Merge pull request #1791 from Gilead-BioStats/fix-1790

Add a function to cleanly convert Params to Labels.

NAMESPACE

@@ -1,5 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(validate_lParamLabels,"NULL")
+S3method(validate_lParamLabels,character)
+S3method(validate_lParamLabels,list)
 export("%>%")
 export(":=")
 export(.data)
@@ -22,6 +25,8 @@ export(MakeBounds)
 export(MakeCharts)
 export(MakeLongMeta)
 export(MakeMetric)
+export(MakeParamLabels)
+export(MakeParamLabelsList)
 export(MakeWideGroups)
 export(MakeWorkflowList)
 export(Make_Timeline)

R/Report_Setup.R

@@ -15,7 +15,6 @@
 #' - `StudyID` (character): The study ID.
 #' - `red_kris` (numeric): The number of red flags.
 #' - `amber_kris` (numeric): The number of amber flags.
-#'
 
 Report_Setup <- function(dfGroups = NULL, dfMetrics = NULL, dfResults = NULL) {
   output <- list()

R/Report_StudyInfo.R

@@ -14,7 +14,6 @@
 #'
 #' @keywords internal
 
-
 Report_StudyInfo <- function(
   lStudy,
   lStudyLabels = NULL
@@ -30,23 +29,27 @@ Report_StudyInfo <- function(
     )
   }
 
-  study_status_table <- lStudy %>% imap_dfr(function(value, param) {
-    data.frame(
-      Description = ifelse(
-        param %in% names(lStudyLabels),
-        lStudyLabels[[param]],
-        param
-      ),
-      Value = ifelse(
-        is.na(value),
-        value,
-        prettyNum(value, drop0trailing = TRUE)
+  lLabels <- MakeParamLabelsList(names(lStudy), lStudyLabels)
+  dfLabels <- data.frame(
+    Param = names(lLabels),
+    Description = unname(unlist(lLabels))
+  )
+
+  study_status_table <- data.frame(
+    Param = names(lStudy),
+    Value = unname(unlist(lStudy))
+  ) %>%
+    dplyr::left_join(dfLabels, by = "Param") %>%
+    dplyr::select(-"Param") %>%
+    dplyr::mutate(
+      Value = dplyr::if_else(
+        is.na(.data$Value),
+        .data$Value,
+        prettyNum(.data$Value, drop0trailing = TRUE)
       )
     )
-  })
 
   show_table <- study_status_table %>%
-    slice(1:5) %>%
     gsm_gt(id = "study_table")
 
   hide_table <- study_status_table %>%

R/aaa-shared.R

@@ -18,6 +18,7 @@ gloss_extra <- function(x) {
 #' @param dfGroups `r gloss_param("dfGroups")`
 #' @param dfInput `r gloss_param("dfInput")`
 #' @param lMetric `r gloss_param("lMetric")`
+#' @param lParamLabels `r gloss_param("lParamLabels")`
 #' @param bDebug `r gloss_param("bDebug")`
 #'
 #'

R/util-MakeParamLabels.R

@@ -0,0 +1,77 @@
+#' Create Labels for Parameters
+#'
+#' @description `r lifecycle::badge("stable")`
+#'
+#'   Convert a vector of parameters to labels in Title Case. `MakeParamLabels`
+#'   adds a `Labels` column to a `data.frame` that has a `Params` column (such
+#'   as `dfGroups`), while `MakeParamLabelsList` returns just the list of named
+#'   parameters.
+#'
+#' @inheritParams shared-params
+#'
+#' @return `dfGroups` with an added `Label` column, or a list of labeled
+#'   parameters.
+#'
+#' @examples
+#' head(gsm::reportingGroups)
+#' MakeParamLabels(head(gsm::reportingGroups))
+#' MakeParamLabels(
+#'   head(gsm::reportingGroups),
+#'   list(ParticipantCount = "Number of Participants")
+#' )
+#' MakeParamLabelsList(head(gsm::reportingGroups$Param))
+#'
+#' @export
+MakeParamLabels <- function(dfGroups, lParamLabels = NULL) {
+  chrParams <- sort(unique(dfGroups$Param))
+  labels <- MakeParamLabelsList(chrParams, lParamLabels)
+  dfLabels <- tibble::enframe(labels, name = "Param", value = "Label")
+  dfLabels$Label <- unlist(dfLabels$Label)
+  return(dplyr::left_join(dfGroups, dfLabels, by = "Param"))
+}
+
+#' @rdname MakeParamLabels
+#' @param chrParams A character vector of parameters, or a list that can be
+#'   coerced to a character vector.
+#' @export
+MakeParamLabelsList <- function(chrParams, lParamLabels = NULL) {
+  chrParams <- unlist(chrParams)
+  lParamLabels <- validate_lParamLabels(lParamLabels)
+  known_params <- intersect(chrParams, names(lParamLabels))
+  new_params <- setdiff(chrParams, names(lParamLabels))
+  labels <- setNames(as.list(chrParams), chrParams)
+  labels[known_params] <- lParamLabels[known_params]
+  labels[new_params] <- ParamToLabel(new_params)
+  return(labels)
+}
+
+validate_lParamLabels <- function(lParamLabels) {
+  UseMethod("validate_lParamLabels")
+}
+
+#' @export
+validate_lParamLabels.NULL <- function(lParamLabels) {
+  return(NULL)
+}
+
+#' @export
+validate_lParamLabels.list <- function(lParamLabels) {
+  if (length(lParamLabels) && rlang::is_named(lParamLabels)) {
+    # Uniquify.
+    return(lParamLabels[unique(names(lParamLabels))])
+  }
+  return(NULL)
+}
+
+#' @export
+validate_lParamLabels.character <- function(lParamLabels) {
+  return(validate_lParamLabels.list(as.list(lParamLabels)))
+}
+
+ParamToLabel <- function(chrParams) {
+  stringr::str_replace_all(chrParams, "[^A-Za-z0-9]", " ") %>%
+    stringr::str_replace_all("([[:lower:]])([[:upper:]])", "\\1 \\2") %>%
+    stringr::str_replace_all(
+      "(^| )([[:lower:]])", toupper
+    )
+}

_pkgdown.yml

@@ -68,6 +68,8 @@ reference:
      -  MakeCharts
      -  MakeMetric
      -  MakeLongMeta
+     -  MakeParamLabels
+     -  MakeParamLabelsList
      -  MakeWideGroups
      -  MakeWorkflowList
      -  ParseThreshold

man/glossary/lParamLabels.yaml

@@ -0,0 +1,3 @@
+class: list
+definition: >
+  Labels for parameters, with the parameters as names, and the label as value.

tests/testthat/test-Report_StudyInfo.R

@@ -30,7 +30,6 @@ test_that("Uses default study labels when lStudyLabels is NULL", {
   expect_true(any(grepl("Study Status", output)))
   expect_true(any(grepl("Show Details", output)))
   expect_true(any(grepl("Unique Study ID", output)))
-  expect_true(any(grepl("protocol_title", output)))
 })
 
 test_that("Uses custom study labels when lStudyLabels is provided", {

tests/testthat/test-util-MakeParamLabels.R

@@ -0,0 +1,126 @@
+test_that("MakeParamLabels generates labels", {
+  dfGroups <- data.frame(Param = c(
+    "param",
+    "Param",
+    "aParam",
+    "b param",
+    "c_param",
+    "paramID"
+  ))
+  dfGroupsMod <- MakeParamLabels(dfGroups)
+  expect_identical(
+    dfGroupsMod$Label,
+    c(
+      "Param",
+      "Param",
+      "A Param",
+      "B Param",
+      "C Param",
+      "Param ID"
+    )
+  )
+})
+
+test_that("MakeParamLabels uses supplied labels", {
+  dfGroups <- data.frame(Param = c(
+    "param",
+    "Param",
+    "aParam",
+    "b param",
+    "c_param",
+    "paramID"
+  ))
+  dfGroupsMod <- MakeParamLabels(
+    dfGroups,
+    list("aParam" = "alpha parameter", "c_param" = "Chi Parameter")
+  )
+  expect_identical(
+    dfGroupsMod$Label,
+    c(
+      "Param",
+      "Param",
+      "alpha parameter",
+      "B Param",
+      "Chi Parameter",
+      "Param ID"
+    )
+  )
+})
+
+test_that("MakeParamLabels works with character labels", {
+  dfGroups <- data.frame(Param = c(
+    "param",
+    "Param",
+    "aParam",
+    "b param",
+    "c_param",
+    "paramID"
+  ))
+  dfGroupsMod <- MakeParamLabels(
+    dfGroups,
+    c("aParam" = "alpha parameter", "c_param" = "Chi Parameter")
+  )
+  expect_identical(
+    dfGroupsMod$Label,
+    c(
+      "Param",
+      "Param",
+      "alpha parameter",
+      "B Param",
+      "Chi Parameter",
+      "Param ID"
+    )
+  )
+})
+
+test_that("MakeParamLabels ignores length-0 labels", {
+  dfGroups <- data.frame(Param = c(
+    "param",
+    "Param",
+    "aParam",
+    "b param",
+    "c_param",
+    "paramID"
+  ))
+  dfGroupsMod <- MakeParamLabels(
+    dfGroups,
+    list()
+  )
+  expect_identical(
+    dfGroupsMod$Label,
+    c(
+      "Param",
+      "Param",
+      "A Param",
+      "B Param",
+      "C Param",
+      "Param ID"
+    )
+  )
+})
+
+test_that("MakeParamLabels works when no labels overlap", {
+  dfGroups <- data.frame(Param = c(
+    "param",
+    "Param",
+    "aParam",
+    "b param",
+    "c_param",
+    "paramID"
+  ))
+  dfGroupsMod <- MakeParamLabels(
+    dfGroups,
+    list(new = "nothing")
+  )
+  expect_identical(
+    dfGroupsMod$Label,
+    c(
+      "Param",
+      "Param",
+      "A Param",
+      "B Param",
+      "C Param",
+      "Param ID"
+    )
+  )
+})