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12
DESCRIPTION
12
DESCRIPTION
@ -1,6 +1,6 @@
|
|||||||
Package: REDCapCAST
|
Package: REDCapCAST
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||||||
Title: REDCap Castellated Data Handling
|
Title: REDCap Castellated Data Handling
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||||||
Version: 24.1.2
|
Version: 24.1.1
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||||||
Authors@R: c(
|
Authors@R: c(
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||||||
person("Andreas Gammelgaard", "Damsbo", email = "agdamsbo@clin.au.dk",
|
person("Andreas Gammelgaard", "Damsbo", email = "agdamsbo@clin.au.dk",
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||||||
role = c("aut", "cre"),comment = c(ORCID = "0000-0002-7559-1154")),
|
role = c("aut", "cre"),comment = c(ORCID = "0000-0002-7559-1154")),
|
||||||
@ -27,13 +27,12 @@ Suggests:
|
|||||||
jsonlite,
|
jsonlite,
|
||||||
testthat,
|
testthat,
|
||||||
Hmisc,
|
Hmisc,
|
||||||
|
readr,
|
||||||
knitr,
|
knitr,
|
||||||
rmarkdown,
|
rmarkdown,
|
||||||
gt,
|
gt,
|
||||||
usethis,
|
usethis,
|
||||||
ggplot2,
|
ggplot2
|
||||||
haven,
|
|
||||||
here
|
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||||||
License: GPL (>= 3)
|
License: GPL (>= 3)
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||||||
Encoding: UTF-8
|
Encoding: UTF-8
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||||||
LazyData: true
|
LazyData: true
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||||||
@ -46,15 +45,12 @@ Imports:
|
|||||||
tidyr,
|
tidyr,
|
||||||
tidyselect,
|
tidyselect,
|
||||||
keyring,
|
keyring,
|
||||||
purrr,
|
purrr
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||||||
readr,
|
|
||||||
stats
|
|
||||||
Collate:
|
Collate:
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||||||
'utils.r'
|
'utils.r'
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||||||
'process_user_input.r'
|
'process_user_input.r'
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||||||
'REDCap_split.r'
|
'REDCap_split.r'
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||||||
'ds2dd.R'
|
'ds2dd.R'
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'ds2dd_detailed.R'
|
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||||||
'easy_redcap.R'
|
'easy_redcap.R'
|
||||||
'read_redcap_tables.R'
|
'read_redcap_tables.R'
|
||||||
'redcap_wider.R'
|
'redcap_wider.R'
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||||||
|
@ -4,11 +4,9 @@ export(REDCap_split)
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export(clean_redcap_name)
|
export(clean_redcap_name)
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export(d2w)
|
export(d2w)
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export(ds2dd)
|
export(ds2dd)
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export(ds2dd_detailed)
|
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export(easy_redcap)
|
export(easy_redcap)
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export(focused_metadata)
|
export(focused_metadata)
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export(get_api_key)
|
export(get_api_key)
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export(guess_time_only_filter)
|
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export(match_fields_to_form)
|
export(match_fields_to_form)
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export(read_redcap_tables)
|
export(read_redcap_tables)
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export(redcap_wider)
|
export(redcap_wider)
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@ -23,6 +21,5 @@ importFrom(keyring,key_get)
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|||||||
importFrom(keyring,key_list)
|
importFrom(keyring,key_list)
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||||||
importFrom(keyring,key_set)
|
importFrom(keyring,key_set)
|
||||||
importFrom(purrr,reduce)
|
importFrom(purrr,reduce)
|
||||||
importFrom(readr,parse_time)
|
|
||||||
importFrom(tidyr,pivot_wider)
|
importFrom(tidyr,pivot_wider)
|
||||||
importFrom(tidyselect,all_of)
|
importFrom(tidyselect,all_of)
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|
12
NEWS.md
12
NEWS.md
@ -1,15 +1,3 @@
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# REDCapCAST 24.1.2
|
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|
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### Functions
|
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||||||
|
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* Fix: `ds2dd()`: uses correct default dd column names. Will be deprecated.
|
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|
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* NEW: `ds2dd_detailed()`: extension of the `ds2dd()`, which serves to preserve as much metadata as possible automatically. Depends on a group of helper functions also introduced. Of special note is the `guess_time_only_filter()`, which will try to guess which columns/variables should be formatted as time only formats. Supports hms time format. DETAILED INSTRUCTION AND VIGNETTE IS PENDING.
|
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|
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### Other
|
|
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|
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||||||
I believe `renv` has now been added and runs correctly. After clone, do `renv::restore()` to install all necessary package to modify the package.
|
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|
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# REDCapCAST 24.1.1
|
# REDCapCAST 24.1.1
|
||||||
|
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||||||
### Functions
|
### Functions
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||||||
|
13
R/ds2dd.R
13
R/ds2dd.R
@ -1,13 +1,8 @@
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|||||||
utils::globalVariables(c("metadata_names"))
|
utils::globalVariables(c("redcapcast_meta"))
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||||||
#' (DEPRECATED) Data set to data dictionary function
|
#' Data set to data dictionary function
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||||||
#'
|
#'
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||||||
#' @description
|
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#' Creates a very basic data dictionary skeleton. Please see `ds2dd_detailed()`
|
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#' for a more advanced function.
|
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#'
|
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#' @details
|
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#' Migrated from stRoke ds2dd(). Fits better with the functionality of
|
#' Migrated from stRoke ds2dd(). Fits better with the functionality of
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#' 'REDCapCAST'.
|
#' 'REDCapCAST'
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#' @param ds data set
|
#' @param ds data set
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#' @param record.id name or column number of id variable, moved to first row of
|
#' @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".
|
#' data dictionary, character of integer. Default is "record_id".
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@ -21,7 +16,7 @@ utils::globalVariables(c("metadata_names"))
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#' @param include.column.names Flag to give detailed output including new
|
#' @param include.column.names Flag to give detailed output including new
|
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#' column names for original data set for upload.
|
#' column names for original data set for upload.
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#' @param metadata Metadata column names. Default is the included
|
#' @param metadata Metadata column names. Default is the included
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#' REDCapCAST::metadata_names.
|
#' REDCapCAST::redcapcast_data.
|
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#'
|
#'
|
||||||
#' @return data.frame or list of data.frame and vector
|
#' @return data.frame or list of data.frame and vector
|
||||||
#' @export
|
#' @export
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|
@ -1,343 +0,0 @@
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utils::globalVariables(c( "stats::setNames", "field_name", "field_type", "select_choices_or_calculations"))
|
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||||||
#' Try at determining which are true time only variables
|
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||||||
#'
|
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||||||
#' @description
|
|
||||||
#' This is just a try at guessing data type based on data class and column names
|
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||||||
#' hoping for a tiny bit of naming consistency. R does not include a time-only
|
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#' data format natively, so the "hms" class from `readr` is used. This
|
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||||||
#' has to be converted to character class before REDCap upload.
|
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||||||
#'
|
|
||||||
#' @param data data set
|
|
||||||
#' @param validate flag to output validation data. Will output list.
|
|
||||||
#' @param sel.pos Positive selection regex string
|
|
||||||
#' @param sel.neg Negative selection regex string
|
|
||||||
#'
|
|
||||||
#' @return character vector or list depending on `validate` flag.
|
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||||||
#' @export
|
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||||||
#'
|
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||||||
#' @examples
|
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||||||
#' data <- redcapcast_data
|
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||||||
#' data |> guess_time_only_filter()
|
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||||||
#' data |> guess_time_only_filter(validate = TRUE) |> lapply(head)
|
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guess_time_only_filter <- function(data, validate = FALSE, sel.pos = "[Tt]i[d(me)]", sel.neg = "[Dd]at[eo]") {
|
|
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datetime_nms <- data |>
|
|
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lapply(\(x)any(c("POSIXct","hms") %in% class(x))) |>
|
|
||||||
(\(x) names(data)[do.call(c, x)])()
|
|
||||||
|
|
||||||
time_only_log <- datetime_nms |> (\(x) {
|
|
||||||
## Detects which are determined true Time only variables
|
|
||||||
## Inspection is necessary
|
|
||||||
grepl(pattern = sel.pos, x = x) &
|
|
||||||
!grepl(pattern = sel.neg, x = x)
|
|
||||||
})()
|
|
||||||
|
|
||||||
if (validate) {
|
|
||||||
list(
|
|
||||||
"is.POSIX" = data[datetime_nms],
|
|
||||||
"is.datetime" = data[datetime_nms[!time_only_log]],
|
|
||||||
"is.time_only" = data[datetime_nms[time_only_log]]
|
|
||||||
)
|
|
||||||
} else {
|
|
||||||
datetime_nms[time_only_log]
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
#' Correction based on time_only_filter function. Introduces new class for easier
|
|
||||||
#' validation labelling.
|
|
||||||
#'
|
|
||||||
#' @description
|
|
||||||
#' Dependens on the data class "hms" introduced with
|
|
||||||
#' `guess_time_only_filter()` and converts these
|
|
||||||
#'
|
|
||||||
#' @param data data set
|
|
||||||
#' @param ... arguments passed on to `guess_time_only_filter()`
|
|
||||||
#'
|
|
||||||
#' @return tibble
|
|
||||||
#' @importFrom readr parse_time
|
|
||||||
#'
|
|
||||||
#' @examples
|
|
||||||
#' data <- redcapcast_data
|
|
||||||
#' ## data |> time_only_correction()
|
|
||||||
time_only_correction <- function(data, ...) {
|
|
||||||
nms <- guess_time_only_filter(data, ...)
|
|
||||||
z <- nms |>
|
|
||||||
lapply(\(y) {
|
|
||||||
readr::parse_time(format(data[[y]], format = "%H:%M:%S"))
|
|
||||||
}) |>
|
|
||||||
suppressMessages(dplyr::bind_cols()) |>
|
|
||||||
stats::setNames(nm = nms)
|
|
||||||
data[nms] <- z
|
|
||||||
data
|
|
||||||
}
|
|
||||||
|
|
||||||
#' Change "hms" to "character" for REDCap upload.
|
|
||||||
#'
|
|
||||||
#' @param data data set
|
|
||||||
#'
|
|
||||||
#' @return data.frame or tibble
|
|
||||||
#'
|
|
||||||
#' @examples
|
|
||||||
#' data <- redcapcast_data
|
|
||||||
#' ## data |> time_only_correction() |> hms2character()
|
|
||||||
hms2character <- function(data) {
|
|
||||||
data |>
|
|
||||||
lapply(function(x) {
|
|
||||||
if ("hms" %in% class(x)) {
|
|
||||||
as.character(x)
|
|
||||||
} else {
|
|
||||||
x
|
|
||||||
}
|
|
||||||
}) |>
|
|
||||||
dplyr::bind_cols()
|
|
||||||
}
|
|
||||||
|
|
||||||
#' Extract data from stata file for data dictionary
|
|
||||||
#'
|
|
||||||
#' @details
|
|
||||||
#' This function is a natural development of the ds2dd() function. It assumes
|
|
||||||
#' that the first column is the ID-column. No checks.
|
|
||||||
#' Please, do always inspect the data dictionary before upload.
|
|
||||||
#'
|
|
||||||
#' Ensure, that the data set is formatted with as much information as possible.
|
|
||||||
#'
|
|
||||||
#' `field.type` can be supplied
|
|
||||||
#'
|
|
||||||
#' @param data data frame
|
|
||||||
#' @param date.format date format, character string. ymd/dmy/mdy. dafault is
|
|
||||||
#' dmy.
|
|
||||||
#' @param add.auto.id flag to add id column
|
|
||||||
#' @param form.name manually specify form name(s). Vector of length 1 or
|
|
||||||
#' ncol(data). Default is NULL and "data" is used.
|
|
||||||
#' @param field.type manually specify field type(s). Vector of length 1 or
|
|
||||||
#' ncol(data). Default is NULL and "text" is used for everything but factors,
|
|
||||||
#' which wil get "radio".
|
|
||||||
#' @param field.label manually specify field label(s). Vector of length 1 or
|
|
||||||
#' ncol(data). Default is NULL and colnames(data) is used or attribute
|
|
||||||
#' `field.label.attr` for haven_labelled data set (imported .dta file with
|
|
||||||
#' `haven::read_dta()`).
|
|
||||||
#' @param field.label.attr attribute name for named labels for haven_labelled
|
|
||||||
#' data set (imported .dta file with `haven::read_dta()`. Default is "label"
|
|
||||||
#' @param field.validation manually specify field validation(s). Vector of
|
|
||||||
#' length 1 or ncol(data). Default is NULL and `levels()` are used for factors
|
|
||||||
#' or attribute `factor.labels.attr` for haven_labelled data set (imported .dta file with
|
|
||||||
#' `haven::read_dta()`).
|
|
||||||
#' @param metadata redcap metadata headings. Default is
|
|
||||||
#' REDCapCAST:::metadata_names.
|
|
||||||
#' @param validate.time Flag to validate guessed time columns
|
|
||||||
#' @param time.var.sel.pos Positive selection regex string passed to
|
|
||||||
#' `gues_time_only_filter()` as sel.pos.
|
|
||||||
#' @param time.var.sel.neg Negative selection regex string passed to
|
|
||||||
#' `gues_time_only_filter()` as sel.neg.
|
|
||||||
#'
|
|
||||||
#' @return list of length 2
|
|
||||||
#' @export
|
|
||||||
#'
|
|
||||||
#' @examples
|
|
||||||
#' data <- redcapcast_data
|
|
||||||
#' data |> ds2dd_detailed(validate.time = TRUE)
|
|
||||||
#' data |> ds2dd_detailed()
|
|
||||||
#' iris |> ds2dd_detailed(add.auto.id = TRUE)
|
|
||||||
#' mtcars |> ds2dd_detailed(add.auto.id = TRUE)
|
|
||||||
ds2dd_detailed <- function(data,
|
|
||||||
add.auto.id = FALSE,
|
|
||||||
date.format = "dmy",
|
|
||||||
form.name = NULL,
|
|
||||||
field.type = NULL,
|
|
||||||
field.label = NULL,
|
|
||||||
field.label.attr ="label",
|
|
||||||
field.validation = NULL,
|
|
||||||
metadata = metadata_names,
|
|
||||||
validate.time = FALSE,
|
|
||||||
time.var.sel.pos = "[Tt]i[d(me)]",
|
|
||||||
time.var.sel.neg = "[Dd]at[eo]") {
|
|
||||||
## Handles the odd case of no id column present
|
|
||||||
if (add.auto.id) {
|
|
||||||
data <- dplyr::tibble(
|
|
||||||
default_trial_id = seq_len(nrow(data)),
|
|
||||||
data
|
|
||||||
)
|
|
||||||
message("A default id column has been added")
|
|
||||||
}
|
|
||||||
|
|
||||||
if (validate.time) {
|
|
||||||
return(data |> guess_time_only_filter(validate = TRUE))
|
|
||||||
}
|
|
||||||
|
|
||||||
if (lapply(data, haven::is.labelled) |> (\(x)do.call(c, x))() |> any()) {
|
|
||||||
message("Data seems to be imported with haven from a Stata (.dta) file and will be treated as such.")
|
|
||||||
data.source <- "dta"
|
|
||||||
} else {
|
|
||||||
data.source <- ""
|
|
||||||
}
|
|
||||||
|
|
||||||
## data classes
|
|
||||||
|
|
||||||
### Only keeps the first class, as time fields (POSIXct/POSIXt) has two classes
|
|
||||||
if (data.source == "dta") {
|
|
||||||
data_classes <-
|
|
||||||
data |>
|
|
||||||
haven::as_factor() |>
|
|
||||||
time_only_correction(sel.pos = time.var.sel.pos, sel.neg = time.var.sel.neg) |>
|
|
||||||
lapply(\(x)class(x)[1]) |>
|
|
||||||
(\(x)do.call(c, x))()
|
|
||||||
} else {
|
|
||||||
data_classes <-
|
|
||||||
data |>
|
|
||||||
time_only_correction(sel.pos = time.var.sel.pos, sel.neg = time.var.sel.neg) |>
|
|
||||||
lapply(\(x)class(x)[1]) |>
|
|
||||||
(\(x)do.call(c, x))()
|
|
||||||
}
|
|
||||||
|
|
||||||
## ---------------------------------------
|
|
||||||
## Building the data dictionary
|
|
||||||
## ---------------------------------------
|
|
||||||
|
|
||||||
## skeleton
|
|
||||||
|
|
||||||
dd <- data.frame(matrix(ncol = length(metadata), nrow = ncol(data))) |>
|
|
||||||
stats::setNames(metadata) |>
|
|
||||||
dplyr::tibble()
|
|
||||||
|
|
||||||
dd$field_name <- gsub(" ", "_", tolower(colnames(data)))
|
|
||||||
|
|
||||||
## form_name
|
|
||||||
if (is.null(form.name)) {
|
|
||||||
dd$form_name <- "data"
|
|
||||||
} else {
|
|
||||||
if (length(form.name) == 1 | length(form.name) == nrow(dd)) {
|
|
||||||
dd$form_name <- form.name
|
|
||||||
} else {
|
|
||||||
stop("Length of supplied 'form.name' has to be one (1) or ncol(data).")
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
## field_label
|
|
||||||
|
|
||||||
if (is.null(field.label)) {
|
|
||||||
if (data.source == "dta") {
|
|
||||||
label <- data |>
|
|
||||||
lapply(function(x) {
|
|
||||||
if (haven::is.labelled(x)) {
|
|
||||||
attributes(x)[[field.label.attr]]
|
|
||||||
} else {
|
|
||||||
NA
|
|
||||||
}
|
|
||||||
}) |>
|
|
||||||
(\(x)do.call(c, x))()
|
|
||||||
} else {
|
|
||||||
label <- data |> colnames()
|
|
||||||
}
|
|
||||||
|
|
||||||
dd <-
|
|
||||||
dd |> dplyr::mutate(field_label = dplyr::if_else(is.na(label), field_name, label))
|
|
||||||
} else {
|
|
||||||
if (length(field.label) == 1 | length(field.label) == nrow(dd)) {
|
|
||||||
dd$field_label <- field.label
|
|
||||||
} else {
|
|
||||||
stop("Length of supplied 'field.label' has to be one (1) or ncol(data).")
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
## field_type
|
|
||||||
|
|
||||||
if (is.null(field.type)) {
|
|
||||||
dd$field_type <- "text"
|
|
||||||
|
|
||||||
dd <-
|
|
||||||
dd |> dplyr::mutate(field_type = dplyr::if_else(data_classes == "factor", "radio", field_type))
|
|
||||||
} else {
|
|
||||||
if (length(field.type) == 1 | length(field.type) == nrow(dd)) {
|
|
||||||
dd$field_type <- field.type
|
|
||||||
} else {
|
|
||||||
stop("Length of supplied 'field.type' has to be one (1) or ncol(data).")
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
## validation
|
|
||||||
|
|
||||||
if (is.null(field.validation)) {
|
|
||||||
dd <-
|
|
||||||
dd |> dplyr::mutate(
|
|
||||||
text_validation_type_or_show_slider_number = dplyr::case_when(
|
|
||||||
data_classes == "Date" ~ paste0("date_", date.format),
|
|
||||||
data_classes ==
|
|
||||||
"hms" ~ "time_hh_mm_ss",
|
|
||||||
## Self invented format after filtering
|
|
||||||
data_classes ==
|
|
||||||
"POSIXct" ~ paste0("datetime_", date.format),
|
|
||||||
data_classes ==
|
|
||||||
"numeric" ~ "number"
|
|
||||||
)
|
|
||||||
)
|
|
||||||
} else {
|
|
||||||
if (length(field.validation) == 1 | length(field.validation) == nrow(dd)) {
|
|
||||||
dd$text_validation_type_or_show_slider_number <- field.validation
|
|
||||||
} else {
|
|
||||||
stop("Length of supplied 'field.validation' has to be one (1) or ncol(data).")
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
## choices
|
|
||||||
|
|
||||||
if (data.source == "dta") {
|
|
||||||
factor_levels <- data |>
|
|
||||||
lapply(function(x) {
|
|
||||||
if (haven::is.labelled(x)) {
|
|
||||||
att <- attributes(x)$labels
|
|
||||||
paste(paste(att, names(att), sep = ", "), collapse = " | ")
|
|
||||||
} else {
|
|
||||||
NA
|
|
||||||
}
|
|
||||||
}) |>
|
|
||||||
(\(x)do.call(c, x))()
|
|
||||||
} else {
|
|
||||||
factor_levels <- data |>
|
|
||||||
lapply(function(x) {
|
|
||||||
if (is.factor(x)) {
|
|
||||||
## Re-factors to avoid confusion with missing levels
|
|
||||||
## Assumes alle relevant levels are represented in the data
|
|
||||||
re_fac <- factor(x)
|
|
||||||
paste(paste(unique(as.numeric(re_fac)), levels(re_fac), sep = ", "), collapse = " | ")
|
|
||||||
} else {
|
|
||||||
NA
|
|
||||||
}
|
|
||||||
}) |>
|
|
||||||
(\(x)do.call(c, x))()
|
|
||||||
}
|
|
||||||
|
|
||||||
dd <-
|
|
||||||
dd |> dplyr::mutate(
|
|
||||||
select_choices_or_calculations = dplyr::if_else(
|
|
||||||
is.na(factor_levels),
|
|
||||||
select_choices_or_calculations,
|
|
||||||
factor_levels
|
|
||||||
)
|
|
||||||
)
|
|
||||||
|
|
||||||
list(
|
|
||||||
data = data |>
|
|
||||||
time_only_correction(sel.pos = time.var.sel.pos, sel.neg = time.var.sel.neg) |>
|
|
||||||
hms2character() |>
|
|
||||||
(\(x)stats::setNames(x, tolower(names(x))))(),
|
|
||||||
meta = dd
|
|
||||||
)
|
|
||||||
}
|
|
||||||
|
|
||||||
### Completion
|
|
||||||
#' Completion marking based on completed upload
|
|
||||||
#'
|
|
||||||
#' @param upload output list from `REDCapR::redcap_write()`
|
|
||||||
#' @param ls output list from `ds2dd_detailed()`
|
|
||||||
#'
|
|
||||||
#' @return list with `REDCapR::redcap_write()` results
|
|
||||||
mark_complete <- function(upload, ls){
|
|
||||||
data <- ls$data
|
|
||||||
meta <- ls$meta
|
|
||||||
forms <- unique(meta$form_name)
|
|
||||||
cbind(data[[1]][data[[1]] %in% upload$affected_ids],
|
|
||||||
data.frame(matrix(2,ncol=length(forms),nrow=upload$records_affected_count))) |>
|
|
||||||
stats::setNames(c(names(data)[1],paste0(forms,"_complete")))
|
|
||||||
}
|
|
@ -10,9 +10,8 @@
|
|||||||
#' \item{redcap_repeat_instrument}{Repeat instrument, character}
|
#' \item{redcap_repeat_instrument}{Repeat instrument, character}
|
||||||
#' \item{redcap_repeat_instance}{Repeat instance, numeric}
|
#' \item{redcap_repeat_instance}{Repeat instance, numeric}
|
||||||
#' \item{cpr}{CPR number, character}
|
#' \item{cpr}{CPR number, character}
|
||||||
#' \item{inclusion}{Inclusion date, Date}
|
#' \item{inclusion}{Inclusion date, date}
|
||||||
#' \item{inclusion_time}{Inclusion time, hms}
|
#' \item{dob}{Date of birth, date}
|
||||||
#' \item{dob}{Date of birth, Date}
|
|
||||||
#' \item{age}{Age decimal, numeric}
|
#' \item{age}{Age decimal, numeric}
|
||||||
#' \item{age_integer}{Age integer, numeric}
|
#' \item{age_integer}{Age integer, numeric}
|
||||||
#' \item{sex}{Legal sex, character}
|
#' \item{sex}{Legal sex, character}
|
||||||
@ -22,10 +21,10 @@
|
|||||||
#' \item{region}{region, character}
|
#' \item{region}{region, character}
|
||||||
#' \item{baseline_data_start_complete}{Completed, character}
|
#' \item{baseline_data_start_complete}{Completed, character}
|
||||||
#' \item{mrs_assessed}{mRS Assessed, character}
|
#' \item{mrs_assessed}{mRS Assessed, character}
|
||||||
#' \item{mrs_date}{Assesment date, Date}
|
#' \item{mrs_date}{Assesment date, date}
|
||||||
#' \item{mrs_score}{Categorical score, numeric}
|
#' \item{mrs_score}{Score, numeric}
|
||||||
#' \item{mrs_complete}{Complete, numeric}
|
#' \item{mrs_complete}{Complete, numeric}
|
||||||
#' \item{event_datetime}{Event datetime, POSIXct}
|
#' \item{event_date}{Event date, date}
|
||||||
#' \item{event_type}{Event type, character}
|
#' \item{event_type}{Event type, character}
|
||||||
#' \item{new_event_complete}{Completed, character}
|
#' \item{new_event_complete}{Completed, character}
|
||||||
#'
|
#'
|
||||||
|
Binary file not shown.
12
man/ds2dd.Rd
12
man/ds2dd.Rd
@ -2,7 +2,7 @@
|
|||||||
% Please edit documentation in R/ds2dd.R
|
% Please edit documentation in R/ds2dd.R
|
||||||
\name{ds2dd}
|
\name{ds2dd}
|
||||||
\alias{ds2dd}
|
\alias{ds2dd}
|
||||||
\title{(DEPRECATED) Data set to data dictionary function}
|
\title{Data set to data dictionary function}
|
||||||
\usage{
|
\usage{
|
||||||
ds2dd(
|
ds2dd(
|
||||||
ds,
|
ds,
|
||||||
@ -11,7 +11,7 @@ ds2dd(
|
|||||||
field.type = "text",
|
field.type = "text",
|
||||||
field.label = NULL,
|
field.label = NULL,
|
||||||
include.column.names = FALSE,
|
include.column.names = FALSE,
|
||||||
metadata = metadata_names
|
metadata = names(redcapcast_meta)
|
||||||
)
|
)
|
||||||
}
|
}
|
||||||
\arguments{
|
\arguments{
|
||||||
@ -34,18 +34,14 @@ names.}
|
|||||||
column names for original data set for upload.}
|
column names for original data set for upload.}
|
||||||
|
|
||||||
\item{metadata}{Metadata column names. Default is the included
|
\item{metadata}{Metadata column names. Default is the included
|
||||||
REDCapCAST::metadata_names.}
|
REDCapCAST::redcapcast_data.}
|
||||||
}
|
}
|
||||||
\value{
|
\value{
|
||||||
data.frame or list of data.frame and vector
|
data.frame or list of data.frame and vector
|
||||||
}
|
}
|
||||||
\description{
|
\description{
|
||||||
Creates a very basic data dictionary skeleton. Please see `ds2dd_detailed()`
|
|
||||||
for a more advanced function.
|
|
||||||
}
|
|
||||||
\details{
|
|
||||||
Migrated from stRoke ds2dd(). Fits better with the functionality of
|
Migrated from stRoke ds2dd(). Fits better with the functionality of
|
||||||
'REDCapCAST'.
|
'REDCapCAST'
|
||||||
}
|
}
|
||||||
\examples{
|
\examples{
|
||||||
redcapcast_data$record_id <- seq_len(nrow(redcapcast_data))
|
redcapcast_data$record_id <- seq_len(nrow(redcapcast_data))
|
||||||
|
@ -1,82 +0,0 @@
|
|||||||
% Generated by roxygen2: do not edit by hand
|
|
||||||
% Please edit documentation in R/ds2dd_detailed.R
|
|
||||||
\name{ds2dd_detailed}
|
|
||||||
\alias{ds2dd_detailed}
|
|
||||||
\title{Extract data from stata file for data dictionary}
|
|
||||||
\usage{
|
|
||||||
ds2dd_detailed(
|
|
||||||
data,
|
|
||||||
add.auto.id = FALSE,
|
|
||||||
date.format = "dmy",
|
|
||||||
form.name = NULL,
|
|
||||||
field.type = NULL,
|
|
||||||
field.label = NULL,
|
|
||||||
field.label.attr = "label",
|
|
||||||
field.validation = NULL,
|
|
||||||
metadata = metadata_names,
|
|
||||||
validate.time = FALSE,
|
|
||||||
time.var.sel.pos = "[Tt]i[d(me)]",
|
|
||||||
time.var.sel.neg = "[Dd]at[eo]"
|
|
||||||
)
|
|
||||||
}
|
|
||||||
\arguments{
|
|
||||||
\item{data}{data frame}
|
|
||||||
|
|
||||||
\item{add.auto.id}{flag to add id column}
|
|
||||||
|
|
||||||
\item{date.format}{date format, character string. ymd/dmy/mdy. dafault is
|
|
||||||
dmy.}
|
|
||||||
|
|
||||||
\item{form.name}{manually specify form name(s). Vector of length 1 or
|
|
||||||
ncol(data). Default is NULL and "data" is used.}
|
|
||||||
|
|
||||||
\item{field.type}{manually specify field type(s). Vector of length 1 or
|
|
||||||
ncol(data). Default is NULL and "text" is used for everything but factors,
|
|
||||||
which wil get "radio".}
|
|
||||||
|
|
||||||
\item{field.label}{manually specify field label(s). Vector of length 1 or
|
|
||||||
ncol(data). Default is NULL and colnames(data) is used or attribute
|
|
||||||
`field.label.attr` for haven_labelled data set (imported .dta file with
|
|
||||||
`haven::read_dta()`).}
|
|
||||||
|
|
||||||
\item{field.label.attr}{attribute name for named labels for haven_labelled
|
|
||||||
data set (imported .dta file with `haven::read_dta()`. Default is "label"}
|
|
||||||
|
|
||||||
\item{field.validation}{manually specify field validation(s). Vector of
|
|
||||||
length 1 or ncol(data). Default is NULL and `levels()` are used for factors
|
|
||||||
or attribute `factor.labels.attr` for haven_labelled data set (imported .dta file with
|
|
||||||
`haven::read_dta()`).}
|
|
||||||
|
|
||||||
\item{metadata}{redcap metadata headings. Default is
|
|
||||||
REDCapCAST:::metadata_names.}
|
|
||||||
|
|
||||||
\item{validate.time}{Flag to validate guessed time columns}
|
|
||||||
|
|
||||||
\item{time.var.sel.pos}{Positive selection regex string passed to
|
|
||||||
`gues_time_only_filter()` as sel.pos.}
|
|
||||||
|
|
||||||
\item{time.var.sel.neg}{Negative selection regex string passed to
|
|
||||||
`gues_time_only_filter()` as sel.neg.}
|
|
||||||
}
|
|
||||||
\value{
|
|
||||||
list of length 2
|
|
||||||
}
|
|
||||||
\description{
|
|
||||||
Extract data from stata file for data dictionary
|
|
||||||
}
|
|
||||||
\details{
|
|
||||||
This function is a natural development of the ds2dd() function. It assumes
|
|
||||||
that the first column is the ID-column. No checks.
|
|
||||||
Please, do always inspect the data dictionary before upload.
|
|
||||||
|
|
||||||
Ensure, that the data set is formatted with as much information as possible.
|
|
||||||
|
|
||||||
`field.type` can be supplied
|
|
||||||
}
|
|
||||||
\examples{
|
|
||||||
data <- redcapcast_data
|
|
||||||
data |> ds2dd_detailed(validate.time = TRUE)
|
|
||||||
data |> ds2dd_detailed()
|
|
||||||
iris |> ds2dd_detailed(add.auto.id = TRUE)
|
|
||||||
mtcars |> ds2dd_detailed(add.auto.id = TRUE)
|
|
||||||
}
|
|
@ -1,36 +0,0 @@
|
|||||||
% Generated by roxygen2: do not edit by hand
|
|
||||||
% Please edit documentation in R/ds2dd_detailed.R
|
|
||||||
\name{guess_time_only_filter}
|
|
||||||
\alias{guess_time_only_filter}
|
|
||||||
\title{Try at determining which are true time only variables}
|
|
||||||
\usage{
|
|
||||||
guess_time_only_filter(
|
|
||||||
data,
|
|
||||||
validate = FALSE,
|
|
||||||
sel.pos = "[Tt]i[d(me)]",
|
|
||||||
sel.neg = "[Dd]at[eo]"
|
|
||||||
)
|
|
||||||
}
|
|
||||||
\arguments{
|
|
||||||
\item{data}{data set}
|
|
||||||
|
|
||||||
\item{validate}{flag to output validation data. Will output list.}
|
|
||||||
|
|
||||||
\item{sel.pos}{Positive selection regex string}
|
|
||||||
|
|
||||||
\item{sel.neg}{Negative selection regex string}
|
|
||||||
}
|
|
||||||
\value{
|
|
||||||
character vector or list depending on `validate` flag.
|
|
||||||
}
|
|
||||||
\description{
|
|
||||||
This is just a try at guessing data type based on data class and column names
|
|
||||||
hoping for a tiny bit of naming consistency. R does not include a time-only
|
|
||||||
data format natively, so the "hms" class from `readr` is used. This
|
|
||||||
has to be converted to character class before REDCap upload.
|
|
||||||
}
|
|
||||||
\examples{
|
|
||||||
data <- redcapcast_data
|
|
||||||
data |> guess_time_only_filter()
|
|
||||||
data |> guess_time_only_filter(validate = TRUE) |> lapply(head)
|
|
||||||
}
|
|
@ -1,21 +0,0 @@
|
|||||||
% Generated by roxygen2: do not edit by hand
|
|
||||||
% Please edit documentation in R/ds2dd_detailed.R
|
|
||||||
\name{hms2character}
|
|
||||||
\alias{hms2character}
|
|
||||||
\title{Change "hms" to "character" for REDCap upload.}
|
|
||||||
\usage{
|
|
||||||
hms2character(data)
|
|
||||||
}
|
|
||||||
\arguments{
|
|
||||||
\item{data}{data set}
|
|
||||||
}
|
|
||||||
\value{
|
|
||||||
data.frame or tibble
|
|
||||||
}
|
|
||||||
\description{
|
|
||||||
Change "hms" to "character" for REDCap upload.
|
|
||||||
}
|
|
||||||
\examples{
|
|
||||||
data <- redcapcast_data
|
|
||||||
## data |> time_only_correction() |> hms2character()
|
|
||||||
}
|
|
@ -1,19 +0,0 @@
|
|||||||
% Generated by roxygen2: do not edit by hand
|
|
||||||
% Please edit documentation in R/ds2dd_detailed.R
|
|
||||||
\name{mark_complete}
|
|
||||||
\alias{mark_complete}
|
|
||||||
\title{Completion marking based on completed upload}
|
|
||||||
\usage{
|
|
||||||
mark_complete(upload, ls)
|
|
||||||
}
|
|
||||||
\arguments{
|
|
||||||
\item{upload}{output list from `REDCapR::redcap_write()`}
|
|
||||||
|
|
||||||
\item{ls}{output list from `ds2dd_detailed()`}
|
|
||||||
}
|
|
||||||
\value{
|
|
||||||
list with `REDCapR::redcap_write()` results
|
|
||||||
}
|
|
||||||
\description{
|
|
||||||
Completion marking based on completed upload
|
|
||||||
}
|
|
@ -12,9 +12,8 @@ A data frame with 22 variables:
|
|||||||
\item{redcap_repeat_instrument}{Repeat instrument, character}
|
\item{redcap_repeat_instrument}{Repeat instrument, character}
|
||||||
\item{redcap_repeat_instance}{Repeat instance, numeric}
|
\item{redcap_repeat_instance}{Repeat instance, numeric}
|
||||||
\item{cpr}{CPR number, character}
|
\item{cpr}{CPR number, character}
|
||||||
\item{inclusion}{Inclusion date, Date}
|
\item{inclusion}{Inclusion date, date}
|
||||||
\item{inclusion_time}{Inclusion time, hms}
|
\item{dob}{Date of birth, date}
|
||||||
\item{dob}{Date of birth, Date}
|
|
||||||
\item{age}{Age decimal, numeric}
|
\item{age}{Age decimal, numeric}
|
||||||
\item{age_integer}{Age integer, numeric}
|
\item{age_integer}{Age integer, numeric}
|
||||||
\item{sex}{Legal sex, character}
|
\item{sex}{Legal sex, character}
|
||||||
@ -24,10 +23,10 @@ A data frame with 22 variables:
|
|||||||
\item{region}{region, character}
|
\item{region}{region, character}
|
||||||
\item{baseline_data_start_complete}{Completed, character}
|
\item{baseline_data_start_complete}{Completed, character}
|
||||||
\item{mrs_assessed}{mRS Assessed, character}
|
\item{mrs_assessed}{mRS Assessed, character}
|
||||||
\item{mrs_date}{Assesment date, Date}
|
\item{mrs_date}{Assesment date, date}
|
||||||
\item{mrs_score}{Categorical score, numeric}
|
\item{mrs_score}{Score, numeric}
|
||||||
\item{mrs_complete}{Complete, numeric}
|
\item{mrs_complete}{Complete, numeric}
|
||||||
\item{event_datetime}{Event datetime, POSIXct}
|
\item{event_date}{Event date, date}
|
||||||
\item{event_type}{Event type, character}
|
\item{event_type}{Event type, character}
|
||||||
\item{new_event_complete}{Completed, character}
|
\item{new_event_complete}{Completed, character}
|
||||||
|
|
||||||
|
@ -1,25 +0,0 @@
|
|||||||
% Generated by roxygen2: do not edit by hand
|
|
||||||
% Please edit documentation in R/ds2dd_detailed.R
|
|
||||||
\name{time_only_correction}
|
|
||||||
\alias{time_only_correction}
|
|
||||||
\title{Correction based on time_only_filter function. Introduces new class for easier
|
|
||||||
validation labelling.}
|
|
||||||
\usage{
|
|
||||||
time_only_correction(data, ...)
|
|
||||||
}
|
|
||||||
\arguments{
|
|
||||||
\item{data}{data set}
|
|
||||||
|
|
||||||
\item{...}{arguments passed on to `guess_time_only_filter()`}
|
|
||||||
}
|
|
||||||
\value{
|
|
||||||
tibble
|
|
||||||
}
|
|
||||||
\description{
|
|
||||||
Dependens on the data class "hms" introduced with
|
|
||||||
`guess_time_only_filter()` and converts these
|
|
||||||
}
|
|
||||||
\examples{
|
|
||||||
data <- redcapcast_data
|
|
||||||
## data |> time_only_correction()
|
|
||||||
}
|
|
Loading…
Reference in New Issue
Block a user