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freq: fix na.rm in groups

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-11-08 16:10:03 +01:00
parent 84e08f516a
commit 9be5e0318b
4 changed files with 11 additions and 4 deletions
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6
R/eucast.R
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@ -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),

5
R/freq.R
View File

@ -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)