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#' @title Create a metadata table
#'
#' @description Create a metadata table from the survey data files.
#'
#' @details A data frame like tibble ojbect is returned.
#' In case you are working with a list of surveys (waves), call
#' \code{\link{metadata_waves_create}}, which is a wrapper around
#' a list of \code{\link{metadata_create}} calls.
#'
#' The structure of the returned tibble:
#' \describe{
#' \item{filename}{The original file name; if present; \code{missing}, if a non-\code{\link{survey}} data frame is used as input \code{survey}.}
#' \item{id}{The ID of the survey, if present; \code{missing}, if a non-\code{\link{survey}} data frame is used as input \code{survey}.}
#' \item{var_name_orig}{The original variable name in SPSS.}
#' \item{class_orig}{The original variable class after importing with\code{\link[haven]{read_spss}}.}
#' \item{label_orig}{The original variable label in SPSS.}
#' \item{labels}{A list of the value labels.}
#' \item{valid_labels}{A list of the value labels that are not marked as missing values.}
#' \item{na_labels}{A list of the value labels that refer to user-defined missing values.}
#' \item{na_range}{An optional range of a continuous missing range, if present in the vector.}
#' \item{n_labels}{Number of categories or unique levels, which may be different from the sum of missing and category labels.}
#' \item{n_valid_labels}{Number of categories in the non-missing range.}
#' \item{n_na_labels}{Number of categories of the variable, should be the sum of the former two.}
#' \item{na_levels}{A list of the user-defined missing values.}
#' }
#'
#' @param survey A survey data frame.
#' @importFrom tibble tibble
#' @importFrom dplyr left_join mutate case_when group_by
#' @importFrom tidyr nest unnest
#' @importFrom labelled na_values na_range val_labels var_label
#' @importFrom purrr map
#' @importFrom assertthat assert_that
#' @importFrom rlang .data
#' @family metadata functions
#' @return A nested data frame with metadata and the range of
#' labels, na_values and the na_range itself.
#' @examples
#' metadata_create (
#' survey = read_rds (
#' system.file("examples", "ZA7576.rds",
#' package = "retroharmonize")
#' )
#' )
#' @export
metadata_create <- function( survey ) {
assert_that(is.survey(survey),
msg = "Parameter 'survey' must be of s3 class survey. See ?is.survey.")
filename <- attr(survey, "filename")
if (is.null(filename)) filename <- "unknown"
id <- attr(survey, "id")
if (is.null(id)) id <- "missing"
if( ncol(survey) == 0) {
# Special case when file could not be read and survey is empty
return(metadata_initialize(filename = filename, id = paste0(filename, " could not be read.")))
}
label_orig <- lapply ( survey, labelled::var_label )
class_orig <- vapply( survey, function(x) class(x)[1], character(1))
metadata <- tibble::tibble (
filename = filename,
id = id,
var_name_orig = names(survey),
class_orig = class_orig,
label_orig = ifelse ( vapply(label_orig, is.null, logical(1)),
"",
unlist(label_orig)) %>%
as.character() %>%
var_label_normalize()
)
fn_valid_range <- function(x) {
labelled::val_labels(x)[!labelled::val_labels(x) %in% labelled::na_values(x)]
}
na_labels <- function(x) {
# labels that refer to na_values
labs <- labelled::val_labels(x)
labs[labs == labelled::na_values(x)]
}
to_list_column <- function(.f = "na_values") {
x <- dplyr::case_when (
.f == "na_labels" ~ sapply ( survey, na_labels),
.f == "na_range" ~ sapply ( survey, labelled::na_range),
.f == "valid_range" ~ sapply ( survey, fn_valid_range),
.f == "labels" ~ sapply ( survey, labelled::val_labels))
x[sapply(x, is.null)] <- NA_character_
names(x) <- names(survey)
#df <- purrr::map(x, list)
#names(df) <- rep(.f, length(df))
x
}
range_df <- tibble::tibble (
var_name_orig = names(survey),
labels = to_list_column(.f = "labels"),
valid_labels = to_list_column(.f = "valid_range"),
na_labels = to_list_column(.f = "na_labels"),
na_range = to_list_column (.f = "na_range")
)
label_length <- function(x) {
ifelse ( is.na(x[[1]])[1] | length(x[[1]]) ==0,
0, length(x[[1]]) )
}
range_df$n_labels <- vapply(1:nrow(range_df), function(x) label_length(range_df$labels[x]), numeric(1))
range_df$n_valid_labels <- vapply(1:nrow(range_df), function(x) label_length(range_df$valid_labels[x]), numeric(1))
range_df$n_na_labels <- vapply(1:nrow(range_df), function(x) label_length(range_df$na_labels[x]), numeric(1))
return_df <- metadata %>%
dplyr::left_join ( range_df %>%
dplyr::group_by ( .data$var_name_orig ) %>%
tidyr::nest() ,
by = "var_name_orig") %>%
tidyr::unnest ( cols = "data" ) %>%
dplyr::ungroup() %>%
dplyr::mutate ( n_na_labels = as.numeric(.data$n_na_labels),
n_valid_labels = as.numeric(.data$n_valid_labels),
n_labels = as.numeric(.data$n_labels)) %>%
as.data.frame()
change_label_to_empty <- function() {
"none" = NA_real_
}
## Avoid the accidental creation of empty CHARACTER lists, because they do not bind with
## numeric lists.
return_df$label_type <- vapply(return_df$labels, function(x) class(x)[1], character(1))
return_dflabels <- ifelse (return_df$label_type == "character" & return_df$n_labels ==0 ,
yes = change_label_to_empty(),
no = return_df$labels )
return_df$valid_labels <- ifelse (return_df$label_type == "character" & return_df$n_labels ==0 ,
yes = change_label_to_empty(),
no = return_df$valid_labels )
return_df$na_labels <- ifelse (return_df$label_type == "character" & return_df$n_labels == 0 ,
yes = change_label_to_empty(),
no = return_df$na_labels )
return_df %>%
select ( -.data$label_type )
}
#' @title Create a metadata table from several surveys
#' @rdname metadata_create
#' @param survey_list A list containing surveys of class survey.
#' @family metadata functions
#' @examples
#' examples_dir <- system.file( "examples", package = "retroharmonize")
#'
#' my_rds_files <- dir( examples_dir)[grepl(".rds",
#' dir(examples_dir))]
#'
#' example_surveys <- read_surveys(file.path(examples_dir, my_rds_files))
#' metadata_waves_create (example_surveys)
#' @export
metadata_waves_create <- function ( survey_list ) {
validate_survey_list( survey_list)
metadata_list <- lapply ( survey_list, metadata_create )
do.call ( rbind, metadata_list )
}
#' @title Initialize a metadata data frame
#'
#' @inheritParams metadata_create
#' @importFrom tibble tibble
#' @return A nested data frame with metadata and the range of
#' labels, na_values and the na_range itself.
#' @keywords internal
metadata_initialize <- function (filename, id ){
tibble::tibble (
filename = filename,
id = id,
class_orig = NA_character_,
var_name_orig = NA_character_,
label_orig = NA_character_,
labels = NA_character_,
valid_labels = list("none" = NA_real_),
na_labels = list("none" = NA_real_),
na_range = list("none" = NA_real_),
n_labels = 0,
n_valid_labels = 0,
n_na_labels = 0 )
}
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