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(v1.3.0.9035) mdro() for EUCAST 3.2, examples cleanup

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dr. M.S. (Matthijs) Berends
2020-09-29 23:35:46 +02:00
parent 68e6e1e329
commit 4e0374af29
94 changed files with 1143 additions and 1165 deletions
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28
R/bug_drug_combinations.R
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@ -26,7 +26,7 @@
#' @inheritParams eucast_rules
#' @param combine_IR logical to indicate whether values R and I should be summed
#' @param add_ab_group logical to indicate where the group of the antimicrobials must be included as a first column
#' @param remove_intrinsic_resistant logical to indicate that rows with 100% resistance for all tested antimicrobials must be removed from the table
#' @param remove_intrinsic_resistant logical to indicate that rows and columns with 100% resistance for all tested antimicrobials must be removed from the table
#' @param FUN the function to call on the `mo` column to transform the microorganism IDs, defaults to [mo_shortname()]
#' @param translate_ab a character of length 1 containing column names of the [antibiotics] data set
#' @param ... arguments passed on to `FUN`
@ -45,13 +45,13 @@
#' format(x, translate_ab = "name (atc)")
#'
#' # Use FUN to change to transformation of microorganism codes
#' x <- bug_drug_combinations(example_isolates,
#' FUN = mo_gramstain)
#' bug_drug_combinations(example_isolates,
#' FUN = mo_gramstain)
#'
#' x <- bug_drug_combinations(example_isolates,
#' FUN = function(x) ifelse(x == as.mo("E. coli"),
#' "E. coli",
#' "Others"))
#' bug_drug_combinations(example_isolates,
#' FUN = function(x) ifelse(x == as.mo("E. coli"),
#' "E. coli",
#' "Others"))
#' }
bug_drug_combinations <- function(x,
col_mo = NULL,
@ -183,13 +183,12 @@ format.bug_drug_combinations <- function(x,
y <- y %pm>%
pm_left_join(mo_group, by = "ab")
}
y <<- y
y <- y %pm>%
pm_distinct(ab, .keep_all = TRUE) %pm>%
pm_select(-mo, -txt) %pm>%
# replace tidyr::pivot_wider() until here
remove_NAs()
select_ab_vars <- function(.data) {
.data[, c("ab_group", "ab_txt", colnames(.data)[!colnames(.data) %in% c("ab_group", "ab_txt", "ab")])]
}
@ -205,12 +204,19 @@ format.bug_drug_combinations <- function(x,
y <- y %pm>%
pm_select(-ab_group) %pm>%
pm_rename("Drug" = ab_txt)
colnames(y)[1] <- translate_AMR(colnames(y)[1], language = get_locale(), only_unknown = FALSE)
colnames(y)[1] <- translate_AMR(colnames(y)[1], language, only_unknown = FALSE)
} else {
y <- y %pm>%
pm_rename("Group" = ab_group,
"Drug" = ab_txt)
colnames(y)[1:2] <- translate_AMR(colnames(y)[1:2], language = get_locale(), only_unknown = FALSE)
}
if (!is.null(language)) {
colnames(y) <- translate_AMR(colnames(y), language, only_unknown = FALSE)
}
if (remove_intrinsic_resistant == TRUE) {
y <- y[, !sapply(y, function(col) all(col %like% "100", na.rm = TRUE) & !any(is.na(col))), drop = FALSE]
}
rownames(y) <- NULL