Merge pull request #7 from metrumresearchgroup/fix-nasum

Fix nasum

DESCRIPTION

@@ -32,7 +32,8 @@ Imports:
     hms,
     lubridate,
     purrr,
-    readr
+    readr,
+    tidyr
 Suggests:
     sessioninfo,
     knitr,

R/nasum.R

@@ -1,21 +1,25 @@
-#' Count Number of \code{NA} Values in List Items
+#' Display a count of NAs by column in a data.frame
 #'
 #' @description 
 #' \code{nasum} Count the number of \code{NA} values in each element of a list-like object.
 #' 
-#' @param x list of vector-like objects; e.g. a data frame
-#' @param simplify logical: coerce to vector result if possible
-#' 
-#' @usage nasum(x,simplify=TRUE)
+#' @param .df the count of NAs will be calculated for each column in this data 
+#' set, with any grouping variables retained
 #' 
 #' @details
 #' Arguments are passed to \code{simplify}, along with a function 
 #' that sums instances of \code{NA}.
 #' 
-#' @author Natalie Hsiang
+#' @author Tim Waterhouse
 #' 
 #' @examples
 #' nasum(Theoph)
 #' 
 #' @export
-nasum <- function(x, simplify=TRUE)sapply(x,FUN=function(y)sum(is.na(y)),simplify=simplify)
+nasum <- function(.df) {
+  .df %>% 
+    dplyr::summarize(dplyr::across(dplyr::everything(), ~ sum(is.na(.))), .groups = "keep") %>% 
+    tidyr::pivot_longer(-dplyr::group_cols(), values_to = "n_NA") %>% 
+    dplyr::ungroup() %>% 
+    dplyr::filter(n_NA > 0)
+}

R/nsub.R

@@ -10,4 +10,8 @@
 #' @author Samuel P Callisto, PhD
 #' 
 #' @export
-nsub <- function(.df, .id="USUBJID") {.df %>% dplyr::distinct({{ .id }}) %>% nrow()}
+nsub <- function(.df, .id) {
+
+  .df %>% dplyr::distinct({{ .id }}) %>% nrow()
+
+  }

tests/testthat/test-nasum.R

@@ -5,9 +5,6 @@ Theoph2$Time = NA_real_
 
 test_that("Finds NA within dataframe [MRG-NASM-001]", {
   Theoph_na <- nasum(Theoph2)
-  expect_equal(Theoph_na[1], setNames(3, "Subject"))
-  expect_equal(Theoph_na[2], setNames(0, "Wt"))
-  expect_equal(Theoph_na[3], setNames(0, "Dose"))
-  expect_equal(Theoph_na[4], setNames(132, "Time"))
-  expect_equal(Theoph_na[5], setNames(5, "conc"))
+  expect_equal(Theoph_na[1], dplyr::tibble(name = c("Subject", "Time", "conc")))
+  expect_equal(Theoph_na[2], dplyr::tibble(n_NA = c(3, 132, 5)))
 })