AMR/R/deprecated.R

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will be removed in a future release.** Using the functions will give a warning with the name of the function it has been replaced by (if there is one).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