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(v0.7.1.9102) lintr

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dr. M.S. (Matthijs) Berends
2019-10-11 17:21:02 +02:00
parent 59af355a89
commit 00cdb498a0
65 changed files with 620 additions and 812 deletions
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12
R/bug_drug_combinations.R
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@ -31,7 +31,7 @@
#' @param ... arguments passed on to \code{FUN}
#' @inheritParams rsi_df
#' @inheritParams base::formatC
#' @importFrom dplyr %>% rename group_by select mutate filter pull
#' @importFrom dplyr %>% rename group_by select mutate filter summarise ungroup
#' @importFrom tidyr spread
# @importFrom clean freq percentage
#' @details The function \code{format} calculates the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S.
@ -46,7 +46,7 @@
#' \donttest{
#' x <- bug_drug_combinations(example_isolates)
#' x
#' format(x)
#' format(x, translate_ab = "name (atc)")
#'
#' # Use FUN to change to transformation of microorganism codes
#' x <- bug_drug_combinations(example_isolates,
@ -76,7 +76,9 @@ bug_drug_combinations <- function(x,
x <- x %>%
as.data.frame(stringsAsFactors = FALSE) %>%
mutate(mo = x %>% pull(col_mo) %>% FUN(...)) %>%
mutate(mo = x %>%
pull(col_mo) %>%
FUN(...)) %>%
group_by(mo) %>%
select_if(is.rsi) %>%
gather("ab", "value", -mo) %>%
@ -112,7 +114,7 @@ format.bug_drug_combinations <- function(x,
if (remove_intrinsic_resistant == TRUE) {
x <- x %>% filter(R != total)
}
if (combine_IR == FALSE | combine_SI == TRUE) {
if (combine_SI == TRUE | combine_IR == FALSE) {
x$isolates <- x$R
} else {
x$isolates <- x$R + x$I
@ -121,7 +123,7 @@ format.bug_drug_combinations <- function(x,
give_ab_name <- function(ab, format, language) {
format <- tolower(format)
ab_txt <- rep(format, length(ab))
for (i in 1:length(ab_txt)) {
for (i in seq_len(length(ab_txt))) {
ab_txt[i] <- gsub("ab", ab[i], ab_txt[i])
ab_txt[i] <- gsub("cid", ab_cid(ab[i]), ab_txt[i])
ab_txt[i] <- gsub("group", ab_group(ab[i], language = language), ab_txt[i])