New argument zeros in ranktransform() (#573)

* init

* minor

* fix lints

Author: etiennebacher

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: datawizard
 Title: Easy Data Wrangling and Statistical Transformations
-Version: 0.13.0.18
+Version: 0.13.0.19
 Authors@R: c(
     person("Indrajeet", "Patil", , "patilindrajeet.science@gmail.com", role = "aut",
            comment = c(ORCID = "0000-0003-1995-6531")),

NEWS.md

@@ -39,6 +39,9 @@ CHANGES
 * `data_summary()` also accepts the results of `bayestestR::ci()` as summary
   function (#483).
 
+* `ranktransform()` has a new argument `zeros` to determine how zeros should be
+  handled when `sign = TRUE` (#573).
+
 BUG FIXES
 
 * `describe_distribution()` no longer errors if the sample was too sparse to compute

R/ranktransform.R

@@ -10,6 +10,9 @@
 #' @param method Treatment of ties. Can be one of `"average"` (default),
 #'   `"first"`, `"last"`, `"random"`, `"max"` or `"min"`. See [rank()] for
 #'   details.
+#' @param zeros How to handle zeros. If `"na"` (default), they are marked as
+#' `NA`. If `"signrank"`, they are kept during the ranking and marked as zeros.
+#' This is only used when `sign = TRUE`.
 #' @param ... Arguments passed to or from other methods.
 #' @inheritParams extract_column_names
 #' @inheritParams standardize.data.frame
@@ -19,8 +22,11 @@
 #' @examples
 #' ranktransform(c(0, 1, 5, -5, -2))
 #'
-#' # Won't work
-#' # ranktransform(c(0, 1, 5, -5, -2), sign = TRUE)
+#' # By default, zeros are converted to NA
+#' suppressWarnings(
+#'   ranktransform(c(0, 1, 5, -5, -2), sign = TRUE)
+#' )
+#' ranktransform(c(0, 1, 5, -5, -2), sign = TRUE, zeros = "signrank")
 #'
 #' head(ranktransform(trees))
 #' @return A rank-transformed object.
@@ -38,13 +44,20 @@ ranktransform <- function(x, ...) {
 ranktransform.numeric <- function(x,
                                   sign = FALSE,
                                   method = "average",
+                                  zeros = "na",
                                   verbose = TRUE,
                                   ...) {
   # no change if all values are `NA`s
   if (all(is.na(x))) {
     return(x)
   }
 
+  zeros <- match.arg(zeros, c("na", "signrank"))
+  method <- match.arg(
+    method,
+    c("average", "first", "last", "random", "max", "min")
+  )
+
   # Warning if only one value and return early
   if (insight::has_single_value(x)) {
     if (is.null(names(x))) {
@@ -54,7 +67,13 @@ ranktransform.numeric <- function(x,
     }
 
     if (verbose) {
-      insight::format_warning(paste0("Variable `", name, "` contains only one unique value and will not be normalized."))
+      insight::format_warning(
+        paste0(
+          "Variable `",
+          name,
+          "` contains only one unique value and will not be normalized."
+        )
+      )
     }
 
     return(x)
@@ -70,16 +89,31 @@ ranktransform.numeric <- function(x,
     }
 
     if (verbose) {
-      insight::format_warning(paste0("Variable `", name, "` contains only two different values. Consider converting it to a factor."))
+      # nolint
+      insight::format_warning(
+        paste0(
+          "Variable `",
+          name,
+          "` contains only two different values. Consider converting it to a factor."
+        )
+      )
     }
   }
 
-
   if (sign) {
-    ZEROES <- x == 0
-    if (any(ZEROES) && verbose) insight::format_warning("Zeros detected. These cannot be sign-rank transformed.")
-    out <- rep(NA, length(x))
-    out[!ZEROES] <- sign(x[!ZEROES]) * rank(abs(x[!ZEROES]), ties.method = method, na.last = "keep")
+    if (zeros == "na") {
+      out <- rep(NA, length(x))
+      ZEROES <- x == 0
+      if (any(ZEROES) && verbose) {
+        insight::format_warning("Zeros detected. These cannot be sign-rank transformed.") # nolint
+      }
+      out[!ZEROES] <- sign(x[!ZEROES]) * rank(abs(x[!ZEROES]),
+        ties.method = method,
+        na.last = "keep"
+      )
+    } else if (zeros == "signrank") {
+      out <- sign(x) * rank(abs(x), ties.method = method, na.last = "keep")
+    }
   } else {
     out <- rank(x, ties.method = method, na.last = "keep")
   }
@@ -102,6 +136,7 @@ ranktransform.grouped_df <- function(x,
                                      method = "average",
                                      ignore_case = FALSE,
                                      regex = FALSE,
+                                     zeros = "na",
                                      verbose = TRUE,
                                      ...) {
   info <- attributes(x)
@@ -143,6 +178,7 @@ ranktransform.data.frame <- function(x,
                                      method = "average",
                                      ignore_case = FALSE,
                                      regex = FALSE,
+                                     zeros = "na",
                                      verbose = TRUE,
                                      ...) {
   # evaluate arguments

man/ranktransform.Rd

@@ -46,6 +46,22 @@ test_that("signed rank works as expected", {
   ))))
 })
 
+test_that("argument 'zeros' works", {
+  x <- c(-1, 0, 2, -3, 4)
+  expect_warning(
+    ranktransform(x, sign = TRUE),
+    "cannot be sign-rank"
+  )
+  expect_identical(
+    ranktransform(x, sign = TRUE, zeros = "signrank"),
+    c(-2, 0, 3, -4, 5)
+  )
+  expect_error(
+    ranktransform(x, sign = TRUE, zeros = "foo"),
+    "should be one of"
+  )
+})
+
 test_that("ranktransform works with data frames", {
   set.seed(123)
   expect_snapshot(ranktransform(BOD))
@@ -58,9 +74,9 @@ test_that("ranktransform works with data frames (grouped data)", {
   skip_if_not_installed("poorman")
 
   set.seed(123)
-  value1 <- sample(1:20, 9, replace = TRUE)
+  value1 <- sample.int(20, 9, replace = TRUE)
   set.seed(456)
-  value2 <- sample(1:20, 9, replace = TRUE)
+  value2 <- sample.int(20, 9, replace = TRUE)
 
   test_df <- data.frame(
     id = rep(c("A", "B", "C"), each = 3),
@@ -69,6 +85,7 @@ test_that("ranktransform works with data frames (grouped data)", {
     stringsAsFactors = FALSE
   )
 
+  # nolint start: nested_pipe_linter
   expect_identical(
     test_df %>%
       poorman::group_by(id) %>%
@@ -81,6 +98,7 @@ test_that("ranktransform works with data frames (grouped data)", {
       stringsAsFactors = FALSE
     )
   )
+  # nolint end
 })
 
 
@@ -99,6 +117,7 @@ test_that("ranktransform works with data frames containing NAs (grouped data)",
     stringsAsFactors = FALSE
   )
 
+  # nolint start: nested_pipe_linter
   expect_identical(
     test_df %>%
       poorman::group_by(id) %>%
@@ -111,6 +130,7 @@ test_that("ranktransform works with data frames containing NAs (grouped data)",
       stringsAsFactors = FALSE
     )
   )
+  # nolint end
 })
 
 # select helpers ------------------------------