R version dependency

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: REDCapCAST
 Title: REDCap Metadata Casting and Castellated Data Handling
-Version: 24.12.1
+Version: 25.1.1
 Authors@R: c(
     person("Andreas Gammelgaard", "Damsbo", email = "agdamsbo@clin.au.dk", 
     role = c("aut", "cre"),comment = c(ORCID = "0000-0002-7559-1154")), 
@@ -21,7 +21,7 @@ Description: Casting metadata for REDCap database creation and handling of
     4) procedures for data integration and interoperability with external 
     sources (Harris et al (2009) <doi:10.1016/j.jbi.2008.08.010>; 
     Harris et al (2019) <doi:10.1016/j.jbi.2019.103208>).
-Depends: R (>= 3.4.0)
+Depends: R (>= 4.1.0)
 Suggests:
     httr,
     jsonlite,
@@ -34,7 +34,8 @@ Suggests:
     roxygen2,
     spelling,
     rhub,
-    rsconnect
+    rsconnect,
+    pkgconfig
 License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true
@@ -50,19 +51,21 @@ Imports:
     purrr,
     readr,
     stats,
-    shiny,
-    haven,
     zip,
     assertthat,
-    openxlsx2,
-    readODS,
     forcats,
     vctrs,
     gt,
     bslib,
     here,
     glue,
-    gtsummary
+    gtsummary,
+    shiny,
+    haven,
+    openxlsx2,
+    readODS
+Language: en-US
+VignetteBuilder: knitr
 Collate: 
     'REDCapCAST-package.R'
     'utils.r'
@@ -82,5 +85,3 @@ Collate:
     'redcapcast_data.R'
     'redcapcast_meta.R'
     'shiny_cast.R'
-Language: en-US
-VignetteBuilder: knitr

NAMESPACE

@@ -28,6 +28,7 @@ export(clean_redcap_name)
 export(compact_vec)
 export(create_html_table)
 export(create_instrument_meta)
+export(cut_string_length)
 export(d2w)
 export(doc2dd)
 export(ds2dd)
@@ -73,11 +74,15 @@ importFrom(REDCapR,redcap_metadata_read)
 importFrom(REDCapR,redcap_read)
 importFrom(forcats,as_factor)
 importFrom(forcats,fct_drop)
+importFrom(haven,read_dta)
 importFrom(keyring,key_get)
 importFrom(keyring,key_list)
 importFrom(keyring,key_set)
 importFrom(openxlsx2,read_xlsx)
 importFrom(purrr,reduce)
+importFrom(readODS,read_ods)
 importFrom(readr,parse_time)
+importFrom(readr,read_csv)
+importFrom(readr,read_rds)
 importFrom(tidyr,pivot_wider)
 importFrom(tidyselect,all_of)

NEWS.md

@@ -1,18 +1,24 @@
-# REDCapCAST 24.12.2
+# REDCapCAST 25.1.1
 
 The newly introduced extension of `forcats::fct_drop()` has been corrected to work as intended as a method.
 
+Conversion of column names to `field_names` are aligning better with REDCap naming.
+
+Shorten variable names above 100 characters (REDCap criteria; note recommended variable name length is <26)
+
+Fixed a params conflict in easy_redcap() when specifying raw_or_label.
+
 # REDCapCAST 24.12.1
 
 This release attempts to solve problems hosting the shiny_cast app, while also implementing functions to preserve as much meta data as possible from the REDCap database when exporting data.
 
 The hosting on shinyapps.io has given a lot of trouble recently. Modified 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.
 
-* 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: A new option to `raw_or_label` in `read_redcap_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()`.
+* CHANGE: the default data export method of `easy_redcap()` has been changed to use the new labelled data export with `read_redcap_tables()`.
 
 # REDCapCAST 24.11.3
 
@@ -165,7 +171,7 @@ The main goal this package is to keep the option to only export a defined subset
 
 ### Functions:
 
-* `read_redcap_tables()` **NEW**: this function is mainly an implementation of the combined use of `REDCapR::readcap_read()` and `REDCap_split()` to maintain the focused nature of `REDCapR::readcap_read()`, to only download the specified data. Also implements tests of valid form names and event names. The usual fall-back solution was to get all data.
+* `read_redcap_tables()` **NEW**: this function is mainly an implementation of the combined use of `REDCapR::redcap_read()` and `REDCap_split()` to maintain the focused nature of `REDCapR::redcap_read()`, to only download the specified data. Also implements tests of valid form names and event names. The usual fall-back solution was to get all data.
 
 * `redcap_wider()` **NEW**: this function pivots the long data frames from `read_redcap_tables()` using `tidyr::pivot_wider()`.
 

R/ds2dd_detailed.R

@@ -1,5 +1,4 @@
 utils::globalVariables(c(
-  "stats::setNames",
   "field_name",
   "field_type",
   "select_choices_or_calculations",
@@ -247,7 +246,7 @@ ds2dd <-
 #'     form.name = sample(c("b", "c"), size = 6, replace = TRUE, prob = rep(.5, 2))
 #'   ) |>
 #'   purrr::pluck("meta")
-#' mtcars |> ds2dd_detailed(add.auto.id = TRUE)
+#' mtcars |> numchar2fct() |> ds2dd_detailed(add.auto.id = TRUE)
 #'
 #' ## Using column name suffix to carry form name
 #' data <- iris |>
@@ -269,6 +268,10 @@ ds2dd_detailed <- function(data,
                            metadata = names(REDCapCAST::redcapcast_meta),
                            convert.logicals = TRUE) {
 
+  short_names <- colnames(data) |> lapply(\(.x) cut_string_length(.x,l=90)) |> purrr::reduce(c)
+
+  data <- stats::setNames(data,short_names)
+
   if (convert.logicals) {
     data <- data |>
       ## Converts logical to factor, which overwrites attributes
@@ -294,7 +297,6 @@ ds2dd_detailed <- function(data,
     dplyr::tibble()
 
   ## form_name and field_name
-
   if (!is.null(form.sep)) {
     if (form.sep != "") {
       parts <- strsplit(names(data), split = form.sep)
@@ -313,11 +315,14 @@ ds2dd_detailed <- function(data,
       dd$field_name <- tolower(dd$field_name)
     } else {
       dd$form_name <- "data"
-      dd$field_name <- gsub(" ", "_", tolower(colnames(data)))
+
+      # dd$field_name <- gsub(" ", "_", tolower(colnames(data)))
+      dd$field_name <- clean_redcap_name(colnames(data))
     }
   } else {
     ## if no form name prefix, the colnames are used as field_names
-    dd$field_name <- gsub(" ", "_", tolower(colnames(data)))
+    # dd$field_name <- gsub(" ", "_", tolower(colnames(data)))
+    dd$field_name <- clean_redcap_name(colnames(data))
 
     if (is.null(form.name)) {
       dd$form_name <- "data"
@@ -425,7 +430,14 @@ ds2dd_detailed <- function(data,
   out <- list(
     data = data |>
       hms2character() |>
-      stats::setNames(dd$field_name),
+      stats::setNames(dd$field_name) |>
+      lapply(\(.x){
+        if (identical("factor",class(.x))){
+          as.numeric(.x)
+        } else {
+          .x
+        }
+      }) |> dplyr::bind_cols(),
     meta = dd
   )
 

R/easy_redcap.R

@@ -28,6 +28,9 @@ get_api_key <- function(key.name, ...) {
 #' \link[keyring]{key_set}, using the default keyring)
 #' @param widen.data argument to widen the exported data
 #' @param uri REDCap database API uri
+#' @param raw_or_label argument passed on to
+#' \link[REDCapCAST]{read_redcap_tables}. Default is "both" to get labelled
+#' data.
 #' @param ... arguments passed on to \link[REDCapCAST]{read_redcap_tables}.
 #'
 #' @return data.frame or list depending on widen.data
@@ -35,16 +38,22 @@ get_api_key <- function(key.name, ...) {
 #'
 #' @examples
 #' \dontrun{
-#' easy_redcap("My_new_project",fields=c("record_id","age","hypertension"))
+#' easy_redcap("My_new_project", fields = c("record_id", "age", "hypertension"))
 #' }
-easy_redcap <- function(project.name, widen.data = TRUE, uri, ...) {
+easy_redcap <- function(project.name,
-  key <- get_api_key(key.name = paste0(project.name, "_REDCAP_API"),
+                        widen.data = TRUE,
-                     prompt = "Provide REDCap API key:")
+                        uri,
+                        raw_or_label = "both",
+                        ...) {
+  key <- get_api_key(
+    key.name = paste0(project.name, "_REDCAP_API"),
+    prompt = "Provide REDCap API key:"
+  )
 
   out <- read_redcap_tables(
     uri = uri,
     token = key,
-    raw_or_label = "both",
+    raw_or_label = raw_or_label,
     ...
   )
 

R/shiny_cast.R

@@ -47,6 +47,12 @@ file_extension <- function(filenames) {
 #' @return tibble
 #' @export
 #'
+#' @importFrom openxlsx2 read_xlsx
+#' @importFrom haven read_dta
+#' @importFrom readODS read_ods
+#' @importFrom readr read_csv read_rds
+#'
+#'
 #' @examples
 #' read_input("https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/data/sample.csv")
 read_input <- function(file, consider.na = c("NA", '""', "")) {
@@ -55,15 +61,15 @@ read_input <- function(file, consider.na = c("NA", '""', "")) {
   tryCatch(
     {
       if (ext == "csv") {
-        df <- readr::read_csv(file = file, na = consider.na)
+        df <- read_csv(file = file, na = consider.na)
       } else if (ext %in% c("xls", "xlsx")) {
-        df <- openxlsx2::read_xlsx(file = file, na.strings = consider.na)
+        df <- read_xlsx(file = file, na.strings = consider.na)
       } else if (ext == "dta") {
-        df <- haven::read_dta(file = file)
+        df <- read_dta(file = file)
       } else if (ext == "ods") {
-        df <- readODS::read_ods(path = file)
+        df <- read_ods(path = file)
       } else if (ext == "rds") {
-        df <- readr::read_rds(file = file)
+        df <- read_rds(file = file)
       }else {
         stop("Input file format has to be on of:
              '.csv', '.xls', '.xlsx', '.dta', '.ods' or '.rds'")

R/utils.r

@@ -97,7 +97,10 @@ focused_metadata <- function(metadata, vars_in_data) {
 #' @return vector or data frame, same format as input
 #' @export
 #'
+#' @examples
+#' "Research!, ne:ws? and c;l-.ls" |> clean_redcap_name()
 clean_redcap_name <- function(x) {
+  gsub("[,.;:?!@]","",
   gsub(
     " ", "_",
     gsub(
@@ -108,6 +111,7 @@ clean_redcap_name <- function(x) {
       )
     )
   )
+  )
 }
 
 
@@ -518,3 +522,22 @@ dummy_fun <- function(...){
     gtsummary::add_difference()
   )
 }
+
+
+#' Cut string to desired length
+#'
+#' @param data data
+#' @param l length
+#'
+#' @returns character string of length l
+#' @export
+#'
+#' @examples
+#' "length" |> cut_string_length(l=3)
+cut_string_length <- function(data,l=100){
+  if (nchar(data)>=l){
+    substr(data,1,l)
+  } else {
+    data
+  }
+}

REDCapCAST.Rproj

@@ -19,4 +19,5 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageCheckArgs: --as-cran
 PackageRoxygenize: rd,collate,namespace,vignette

cran-comments.md

@@ -1,8 +1,9 @@
-── R CMD check results ─────────────────────────────────────────────────────────────────────────────── REDCapCAST 24.11.1 ────
+── R CMD check results ─────────────────────────────────────────────────────────────────────── REDCapCAST 25.1.1 ────
-Duration: 23.8s
+Duration: 31.2s
 
 0 errors ✔ | 0 warnings ✔ | 0 notes ✔
 
 R CMD check succeeded
+
 ## Test environments
 Rhubv2 runs and checks out.

inst/WORDLIST

@@ -68,6 +68,7 @@ natively
 ncol
 og
 param
+params
 pegeler
 perl
 pos

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: 9461113
+bundleId: 9642648
 url: https://agdamsbo.shinyapps.io/redcapcast/
 version: 1

man/REDCapCAST-package.Rd

@@ -6,8 +6,6 @@
 \alias{REDCapCAST-package}
 \title{REDCapCAST: REDCap Metadata Casting and Castellated Data Handling}
 \description{
-\if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}}
-
 Casting metadata for REDCap database creation and handling of castellated data using repeated instruments and longitudinal projects in 'REDCap'. Keeps a focused data export approach, by allowing to only export required data from the database. Also for casting new REDCap databases based on datasets from other sources. Originally forked from the R part of 'REDCapRITS' by Paul Egeler. See \url{https://github.com/pegeler/REDCapRITS}. 'REDCap' (Research Electronic Data Capture) is a secure, web-based software platform designed to support data capture for research studies, providing 1) an intuitive interface for validated data capture; 2) audit trails for tracking data manipulation and export procedures; 3) automated export procedures for seamless data downloads to common statistical packages; and 4) procedures for data integration and interoperability with external sources (Harris et al (2009) \doi{10.1016/j.jbi.2008.08.010}; Harris et al (2019) \doi{10.1016/j.jbi.2019.103208}).
 }
 \seealso{

man/clean_redcap_name.Rd

@@ -17,3 +17,6 @@ Stepwise removal on non-alphanumeric characters, trailing white space,
 substitutes spaces for underscores and converts to lower case.
 Trying to make up for different naming conventions.
 }
+\examples{
+"Research!, ne:ws? and c;l-.ls" |> clean_redcap_name()
+}

man/cut_string_length.Rd

@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.r
+\name{cut_string_length}
+\alias{cut_string_length}
+\title{Cut string to desired length}
+\usage{
+cut_string_length(data, l = 100)
+}
+\arguments{
+\item{data}{data}
+
+\item{l}{length}
+}
+\value{
+character string of length l
+}
+\description{
+Cut string to desired length
+}
+\examples{
+"length" |> cut_string_length(l=3)
+}

man/ds2dd_detailed.Rd

@@ -91,7 +91,7 @@ iris |>
     form.name = sample(c("b", "c"), size = 6, replace = TRUE, prob = rep(.5, 2))
   ) |>
   purrr::pluck("meta")
-mtcars |> ds2dd_detailed(add.auto.id = TRUE)
+mtcars |> numchar2fct() |> ds2dd_detailed(add.auto.id = TRUE)
 
 ## Using column name suffix to carry form name
 data <- iris |>

man/easy_redcap.Rd

@@ -4,7 +4,7 @@
 \alias{easy_redcap}
 \title{Secure API key storage and data acquisition in one}
 \usage{
-easy_redcap(project.name, widen.data = TRUE, uri, ...)
+easy_redcap(project.name, widen.data = TRUE, uri, raw_or_label = "both", ...)
 }
 \arguments{
 \item{project.name}{The name of the current project (for key storage with
@@ -14,6 +14,10 @@ easy_redcap(project.name, widen.data = TRUE, uri, ...)
 
 \item{uri}{REDCap database API uri}
 
+\item{raw_or_label}{argument passed on to
+\link[REDCapCAST]{read_redcap_tables}. Default is "both" to get labelled
+data.}
+
 \item{...}{arguments passed on to \link[REDCapCAST]{read_redcap_tables}.}
 }
 \value{
@@ -24,6 +28,6 @@ Secure API key storage and data acquisition in one
 }
 \examples{
 \dontrun{
-easy_redcap("My_new_project",fields=c("record_id","age","hypertension"))
+easy_redcap("My_new_project", fields = c("record_id", "age", "hypertension"))
 }
 }

vignettes/REDCapCAST.Rmd

@@ -37,7 +37,7 @@ shiny_cast()
 
 To get you started, the easiest way possible, you can use the `easy_redcap()` function (example below).
 
-You will need an API-key for your REDCap server, the uri/URL/address for the API connection (usually the adress used for accessing your institutions REDCap servar, with an appended "/api/").
+You will need an API-key for your REDCap server, the uri/URL/address for the API connection (usually the address used for accessing your institutions REDCap server, with an appended "/api/").
 
 This function includes a few convenience features to ease your further work.