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503 lines
20 KiB
R
Executable File
503 lines
20 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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#' Deprecated Functions
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#'
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#' These functions are so-called '[Deprecated]'. **They will be removed in a future release.** Using the functions will give a warning with the name of the function it has been replaced by (if there is one).
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#' @details All antibiotic class selectors (such as [carbapenems()], [aminoglycosides()]) can now be used for filtering as well, making all their accompanying `filter_*()` functions redundant (such as [filter_carbapenems()], [filter_aminoglycosides()]).
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#' @inheritSection lifecycle Retired Lifecycle
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#' @inheritSection AMR Read more on Our Website!
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#' @keywords internal
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#' @name AMR-deprecated
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#' @export
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p_symbol <- function(p, emptychar = " ") {
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.Deprecated(package = "AMR", new = "cleaner::p_symbol")
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p <- as.double(p)
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s <- rep(NA_character_, length(p))
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s[p <= 1] <- emptychar
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s[p <= 0.100] <- "."
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s[p <= 0.050] <- "*"
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s[p <= 0.010] <- "**"
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s[p <= 0.001] <- "***"
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s
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}
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#' @name AMR-deprecated
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#' @export
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filter_first_weighted_isolate <- function(x = NULL,
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col_date = NULL,
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col_patient_id = NULL,
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col_mo = NULL,
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...) {
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.Deprecated(old = "filter_first_weighted_isolate()",
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new = "filter_first_isolate()",
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package = "AMR")
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if (is_null_or_grouped_tbl(x)) {
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# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
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# is also fix for using a grouped df as input (a dot as first argument)
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x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
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}
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meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
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meet_criteria(col_date, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
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meet_criteria(col_patient_id, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
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meet_criteria(col_mo, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
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filter_first_isolate(x = x, col_date = col_date, col_patient_id = col_patient_id, col_mo = col_mo, ...)
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}
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#' @name AMR-deprecated
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#' @export
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key_antibiotics <- function(x = NULL,
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col_mo = NULL,
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universal_1 = guess_ab_col(x, "amoxicillin"),
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universal_2 = guess_ab_col(x, "amoxicillin/clavulanic acid"),
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universal_3 = guess_ab_col(x, "cefuroxime"),
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universal_4 = guess_ab_col(x, "piperacillin/tazobactam"),
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universal_5 = guess_ab_col(x, "ciprofloxacin"),
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universal_6 = guess_ab_col(x, "trimethoprim/sulfamethoxazole"),
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GramPos_1 = guess_ab_col(x, "vancomycin"),
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GramPos_2 = guess_ab_col(x, "teicoplanin"),
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GramPos_3 = guess_ab_col(x, "tetracycline"),
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GramPos_4 = guess_ab_col(x, "erythromycin"),
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GramPos_5 = guess_ab_col(x, "oxacillin"),
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GramPos_6 = guess_ab_col(x, "rifampin"),
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GramNeg_1 = guess_ab_col(x, "gentamicin"),
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GramNeg_2 = guess_ab_col(x, "tobramycin"),
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GramNeg_3 = guess_ab_col(x, "colistin"),
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GramNeg_4 = guess_ab_col(x, "cefotaxime"),
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GramNeg_5 = guess_ab_col(x, "ceftazidime"),
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GramNeg_6 = guess_ab_col(x, "meropenem"),
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warnings = TRUE,
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...) {
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.Deprecated(old = "key_antibiotics()",
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new = "key_antimicrobials()",
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package = "AMR")
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if (is_null_or_grouped_tbl(x)) {
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# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
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# is also fix for using a grouped df as input (a dot as first argument)
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x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
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}
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key_antimicrobials(x = x,
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col_mo = col_mo,
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universal = c(universal_1, universal_2, universal_3, universal_4, universal_5, universal_6),
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gram_negative = c(GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6),
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gram_positive = c(GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6),
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antifungal = NULL,
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only_rsi_columns = FALSE,
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...)
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}
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#' @name AMR-deprecated
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#' @export
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key_antibiotics_equal <- function(y,
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z,
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type = "keyantimicrobials",
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ignore_I = TRUE,
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points_threshold = 2,
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info = FALSE,
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na.rm = TRUE,
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...) {
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.Deprecated(old = "key_antibiotics_equal()",
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new = "antimicrobials_equal()",
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package = "AMR")
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antimicrobials_equal(y = y,
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z = z,
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type = type,
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ignore_I = ignore_I,
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points_threshold = points_threshold,
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info = info)
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}
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#' @name AMR-deprecated
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#' @export
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filter_ab_class <- function(x,
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ab_class,
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result = NULL,
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scope = "any",
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only_rsi_columns = FALSE,
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...) {
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.call_depth <- list(...)$`.call_depth`
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if (is.null(.call_depth)) {
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.call_depth <- 0
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}
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.x_name <- list(...)$`.x_name`
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if (is.null(.x_name)) {
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.x_name <- deparse(substitute(x))
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}
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.fn <- list(...)$`.fn`
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if (is.null(.fn)) {
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.fn <- "filter_ab_class"
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}
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.fn_old <- .fn
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# new way: using the ab selectors
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.fn <- gsub("filter_", "", .fn, fixed = TRUE)
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.fn <- gsub("^([1-5][a-z]+)_cephalosporins", "cephalosporins_\\1", .fn)
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if (missing(x) || is_null_or_grouped_tbl(x)) {
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# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
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# is also fix for using a grouped df as input (a dot as first argument)
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x <- get_current_data(arg_name = "x", call = -2 - .call_depth)
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.x_name <- "your_data"
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}
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meet_criteria(x, allow_class = "data.frame", .call_depth = .call_depth)
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meet_criteria(ab_class, allow_class = "character", has_length = 1, .call_depth = .call_depth)
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if (!is.null(result)) {
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# make result = "SI" works too:
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result <- toupper(unlist(strsplit(result, "")))
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}
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meet_criteria(result, allow_class = "character", has_length = c(1, 2, 3), is_in = c("S", "I", "R"), allow_NULL = TRUE, .call_depth = .call_depth)
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meet_criteria(scope, allow_class = "character", has_length = 1, is_in = c("all", "any"), .call_depth = .call_depth)
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1, .call_depth = .call_depth)
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if (is.null(result)) {
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result <- c("S", "I", "R")
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}
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# get e.g. carbapenems() from filter_carbapenems()
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fn <- get(.fn, envir = asNamespace("AMR"))
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if (scope == "any") {
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scope_fn <- any
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} else {
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scope_fn <- all
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}
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# be nice here, be VERY extensive about how the AB selectors have taken over this function
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deprecated_fn <- paste0(.fn, "(", ifelse(.fn == "ab_class", paste0("\"", ab_class, "\""), ""), ")",
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ifelse(length(result) > 1,
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paste0(", c(", paste0("\"", result, "\"", collapse = ", "), ")"),
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ifelse(is.null(result),
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"",
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paste0(" == \"", result, "\""))))
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if (.x_name == ".") {
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.x_name <- "your_data"
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}
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warning_(paste0("`", .fn_old, "()` is deprecated. Use the antibiotic selector `", .fn, "()` instead.\n",
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"In dplyr:\n",
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" - ", .x_name, " %>% filter(", scope, "(", deprecated_fn, "))\n",
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ifelse(length(result) > 1,
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paste0(" - ", .x_name, " %>% filter(", scope, "(",
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.fn, "(", ifelse(.fn == "ab_class", paste0("\"", ab_class, "\""), ""), ") == \"R\"))\n"),
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""),
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"In base R:\n",
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" - ", .x_name, "[", scope, "(", deprecated_fn, "), ]\n",
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ifelse(length(result) > 1,
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paste0(" - ", .x_name, "[", scope, "(",
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.fn, "(", ifelse(.fn == "ab_class", paste0("\"", ab_class, "\""), ""), ") == \"R\"), ]\n"),
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""),
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" - subset(", .x_name, ", ", scope, "(", deprecated_fn, "))",
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ifelse(length(result) > 1,
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paste0("\n - subset(", .x_name, ", ", scope, "(",
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.fn, "(", ifelse(.fn == "ab_class", paste0("\"", ab_class, "\""), ""), ") == \"R\"))"),
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"")),
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call = FALSE)
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if (.fn == "ab_class") {
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subset(x, scope_fn(fn(ab_class = ab_class), result))
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} else {
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subset(x, scope_fn(fn(), result))
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}
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}
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#' @name AMR-deprecated
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#' @export
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filter_aminoglycosides <- function(x,
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result = NULL,
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scope = "any",
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only_rsi_columns = FALSE,
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...) {
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filter_ab_class(x = x,
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ab_class = "aminoglycoside",
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result = result,
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scope = scope,
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only_rsi_columns = only_rsi_columns,
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.call_depth = 1,
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.fn = "filter_aminoglycosides",
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.x_name = deparse(substitute(x)),
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...)
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}
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#' @name AMR-deprecated
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#' @export
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filter_betalactams <- function(x,
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result = NULL,
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scope = "any",
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only_rsi_columns = FALSE,
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...) {
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filter_ab_class(x = x,
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ab_class = "carbapenem|cephalosporin|penicillin",
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result = result,
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scope = scope,
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only_rsi_columns = only_rsi_columns,
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.call_depth = 1,
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.fn = "filter_betalactams",
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.x_name = deparse(substitute(x)),
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...)
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}
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#' @name AMR-deprecated
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#' @export
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filter_carbapenems <- function(x,
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result = NULL,
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scope = "any",
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only_rsi_columns = FALSE,
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...) {
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filter_ab_class(x = x,
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ab_class = "carbapenem",
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result = result,
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scope = scope,
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only_rsi_columns = only_rsi_columns,
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.call_depth = 1,
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.fn = "filter_carbapenems",
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.x_name = deparse(substitute(x)),
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...)
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}
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#' @name AMR-deprecated
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#' @export
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filter_cephalosporins <- function(x,
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result = NULL,
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scope = "any",
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only_rsi_columns = FALSE,
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...) {
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filter_ab_class(x = x,
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ab_class = "cephalosporin",
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result = result,
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scope = scope,
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only_rsi_columns = only_rsi_columns,
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.call_depth = 1,
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.fn = "filter_cephalosporins",
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.x_name = deparse(substitute(x)),
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...)
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}
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#' @name AMR-deprecated
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#' @export
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filter_1st_cephalosporins <- function(x,
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result = NULL,
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scope = "any",
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only_rsi_columns = FALSE,
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...) {
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filter_ab_class(x = x,
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ab_class = "cephalosporins (1st gen.)",
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result = result,
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scope = scope,
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only_rsi_columns = only_rsi_columns,
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.call_depth = 1,
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.fn = "filter_1st_cephalosporins",
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.x_name = deparse(substitute(x)),
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...)
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}
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#' @name AMR-deprecated
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#' @export
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filter_2nd_cephalosporins <- function(x,
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result = NULL,
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scope = "any",
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only_rsi_columns = FALSE,
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...) {
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filter_ab_class(x = x,
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ab_class = "cephalosporins (2nd gen.)",
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result = result,
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scope = scope,
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only_rsi_columns = only_rsi_columns,
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.call_depth = 1,
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.fn = "filter_2nd_cephalosporins",
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.x_name = deparse(substitute(x)),
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...)
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}
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#' @name AMR-deprecated
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#' @export
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filter_3rd_cephalosporins <- function(x,
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result = NULL,
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scope = "any",
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only_rsi_columns = FALSE,
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...) {
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filter_ab_class(x = x,
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ab_class = "cephalosporins (3rd gen.)",
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result = result,
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scope = scope,
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only_rsi_columns = only_rsi_columns,
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.call_depth = 1,
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.fn = "filter_3rd_cephalosporins",
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.x_name = deparse(substitute(x)),
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...)
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}
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#' @name AMR-deprecated
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#' @export
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filter_4th_cephalosporins <- function(x,
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result = NULL,
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scope = "any",
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only_rsi_columns = FALSE,
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...) {
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filter_ab_class(x = x,
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ab_class = "cephalosporins (4th gen.)",
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result = result,
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scope = scope,
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only_rsi_columns = only_rsi_columns,
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.call_depth = 1,
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.fn = "filter_4th_cephalosporins",
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.x_name = deparse(substitute(x)),
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...)
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}
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#' @name AMR-deprecated
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#' @export
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filter_5th_cephalosporins <- function(x,
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result = NULL,
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scope = "any",
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only_rsi_columns = FALSE,
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...) {
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filter_ab_class(x = x,
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ab_class = "cephalosporins (5th gen.)",
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result = result,
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scope = scope,
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only_rsi_columns = only_rsi_columns,
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.call_depth = 1,
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.fn = "filter_5th_cephalosporins",
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.x_name = deparse(substitute(x)),
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...)
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}
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#' @name AMR-deprecated
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#' @export
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filter_fluoroquinolones <- function(x,
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result = NULL,
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scope = "any",
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only_rsi_columns = FALSE,
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...) {
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filter_ab_class(x = x,
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ab_class = "fluoroquinolone",
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result = result,
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scope = scope,
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only_rsi_columns = only_rsi_columns,
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.call_depth = 1,
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.fn = "filter_fluoroquinolones",
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.x_name = deparse(substitute(x)),
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...)
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}
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#' @name AMR-deprecated
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#' @export
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filter_glycopeptides <- function(x,
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result = NULL,
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scope = "any",
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only_rsi_columns = FALSE,
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...) {
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filter_ab_class(x = x,
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ab_class = "glycopeptide",
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result = result,
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scope = scope,
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only_rsi_columns = only_rsi_columns,
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.call_depth = 1,
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.fn = "filter_glycopeptides",
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.x_name = deparse(substitute(x)),
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...)
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}
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#' @name AMR-deprecated
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#' @export
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filter_macrolides <- function(x,
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result = NULL,
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scope = "any",
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only_rsi_columns = FALSE,
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...) {
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filter_ab_class(x = x,
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ab_class = "macrolide",
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result = result,
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scope = scope,
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only_rsi_columns = only_rsi_columns,
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.call_depth = 1,
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.fn = "filter_macrolides",
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.x_name = deparse(substitute(x)),
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...)
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}
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#' @name AMR-deprecated
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#' @export
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filter_oxazolidinones <- function(x,
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result = NULL,
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scope = "any",
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only_rsi_columns = FALSE,
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...) {
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filter_ab_class(x = x,
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ab_class = "oxazolidinone",
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result = result,
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scope = scope,
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only_rsi_columns = only_rsi_columns,
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.call_depth = 1,
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.fn = "filter_oxazolidinones",
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.x_name = deparse(substitute(x)),
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...)
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}
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#' @name AMR-deprecated
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#' @export
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filter_penicillins <- function(x,
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result = NULL,
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scope = "any",
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only_rsi_columns = FALSE,
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...) {
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filter_ab_class(x = x,
|
|
ab_class = "penicillin",
|
|
result = result,
|
|
scope = scope,
|
|
only_rsi_columns = only_rsi_columns,
|
|
.call_depth = 1,
|
|
.fn = "filter_penicillins",
|
|
.x_name = deparse(substitute(x)),
|
|
...)
|
|
}
|
|
|
|
#' @name AMR-deprecated
|
|
#' @export
|
|
filter_tetracyclines <- function(x,
|
|
result = NULL,
|
|
scope = "any",
|
|
only_rsi_columns = FALSE,
|
|
...) {
|
|
filter_ab_class(x = x,
|
|
ab_class = "tetracycline",
|
|
result = result,
|
|
scope = scope,
|
|
only_rsi_columns = only_rsi_columns,
|
|
.call_depth = 1,
|
|
.fn = "filter_tetracyclines",
|
|
.x_name = deparse(substitute(x)),
|
|
...)
|
|
}
|