mirror of
https://github.com/agdamsbo/REDCapCAST.git
synced 2024-11-21 21:10:22 +01:00
styling and new function is.repeated_longitudinal()
This commit is contained in:
parent
3e356004d4
commit
e1509188ff
@ -139,6 +139,8 @@ REDCap_split <- function(records,
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)
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)
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if ("redcap_repeat_instrument" %in% vars_in_data) {
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# Variables to be at the beginning of each repeating instrument
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repeat_instrument_fields <- grep("^redcap_repeat.*",
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@ -197,6 +199,5 @@ REDCap_split <- function(records,
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}
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out
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}
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316
R/utils.r
316
R/utils.r
@ -1,5 +1,3 @@
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#' focused_metadata
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#' @description Extracts limited metadata for variables in a dataset
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#' @param metadata A dataframe containing metadata
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@ -8,7 +6,6 @@
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#' @export
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#'
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focused_metadata <- function(metadata, vars_in_data) {
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if (any(c("tbl_df", "tbl") %in% class(metadata))) {
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metadata <- data.frame(metadata)
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}
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@ -17,9 +14,11 @@ focused_metadata <- function(metadata, vars_in_data) {
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field_type <- grepl(".*[Ff]ield[._][Tt]ype$", names(metadata))
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fields <-
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metadata[!metadata[, field_type] %in% c("descriptive", "checkbox") &
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metadata[, field_name] %in% vars_in_data,
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field_name]
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metadata[
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!metadata[, field_type] %in% c("descriptive", "checkbox") &
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metadata[, field_name] %in% vars_in_data,
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field_name
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]
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# Process checkbox fields
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if (any(metadata[, field_type] == "checkbox")) {
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@ -29,19 +28,22 @@ focused_metadata <- function(metadata, vars_in_data) {
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# Processing
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checkbox_basenames <-
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metadata[metadata[, field_type] == "checkbox" &
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metadata[, field_name] %in% vars_check,
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field_name]
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metadata[
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metadata[, field_type] == "checkbox" &
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metadata[, field_name] %in% vars_check,
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field_name
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]
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fields <- c(fields, checkbox_basenames)
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}
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# Process instrument status fields
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form_names <-
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unique(metadata[, grepl(".*[Ff]orm[._][Nn]ame$",
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names(metadata))][metadata[, field_name]
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%in% fields])
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unique(metadata[, grepl(
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".*[Ff]orm[._][Nn]ame$",
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names(metadata)
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)][metadata[, field_name]
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%in% fields])
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form_complete_fields <- paste0(form_names, "_complete")
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@ -54,33 +56,34 @@ focused_metadata <- function(metadata, vars_in_data) {
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timestamp_fields <- timestamps
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fields <- c(fields, timestamp_fields)
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}
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# Process ".*\\.factor" fields supplied by REDCap's export data R script
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if (any(grepl("\\.factor$", vars_in_data))) {
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factor_fields <-
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do.call("rbind",
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apply(fields,
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1,
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function(x, y) {
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field_indices <- grepl(paste0("^", x[1], "\\.factor$"), y)
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if (any(field_indices))
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data.frame(
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field_name = y[field_indices],
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form_name = x[2],
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stringsAsFactors = FALSE,
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row.names = NULL
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)
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},
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y = vars_in_data))
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do.call(
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"rbind",
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apply(fields,
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1,
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function(x, y) {
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field_indices <- grepl(paste0("^", x[1], "\\.factor$"), y)
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if (any(field_indices)) {
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data.frame(
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field_name = y[field_indices],
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form_name = x[2],
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stringsAsFactors = FALSE,
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row.names = NULL
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)
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}
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},
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y = vars_in_data
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)
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)
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fields <- c(fields, factor_fields[, 1])
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}
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metadata[metadata[, field_name] %in% fields, ]
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}
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#' clean_redcap_name
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@ -94,13 +97,18 @@ focused_metadata <- function(metadata, vars_in_data) {
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#' @return vector or data frame, same format as input
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#' @export
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#'
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clean_redcap_name <- function(x){
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gsub(" ", "_",
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gsub("[' ']$","",
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gsub("[^a-z0-9' '_]", "",
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tolower(x)
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)))}
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clean_redcap_name <- function(x) {
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gsub(
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" ", "_",
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gsub(
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"[' ']$", "",
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gsub(
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"[^a-z0-9' '_]", "",
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tolower(x)
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)
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)
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)
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}
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#' Sanitize list of data frames
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@ -116,15 +124,18 @@ clean_redcap_name <- function(x){
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#'
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sanitize_split <- function(l,
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generic.names = c(
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"record_id",
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"redcap_event_name",
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"redcap_repeat_instrument",
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"redcap_repeat_instance"
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)) {
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generic.names <- c(get_id_name(l),
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generic.names,
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paste0(names(l), "_complete"))
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lapply(l, function(i) {
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if (ncol(i) > 2) {
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s <- data.frame(i[, !colnames(i) %in% generic.names])
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i[!apply(is.na(s), MARGIN = 1, FUN = all),]
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i[!apply(is.na(s), MARGIN = 1, FUN = all), ]
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} else {
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i
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}
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@ -132,6 +143,19 @@ sanitize_split <- function(l,
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}
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#' Get the id name
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#'
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#' @param data data frame or list
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#'
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#' @return character vector
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get_id_name <- function(data) {
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if ("list" %in% class(data)) {
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do.call(c, lapply(data, names))[[1]]
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} else {
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names(data)[[1]]
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}
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}
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#' Match fields to forms
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#'
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#' @param metadata A data frame containing field names and form names
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@ -143,20 +167,23 @@ sanitize_split <- function(l,
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#'
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#'
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match_fields_to_form <- function(metadata, vars_in_data) {
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metadata <- data.frame(metadata)
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field_form_name <- grepl(".*([Ff]ield|[Ff]orm)[._][Nn]ame$",names(metadata))
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field_type <- grepl(".*[Ff]ield[._][Tt]ype$",names(metadata))
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field_form_name <- grepl(".*([Ff]ield|[Ff]orm)[._][Nn]ame$", names(metadata))
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field_type <- grepl(".*[Ff]ield[._][Tt]ype$", names(metadata))
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fields <- metadata[!metadata[,field_type] %in% c("descriptive", "checkbox"),
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field_form_name]
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fields <- metadata[
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!metadata[, field_type] %in% c("descriptive", "checkbox"),
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field_form_name
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]
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names(fields) <- c("field_name", "form_name")
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# Process instrument status fields
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form_names <- unique(metadata[,grepl(".*[Ff]orm[._][Nn]ame$",
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names(metadata))])
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form_names <- unique(metadata[, grepl(
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".*[Ff]orm[._][Nn]ame$",
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names(metadata)
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)])
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form_complete_fields <- data.frame(
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field_name = paste0(form_names, "_complete"),
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form_name = form_names,
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@ -176,57 +203,65 @@ match_fields_to_form <- function(metadata, vars_in_data) {
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)
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fields <- rbind(fields, timestamp_fields)
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}
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# Process checkbox fields
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if (any(metadata[,field_type] == "checkbox")) {
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checkbox_basenames <- metadata[metadata[,field_type] == "checkbox",
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field_form_name]
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if (any(metadata[, field_type] == "checkbox")) {
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checkbox_basenames <- metadata[
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metadata[, field_type] == "checkbox",
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field_form_name
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]
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checkbox_fields <-
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do.call("rbind",
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apply(checkbox_basenames,
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1,
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function(x, y)
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data.frame(
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field_name =
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y[grepl(paste0("^", x[1], "___((?!\\.factor).)+$"),
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y, perl = TRUE)],
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form_name = x[2],
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stringsAsFactors = FALSE,
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row.names = NULL
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),
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y = vars_in_data))
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do.call(
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"rbind",
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apply(checkbox_basenames,
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1,
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function(x, y) {
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data.frame(
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field_name =
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y[grepl(paste0("^", x[1], "___((?!\\.factor).)+$"),
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y,
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perl = TRUE
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)],
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form_name = x[2],
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stringsAsFactors = FALSE,
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row.names = NULL
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)
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},
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y = vars_in_data
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)
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)
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fields <- rbind(fields, checkbox_fields)
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}
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# Process ".*\\.factor" fields supplied by REDCap's export data R script
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if (any(grepl("\\.factor$", vars_in_data))) {
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factor_fields <-
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do.call("rbind",
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apply(fields,
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1,
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function(x, y) {
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field_indices <- grepl(paste0("^", x[1], "\\.factor$"), y)
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if (any(field_indices))
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data.frame(
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field_name = y[field_indices],
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form_name = x[2],
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stringsAsFactors = FALSE,
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row.names = NULL
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)
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},
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y = vars_in_data))
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do.call(
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"rbind",
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apply(fields,
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1,
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function(x, y) {
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field_indices <- grepl(paste0("^", x[1], "\\.factor$"), y)
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if (any(field_indices)) {
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data.frame(
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field_name = y[field_indices],
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form_name = x[2],
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stringsAsFactors = FALSE,
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row.names = NULL
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)
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}
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},
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y = vars_in_data
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)
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)
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fields <- rbind(fields, factor_fields)
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}
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fields
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}
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#' Split a data frame into separate tables for each form
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@ -256,10 +291,12 @@ match_fields_to_form <- function(metadata, vars_in_data) {
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#'
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#' # Create the fields
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#' fields <- matrix(
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#' c("form_a_name", "form_a",
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#' c(
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#' "form_a_name", "form_a",
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#' "form_a_age", "form_a",
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#' "form_b_name", "form_b",
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#' "form_b_gender", "form_b"),
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#' "form_b_gender", "form_b"
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#' ),
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#' ncol = 2, byrow = TRUE
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#' )
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#'
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@ -269,14 +306,17 @@ split_non_repeating_forms <-
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function(table, universal_fields, fields) {
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forms <- unique(fields[[2]])
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x <- lapply(forms,
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function (x) {
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table[names(table) %in% union(universal_fields,
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fields[fields[, 2] == x, 1])]
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})
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x <- lapply(
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forms,
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function(x) {
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table[names(table) %in% union(
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universal_fields,
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fields[fields[, 2] == x, 1]
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)]
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}
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)
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structure(x, names = forms)
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}
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@ -295,7 +335,7 @@ split_non_repeating_forms <-
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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(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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@ -306,26 +346,33 @@ strsplitx <- function(x,
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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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out <- base::strsplit(
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x = x,
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split = paste0("(?<=.)(?=", split, ")"),
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perl = TRUE,
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...
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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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out <- base::strsplit(
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x = x,
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split = paste0("(?<=", split, ")"),
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perl = TRUE,
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...
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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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out <- base::strsplit(gsub(
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"~~", "~", # Removes double ~
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gsub(
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"^~", "", # 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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)
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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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@ -345,37 +392,36 @@ strsplitx <- function(x,
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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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#' 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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#' 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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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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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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"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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paste0("e", nt),
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"to",
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"tre",
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"fire",
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@ -401,15 +447,14 @@ d2w <- function(x, lang = "en", neutrum=FALSE, everything=FALSE) {
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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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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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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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@ -426,19 +471,20 @@ d2w <- function(x, lang = "en", neutrum=FALSE, everything=FALSE) {
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#' @return logical
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#' @examples
|
||||
#' is.repeated_longitudinal(c("record_id", "age", "record_id", "gender"))
|
||||
#'
|
||||
#' is.repeated_longitudinal(redcapcast_data)
|
||||
#' is.repeated_longitudinal(list(redcapcast_data))
|
||||
is.repeated_longitudinal <- function(data, generics = c(
|
||||
"redcap_event_name",
|
||||
"redcap_repeat_instrument",
|
||||
"redcap_repeat_instance"
|
||||
)) {
|
||||
if (is.list(data)) {
|
||||
"redcap_event_name",
|
||||
"redcap_repeat_instrument",
|
||||
"redcap_repeat_instance"
|
||||
)) {
|
||||
if ("list" %in% class(data)) {
|
||||
names <- data |>
|
||||
lapply(names) |>
|
||||
purrr::list_c()
|
||||
} else if (is.data.frame(data)) {
|
||||
} else if ("data.frame" %in% class(data)) {
|
||||
names <- names(data)
|
||||
} else if (is.vector(data)) {
|
||||
} else if ("character" %in% class(data)) {
|
||||
names <- data
|
||||
}
|
||||
any(generics %in% names)
|
||||
|
||||
@ -6,7 +6,7 @@
|
||||
\usage{
|
||||
sanitize_split(
|
||||
l,
|
||||
generic.names = c("record_id", "redcap_event_name", "redcap_repeat_instrument",
|
||||
generic.names = c("redcap_event_name", "redcap_repeat_instrument",
|
||||
"redcap_repeat_instance")
|
||||
)
|
||||
}
|
||||
|
||||
@ -36,10 +36,12 @@ universal_fields <- c("id")
|
||||
|
||||
# Create the fields
|
||||
fields <- matrix(
|
||||
c("form_a_name", "form_a",
|
||||
c(
|
||||
"form_a_name", "form_a",
|
||||
"form_a_age", "form_a",
|
||||
"form_b_name", "form_b",
|
||||
"form_b_gender", "form_b"),
|
||||
"form_b_gender", "form_b"
|
||||
),
|
||||
ncol = 2, byrow = TRUE
|
||||
)
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user