }
 
   ## Applying labels
   attr_l <- attr(x = data, which = label, exact = TRUE)
@@ -227,8 +236,21 @@ named_levels <- function(data, label = "labels", na.label = NULL, na.value = 99)
   out
 }
 
-is.roman <- function(data){
-  identical(data,as.character(utils::as.roman(data)))
+#' Test if vector can be interpreted as roman numerals
+#'
+#' @param data character vector
+#'
+#' @return logical
+#' @export
+#'
+#' @examples
+#' sample(1:100,10) |> as.roman() |> possibly_roman()
+#' sample(c(TRUE,FALSE),10,TRUE)|> possibly_roman()
+#' rep(NA,10)|> possibly_roman()
+possibly_roman <- function(data){
+  # browser()
+  if (all(is.na(data))) return(FALSE)
+  identical(as.character(data),as.character(utils::as.roman(data)))
 }
 
 

R/ds2dd_detailed.R

@@ -141,10 +141,15 @@ hms2character <- function(data) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
-#' data <- REDCapCAST::redcapcast_data
-#' data |> ds2dd_detailed()
+#' ## Basic parsing with default options
+#' REDCapCAST::redcapcast_data |>
+#'   dplyr::select(-dplyr::starts_with("redcap_")) |>
+#'   ds2dd_detailed()
+#'
+#' ## Adding a record_id field
 #' iris |> ds2dd_detailed(add.auto.id = TRUE)
+#'
+#' ## Passing form name information to function
 #' iris |>
 #'   ds2dd_detailed(
 #'     add.auto.id = TRUE,
@@ -152,13 +157,14 @@ hms2character <- function(data) {
 #'   ) |>
 #'   purrr::pluck("meta")
 #' mtcars |> ds2dd_detailed(add.auto.id = TRUE)
+#'
+#' ## Using column name suffix to carry form name
 #' data <- iris |>
 #'   ds2dd_detailed(add.auto.id = TRUE) |>
 #'   purrr::pluck("data")
 #' names(data) <- glue::glue("{sample(x = c('a','b'),size = length(names(data)),
 #' replace=TRUE,prob = rep(x=.5,2))}__{names(data)}")
 #' data |> ds2dd_detailed(form.sep = "__")
-#' }
 ds2dd_detailed <- function(data,
                            add.auto.id = FALSE,
                            date.format = "dmy",
@@ -171,24 +177,18 @@ ds2dd_detailed <- function(data,
                            field.validation = NULL,
                            metadata = names(REDCapCAST::redcapcast_meta),
                            convert.logicals = TRUE) {
+  # Repair empty columns
+  # These where sometimes classed as factors or
+  # if (any(sapply(data,all_na))){
+  #   data <- data |>
+  #     ## Converts logical to factor, which overwrites attributes
+  #     dplyr::mutate(dplyr::across(dplyr::where(all_na), as.character))
+  # }
 
   if (convert.logicals) {
-    # Labels/attributes are saved
-    # labels <- lapply(data, \(.x){
-    #   get_attr(.x, attr = NULL)
-    # })
-
     data <- data |>
       ## Converts logical to factor, which overwrites attributes
       dplyr::mutate(dplyr::across(dplyr::where(is.logical), as_factor))
-
-    # Old attributes are appended
-    # data <- purrr::imap(no_attr,\(.x,.i){
-    #   attributes(.x) <- c(attributes(.x),labels[[.i]])
-    #   .x
-    # }) |>
-    #   dplyr::bind_cols()
-
   }
 
   ## Handles the odd case of no id column present
@@ -197,9 +197,6 @@ ds2dd_detailed <- function(data,
       record_id = seq_len(nrow(data)),
       data
     )
-    # set_attr(data$record_id,label="ID",attr="label")
-
-    message("A default id column has been added")
   }
 
   ## ---------------------------------------
@@ -227,6 +224,9 @@ ds2dd_detailed <- function(data,
         dd$form_name <- clean_redcap_name(Reduce(c, lapply(parts, \(.x) .x[[length(.x)]])))
         dd$field_name <- Reduce(c, lapply(parts, \(.x) paste(.x[seq_len(length(.x) - 1)], collapse = form.sep)))
       }
+      ## To preserve original
+      colnames(data) <- dd$field_name
+      dd$field_name <- tolower(dd$field_name)
     } else {
       dd$form_name <- "data"
       dd$field_name <- gsub(" ", "_", tolower(colnames(data)))
@@ -251,14 +251,20 @@ ds2dd_detailed <- function(data,
   if (is.null(field.label)) {
     dd$field_label <- data |>
       sapply(function(x) {
-        get_attr(x, attr = field.label.attr)
+        get_attr(x, attr = field.label.attr) |>
+          compact_vec()
       })
 
     dd <-
-      dd |> dplyr::mutate(field_label = dplyr::if_else(is.na(field_label),
-        field_name, field_label
-      ))
+      dd |>
+      dplyr::mutate(
+        field_label = dplyr::if_else(is.na(field_label),
+          colnames(data),
+          field_label
+        )
+      )
   } else {
+    ## It really should be unique for each: same length as number of variables
     if (length(field.label) == 1 || length(field.label) == nrow(dd)) {
       dd$field_label <- field.label
     } else {
@@ -312,23 +318,16 @@ ds2dd_detailed <- function(data,
   ## choices
 
   factor_levels <- data |>
-      lapply(function(x) {
+    sapply(function(x) {
       if (is.factor(x)) {
         ## Custom function to ensure factor order and keep original values
         ## Avoiding refactoring to keep as much information as possible
-          lvls <- sort(named_levels(x))
-          paste(
-            paste(lvls,
-              names(lvls),
-              sep = ", "
-            ),
-            collapse = " | "
-          )
+        sort(named_levels(x)) |>
+          vec2choice()
       } else {
         NA
       }
-      }) |>
-      (\(x)do.call(c, x))()
+    })
 
   dd <-
     dd |> dplyr::mutate(
@@ -346,10 +345,22 @@ ds2dd_detailed <- function(data,
     meta = dd
   )
 
-  class(out) <- c("REDCapCAST",class(out))
+  class(out) <- c("REDCapCAST", class(out))
   out
 }
 
+#' Check if vector is all NA
+#'
+#' @param data vector of data.frame
+#'
+#' @return logical
+#' @export
+#'
+#' @examples
+#' rep(NA,4) |> all_na()
+all_na <- function(data){
+  all(is.na(data))
+}
 
 #' Guess time variables based on naming pattern
 #'
@@ -423,11 +434,9 @@ mark_complete <- function(upload, ls) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
 #' mtcars |>
 #'   parse_data() |>
 #'   str()
-#' }
 parse_data <- function(data,
                        guess_type = TRUE,
                        col_types = NULL,
@@ -483,7 +492,6 @@ parse_data <- function(data,
 #' @importFrom forcats as_factor
 #'
 #' @examples
-#' \dontrun{
 #' sample(seq_len(4), 20, TRUE) |>
 #'   var2fct(6) |>
 #'   summary()
@@ -491,7 +499,6 @@ parse_data <- function(data,
 #'   var2fct(6) |>
 #'   summary()
 #' sample(letters[1:4], 20, TRUE) |> var2fct(6)
-#' }
 var2fct <- function(data, unique.n) {
   if (length(unique(data)) <= unique.n) {
     as_factor(data)
@@ -540,5 +547,59 @@ numchar2fct <- function(data, numeric.threshold = 6, character.throshold = 6) {
 }
 
 
+#' Named vector to REDCap choices (`wrapping compact_vec()`)
+#'
+#' @param data named vector
+#'
+#' @return character string
+#' @export
+#'
+#' @examples
+#' sample(seq_len(4), 20, TRUE) |>
+#'   as_factor() |>
+#'   named_levels() |>
+#'   sort() |>
+#'   vec2choice()
+vec2choice <- function(data) {
+  compact_vec(data,nm.sep = ", ",val.sep = " | ")
+}
 
+#' Compacting a vector of any length with or without names
+#'
+#' @param data vector, optionally named
+#' @param nm.sep string separating name from value if any
+#' @param val.sep string separating values
+#'
+#' @return character string
+#' @export
+#'
+#' @examples
+#' sample(seq_len(4), 20, TRUE) |>
+#'   as_factor() |>
+#'   named_levels() |>
+#'   sort() |>
+#'   compact_vec()
+#' 1:6 |> compact_vec()
+#' "test" |> compact_vec()
+#' sample(letters[1:9], 20, TRUE) |> compact_vec()
+compact_vec <- function(data,nm.sep=": ",val.sep="; ") {
+  # browser()
+  if (all(is.na(data))) {
+    return(data)
+  }
 
+  if (length(names(data)) > 0) {
+    paste(
+      paste(data,
+        names(data),
+        sep = nm.sep
+      ),
+      collapse = val.sep
+    )
+  } else {
+    paste(
+      data,
+      collapse = val.sep
+    )
+  }
+}

R/shiny_cast.R

@@ -21,7 +21,6 @@ shiny_cast <- function(...) {
 }
 
 
-
 #' DEPRECATED Helper to import files correctly
 #'
 #' @param filenames file names

inst/shiny-examples/casting/rsconnect/shinyapps.io/agdamsbo/redcapcast.dcf

@@ -5,6 +5,6 @@ account: agdamsbo
 server: shinyapps.io
 hostUrl: https://api.shinyapps.io/v1
 appId: 11351429
-bundleId: 9392320
+bundleId: 9392352
 url: https://agdamsbo.shinyapps.io/redcapcast/
 version: 1

inst/shiny-examples/casting/server.R

@@ -63,7 +63,7 @@ server <- function(input, output, session) {
     v$file <- "loaded"
     ds2dd_detailed(
       data = dat(),
-      add.auto.id = input$add_id=="yes"
+      add.auto.id = input$add_id == "yes"
     )
   })
 
@@ -132,7 +132,8 @@ server <- function(input, output, session) {
     content = function(file) {
       export_redcap_instrument(purrr::pluck(dd(), "meta"),
         file = file,
-                               record.id = ifelse(input$add_id=="none",NA,names(dat())[1]))
+        record.id = ifelse(input$add_id == "none", NA, names(dat())[1])
+      )
     }
   )
 

inst/shiny-examples/casting/ui.R

@@ -2,6 +2,5 @@ ui <-
   bslib::page(
     theme = bslib::bs_theme(preset = "united"),
     title = "REDCap database creator",
-nav_bar_page()
+    nav_bar_page()
   )
-

man/all_na.Rd

@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ds2dd_detailed.R
+\name{all_na}
+\alias{all_na}
+\title{Check if vector is all NA}
+\usage{
+all_na(data)
+}
+\arguments{
+\item{data}{vector of data.frame}
+}
+\value{
+logical
+}
+\description{
+Check if vector is all NA
+}
+\examples{
+rep(NA,4) |> all_na()
+}

man/compact_vec.Rd

@@ -0,0 +1,31 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ds2dd_detailed.R
+\name{compact_vec}
+\alias{compact_vec}
+\title{Compacting a vector of any length with or without names}
+\usage{
+compact_vec(data, nm.sep = ": ", val.sep = "; ")
+}
+\arguments{
+\item{data}{vector, optionally named}
+
+\item{nm.sep}{string separating name from value if any}
+
+\item{val.sep}{string separating values}
+}
+\value{
+character string
+}
+\description{
+Compacting a vector of any length with or without names
+}
+\examples{
+sample(seq_len(4), 20, TRUE) |>
+  as_factor() |>
+  named_levels() |>
+  sort() |>
+  compact_vec()
+1:6 |> compact_vec()
+"test" |> compact_vec()
+sample(letters[1:9], 20, TRUE) |> compact_vec()
+}

man/ds2dd_detailed.Rd

@@ -75,10 +75,15 @@ Ensure, that the data set is formatted with as much information as possible.
 `field.type` can be supplied
 }
 \examples{
-\dontrun{
-data <- REDCapCAST::redcapcast_data
-data |> ds2dd_detailed()
+## Basic parsing with default options
+REDCapCAST::redcapcast_data |>
+  dplyr::select(-dplyr::starts_with("redcap_")) |>
+  ds2dd_detailed()
+
+## Adding a record_id field
 iris |> ds2dd_detailed(add.auto.id = TRUE)
+
+## Passing form name information to function
 iris |>
   ds2dd_detailed(
     add.auto.id = TRUE,
@@ -86,6 +91,8 @@ iris |>
   ) |>
   purrr::pluck("meta")
 mtcars |> ds2dd_detailed(add.auto.id = TRUE)
+
+## Using column name suffix to carry form name
 data <- iris |>
   ds2dd_detailed(add.auto.id = TRUE) |>
   purrr::pluck("data")
@@ -93,4 +100,3 @@ names(data) <- glue::glue("{sample(x = c('a','b'),size = length(names(data)),
 replace=TRUE,prob = rep(x=.5,2))}__{names(data)}")
 data |> ds2dd_detailed(form.sep = "__")
 }
-}

man/parse_data.Rd

@@ -33,9 +33,7 @@ data.frame or tibble
 Helper to auto-parse un-formatted data with haven and readr
 }
 \examples{
-\dontrun{
 mtcars |>
   parse_data() |>
   str()
 }
-}

man/possibly_roman.Rd

@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/as_factor.R
+\name{possibly_roman}
+\alias{possibly_roman}
+\title{Test if vector can be interpreted as roman numerals}
+\usage{
+possibly_roman(data)
+}
+\arguments{
+\item{data}{character vector}
+}
+\value{
+logical
+}
+\description{
+Test if vector can be interpreted as roman numerals
+}
+\examples{
+sample(1:100,10) |> as.roman() |> possibly_roman()
+sample(c(TRUE,FALSE),10,TRUE)|> possibly_roman()
+rep(NA,10)|> possibly_roman()
+}

man/var2fct.Rd

@@ -19,7 +19,6 @@ This is a wrapper of forcats::as_factor, which sorts numeric vectors before
 factoring, but levels character vectors in order of appearance.
 }
 \examples{
-\dontrun{
 sample(seq_len(4), 20, TRUE) |>
   var2fct(6) |>
   summary()
@@ -28,4 +27,3 @@ sample(letters, 20) |>
   summary()
 sample(letters[1:4], 20, TRUE) |> var2fct(6)
 }
-}

man/vec2choice.Rd

@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ds2dd_detailed.R
+\name{vec2choice}
+\alias{vec2choice}
+\title{Named vector to REDCap choices (`wrapping compact_vec()`)}
+\usage{
+vec2choice(data)
+}
+\arguments{
+\item{data}{named vector}
+}
+\value{
+character string
+}
+\description{
+Named vector to REDCap choices (`wrapping compact_vec()`)
+}
+\examples{
+sample(seq_len(4), 20, TRUE) |>
+  as_factor() |>
+  named_levels() |>
+  sort() |>
+  vec2choice()
+}