From c3b54b08606cc0f9df6dca750b457775608cb44f Mon Sep 17 00:00:00 2001
From: Andreas Gammelgaard Damsbo <andreas@gdamsbo.dk>
Date: Wed, 20 Nov 2024 12:09:13 +0100
Subject: [PATCH] as_factor functions to preserve attributes

---
 R/as_factor.R           | 249 ++++++++++++++++++++++++++++++++++++++++
 R/ds2dd_detailed.R      | 117 +++----------------
 man/as_factor.Rd        |  51 ++++++++
 man/fct2num.Rd          |  34 ++++++
 man/get_attr.Rd         |   2 +-
 man/haven_all_levels.Rd |   2 +-
 man/named_levels.Rd     |  25 ++++
 man/set_attr.Rd         |   2 +-
 8 files changed, 378 insertions(+), 104 deletions(-)
 create mode 100644 R/as_factor.R
 create mode 100644 man/as_factor.Rd
 create mode 100644 man/fct2num.Rd
 create mode 100644 man/named_levels.Rd

diff --git a/R/as_factor.R b/R/as_factor.R
new file mode 100644
index 0000000..5e4e912
--- /dev/null
+++ b/R/as_factor.R
@@ -0,0 +1,249 @@
+#' Convert labelled vectors to factors while preserving attributes
+#'
+#' This extends [forcats::as_factor()] as well as [haven::as_factor()], by appending
+#' original attributes except for "class" after converting to factor to avoid
+#' ta loss in case of rich formatted and labelled data.
+#'
+#' Please refer to parent functions for extended documentation.
+#'
+#' @param x Object to coerce to a factor.
+#' @param ... Other arguments passed down to method.
+#' @export
+#' @examples
+#' # will preserve all attributes but class
+#' c(1, 4, 3, "A", 7, 8, 1) |> as_factor()
+#' structure(c(1, 2, 3, 2, 10, 9),
+#'   labels = c(Unknown = 9, Refused = 10)
+#' ) |>
+#'   as_factor()
+#'
+#' structure(c(1, 2, 3, 2, 10, 9),
+#'   labels = c(Unknown = 9, Refused = 10),
+#'   class = "haven_labelled"
+#' ) |>
+#'   as_factor()
+#'
+#' @importFrom forcats as_factor
+#' @importFrom rlang check_dots_used
+#' @export
+#' @name as_factor
+as_factor <- function(x, ...) {
+  rlang::check_dots_used()
+  UseMethod("as_factor")
+}
+
+#' @rdname as_factor
+#' @export
+as_factor.logical <- function(x, ...) {
+  labels <- get_attr(x)
+  x <- forcats::as_factor(x, ...)
+  set_attr(x, labels[-match("class", names(labels))])
+}
+
+#' @rdname as_factor
+#' @export
+as_factor.numeric <- function(x, ...) {
+  labels <- get_attr(x)
+  x <- forcats::as_factor(x, ...)
+  set_attr(x, labels[-match("class", names(labels))])
+}
+
+#' @rdname as_factor
+#' @export
+as_factor.character <- function(x, ...) {
+  labels <- get_attr(x)
+  x <- forcats::as_factor(x, ...)
+  set_attr(x, labels[-match("class", names(labels))])
+}
+
+#' @rdname as_factor
+#' @export
+as_factor.haven_labelled <- function(x, ...) {
+  labels <- get_attr(x)
+  x <- haven::as_factor(x, ...)
+  set_attr(x, labels[-match("class", names(labels))])
+}
+
+#' @export
+#' @rdname as_factor
+as_factor.labelled <- as_factor.haven_labelled
+
+
+
+#' Get named vector of factor levels and values
+#'
+#' @param data factor
+#' @param label character string of attribute with named vector of factor labels
+#'
+#' @return named vector
+#' @export
+#'
+#' @examples
+#' structure(c(1, 2, 3, 2, 10, 9),
+#'   labels = c(Unknown = 9, Refused = 10),
+#'   class = "haven_labelled"
+#' ) |> as_factor() |> named_levels()
+named_levels <- function(data, label = "labels",na.label=NULL, na.value=99) {
+  stopifnot(is.factor(data))
+  if (!is.null(na.label)){
+    attrs <- attributes(data)
+    lvls <- as.character(data)
+    lvls[is.na(lvls)] <- na.label
+    vals <- as.numeric(data)
+    vals[is.na(vals)] <- na.value
+
+    lbls <- data.frame(
+      name = lvls,
+      value = vals
+    ) |> unique() |>
+      (\(d){
+        stats::setNames(d$value, d$name)
+      })() |>
+      sort()
+
+    data <- do.call(structure,
+            c(list(.Data=match(vals,lbls)),
+              attrs[-match("levels", names(attrs))],
+              list(levels=names(lbls),
+                   labels=lbls)))
+  }
+
+  d <- data.frame(
+    name = levels(data)[data],
+    value = as.numeric(data)
+  ) |>
+    unique()
+
+  ## Applying labels
+  attr_l <- attr(x = data, which = label, exact = TRUE)
+  if (length(attr_l) != 0) {
+    d$value[match(names(attr_l), d$name)] <- unname(attr_l)
+  }
+
+  out <- stats::setNames(d$value, d$name)
+  ## Sort if levels are numeric
+  ## Else, they appear in order of appearance
+  if (identical(
+    levels(data),
+    suppressWarnings(as.character(as.numeric(levels(data))))
+  )) {
+    out <- out |> sort()
+  }
+  out
+}
+
+
+#' Allows conversion of factor to numeric values preserving original levels
+#'
+#' @param data vector
+#'
+#' @return numeric vector
+#' @export
+#'
+#' @examples
+#' c(1, 4, 3, "A", 7, 8, 1) |>
+#' as_factor() |> fct2num()
+#'
+#' structure(c(1, 2, 3, 2, 10, 9),
+#'   labels = c(Unknown = 9, Refused = 10),
+#'   class = "haven_labelled"
+#' ) |>
+#'   as_factor() |>
+#'   fct2num()
+#'
+#' structure(c(1, 2, 3, 2, 10, 9),
+#'   labels = c(Unknown = 9, Refused = 10)
+#' ) |>
+#'   as_factor() |>
+#'   fct2num()
+fct2num <- function(data) {
+  stopifnot(is.factor(data))
+  as.numeric(named_levels(data))[match(data, names(named_levels(data)))]
+}
+
+#' Extract attribute. Returns NA if none
+#'
+#' @param data vector
+#' @param attr attribute name
+#'
+#' @return character vector
+#' @export
+#'
+#' @examples
+#' attr(mtcars$mpg, "label") <- "testing"
+#' sapply(mtcars, get_attr)
+#' lapply(mtcars, \(.x)get_attr(.x, NULL))
+#' mtcars |>
+#'   numchar2fct(numeric.threshold = 6) |>
+#'   ds2dd_detailed()
+get_attr <- function(data, attr = NULL) {
+  if (is.null(attr)) {
+    attributes(data)
+  } else {
+    a <- attr(data, attr, exact = TRUE)
+    if (is.null(a)) {
+      NA
+    } else {
+      a
+    }
+  }
+}
+
+
+#' Set attributes for named attribute. Appends if attr is NULL
+#'
+#' @param data vector
+#' @param label label
+#' @param attr attribute name
+#'
+#' @return vector with attribute
+#' @export
+#'
+set_attr <- function(data, label, attr = NULL) {
+  if (is.null(attr)) {
+    ## Has to be list...
+    stopifnot(is.list(label))
+    ## ... with names
+    stopifnot(length(label)==length(names(label)))
+    attributes(data) <- c(attributes(data),label)
+  } else {
+    attr(data, attr) <- label
+  }
+  data
+}
+
+#' Finish incomplete haven attributes substituting missings with values
+#'
+#' @param data haven labelled variable
+#'
+#' @return named vector
+#' @export
+#'
+#' @examples
+#' ds <- structure(c(1, 2, 3, 2, 10, 9),
+#'   labels = c(Unknown = 9, Refused = 10),
+#'   class = "haven_labelled"
+#' )
+#' haven::is.labelled(ds)
+#' attributes(ds)
+#' ds |> haven_all_levels()
+haven_all_levels <- function(data) {
+  stopifnot(haven::is.labelled(data))
+  if (length(attributes(data)$labels) == length(unique(data))) {
+    out <- attributes(data)$labels
+  } else {
+    att <- attributes(data)$labels
+    out <- c(unique(data[!data %in% att]), att) |>
+      stats::setNames(c(unique(data[!data %in% att]), names(att)))
+  }
+  out
+}
+
+# readr::read_rds("/Users/au301842/PAaSO/labelled_test.rds") |> ds2dd_detailed()
+#' sample(c(TRUE,FALSE,NA),20,TRUE) |> set_attr("hidden","status") |> trial_fct() |> named_levels(na.label = "Missing") |> sort()
+# trial_fct <- function(x){
+#   labels <- get_attr(x)
+#   x <- factor(x, levels = c("FALSE", "TRUE"))
+#   set_attr(x, labels[-match("class", names(labels))])
+# }
+
diff --git a/R/ds2dd_detailed.R b/R/ds2dd_detailed.R
index e01c9cd..13a515d 100644
--- a/R/ds2dd_detailed.R
+++ b/R/ds2dd_detailed.R
@@ -172,20 +172,20 @@ ds2dd_detailed <- function(data,
 
   if (convert.logicals) {
     # Labels/attributes are saved
-    labels <- lapply(data, \(.x){
-      get_attr(.x, attr = NULL)
-    })
+    # labels <- lapply(data, \(.x){
+    #   get_attr(.x, attr = NULL)
+    # })
 
-    no_attr <- data |>
+    data <- data |>
       ## Converts logical to factor, which overwrites attributes
-      dplyr::mutate(dplyr::across(dplyr::where(is.logical), forcats::as_factor))
+      dplyr::mutate(dplyr::across(dplyr::where(is.logical), as_factor))
 
     # Old attributes are appended
-    data <- purrr::imap(no_attr,\(.x,.i){
-      attributes(.x) <- c(attributes(.x),labels[[.i]])
-      .x
-    }) |>
-      dplyr::bind_cols()
+    # data <- purrr::imap(no_attr,\(.x,.i){
+    #   attributes(.x) <- c(attributes(.x),labels[[.i]])
+    #   .x
+    # }) |>
+    #   dplyr::bind_cols()
 
   }
 
@@ -262,7 +262,6 @@ ds2dd_detailed <- function(data,
     }
   }
 
-
   data_classes <- do.call(c, lapply(data, \(.x)class(.x)[1]))
 
   ## field_type
@@ -308,27 +307,15 @@ ds2dd_detailed <- function(data,
 
   ## choices
 
-  if (any(do.call(c, lapply(data, haven::is.labelled)))) {
-    factor_levels <- data |>
-      lapply(function(x) {
-        if (haven::is.labelled(x)) {
-          att <- haven_all_levels(x)
-          paste(paste(att, names(att), sep = ", "), collapse = " | ")
-        } else {
-          NA
-        }
-      }) |>
-      (\(x)do.call(c, x))()
-  } else {
-    factor_levels <- data |>
+  factor_levels <- data |>
       lapply(function(x) {
         if (is.factor(x)) {
-          ## Re-factors to avoid confusion with missing levels
-          ## Assumes all relevant levels are represented in the data
-          re_fac <- factor(x)
+          ## Custom function to ensure factor order and keep original values
+          ## Avoiding refactoring to keep as much information as possible
+          lvls <- sort(named_levels(x))
           paste(
-            paste(seq_along(levels(re_fac)),
-              levels(re_fac),
+            paste(lvls,
+              names(lvls),
               sep = ", "
             ),
             collapse = " | "
@@ -338,7 +325,6 @@ ds2dd_detailed <- function(data,
         }
       }) |>
       (\(x)do.call(c, x))()
-  }
 
   dd <-
     dd |> dplyr::mutate(
@@ -357,33 +343,6 @@ ds2dd_detailed <- function(data,
   )
 }
 
-#' Finish incomplete haven attributes substituting missings with values
-#'
-#' @param data haven labelled variable
-#'
-#' @return named vector
-#' @export
-#'
-#' @examples
-#' ds <- structure(c(1, 2, 3, 2, 10, 9),
-#'   labels = c(Unknown = 9, Refused = 10),
-#'   class = "haven_labelled"
-#' )
-#' haven::is.labelled(ds)
-#' attributes(ds)
-#' ds |> haven_all_levels()
-haven_all_levels <- function(data) {
-  stopifnot(haven::is.labelled(data))
-  if (length(attributes(data)$labels) == length(unique(data))) {
-    out <- attributes(data)$labels
-  } else {
-    att <- attributes(data)$labels
-    out <- c(unique(data[!data %in% att]), att) |>
-      stats::setNames(c(unique(data[!data %in% att]), names(att)))
-  }
-  out
-}
-
 
 #' Guess time variables based on naming pattern
 #'
@@ -567,50 +526,6 @@ numchar2fct <- function(data, numeric.threshold = 6, character.throshold = 6) {
     )
 }
 
-#' Extract attribute. Returns NA if none
-#'
-#' @param data vector
-#' @param attr attribute name
-#'
-#' @return character vector
-#' @export
-#'
-#' @examples
-#' attr(mtcars$mpg, "label") <- "testing"
-#' sapply(mtcars, get_attr)
-#' lapply(mtcars, \(.x)get_attr(.x, NULL))
-#' mtcars |>
-#'   numchar2fct(numeric.threshold = 6) |>
-#'   ds2dd_detailed()
-get_attr <- function(data, attr = NULL) {
-  if (is.null(attr)) {
-    attributes(data)
-  } else {
-    a <- attr(data, attr, exact = TRUE)
-    if (is.null(a)) {
-      NA
-    } else {
-      a
-    }
-  }
-}
 
 
-#' Set attributes for named attribute. Appends if attr is NULL
-#'
-#' @param data vector
-#' @param label label
-#' @param attr attribute name
-#'
-#' @return vector with attribute
-#' @export
-#'
-set_attr <- function(data, label, attr = NULL) {
-  if (is.null(attr)) {
-    attributes(data) <- c(attributes(data),label)
-  } else {
-    attr(data, attr) <- label
-  }
-  data
-}
 
diff --git a/man/as_factor.Rd b/man/as_factor.Rd
new file mode 100644
index 0000000..a681fc9
--- /dev/null
+++ b/man/as_factor.Rd
@@ -0,0 +1,51 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/as_factor.R
+\name{as_factor}
+\alias{as_factor}
+\alias{as_factor.logical}
+\alias{as_factor.numeric}
+\alias{as_factor.character}
+\alias{as_factor.haven_labelled}
+\alias{as_factor.labelled}
+\title{Convert labelled vectors to factors while preserving attributes}
+\usage{
+as_factor(x, ...)
+
+\method{as_factor}{logical}(x, ...)
+
+\method{as_factor}{numeric}(x, ...)
+
+\method{as_factor}{character}(x, ...)
+
+\method{as_factor}{haven_labelled}(x, ...)
+
+\method{as_factor}{labelled}(x, ...)
+}
+\arguments{
+\item{x}{Object to coerce to a factor.}
+
+\item{...}{Other arguments passed down to method.}
+}
+\description{
+This extends [forcats::as_factor()] as well as [haven::as_factor()], by appending
+original attributes except for "class" after converting to factor to avoid
+ta loss in case of rich formatted and labelled data.
+}
+\details{
+Please refer to parent functions for extended documentation.
+}
+\examples{
+# will preserve all attributes but class
+c(1, 4, 3, "A", 7, 8, 1) |> as_factor()
+structure(c(1, 2, 3, 2, 10, 9),
+  labels = c(Unknown = 9, Refused = 10)
+) |>
+  as_factor()
+
+structure(c(1, 2, 3, 2, 10, 9),
+  labels = c(Unknown = 9, Refused = 10),
+  class = "haven_labelled"
+) |>
+  as_factor()
+
+}
diff --git a/man/fct2num.Rd b/man/fct2num.Rd
new file mode 100644
index 0000000..2d6c99e
--- /dev/null
+++ b/man/fct2num.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/as_factor.R
+\name{fct2num}
+\alias{fct2num}
+\title{Allows conversion of factor to numeric values preserving original levels}
+\usage{
+fct2num(data)
+}
+\arguments{
+\item{data}{vector}
+}
+\value{
+numeric vector
+}
+\description{
+Allows conversion of factor to numeric values preserving original levels
+}
+\examples{
+c(1, 4, 3, "A", 7, 8, 1) |>
+as_factor() |> fct2num()
+
+structure(c(1, 2, 3, 2, 10, 9),
+  labels = c(Unknown = 9, Refused = 10),
+  class = "haven_labelled"
+) |>
+  as_factor() |>
+  fct2num()
+
+structure(c(1, 2, 3, 2, 10, 9),
+  labels = c(Unknown = 9, Refused = 10)
+) |>
+  as_factor() |>
+  fct2num()
+}
diff --git a/man/get_attr.Rd b/man/get_attr.Rd
index a0a5f5e..b6757f6 100644
--- a/man/get_attr.Rd
+++ b/man/get_attr.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ds2dd_detailed.R
+% Please edit documentation in R/as_factor.R
 \name{get_attr}
 \alias{get_attr}
 \title{Extract attribute. Returns NA if none}
diff --git a/man/haven_all_levels.Rd b/man/haven_all_levels.Rd
index 6805752..7eccfde 100644
--- a/man/haven_all_levels.Rd
+++ b/man/haven_all_levels.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ds2dd_detailed.R
+% Please edit documentation in R/as_factor.R
 \name{haven_all_levels}
 \alias{haven_all_levels}
 \title{Finish incomplete haven attributes substituting missings with values}
diff --git a/man/named_levels.Rd b/man/named_levels.Rd
new file mode 100644
index 0000000..e1481f6
--- /dev/null
+++ b/man/named_levels.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/as_factor.R
+\name{named_levels}
+\alias{named_levels}
+\title{Get named vector of factor levels and values}
+\usage{
+named_levels(data, label = "labels", na.label = NULL, na.value = 99)
+}
+\arguments{
+\item{data}{factor}
+
+\item{label}{character string of attribute with named vector of factor labels}
+}
+\value{
+named vector
+}
+\description{
+Get named vector of factor levels and values
+}
+\examples{
+structure(c(1, 2, 3, 2, 10, 9),
+  labels = c(Unknown = 9, Refused = 10),
+  class = "haven_labelled"
+) |> as_factor() |> named_levels()
+}
diff --git a/man/set_attr.Rd b/man/set_attr.Rd
index 8fcf43c..a7b3884 100644
--- a/man/set_attr.Rd
+++ b/man/set_attr.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ds2dd_detailed.R
+% Please edit documentation in R/as_factor.R
 \name{set_attr}
 \alias{set_attr}
 \title{Set attributes for named attribute. Appends if attr is NULL}