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cleaning and fixes for a minor release

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Andreas Gammelgaard Damsbo 2025-01-29 10:04:38 +01:00
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8
DESCRIPTION
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@ -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")),
@ -65,9 +65,9 @@ Imports:
gtsummary
Collate:
'REDCapCAST-package.R'
'utils.r'
'process_user_input.r'
'REDCap_split.r'
'utils.R'
'process_user_input.R'
'REDCap_split.R'
'as_factor.R'
'doc2dd.R'
'ds2dd_detailed.R'

1
NAMESPACE
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@ -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)

14
NEWS.md
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@ -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()`.

2
R/REDCap_split.r
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@ -80,7 +80,7 @@
#' \item \code{'all'}: a data.frame for each instrument, regardless of
#' whether it is a repeating instrument or not.
#' }
#' @include process_user_input.r utils.r
#' @include process_user_input.R utils.R
#' @export
REDCap_split <- function(records,
metadata,

24
R/ds2dd_detailed.R
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@ -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
)

19
R/easy_redcap.R
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@ -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, ...) {
key <- get_api_key(key.name = paste0(project.name, "_REDCAP_API"),
prompt = "Provide REDCap API key:")
easy_redcap <- function(project.name,
widen.data = TRUE,
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,
...
)

2
R/read_redcap_tables.R
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@ -31,7 +31,7 @@
#'
#' @return list of instruments
#' @importFrom REDCapR redcap_metadata_read redcap_read redcap_event_instruments
#' @include utils.r
#' @include utils.R
#' @export
#'
#' @examples

23
R/utils.r
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@ -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
}
}

1
inst/WORDLIST
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@ -68,6 +68,7 @@ natively
ncol
og
param
params
pegeler
perl
pos

2
inst/shiny-examples/casting/rsconnect/shinyapps.io/agdamsbo/redcapcast.dcf
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@ -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

2
man/REDCap_split.Rd
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@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/REDCap_split.r
% Please edit documentation in R/REDCap_split.R
\name{REDCap_split}
\alias{REDCap_split}
\title{Split REDCap repeating instruments table into multiple tables}

5
man/clean_redcap_name.Rd
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@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/utils.r
% Please edit documentation in R/utils.R
\name{clean_redcap_name}
\alias{clean_redcap_name}
\title{clean_redcap_name}
@ -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()
}

22
man/cut_string_length.Rd Normal file
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@ -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)
}

2
man/d2w.Rd
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@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/utils.r
% Please edit documentation in R/utils.R
\name{d2w}
\alias{d2w}
\title{Convert single digits to words}

2
man/ds2dd_detailed.Rd
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@ -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 |>

8
man/easy_redcap.Rd
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@ -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"))
}
}

2
man/focused_metadata.Rd
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@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/utils.r
% Please edit documentation in R/utils.R
\name{focused_metadata}
\alias{focused_metadata}
\title{focused_metadata}

2
man/get_id_name.Rd
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@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/utils.r
% Please edit documentation in R/utils.R
\name{get_id_name}
\alias{get_id_name}
\title{Get the id name}

2
man/is_repeated_longitudinal.Rd
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@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/utils.r
% Please edit documentation in R/utils.R
\name{is_repeated_longitudinal}
\alias{is_repeated_longitudinal}
\title{Test if repeatable or longitudinal}

2
man/match_fields_to_form.Rd
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@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/utils.r
% Please edit documentation in R/utils.R
\name{match_fields_to_form}
\alias{match_fields_to_form}
\title{Match fields to forms}

2
man/process_user_input.Rd
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@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/process_user_input.r
% Please edit documentation in R/process_user_input.R
\name{process_user_input}
\alias{process_user_input}
\title{User input processing}

2
man/process_user_input.character.Rd
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@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/process_user_input.r
% Please edit documentation in R/process_user_input.R
\name{process_user_input.character}
\alias{process_user_input.character}
\title{User input processing character}

2
man/process_user_input.data.frame.Rd
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@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/process_user_input.r
% Please edit documentation in R/process_user_input.R
\name{process_user_input.data.frame}
\alias{process_user_input.data.frame}
\title{User input processing data.frame}

2
man/process_user_input.default.Rd
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@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/process_user_input.r
% Please edit documentation in R/process_user_input.R
\name{process_user_input.default}
\alias{process_user_input.default}
\title{User input processing default}

2
man/process_user_input.response.Rd
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@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/process_user_input.r
% Please edit documentation in R/process_user_input.R
\name{process_user_input.response}
\alias{process_user_input.response}
\title{User input processing response}

2
man/sanitize_split.Rd
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@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/utils.r
% Please edit documentation in R/utils.R
\name{sanitize_split}
\alias{sanitize_split}
\title{Sanitize list of data frames}

2
man/split_non_repeating_forms.Rd
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@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/utils.r
% Please edit documentation in R/utils.R
\name{split_non_repeating_forms}
\alias{split_non_repeating_forms}
\title{Split a data frame into separate tables for each form}

2
man/strsplitx.Rd
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@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/utils.r
% Please edit documentation in R/utils.R
\name{strsplitx}
\alias{strsplitx}
\title{Extended string splitting}

2
vignettes/REDCapCAST.Rmd
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@ -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.