Add na.rm option to remove the strata variable in rows

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: visR
 Title: Clinical Graphs and Tables Adhering to Graphical Principles
-Version: 0.2.0.9003
+Version: 0.2.0.9004
 Authors@R: c(
     person(given = "Mark",
            family = "Baillie", 
@@ -101,6 +101,6 @@ VignetteBuilder:
 biocViews:
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.0
 LazyData: true
 Language: en-US

NEWS.md

@@ -11,6 +11,7 @@
 ### Other Updates
 * Stratifying variable names have been removed from legend in `visr.survfit()` figures, and the legend title now describes the stratifying variable(s). (#343)
 * `add_risktable` has a rowgutter argument to allow spacing between plot and risktables
+* The strata variable is now removed from the body of `tableone()` results. (#254) 
 
 * Improved documentation for `visr()` and other generic functions. (#301)
 

R/get_tableone.R

@@ -84,7 +84,9 @@ get_tableone.default <- function(data, strata = NULL, overall=TRUE, summary_func
   summary_FUN <- match.fun(summary_function)
 
   if(overall & !is.null(strata)){
-    overall_table1 <- get_tableone(data, strata = NULL, overall = FALSE, summary_function = summary_function)
+    overall_table1 <- get_tableone(data, strata = NULL, overall = FALSE, summary_function = summary_function) %>%
+      dplyr::filter(!(variable %in% strata))
+
     combine_dfs <- TRUE
   }
   else{

README.md

@@ -44,7 +44,7 @@ coverage](https://codecov.io/gh/openpharma/visR/branch/develop/graph/badge.svg)]
 [![pkgdown](https://github.com/openpharma/visR/actions/workflows/makedocs.yml/badge.svg)](https://github.com/openpharma/visR/actions/workflows/makedocs.yml)
 [![CRAN
 status](https://www.r-pkg.org/badges/version/visR)](https://CRAN.R-project.org/package=visR)
-<a href=https://github.com/pharmaR/riskmetric><img src=https://img.shields.io/badge/riskmetric-0.54-green></img></a>
+<a href=https://github.com/pharmaR/riskmetric><img src=https://img.shields.io/badge/riskmetric-0.53-green></img></a>
 <!-- badges: end -->
 
 ## Installation

inst/WORDLIST

@@ -12,6 +12,7 @@ Chisq
 Codecov
 Covid
 DT
+FFFFFF
 Kaplan
 Karnakata
 Lifecycle
@@ -65,19 +66,26 @@ io
 kable
 linetype
 magrittr
+md
 mskcc
+nums
 openpharma
 pkgdown
 psp
 pst
 purrr
 pvalue
+px
 repo
+rgba
+rgmrgujyos
 riskmetric
 risktable
 risktables
 rowgutter
 rtf
+sourcenote
+sourcenotes
 src
 statlist
 strata's
@@ -86,9 +94,11 @@ stype
 survdiff
 survfit
 tableone
+td
 th
 tibble
 tidycmprsk
+uncert
 visR's
 visualisation
 visualisations

tests/testthat/test-get_tableone.R

@@ -24,6 +24,9 @@
 #' T4.3 An error when the `summary_function` is a function not build for it
 #' T4.4 An error when the `summary_function` is `summarize_long`
 #' T4.5 No error when the `summary_function` is `summarize_short`
+#' T5. The tableone removes strata variables in rows that leads NA values
+#' T5.1 An error when the the table includes one strata variable
+#' T5.2 An error when the the table includes multiple strata variables
 
 # Requirement T1 ----------------------------------------------------------
 
@@ -39,18 +42,18 @@ testthat::test_that("T1.1. No error when `data` is of class `data.frame`", {
 testthat::test_that("T1.2. No error when `data` is of class `tibble`", {
 
   data <- dplyr::as_tibble(adtte)
-  
+
   testthat::expect_error(visR::get_tableone(data = data), NA)
 
 })
 
 testthat::test_that("T1.3 No error when `data` is of class `data.table`", {
 
   if (nzchar(find.package("data.table"))) {
-    
+
     data <- data.table::as.data.table(adtte)
     testthat::expect_error(visR::get_tableone(data = data), NA)
-    
+
   }
 })
 
@@ -85,18 +88,18 @@ testthat::test_that("T2.2 An error when `strata` is a string that is not a colna
 
 testthat::test_that("T2.3 Additional colnames in the tableone are the `strata` values (for one `strata`)", {
 
-  trtp_colnames <- colnames(visR::get_tableone(data = adtte, 
+  trtp_colnames <- colnames(visR::get_tableone(data = adtte,
                                                strata = c("TRTP")))[4:6]
   testthat::expect_equal(trtp_colnames, levels(adtte$TRTP))
 
 })
 
 testthat::test_that("T2.4 Additional colnames in the tableone are the crossproduct of all `strata` values (for more than one `strata`)", {
 
-  mapply_colnames <- c(mapply(function(x, y) paste(x, y, sep = "_"), 
+  mapply_colnames <- c(mapply(function(x, y) paste(x, y, sep = "_"),
                             levels(adtte$TRTP),
                             MoreArgs = list(levels(adtte$SEX))))
-  visR_colnames <- colnames(visR::get_tableone(data = adtte, 
+  visR_colnames <- colnames(visR::get_tableone(data = adtte,
                                                strata = c("TRTP", "SEX")))[4:9]
   testthat::expect_equal(mapply_colnames, visR_colnames)
 
@@ -107,30 +110,30 @@ testthat::test_that("T2.4 Additional colnames in the tableone are the crossprodu
 testthat::context("get_tableone - T3. The tableone includes expected columnnames")
 
 testthat::test_that("T3.1 Tableone by default includes columns `variable`, `statistic`, and `Total`", {
-  
+
   tableone_colnames <- colnames(visR::get_tableone(data = adtte))
-  
+
   testthat::expect_equal(tableone_colnames, c("variable", "statistic", "Total"))
 
 })
 
 testthat::test_that("T3.2 Tableone still includes the colum `Total` if `overall` is FALSE but no `strata` is given", {
-  
+
   tableone_colnames <- colnames(visR::get_tableone(data = adtte, overall = FALSE))
-  
+
   testthat::expect_equal(tableone_colnames, c("variable", "statistic", "Total"))
 
 })
 
 testthat::test_that("T3.3 Tableone does not include the colum `Total` if `overall` is FALSE and a `strata` is given", {
 
-  tblone_colnames <- colnames(visR::get_tableone(data = adtte, 
-                                                 overall = FALSE, 
+  tblone_colnames <- colnames(visR::get_tableone(data = adtte,
+                                                 overall = FALSE,
                                                  strata = c("TRTP")))
-  
-  testthat::expect_equal(tblone_colnames, 
+
+  testthat::expect_equal(tblone_colnames,
                          c("variable", "statistic", levels(adtte$TRTP)))
-  
+
 })
 
 # Requirement T4 ---------------------------------------------------------------
@@ -139,38 +142,69 @@ testthat::context("get_tableone - T4. The function only accepts suitable summary
 
 testthat::test_that("T4.1 An error when the `summary_function` is NULL", {
 
-  testthat::expect_error(visR::get_tableone(data = adtte, 
+  testthat::expect_error(visR::get_tableone(data = adtte,
                                             summary_function = NULL))
 
 })
 
 testthat::test_that("T4.2 An error when the `summary_function` is a string", {
 
-  testthat::expect_error(visR::get_tableone(data = adtte, 
+  testthat::expect_error(visR::get_tableone(data = adtte,
                                             summary_function = "A"))
 
 })
 
 testthat::test_that("T4.3 An error when the `summary_function` is a function not build for it", {
 
-  testthat::expect_error(visR::get_tableone(data = adtte, 
+  testthat::expect_error(visR::get_tableone(data = adtte,
                                             summary_function = sum))
 
 })
 
 testthat::test_that("T4.4 An error when the `summary_function` is `summarize_long`", {
 
-  testthat::expect_error(visR::get_tableone(data = adtte, 
+  testthat::expect_error(visR::get_tableone(data = adtte,
                                             summary_function = summarize_long))
 
 })
 
 
 testthat::test_that("T4.5 No error when the `summary_function` is `summarize_short`", {
 
-  testthat::expect_error(visR::get_tableone(data = adtte, 
+  testthat::expect_error(visR::get_tableone(data = adtte,
                                             summary_function = summarize_short), NA)
 
 })
 
+# Requirement T5 ---------------------------------------------------------------
+
+testthat::context("get_tableone - T5. The tableone removes strata variables in rows that leads NA values")
+
+testthat::test_that("T5.1 An error when the the table includes one strata variable", {
+
+  strata <- c("SEX")
+
+  table <- adtte %>%
+    visR::get_tableone(strata = strata)
+
+  testthat::expect_true(sum(strata %in% unique(table$variable)) == 0)
+
+})
+
+testthat::test_that("T5.2 An error when the the table includes multiple strata variables", {
+
+  strata <- c("SEX", "RACE")
+
+  table <- adtte %>%
+    visR::get_tableone(strata = strata)
+
+  testthat::expect_true(sum(strata %in% unique(table$variable)) == 0)
+
+  table <- adtte %>%
+    visR::get_tableone(strata = strata, overall = FALSE)
+
+  testthat::expect_true(sum(strata %in% unique(table$variable)) == 0)
+
+})
+
 # END OF CODE -------------------------------------------------------------