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mirror of https://github.com/msberends/AMR.git synced 2025-07-09 13:42:04 +02:00

(v1.1.0.9004) lose dependencies

This commit is contained in:
2020-05-16 13:05:47 +02:00
parent 9fce546901
commit 7f3da74b17
111 changed files with 3211 additions and 2345 deletions

View File

@ -32,7 +32,6 @@
#' @param ... arguments passed on to `FUN`
#' @inheritParams rsi_df
#' @inheritParams base::formatC
#' @importFrom dplyr %>% rename group_by select mutate filter summarise ungroup
#' @importFrom tidyr pivot_longer
#' @details The function [format()] calculates the resistance per bug-drug combination. Use `combine_IR = FALSE` (default) to test R vs. S+I and `combine_IR = TRUE` to test R+I vs. S.
#'
@ -74,13 +73,15 @@ bug_drug_combinations <- function(x,
stop("`col_mo` must be set.", call. = FALSE)
}
x <- x %>%
as.data.frame(stringsAsFactors = FALSE) %>%
mutate(mo = x %>%
pull(col_mo) %>%
FUN(...)) %>%
group_by(mo) %>%
select_if(is.rsi) %>%
select_rsi <- function(.data) {
.data[, c(col_mo, names(which(sapply(.data, is.rsi))))]
}
x <- x %>% as.data.frame(stringsAsFactors = FALSE)
x$mo <- FUN(x[, col_mo, drop = TRUE])
x <- x %>%
select_rsi() %>%
pivot_longer(-mo, names_to = "ab") %>%
group_by(mo, ab) %>%
summarise(S = sum(value == "S", na.rm = TRUE),
@ -93,9 +94,7 @@ bug_drug_combinations <- function(x,
structure(.Data = x, class = c("bug_drug_combinations", class(x)))
}
#' @importFrom dplyr everything rename %>% ungroup group_by summarise mutate_all arrange everything lag
#' @importFrom tidyr pivot_wider
#' @importFrom cleaner percentage
#' @exportMethod format.bug_drug_combinations
#' @export
#' @rdname bug_drug_combinations
@ -110,10 +109,10 @@ format.bug_drug_combinations <- function(x,
decimal.mark = getOption("OutDec"),
big.mark = ifelse(decimal.mark == ",", ".", ","),
...) {
x <- x %>% filter(total >= minimum)
x <- x %>% subset(total >= minimum)
if (remove_intrinsic_resistant == TRUE) {
x <- x %>% filter(R != total)
x <- x %>% subset(R != total)
}
if (combine_SI == TRUE | combine_IR == FALSE) {
x$isolates <- x$R
@ -137,26 +136,46 @@ format.bug_drug_combinations <- function(x,
ab_txt
}
remove_NAs <- function(.data) {
as.data.frame(sapply(.data, function(x) ifelse(is.na(x), "", x), simplify = FALSE))
}
create_var <- function(.data, ...) {
dots <- list(...)
for (i in seq_len(length(dots))) {
.data[, names(dots)[i]] <- dots[[i]]
}
.data
}
y <- x %>%
mutate(ab = as.ab(ab),
ab_txt = give_ab_name(ab = ab, format = translate_ab, language = language)) %>%
create_var(ab = as.ab(x$ab),
ab_txt = give_ab_name(ab = x$ab, format = translate_ab, language = language)) %>%
group_by(ab, ab_txt, mo) %>%
summarise(isolates = sum(isolates, na.rm = TRUE),
total = sum(total, na.rm = TRUE)) %>%
ungroup() %>%
mutate(txt = paste0(percentage(isolates / total, decimal.mark = decimal.mark, big.mark = big.mark),
" (", trimws(format(isolates, big.mark = big.mark)), "/",
trimws(format(total, big.mark = big.mark)), ")")) %>%
ungroup()
y <- y %>%
create_var(txt = paste0(percentage(y$isolates / y$total, decimal.mark = decimal.mark, big.mark = big.mark),
" (", trimws(format(y$isolates, big.mark = big.mark)), "/",
trimws(format(y$total, big.mark = big.mark)), ")")) %>%
select(ab, ab_txt, mo, txt) %>%
arrange(mo) %>%
pivot_wider(names_from = mo, values_from = txt) %>%
mutate_all(~ifelse(is.na(.), "", .)) %>%
mutate(ab_group = ab_group(ab, language = language),
ab_txt) %>%
select(ab_group, ab_txt, everything(), -ab) %>%
arrange(ab_group, ab_txt) %>%
mutate(ab_group = ifelse(ab_group != lag(ab_group) | is.na(lag(ab_group)), ab_group, ""))
remove_NAs()
select_ab_vars <- function(.data) {
.data[, c("ab_group", "ab_txt", colnames(.data)[!colnames(.data) %in% c("ab_group", "ab_txt", "ab")])]
}
y <- y %>%
create_var(ab_group = ab_group(y$ab, language = language)) %>%
select_ab_vars() %>%
arrange(ab_group, ab_txt)
y <- y %>%
create_var(ab_group = ifelse(y$ab_group != lag(y$ab_group) | is.na(lag(y$ab_group)), y$ab_group, ""))
if (add_ab_group == FALSE) {
y <- y %>% select(-ab_group) %>% rename("Drug" = ab_txt)
colnames(y)[1] <- translate_AMR(colnames(y)[1], language = get_locale(), only_unknown = FALSE)
@ -170,8 +189,7 @@ format.bug_drug_combinations <- function(x,
#' @exportMethod print.bug_drug_combinations
#' @export
#' @importFrom crayon blue
print.bug_drug_combinations <- function(x, ...) {
print(as.data.frame(x, stringsAsFactors = FALSE))
message(blue("NOTE: Use 'format()' on this result to get a publicable/printable format."))
message(font_blue("NOTE: Use 'format()' on this result to get a publicable/printable format."))
}