freq: fix na.rm in groups

NAMESPACE

@@ -173,6 +173,7 @@ importFrom(crayon,green)
 importFrom(crayon,italic)
 importFrom(crayon,red)
 importFrom(crayon,silver)
+importFrom(crayon,strip_style)
 importFrom(curl,nslookup)
 importFrom(data.table,as.data.table)
 importFrom(data.table,data.table)
@@ -190,6 +191,7 @@ importFrom(dplyr,desc)
 importFrom(dplyr,everything)
 importFrom(dplyr,filter)
 importFrom(dplyr,filter_all)
+importFrom(dplyr,filter_at)
 importFrom(dplyr,full_join)
 importFrom(dplyr,funs)
 importFrom(dplyr,group_by)

R/eucast.R

@@ -97,7 +97,7 @@
 #' @rdname EUCAST
 #' @export
 #' @importFrom dplyr %>% select pull mutate_at vars
-#' @importFrom crayon bold bgGreen bgYellow bgRed black green blue italic
+#' @importFrom crayon bold bgGreen bgYellow bgRed black green blue italic strip_style
 #' @return The input of \code{tbl}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{data.frame} with verbose info.
 #' @source
 #'   \itemize{
@@ -376,8 +376,8 @@ EUCAST_rules <- function(tbl,
       if (verbose == TRUE) {
         for (i in 1:length(cols)) {
           # add new row for every affected column
-          verbose_new <- data.frame(rule_type = rule[1],
-                                    rule_set = rule[2],
+          verbose_new <- data.frame(rule_type = strip_style(rule[1]),
+                                    rule_set = strip_style(rule[2]),
                                     force_to = to,
                                     found = length(before),
                                     changed = sum(before != after, na.rm = TRUE),

R/freq.R

@@ -59,7 +59,7 @@
 #' The function \code{top_freq} uses \code{\link[dplyr]{top_n}} internally and will include more than \code{n} rows if there are ties.
 #' @importFrom stats fivenum sd mad
 #' @importFrom grDevices boxplot.stats
-#' @importFrom dplyr %>% arrange arrange_at desc funs group_by mutate mutate_at n_distinct pull select summarise tibble ungroup vars
+#' @importFrom dplyr %>% arrange arrange_at desc filter_at funs group_by mutate mutate_at n_distinct pull select summarise tibble ungroup vars all_vars
 #' @importFrom utils browseVignettes
 #' @importFrom hms is.hms
 #' @importFrom crayon red green silver
@@ -206,6 +206,9 @@ frequency_tbl <- function(x,
         df <- x %>%
           group_by_at(vars(x.group_cols)) %>%
           summarise(count = n())
+        if (na.rm == TRUE) {
+          df <- df %>% filter_at(vars(cols), all_vars(!is.na(.)))
+        }
         if (!missing(sort.count)) {
           if (sort.count == TRUE) {
             df <- df %>% arrange_at(c(x.group, "count"), desc)

tests/testthat/test-freq.R

@@ -63,6 +63,8 @@ test_that("frequency table works", {
 
   # grouping variable
   expect_output(print(septic_patients %>% group_by(gender) %>% freq(hospital_id)))
+  expect_output(print(septic_patients %>% group_by(gender) %>% freq(amox, quote = TRUE)))
+  expect_output(print(septic_patients %>% group_by(gender) %>% freq(amox, markdown = TRUE)))
 
   # top 5
   expect_equal(