CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 23.6.1
+Date: 2023-06-05 06:44:45 UTC
+SHA: f2d5b8f6007b7f953c525e58e8b47ec8d702d9be

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: REDCapCAST
 Title: REDCap Castellated Data Handling
-Version: 23.6.2
+Version: 23.6.1
 Authors@R: c(
     person("Andreas Gammelgaard", "Damsbo", email = "agdamsbo@clin.au.dk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7559-1154")),
@@ -48,7 +48,6 @@ Collate:
     'utils.r'
     'process_user_input.r'
     'REDCap_split.r'
-    'ds2dd.R'
     'read_redcap_tables.R'
     'redcap_wider.R'
     'redcapcast_data.R'

NAMESPACE

@@ -2,15 +2,12 @@
 
 export(REDCap_split)
 export(clean_redcap_name)
-export(d2w)
-export(ds2dd)
 export(focused_metadata)
 export(match_fields_to_form)
 export(read_redcap_tables)
 export(redcap_wider)
 export(sanitize_split)
 export(split_non_repeating_forms)
-export(strsplitx)
 importFrom(REDCapR,redcap_event_instruments)
 importFrom(REDCapR,redcap_metadata_read)
 importFrom(REDCapR,redcap_read)

NEWS.md

@@ -1,16 +1,3 @@
-# REDCapCAST 23.6.2
-
-This version marks the introduction of a few helper functions to handle database creation.
-
-### Functions
-
-* New: `ds2dd()` function migrating from the `stRoke`-package. Assists in building a data dictionary for REDCap from a dataset.
-
-* New: `strsplitx()` function to ease the string splitting as an extension of `base::strsplit()`. Inspiration from https://stackoverflow.com/a/11014253/21019325 and https://www.r-bloggers.com/2018/04/strsplit-but-keeping-the-delimiter/. 
-
-* New: `d2n()` function converts single digits to written numbers. Used to sanitize variable and form names in REDCap database creation. For more universal number to word I would suggest `english::word()` or `xfun::numbers_to_words()`, though I have not been testing these.
-
-
 # REDCapCAST 23.6.1
 
 ### Documentation:

R/ds2dd.R

@@ -1,84 +0,0 @@
-utils::globalVariables(c("redcapcast_meta"))
-#' Data set to data dictionary function
-#'
-#' Migrated from stRoke ds2dd(). Fits better with the functionality of
-#' 'REDCapCAST'
-#' @param ds data set
-#' @param record.id name or column number of id variable, moved to first row of
-#' data dictionary, character of integer. Default is "record_id".
-#' @param form.name vector of form names, character string, length 1 or length
-#' equal to number of variables. Default is "basis".
-#' @param field.type vector of field types, character string, length 1 or length
-#' equal to number of variables. Default is "text.
-#' @param field.label vector of form names, character string, length 1 or length
-#' equal to number of variables. Default is NULL and is then identical to field
-#' names.
-#' @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::redcapcast_data.
-#'
-#' @return data.frame or list of data.frame and vector
-#' @export
-#'
-#' @examples
-#' redcapcast_data$record_id <- seq_len(nrow(redcapcast_data))
-#' ds2dd(redcapcast_data, include.column.names=TRUE)
-
-ds2dd <-
-  function(ds,
-           record.id = "record_id",
-           form.name = "basis",
-           field.type = "text",
-           field.label = NULL,
-           include.column.names = FALSE,
-           metadata = names(redcapcast_meta)) {
-    dd <- data.frame(matrix(ncol = length(metadata), nrow = ncol(ds)))
-    colnames(dd) <- metadata
-
-    if (is.character(record.id) & !record.id %in% colnames(ds)) {
-      stop("Provided record.id is not a variable name in provided data set.")
-    }
-
-    # renaming to lower case and substitute spaces with underscore
-    field.name <- gsub(" ", "_", tolower(colnames(ds)))
-
-    # handles both character and integer
-    colsel <-
-      colnames(ds) == colnames(ds[record.id])
-
-    if (summary(colsel)[3] != 1) {
-      stop("Provided record.id has to be or refer to a uniquely named column.")
-    }
-
-    dd[, "field_name"] <-
-      c(field.name[colsel], field.name[!colsel])
-
-    if (length(form.name) > 1 & length(form.name) != ncol(ds)) {
-      stop(
-        "Provided form.name should be of length 1 (value is reused) or equal
-        length as number of variables in data set."
-      )
-    }
-    dd[, "form_name"] <- form.name
-
-    if (length(field.type) > 1 & length(field.type) != ncol(ds)) {
-      stop(
-        "Provided field.type should be of length 1 (value is reused) or equal
-        length as number of variables in data set."
-      )
-    }
-
-    dd[, "field_type"] <- field.type
-
-    if (is.null(field.label)) {
-      dd[, "field_label"] <- dd[, "field_name"]
-    } else
-      dd[, "field_label"] <- field.label
-
-    if (include.column.names){
-      list("DataDictionary"=dd,"Column names"=field.name)
-    } else dd
-  }
-
-

R/utils.r

@@ -276,141 +276,3 @@ split_non_repeating_forms <-
     structure(x, names = forms)
 
   }
-
-
-#' Extended string splitting
-#'
-#' Can be used as a substitute of the base function. Main claim to fame is
-#' easing the split around the defined delimiter, see example.
-#' @param x data
-#' @param split delimiter
-#' @param type Split type. Can be c("classic", "before", "after", "around")
-#' @param perl perl param from strsplit()
-#' @param ... additional parameters are passed to base strsplit handling splits
-#'
-#' @return list
-#' @export
-#'
-#' @examples
-#' test <- c("12 months follow-up", "3 steps", "mRS 6 weeks", "Counting to 231 now")
-#' strsplitx(test,"[0-9]",type="around")
-strsplitx <- function(x,
-                      split,
-                      type = "classic",
-                      perl = FALSE,
-                      ...) {
-  if (type == "classic") {
-    # use base::strsplit
-    out <- base::strsplit(x = x, split = split, perl = perl, ...)
-  } else if (type == "before") {
-    # split before the delimiter and keep it
-    out <- base::strsplit(x = x,
-                          split = paste0("(?<=.)(?=", split, ")"),
-                          perl = TRUE,
-                          ...)
-  } else if (type == "after") {
-    # split after the delimiter and keep it
-    out <- base::strsplit(x = x,
-                          split = paste0("(?<=", split, ")"),
-                          perl = TRUE,
-                          ...)
-  } else if (type == "around") {
-    # split around the defined delimiter
-
-    out <- base::strsplit(gsub("~~", "~", # Removes double ~
-                               gsub("^~", "", # Removes leading ~
-                                    gsub(
-                                      # Splits and inserts ~ at all delimiters
-                                      paste0("(", split, ")"), "~\\1~", x
-                                    ))), "~")
-
-  } else {
-    # wrong type input
-    stop("type must be 'classic', 'after', 'before' or 'around'!")
-  }
-
-  out
-}
-
-#' Convert single digits to words
-#'
-#' @param x data. Handle vectors, data.frames and lists
-#' @param lang language. Danish (da) and English (en), Default is "en"
-#' @param neutrum for numbers depending on counted word
-#' @param everything flag to also split numbers >9 to single digits
-#'
-#' @return returns characters in same format as input
-#' @export
-#'
-#' @examples
-#' d2w(c(2:8,21))
-#' d2w(data.frame(2:7,3:8,1),lang="da",neutrum=TRUE)
-#'
-#' ## If everything=T, also larger numbers are reduced.
-#' ## Elements in the list are same length as input
-#' d2w(list(2:8,c(2,6,4,23),2), everything=TRUE)
-#'
-d2w <- function(x, lang = "en", neutrum=FALSE, everything=FALSE) {
-
-  # In Danish the written 1 depends on the counted word
-  if (neutrum) nt <- "t" else nt <- "n"
-
-  # A sapply() call with nested lapply() to handle vectors, data.frames and lists
-  convert <- function(x, lang, neutrum) {
-    zero_nine = data.frame(
-      num = 0:9,
-      en = c(
-        'zero',
-        'one',
-        'two',
-        'three',
-        'four',
-        'five',
-        'six',
-        'seven',
-        'eight',
-        'nine'
-      ),
-      da = c(
-        "nul",
-        paste0("e",nt),
-        "to",
-        "tre",
-        "fire",
-        "fem",
-        "seks",
-        "syv",
-        "otte",
-        "ni"
-      )
-    )
-
-    wrd <- lapply(x, function(i) {
-      zero_nine[, tolower(lang)][zero_nine[, 1] == i]
-    })
-
-    sub <- lengths(wrd) == 1
-
-    x[sub] <- wrd[sub]
-
-    unlist(x)
-  }
-
-  # Also converts numbers >9 to single digits and writes out
-  # Uses strsplitx()
-  if (everything) {
-    out <- sapply(x,function(y){
-      do.call(c,lapply(y,function(z){
-        v <- strsplitx(z,"[0-9]",type="around")
-        Reduce(paste,sapply(v,convert,lang = lang, neutrum = neutrum))
-      }))
-
-    })
-  } else {
-  out <- sapply(x,convert,lang = lang, neutrum = neutrum)
-  }
-
-  if (is.data.frame(x)) out <- data.frame(out)
-
-  out
-}

cran-comments.md

@@ -1,22 +1,54 @@
-results$cran_summary()
-For a CRAN submission we recommend that you fix all NOTEs, WARNINGs and ERRORs.
 ## Test environments
 - R-hub windows-x86_64-devel (r-devel)
 - R-hub ubuntu-gcc-release (r-release)
 - R-hub fedora-clang-devel (r-devel)
 
 ## R CMD check results
+❯ On windows-x86_64-devel (r-devel)
+  checking CRAN incoming feasibility ... [17s] NOTE
+  Maintainer: 'Andreas Gammelgaard Damsbo <agdamsbo@clin.au.dk>'
+  
+  New submission
+  
+  Possibly misspelled words in DESCRIPTION:
+    Egeler (8:45)
+    REDCap (2:8, 10:39, 11:30, 14:5)
+    REDCapRITS (8:26)
+    interoperability (19:44)
+
 ❯ On windows-x86_64-devel (r-devel)
   checking for non-standard things in the check directory ... NOTE
-    ''NULL''
+  Found the following files/directories:
 
 ❯ On windows-x86_64-devel (r-devel)
   checking for detritus in the temp directory ... NOTE
   Found the following files/directories:
     'lastMiKTeXException'
 
+❯ On ubuntu-gcc-release (r-release)
+  checking CRAN incoming feasibility ... [6s/24s] NOTE
+  Maintainer: ‘Andreas Gammelgaard Damsbo <agdamsbo@clin.au.dk>’
+  
+  New submission
+  
+  Possibly misspelled words in DESCRIPTION:
+    Egeler (8:45)
+    REDCap (2:8, 10:39, 11:30, 14:5)
+    REDCapRITS (8:26)
+
 ❯ On ubuntu-gcc-release (r-release), fedora-clang-devel (r-devel)
   checking HTML version of manual ... NOTE
   Skipping checking HTML validation: no command 'tidy' found
 
-0 errors ✔ | 0 warnings ✔ | 3 notes ✖
+❯ On fedora-clang-devel (r-devel)
+  checking CRAN incoming feasibility ... [7s/21s] NOTE
+  Maintainer: ‘Andreas Gammelgaard Damsbo <agdamsbo@clin.au.dk>’
+  
+  New submission
+  
+  Possibly misspelled words in DESCRIPTION:
+    Egeler (8:45)
+    REDCap (2:8, 10:39, 11:30, 14:5)
+    REDCapRITS (8:26)
+
+0 errors ✔ | 0 warnings ✔ | 6 notes ✖

inst/WORDLIST

@@ -1,13 +1,11 @@
 Assesment
 CMD
 Codecov
-DOI
 DataDictionary
 GStat
 GithubActions
 JSON
 Lifecycle
-METACRAN
 Pivotting
 README
 REDCap
@@ -16,13 +14,11 @@ REDCapRITS
 SpectrumHealthResearch
 al
 api
-da
 demonstrational
 descirption
 desireable
 doi
 dplyr
-ds
 et
 immprovements
 jbi
@@ -31,11 +27,6 @@ matadata
 md
 nad
 og
-param
-perl
-redcapcast
-stRoke
-strsplit
 thorugh
 tidyverse
 uri

man/d2w.Rd

@@ -1,32 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.r
-\name{d2w}
-\alias{d2w}
-\title{Convert single digits to words}
-\usage{
-d2w(x, lang = "en", neutrum = FALSE, everything = FALSE)
-}
-\arguments{
-\item{x}{data. Handle vectors, data.frames and lists}
-
-\item{lang}{language. Danish (da) and English (en), Default is "en"}
-
-\item{neutrum}{for numbers depending on counted word}
-
-\item{everything}{flag to also split numbers >9 to single digits}
-}
-\value{
-returns characters in same format as input
-}
-\description{
-Convert single digits to words
-}
-\examples{
-d2w(c(2:8,21))
-d2w(data.frame(2:7,3:8,1),lang="da",neutrum=TRUE)
-
-## If everything=T, also larger numbers are reduced.
-## Elements in the list are same length as input
-d2w(list(2:8,c(2,6,4,23),2), everything=TRUE)
-
-}

man/ds2dd.Rd

@@ -1,49 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ds2dd.R
-\name{ds2dd}
-\alias{ds2dd}
-\title{Data set to data dictionary function}
-\usage{
-ds2dd(
-  ds,
-  record.id = "record_id",
-  form.name = "basis",
-  field.type = "text",
-  field.label = NULL,
-  include.column.names = FALSE,
-  metadata = names(redcapcast_meta)
-)
-}
-\arguments{
-\item{ds}{data set}
-
-\item{record.id}{name or column number of id variable, moved to first row of
-data dictionary, character of integer. Default is "record_id".}
-
-\item{form.name}{vector of form names, character string, length 1 or length
-equal to number of variables. Default is "basis".}
-
-\item{field.type}{vector of field types, character string, length 1 or length
-equal to number of variables. Default is "text.}
-
-\item{field.label}{vector of form names, character string, length 1 or length
-equal to number of variables. Default is NULL and is then identical to field
-names.}
-
-\item{include.column.names}{Flag to give detailed output including new
-column names for original data set for upload.}
-
-\item{metadata}{Metadata column names. Default is the included
-REDCapCAST::redcapcast_data.}
-}
-\value{
-data.frame or list of data.frame and vector
-}
-\description{
-Migrated from stRoke ds2dd(). Fits better with the functionality of
-'REDCapCAST'
-}
-\examples{
-redcapcast_data$record_id <- seq_len(nrow(redcapcast_data))
-ds2dd(redcapcast_data, include.column.names=TRUE)
-}

man/strsplitx.Rd

@@ -1,30 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.r
-\name{strsplitx}
-\alias{strsplitx}
-\title{Extended string splitting}
-\usage{
-strsplitx(x, split, type = "classic", perl = FALSE, ...)
-}
-\arguments{
-\item{x}{data}
-
-\item{split}{delimiter}
-
-\item{type}{Split type. Can be c("classic", "before", "after", "around")}
-
-\item{perl}{perl param from strsplit()}
-
-\item{...}{additional parameters are passed to base strsplit handling splits}
-}
-\value{
-list
-}
-\description{
-Can be used as a substitute of the base function. Main claim to fame is
-easing the split around the defined delimiter, see example.
-}
-\examples{
-test <- c("12 months follow-up", "3 steps", "mRS 6 weeks", "Counting to 231 now")
-strsplitx(test,"[0-9]",type="around")
-}

tests/testthat/test-utils.R

@@ -1,20 +0,0 @@
-test_that("strsplitx works", {
-  expect_equal(2 * 2, 4)
-  test <- c("12 months follow-up", "3 steps", "mRS 6 weeks", "Counting to 231 now")
-  expect_length(strsplitx(test,"[0-9]",type="around")[[1]],3)
-
-  expect_equal(strsplitx(test,"[0-9]",type="classic")[[2]][1],"")
-  expect_length(strsplitx(test,"[0-9]",type="classic")[[4]],4)
-
-  expect_length(strsplitx(test,"[0-9]",type="classic")[[4]],4)
-})
-
-test_that("d2w works", {
-
-  expect_length(d2w(c(2:8,21)),8)
-
-  expect_equal(d2w(data.frame(2:7,3:8,1),lang="da",
-                              neutrum=TRUE)[1,3],"et")
-
-  expect_equal(d2w(list(2:8,c(2,6,4,23),2), everything=T)[[2]][4],"two three")
-})