mirror of
https://github.com/agdamsbo/REDCapCAST.git
synced 2024-11-22 05:20:23 +01:00
403 lines
12 KiB
R
403 lines
12 KiB
R
utils::globalVariables(c(
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"stats::setNames",
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"field_name",
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"field_type",
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"select_choices_or_calculations",
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"field_label"
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))
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#' Try at determining which are true time only variables
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#'
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#' @description
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#' 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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#'
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#' @param data data set
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#' @param validate flag to output validation data. Will output list.
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#' @param sel.pos Positive selection regex string
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#' @param sel.neg Negative selection regex string
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#'
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#' @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 |>
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#' guess_time_only_filter(validate = TRUE) |>
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#' lapply(head)
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guess_time_only_filter <- function(data,
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validate = FALSE,
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sel.pos = "[Tt]i[d(me)]",
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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))) |>
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(\(x) names(data)[do.call(c, x)])()
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time_only_log <- datetime_nms |> (\(x) {
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## Detects which are determined true Time only variables
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## Inspection is necessary
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grepl(pattern = sel.pos, x = x) &
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!grepl(pattern = sel.neg, x = x)
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})()
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if (validate) {
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list(
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"is.POSIX" = data[datetime_nms],
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"is.datetime" = data[datetime_nms[!time_only_log]],
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"is.time_only" = data[datetime_nms[time_only_log]]
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)
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} else {
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datetime_nms[time_only_log]
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}
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}
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#' Correction based on time_only_filter function
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#'
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#'
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#' @param data data set
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#' @param ... arguments passed on to `guess_time_only_filter()`
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#'
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#' @return tibble
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#' @importFrom readr parse_time
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#'
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#' @examples
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#' data <- redcapcast_data
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#' ## data |> time_only_correction()
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time_only_correction <- function(data, ...) {
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nms <- guess_time_only_filter(data, ...)
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z <- nms |>
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lapply(\(y) {
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readr::parse_time(format(data[[y]], format = "%H:%M:%S"))
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}) |>
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suppressMessages(dplyr::bind_cols()) |>
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stats::setNames(nm = nms)
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data[nms] <- z
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data
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}
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#' Change "hms" to "character" for REDCap upload.
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#'
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#' @param data data set
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#'
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#' @return data.frame or tibble
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#'
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#' @examples
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#' data <- redcapcast_data
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#' ## data |> time_only_correction() |> hms2character()
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hms2character <- function(data) {
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data |>
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lapply(function(x) {
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if ("hms" %in% class(x)) {
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as.character(x)
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} else {
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x
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}
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}) |>
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dplyr::bind_cols()
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}
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#' Extract data from stata file for data dictionary
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#'
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#' @details
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#' This function is a natural development of the ds2dd() function. It assumes
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#' that the first column is the ID-column. No checks.
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#' Please, do always inspect the data dictionary before upload.
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#'
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#' Ensure, that the data set is formatted with as much information as possible.
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#'
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#' `field.type` can be supplied
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#'
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#' @param data data frame
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#' @param date.format date format, character string. ymd/dmy/mdy. dafault is
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#' dmy.
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#' @param add.auto.id flag to add id column
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#' @param form.name manually specify form name(s). Vector of length 1 or
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#' ncol(data). Default is NULL and "data" is used.
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#' @param form.sep If supplied dataset has form names as suffix or prefix to the
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#' column/variable names, the seperator can be specified. If supplied, the
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#' form.sep is ignored. Default is NULL.
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#' @param form.prefix Flag to set if form is prefix (TRUE) or suffix (FALSE) to
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#' the column names. Assumes all columns have pre- or suffix if specified.
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#' @param field.type manually specify field type(s). Vector of length 1 or
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#' ncol(data). Default is NULL and "text" is used for everything but factors,
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#' which wil get "radio".
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#' @param field.label manually specify field label(s). Vector of length 1 or
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#' ncol(data). Default is NULL and colnames(data) is used or attribute
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#' `field.label.attr` for haven_labelled data set (imported .dta file with
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#' `haven::read_dta()`).
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#' @param field.label.attr attribute name for named labels for haven_labelled
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#' data set (imported .dta file with `haven::read_dta()`. Default is "label"
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#' @param field.validation manually specify field validation(s). Vector of
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#' length 1 or ncol(data). Default is NULL and `levels()` are used for factors
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#' or attribute `factor.labels.attr` for haven_labelled data set (imported .dta
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#' file with `haven::read_dta()`).
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#' @param metadata redcap metadata headings. Default is
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#' REDCapCAST:::metadata_names.
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#' @param validate.time Flag to validate guessed time columns
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#' @param time.var.sel.pos Positive selection regex string passed to
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#' `gues_time_only_filter()` as sel.pos.
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#' @param time.var.sel.neg Negative selection regex string passed to
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#' `gues_time_only_filter()` as sel.neg.
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#'
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#' @return list of length 2
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#' @export
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#'
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#' @examples
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#' data <- REDCapCAST::redcapcast_data
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#' data |> ds2dd_detailed(validate.time = TRUE)
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#' data |> ds2dd_detailed()
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#' iris |> ds2dd_detailed(add.auto.id = TRUE)
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#' mtcars |> ds2dd_detailed(add.auto.id = TRUE)
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#' data <- iris |>
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#' ds2dd_detailed(add.auto.id = TRUE) |>
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#' purrr::pluck("data")
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#' names(data) <- glue::glue("{sample(x = c('a','b'),size = length(names(data)),
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#' replace=TRUE,prob = rep(x=.5,2))}__{names(data)}")
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#' data |> ds2dd_detailed(form.sep="__")
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ds2dd_detailed <- function(data,
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add.auto.id = FALSE,
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date.format = "dmy",
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form.name = NULL,
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form.sep = NULL,
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form.prefix = TRUE,
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field.type = NULL,
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field.label = NULL,
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field.label.attr = "label",
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field.validation = NULL,
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metadata = names(REDCapCAST::redcapcast_meta),
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validate.time = FALSE,
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time.var.sel.pos = "[Tt]i[d(me)]",
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time.var.sel.neg = "[Dd]at[eo]") {
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## Handles the odd case of no id column present
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if (add.auto.id) {
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data <- dplyr::tibble(
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record_id = seq_len(nrow(data)),
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data
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)
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message("A default id column has been added")
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}
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if (validate.time) {
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return(data |> guess_time_only_filter(validate = TRUE))
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}
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if (lapply(data, haven::is.labelled) |> (\(x)do.call(c, x))() |> any()) {
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message("Data seems to be imported with haven from a Stata (.dta) file and
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will be treated as such.")
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data.source <- "dta"
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} else {
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data.source <- ""
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}
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## data classes
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### Only keeps the first class, as time fields (POSIXct/POSIXt) has two
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### classes
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if (data.source == "dta") {
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data_classes <-
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data |>
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haven::as_factor() |>
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time_only_correction(
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sel.pos = time.var.sel.pos,
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sel.neg = time.var.sel.neg
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) |>
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lapply(\(x)class(x)[1]) |>
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(\(x)do.call(c, x))()
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} else {
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data_classes <-
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data |>
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time_only_correction(
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sel.pos = time.var.sel.pos,
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sel.neg = time.var.sel.neg
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) |>
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lapply(\(x)class(x)[1]) |>
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(\(x)do.call(c, x))()
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}
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## ---------------------------------------
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## Building the data dictionary
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## ---------------------------------------
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## skeleton
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dd <- data.frame(matrix(ncol = length(metadata), nrow = ncol(data))) |>
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stats::setNames(metadata) |>
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dplyr::tibble()
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## form_name and field_name
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if (!is.null(form.sep)) {
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if (form.sep!=""){
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suppressMessages(nms <- strsplit(names(data), split = form.sep) |>
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dplyr::bind_cols())
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## Assumes form.sep only occurs once and form.prefix defines if form is prefix or suffix
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dd$form_name <- clean_redcap_name(dplyr::slice(nms,ifelse(form.prefix, 1, 2)))
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## The other split part is used as field names
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dd$field_name <- dplyr::slice(nms,ifelse(!form.prefix, 1, 2)) |> as.character()
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} else {
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dd$form_name <- "data"
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dd$field_name <- gsub(" ", "_", tolower(colnames(data)))
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}
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} else if (is.null(form.sep)) {
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## if no form name prefix, the colnames are used as field_names
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dd$field_name <- gsub(" ", "_", tolower(colnames(data)))
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} else if (is.null(form.name)) {
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dd$form_name <- "data"
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} else {
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if (length(form.name) == 1 || length(form.name) == nrow(dd)) {
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dd$form_name <- form.name
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} else {
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stop("Length of supplied 'form.name' has to be one (1) or ncol(data).")
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}
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}
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## field_label
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if (is.null(field.label)) {
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if (data.source == "dta") {
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dd$field_label <- data |>
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lapply(function(x) {
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if (haven::is.labelled(x)) {
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attributes(x)[[field.label.attr]]
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} else {
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NA
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}
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}) |>
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(\(x)do.call(c, x))()
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}
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dd <-
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dd |> dplyr::mutate(field_label = dplyr::if_else(is.na(field_label),
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field_name, field_label
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))
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} else {
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if (length(field.label) == 1 || length(field.label) == nrow(dd)) {
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dd$field_label <- field.label
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} else {
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stop("Length of supplied 'field.label' has to be one (1) or ncol(data).")
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}
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}
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## field_type
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if (is.null(field.type)) {
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dd$field_type <- "text"
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dd <-
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dd |> dplyr::mutate(field_type = dplyr::if_else(data_classes == "factor",
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"radio", field_type
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))
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} else {
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if (length(field.type) == 1 || length(field.type) == nrow(dd)) {
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dd$field_type <- field.type
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} else {
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stop("Length of supplied 'field.type' has to be one (1) or ncol(data).")
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}
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}
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## validation
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if (is.null(field.validation)) {
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dd <-
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dd |> dplyr::mutate(
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text_validation_type_or_show_slider_number = dplyr::case_when(
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data_classes == "Date" ~ paste0("date_", date.format),
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data_classes ==
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"hms" ~ "time_hh_mm_ss",
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## Self invented format after filtering
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data_classes ==
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"POSIXct" ~ paste0("datetime_", date.format),
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data_classes ==
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"numeric" ~ "number"
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)
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)
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} else {
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if (length(field.validation) == 1 || length(field.validation) == nrow(dd)) {
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dd$text_validation_type_or_show_slider_number <- field.validation
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} else {
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stop("Length of supplied 'field.validation'
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has to be one (1) or ncol(data).")
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}
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}
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## choices
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if (data.source == "dta") {
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factor_levels <- data |>
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lapply(function(x) {
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if (haven::is.labelled(x)) {
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att <- attributes(x)$labels
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paste(paste(att, names(att), sep = ", "), collapse = " | ")
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} else {
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NA
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}
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}) |>
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(\(x)do.call(c, x))()
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} else {
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factor_levels <- data |>
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lapply(function(x) {
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if (is.factor(x)) {
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## Re-factors to avoid confusion with missing levels
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## Assumes all relevant levels are represented in the data
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re_fac <- factor(x)
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paste(
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paste(seq_along(levels(re_fac)),
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levels(re_fac),
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sep = ", "
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),
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collapse = " | "
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)
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} else {
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NA
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}
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}) |>
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(\(x)do.call(c, x))()
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}
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dd <-
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dd |> dplyr::mutate(
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select_choices_or_calculations = dplyr::if_else(
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is.na(factor_levels),
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select_choices_or_calculations,
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factor_levels
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)
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)
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list(
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data = data |>
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time_only_correction(
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sel.pos = time.var.sel.pos,
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sel.neg = time.var.sel.neg
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) |>
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hms2character() |>
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stats::setNames(dd$field_name),
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meta = dd
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)
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}
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### Completion
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#' Completion marking based on completed upload
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#'
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#' @param upload output list from `REDCapR::redcap_write()`
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#' @param ls output list from `ds2dd_detailed()`
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#'
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#' @return list with `REDCapR::redcap_write()` results
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mark_complete <- function(upload, ls) {
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data <- ls$data
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meta <- ls$meta
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forms <- unique(meta$form_name)
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cbind(
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data[[1]][data[[1]] %in% upload$affected_ids],
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data.frame(matrix(2,
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ncol = length(forms),
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nrow = upload$records_affected_count
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))
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) |>
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stats::setNames(c(names(data)[1], paste0(forms, "_complete")))
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}
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