mirror of
https://github.com/agdamsbo/REDCapCAST.git
synced 2024-11-22 13:30:23 +01:00
three new functions and new version
This commit is contained in:
parent
ee396fb811
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@ -1,6 +1,6 @@
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Package: REDCapCAST
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Title: REDCap Castellated Data Handling
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Version: 23.6.1
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Version: 23.6.2
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Authors@R: c(
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person("Andreas Gammelgaard", "Damsbo", email = "agdamsbo@clin.au.dk", role = c("aut", "cre"),
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comment = c(ORCID = "0000-0002-7559-1154")),
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@ -48,6 +48,7 @@ Collate:
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'utils.r'
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'process_user_input.r'
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'REDCap_split.r'
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'ds2dd.R'
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'read_redcap_tables.R'
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'redcap_wider.R'
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'redcapcast_data.R'
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@ -2,12 +2,15 @@
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export(REDCap_split)
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export(clean_redcap_name)
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export(d2w)
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export(ds2dd)
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export(focused_metadata)
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export(match_fields_to_form)
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export(read_redcap_tables)
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export(redcap_wider)
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export(sanitize_split)
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export(split_non_repeating_forms)
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export(strsplitx)
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importFrom(REDCapR,redcap_event_instruments)
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importFrom(REDCapR,redcap_metadata_read)
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importFrom(REDCapR,redcap_read)
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13
NEWS.md
13
NEWS.md
@ -1,3 +1,16 @@
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# REDCapCAST 23.6.2
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This version marks the introduction of a few helper functions to handle database creation.
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### Functions
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* New: `ds2dd()` function migrating from the `stRoke`-package. Assists in building a data dictionary for REDCap from a dataset.
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* 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/.
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* 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.
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# REDCapCAST 23.6.1
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### Documentation:
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84
R/ds2dd.R
Normal file
84
R/ds2dd.R
Normal file
@ -0,0 +1,84 @@
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utils::globalVariables(c("redcapcast_meta"))
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#' Data set to data dictionary function
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#'
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#' Migrated from stRoke ds2dd(). Fits better with the functionality of
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#' 'REDCapCAST'
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#' @param ds data set
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#' @param record.id name or column number of id variable, moved to first row of
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#' data dictionary, character of integer. Default is "record_id".
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#' @param form.name vector of form names, character string, length 1 or length
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#' equal to number of variables. Default is "basis".
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#' @param field.type vector of field types, character string, length 1 or length
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#' equal to number of variables. Default is "text.
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#' @param field.label vector of form names, character string, length 1 or length
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#' equal to number of variables. Default is NULL and is then identical to field
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#' names.
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#' @param include.column.names Flag to give detailed output including new
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#' column names for original data set for upload.
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#' @param metadata Metadata column names. Default is the included
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#' REDCapCAST::redcapcast_data.
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#'
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#' @return data.frame or list of data.frame and vector
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#' @export
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#'
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#' @examples
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#' redcapcast_data$record_id <- seq_len(nrow(redcapcast_data))
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#' ds2dd(redcapcast_data, include.column.names=TRUE)
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ds2dd <-
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function(ds,
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record.id = "record_id",
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form.name = "basis",
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field.type = "text",
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field.label = NULL,
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include.column.names = FALSE,
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metadata = names(redcapcast_meta)) {
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dd <- data.frame(matrix(ncol = length(metadata), nrow = ncol(ds)))
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colnames(dd) <- metadata
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if (is.character(record.id) & !record.id %in% colnames(ds)) {
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stop("Provided record.id is not a variable name in provided data set.")
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}
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# renaming to lower case and substitute spaces with underscore
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field.name <- gsub(" ", "_", tolower(colnames(ds)))
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# handles both character and integer
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colsel <-
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colnames(ds) == colnames(ds[record.id])
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if (summary(colsel)[3] != 1) {
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stop("Provided record.id has to be or refer to a uniquely named column.")
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}
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dd[, "field_name"] <-
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c(field.name[colsel], field.name[!colsel])
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if (length(form.name) > 1 & length(form.name) != ncol(ds)) {
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stop(
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"Provided form.name should be of length 1 (value is reused) or equal
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length as number of variables in data set."
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)
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}
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dd[, "form_name"] <- form.name
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if (length(field.type) > 1 & length(field.type) != ncol(ds)) {
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stop(
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"Provided field.type should be of length 1 (value is reused) or equal
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length as number of variables in data set."
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)
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}
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dd[, "field_type"] <- field.type
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if (is.null(field.label)) {
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dd[, "field_label"] <- dd[, "field_name"]
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} else
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dd[, "field_label"] <- field.label
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if (include.column.names){
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list("DataDictionary"=dd,"Column names"=field.name)
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} else dd
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}
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138
R/utils.r
138
R/utils.r
@ -276,3 +276,141 @@ split_non_repeating_forms <-
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structure(x, names = forms)
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}
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#' Extended string splitting
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#'
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#' Can be used as a substitute of the base function. Main claim to fame is
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#' easing the split around the defined delimiter, see example.
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#' @param x data
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#' @param split delimiter
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#' @param type Split type. Can be c("classic", "before", "after", "around")
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#' @param perl perl param from strsplit()
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#' @param ... additional parameters are passed to base strsplit handling splits
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#'
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#' @return list
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#' @export
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#'
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#' @examples
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#' test <- c("12 months follow-up", "3 steps", "mRS 6 weeks", "Counting to 231 now")
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#' strsplitx(test,"[0-9]",type="around")
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strsplitx <- function(x,
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split,
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type = "classic",
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perl = FALSE,
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...) {
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if (type == "classic") {
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# use base::strsplit
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out <- base::strsplit(x = x, split = split, perl = perl, ...)
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} else if (type == "before") {
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# split before the delimiter and keep it
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out <- base::strsplit(x = x,
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split = paste0("(?<=.)(?=", split, ")"),
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perl = TRUE,
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...)
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} else if (type == "after") {
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# split after the delimiter and keep it
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out <- base::strsplit(x = x,
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split = paste0("(?<=", split, ")"),
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perl = TRUE,
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...)
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} else if (type == "around") {
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# split around the defined delimiter
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out <- base::strsplit(gsub("~~", "~", # Removes double ~
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gsub("^~", "", # Removes leading ~
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gsub(
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# Splits and inserts ~ at all delimiters
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paste0("(", split, ")"), "~\\1~", x
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))), "~")
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} else {
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# wrong type input
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stop("type must be 'classic', 'after', 'before' or 'around'!")
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}
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out
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}
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#' Convert single digits to words
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#'
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#' @param x data. Handle vectors, data.frames and lists
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#' @param lang language. Danish (da) and English (en), Default is "en"
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#' @param neutrum for numbers depending on counted word
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#' @param everything flag to also split numbers >9 to single digits
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#'
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#' @return returns characters in same format as input
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#' @export
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#'
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#' @examples
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#' d2w(c(2:8,21))
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#' d2w(data.frame(2:7,3:8,1),lang="da",neutrum=TRUE)
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#'
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#' ## If everything=T, also larger numbers are reduced.
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#' ## Elements in the list are same length as input
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#' d2w(list(2:8,c(2,6,4,23),2), everything=TRUE)
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#'
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d2w <- function(x, lang = "en", neutrum=FALSE, everything=FALSE) {
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# In Danish the written 1 depends on the counted word
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if (neutrum) nt <- "t" else nt <- "n"
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# A sapply() call with nested lapply() to handle vectors, data.frames and lists
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convert <- function(x, lang, neutrum) {
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zero_nine = data.frame(
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num = 0:9,
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en = c(
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'zero',
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'one',
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'two',
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'three',
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'four',
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'five',
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'six',
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'seven',
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'eight',
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'nine'
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),
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da = c(
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"nul",
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paste0("e",nt),
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"to",
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"tre",
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"fire",
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"fem",
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"seks",
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"syv",
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"otte",
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"ni"
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)
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)
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wrd <- lapply(x, function(i) {
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zero_nine[, tolower(lang)][zero_nine[, 1] == i]
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})
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sub <- lengths(wrd) == 1
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x[sub] <- wrd[sub]
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unlist(x)
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}
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# Also converts numbers >9 to single digits and writes out
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# Uses strsplitx()
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if (everything) {
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out <- sapply(x,function(y){
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do.call(c,lapply(y,function(z){
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v <- strsplitx(z,"[0-9]",type="around")
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Reduce(paste,sapply(v,convert,lang = lang, neutrum = neutrum))
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}))
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})
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} else {
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out <- sapply(x,convert,lang = lang, neutrum = neutrum)
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}
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if (is.data.frame(x)) out <- data.frame(out)
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out
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}
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@ -1,54 +1,41 @@
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## Test environments
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- R-hub windows-x86_64-devel (r-devel)
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- R-hub ubuntu-gcc-release (r-release)
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- R-hub fedora-clang-devel (r-devel)
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## rhub::check_for_cran() results
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## R CMD check results
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❯ On windows-x86_64-devel (r-devel)
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checking CRAN incoming feasibility ... [17s] NOTE
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Maintainer: 'Andreas Gammelgaard Damsbo <agdamsbo@clin.au.dk>'
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New submission
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Possibly misspelled words in DESCRIPTION:
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Egeler (8:45)
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REDCap (2:8, 10:39, 11:30, 14:5)
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REDCapRITS (8:26)
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interoperability (19:44)
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── REDCapCAST 23.6.2: NOTE
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❯ On windows-x86_64-devel (r-devel)
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checking for non-standard things in the check directory ... NOTE
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Found the following files/directories:
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Build ID: REDCapCAST_23.6.2.tar.gz-a738190c0d8a4e76b9212e4915625f96
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Platform: Windows Server 2022, R-devel, 64 bit
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Submitted: 56m 54.3s ago
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Build time: 4m 25.1s
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❯ On windows-x86_64-devel (r-devel)
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checking for detritus in the temp directory ... NOTE
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❯ checking for non-standard things in the check directory ... NOTE
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''NULL''
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❯ checking for detritus in the temp directory ... NOTE
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Found the following files/directories:
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'lastMiKTeXException'
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❯ On ubuntu-gcc-release (r-release)
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checking CRAN incoming feasibility ... [6s/24s] NOTE
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Maintainer: ‘Andreas Gammelgaard Damsbo <agdamsbo@clin.au.dk>’
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New submission
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Possibly misspelled words in DESCRIPTION:
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Egeler (8:45)
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REDCap (2:8, 10:39, 11:30, 14:5)
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REDCapRITS (8:26)
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0 errors ✔ | 0 warnings ✔ | 2 notes ✖
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❯ On ubuntu-gcc-release (r-release), fedora-clang-devel (r-devel)
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checking HTML version of manual ... NOTE
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── REDCapCAST 23.6.2: NOTE
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Build ID: REDCapCAST_23.6.2.tar.gz-a9243a74abae4f04b2a0e29a2751c420
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Platform: Ubuntu Linux 20.04.1 LTS, R-release, GCC
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Submitted: 56m 54.4s ago
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Build time: 32m 6.5s
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❯ checking HTML version of manual ... NOTE
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Skipping checking HTML validation: no command 'tidy' found
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❯ On fedora-clang-devel (r-devel)
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checking CRAN incoming feasibility ... [7s/21s] NOTE
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Maintainer: ‘Andreas Gammelgaard Damsbo <agdamsbo@clin.au.dk>’
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New submission
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Possibly misspelled words in DESCRIPTION:
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Egeler (8:45)
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REDCap (2:8, 10:39, 11:30, 14:5)
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REDCapRITS (8:26)
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0 errors ✔ | 0 warnings ✔ | 1 note ✖
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0 errors ✔ | 0 warnings ✔ | 6 notes ✖
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── REDCapCAST 23.6.2: NOTE
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Build ID: REDCapCAST_23.6.2.tar.gz-ba8ade3478c6494b8a8daee08a502f2b
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Platform: Fedora Linux, R-devel, clang, gfortran
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Submitted: 56m 54.4s ago
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Build time: 29m 25.6s
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❯ checking HTML version of manual ... NOTE
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Skipping checking HTML validation: no command 'tidy' found
|
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0 errors ✔ | 0 warnings ✔ | 1 note ✖
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@ -1,11 +1,13 @@
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Assesment
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CMD
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Codecov
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DOI
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DataDictionary
|
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GStat
|
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GithubActions
|
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JSON
|
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Lifecycle
|
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METACRAN
|
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Pivotting
|
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README
|
||||
REDCap
|
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@ -14,11 +16,13 @@ REDCapRITS
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SpectrumHealthResearch
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al
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api
|
||||
da
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demonstrational
|
||||
descirption
|
||||
desireable
|
||||
doi
|
||||
dplyr
|
||||
ds
|
||||
et
|
||||
immprovements
|
||||
jbi
|
||||
@ -27,6 +31,11 @@ matadata
|
||||
md
|
||||
nad
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||||
og
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||||
param
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||||
perl
|
||||
redcapcast
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stRoke
|
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strsplit
|
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thorugh
|
||||
tidyverse
|
||||
uri
|
||||
|
||||
32
man/d2w.Rd
Normal file
32
man/d2w.Rd
Normal file
@ -0,0 +1,32 @@
|
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% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/utils.r
|
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\name{d2w}
|
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\alias{d2w}
|
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\title{Convert single digits to words}
|
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\usage{
|
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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"}
|
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|
||||
\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{
|
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Convert single digits to words
|
||||
}
|
||||
\examples{
|
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d2w(c(2:8,21))
|
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d2w(data.frame(2:7,3:8,1),lang="da",neutrum=TRUE)
|
||||
|
||||
## If everything=T, also larger numbers are reduced.
|
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## Elements in the list are same length as input
|
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d2w(list(2:8,c(2,6,4,23),2), everything=TRUE)
|
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|
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}
|
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49
man/ds2dd.Rd
Normal file
49
man/ds2dd.Rd
Normal file
@ -0,0 +1,49 @@
|
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% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/ds2dd.R
|
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\name{ds2dd}
|
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\alias{ds2dd}
|
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\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)
|
||||
}
|
||||
30
man/strsplitx.Rd
Normal file
30
man/strsplitx.Rd
Normal file
@ -0,0 +1,30 @@
|
||||
% 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")
|
||||
}
|
||||
20
tests/testthat/test-utils.R
Normal file
20
tests/testthat/test-utils.R
Normal file
@ -0,0 +1,20 @@
|
||||
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")
|
||||
})
|
||||
Loading…
Reference in New Issue
Block a user