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Remove RSI from package, add extra MIC scale functions

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dr. M.S. (Matthijs) Berends
2023-12-03 11:34:48 +01:00
parent 6f417d0ef2
commit c7461766ce
21 changed files with 260 additions and 580 deletions
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108
R/ab_selectors.R
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@ -226,10 +226,6 @@ ab_class <- function(ab_class,
meet_criteria(ab_class, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec(NULL, only_sir_columns = only_sir_columns, ab_class_args = ab_class, only_treatable = only_treatable)
}
@ -242,10 +238,6 @@ ab_selector <- function(filter,
...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
# get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
# but it only takes a couple of milliseconds
@ -277,10 +269,6 @@ ab_selector <- function(filter,
aminoglycosides <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("aminoglycosides", only_sir_columns = only_sir_columns, only_treatable = only_treatable)
}
@ -288,10 +276,6 @@ aminoglycosides <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...
#' @export
aminopenicillins <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("aminopenicillins", only_sir_columns = only_sir_columns)
}
@ -299,10 +283,6 @@ aminopenicillins <- function(only_sir_columns = FALSE, ...) {
#' @export
antifungals <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("antifungals", only_sir_columns = only_sir_columns)
}
@ -310,10 +290,6 @@ antifungals <- function(only_sir_columns = FALSE, ...) {
#' @export
antimycobacterials <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("antimycobacterials", only_sir_columns = only_sir_columns)
}
@ -322,10 +298,6 @@ antimycobacterials <- function(only_sir_columns = FALSE, ...) {
betalactams <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("betalactams", only_sir_columns = only_sir_columns, only_treatable = only_treatable)
}
@ -334,10 +306,6 @@ betalactams <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
carbapenems <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("carbapenems", only_sir_columns = only_sir_columns, only_treatable = only_treatable)
}
@ -345,10 +313,6 @@ carbapenems <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
#' @export
cephalosporins <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("cephalosporins", only_sir_columns = only_sir_columns)
}
@ -356,10 +320,6 @@ cephalosporins <- function(only_sir_columns = FALSE, ...) {
#' @export
cephalosporins_1st <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("cephalosporins_1st", only_sir_columns = only_sir_columns)
}
@ -367,10 +327,6 @@ cephalosporins_1st <- function(only_sir_columns = FALSE, ...) {
#' @export
cephalosporins_2nd <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("cephalosporins_2nd", only_sir_columns = only_sir_columns)
}
@ -378,10 +334,6 @@ cephalosporins_2nd <- function(only_sir_columns = FALSE, ...) {
#' @export
cephalosporins_3rd <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("cephalosporins_3rd", only_sir_columns = only_sir_columns)
}
@ -389,10 +341,6 @@ cephalosporins_3rd <- function(only_sir_columns = FALSE, ...) {
#' @export
cephalosporins_4th <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("cephalosporins_4th", only_sir_columns = only_sir_columns)
}
@ -400,10 +348,6 @@ cephalosporins_4th <- function(only_sir_columns = FALSE, ...) {
#' @export
cephalosporins_5th <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("cephalosporins_5th", only_sir_columns = only_sir_columns)
}
@ -411,10 +355,6 @@ cephalosporins_5th <- function(only_sir_columns = FALSE, ...) {
#' @export
fluoroquinolones <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("fluoroquinolones", only_sir_columns = only_sir_columns)
}
@ -422,10 +362,6 @@ fluoroquinolones <- function(only_sir_columns = FALSE, ...) {
#' @export
glycopeptides <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("glycopeptides", only_sir_columns = only_sir_columns)
}
@ -433,10 +369,6 @@ glycopeptides <- function(only_sir_columns = FALSE, ...) {
#' @export
lincosamides <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("lincosamides", only_sir_columns = only_sir_columns)
}
@ -444,10 +376,6 @@ lincosamides <- function(only_sir_columns = FALSE, ...) {
#' @export
lipoglycopeptides <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("lipoglycopeptides", only_sir_columns = only_sir_columns)
}
@ -455,10 +383,6 @@ lipoglycopeptides <- function(only_sir_columns = FALSE, ...) {
#' @export
macrolides <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("macrolides", only_sir_columns = only_sir_columns)
}
@ -466,10 +390,6 @@ macrolides <- function(only_sir_columns = FALSE, ...) {
#' @export
oxazolidinones <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("oxazolidinones", only_sir_columns = only_sir_columns)
}
@ -477,10 +397,6 @@ oxazolidinones <- function(only_sir_columns = FALSE, ...) {
#' @export
penicillins <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("penicillins", only_sir_columns = only_sir_columns)
}
@ -489,10 +405,6 @@ penicillins <- function(only_sir_columns = FALSE, ...) {
polymyxins <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("polymyxins", only_sir_columns = only_sir_columns, only_treatable = only_treatable)
}
@ -500,10 +412,6 @@ polymyxins <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
#' @export
streptogramins <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("streptogramins", only_sir_columns = only_sir_columns)
}
@ -511,10 +419,6 @@ streptogramins <- function(only_sir_columns = FALSE, ...) {
#' @export
quinolones <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("quinolones", only_sir_columns = only_sir_columns)
}
@ -522,10 +426,6 @@ quinolones <- function(only_sir_columns = FALSE, ...) {
#' @export
tetracyclines <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("tetracyclines", only_sir_columns = only_sir_columns)
}
@ -533,10 +433,6 @@ tetracyclines <- function(only_sir_columns = FALSE, ...) {
#' @export
trimethoprims <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("trimethoprims", only_sir_columns = only_sir_columns)
}
@ -544,10 +440,6 @@ trimethoprims <- function(only_sir_columns = FALSE, ...) {
#' @export
ureidopenicillins <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if ("only_rsi_columns" %in% names(list(...))) {
deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
only_sir_columns <- list(...)$only_rsi_columns
}
ab_select_exec("ureidopenicillins", only_sir_columns = only_sir_columns)
}