AMR/R/ab_class_selectors.R

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R

# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
# #
# 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. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
#' Antibiotic Class Selectors
#'
#' These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.
#' @inheritSection lifecycle Stable Lifecycle
#' @param ab_class an antimicrobial class, such as `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value.
#' @param only_rsi_columns a [logical] to indicate whether only columns of class `<rsi>` must be selected (defaults to `FALSE`), see [as.rsi()]
#' @details
#' These functions can be used in data set calls for selecting columns and filtering rows. They are heavily inspired by the [Tidyverse selection helpers][tidyselect::language] such as [`everything()`][tidyselect::everything()], but also work in base \R and not only in `dplyr` verbs. Nonetheless, they are very convenient to use with `dplyr` functions such as [`select()`][dplyr::select()], [`filter()`][dplyr::filter()] and [`summarise()`][dplyr::summarise()], see *Examples*.
#'
#' All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) in the [antibiotics] data set. This means that a selector such as [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. Use the [ab_class()] function to filter/select on a manually defined antibiotic class.
#'
#' @section Full list of supported agents:
#'
#' `r paste0("* ", sapply(c("AMINOGLYCOSIDES", "AMINOPENICILLINS", "BETALACTAMS", "CARBAPENEMS", "CEPHALOSPORINS", "CEPHALOSPORINS_1ST", "CEPHALOSPORINS_2ND", "CEPHALOSPORINS_3RD", "CEPHALOSPORINS_4TH", "CEPHALOSPORINS_5TH", "FLUOROQUINOLONES", "GLYCOPEPTIDES", "LINCOSAMIDES", "LIPOGLYCOPEPTIDES", "MACROLIDES", "OXAZOLIDINONES", "PENICILLINS", "POLYMYXINS", "STREPTOGRAMINS", "QUINOLONES", "TETRACYCLINES", "UREIDOPENICILLINS"), function(x) paste0("``", tolower(x), "()`` can select ", vector_and(paste0(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), " (", eval(parse(text = x), envir = asNamespace("AMR")), ")"), quotes = FALSE))), "\n", collapse = "")`
#' @rdname antibiotic_class_selectors
#' @name antibiotic_class_selectors
#' @export
#' @inheritSection AMR Reference Data Publicly Available
#' @inheritSection AMR Read more on Our Website!
#' @examples
#' # `example_isolates` is a data set available in the AMR package.
#' # See ?example_isolates.
#'
#' # base R ------------------------------------------------------------------
#'
#' # select columns 'IPM' (imipenem) and 'MEM' (meropenem)
#' example_isolates[, carbapenems()]
#'
#' # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
#' example_isolates[, c("mo", aminoglycosides())]
#'
#' # filter using any() or all()
#' example_isolates[any(carbapenems() == "R"), ]
#' subset(example_isolates, any(carbapenems() == "R"))
#'
#' # filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
#' example_isolates[any(carbapenems()), ]
#' example_isolates[all(carbapenems()), ]
#'
#' # filter with multiple antibiotic selectors using c()
#' example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]
#'
#' # filter + select in one go: get penicillins in carbapenems-resistant strains
#' example_isolates[any(carbapenems() == "R"), penicillins()]
#'
#'
#' # dplyr -------------------------------------------------------------------
#' \donttest{
#' if (require("dplyr")) {
#'
#' # get AMR for all aminoglycosides e.g., per hospital:
#' example_isolates %>%
#' group_by(hospital_id) %>%
#' summarise(across(aminoglycosides(), resistance))
#'
#' # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
#' example_isolates %>%
#' select(carbapenems())
#'
#' # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
#' example_isolates %>%
#' select(mo, aminoglycosides())
#'
#' # any() and all() work in dplyr's filter() too:
#' example_isolates %>%
#' filter(any(aminoglycosides() == "R"),
#' all(cephalosporins_2nd() == "R"))
#'
#' # also works with c():
#' example_isolates %>%
#' filter(any(c(carbapenems(), aminoglycosides()) == "R"))
#'
#' # not setting any/all will automatically apply all():
#' example_isolates %>%
#' filter(aminoglycosides() == "R")
#' #> i Assuming a filter on all 4 aminoglycosides.
#'
#' # this will select columns 'mo' and all antimycobacterial drugs ('RIF'):
#' example_isolates %>%
#' select(mo, ab_class("mycobact"))
#'
#' # get bug/drug combinations for only macrolides in Gram-positives:
#' example_isolates %>%
#' filter(mo_is_gram_positive()) %>%
#' select(mo, macrolides()) %>%
#' bug_drug_combinations() %>%
#' format()
#'
#' data.frame(some_column = "some_value",
#' J01CA01 = "S") %>% # ATC code of ampicillin
#' select(penicillins()) # only the 'J01CA01' column will be selected
#'
#'
#' # with dplyr 1.0.0 and higher (that adds 'across()'), this is all equal:
#' example_isolates[carbapenems() == "R", ]
#' example_isolates %>% filter(carbapenems() == "R")
#' example_isolates %>% filter(across(carbapenems(), ~.x == "R"))
#' }
#' }
ab_class <- function(ab_class,
only_rsi_columns = FALSE) {
meet_criteria(ab_class, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector(NULL, only_rsi_columns = only_rsi_columns, ab_class = ab_class)
}
#' @rdname antibiotic_class_selectors
#' @export
aminoglycosides <- function(only_rsi_columns = FALSE) {
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector("aminoglycosides", only_rsi_columns = only_rsi_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
aminopenicillins <- function(only_rsi_columns = FALSE) {
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector("aminopenicillins", only_rsi_columns = only_rsi_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
betalactams <- function(only_rsi_columns = FALSE) {
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector("betalactams", only_rsi_columns = only_rsi_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
carbapenems <- function(only_rsi_columns = FALSE) {
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector("carbapenems", only_rsi_columns = only_rsi_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
cephalosporins <- function(only_rsi_columns = FALSE) {
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector("cephalosporins", only_rsi_columns = only_rsi_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
cephalosporins_1st <- function(only_rsi_columns = FALSE) {
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector("cephalosporins_1st", only_rsi_columns = only_rsi_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
cephalosporins_2nd <- function(only_rsi_columns = FALSE) {
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector("cephalosporins_2nd", only_rsi_columns = only_rsi_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
cephalosporins_3rd <- function(only_rsi_columns = FALSE) {
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector("cephalosporins_3rd", only_rsi_columns = only_rsi_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
cephalosporins_4th <- function(only_rsi_columns = FALSE) {
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector("cephalosporins_4th", only_rsi_columns = only_rsi_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
cephalosporins_5th <- function(only_rsi_columns = FALSE) {
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector("cephalosporins_5th", only_rsi_columns = only_rsi_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
fluoroquinolones <- function(only_rsi_columns = FALSE) {
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector("fluoroquinolones", only_rsi_columns = only_rsi_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
glycopeptides <- function(only_rsi_columns = FALSE) {
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector("glycopeptides", only_rsi_columns = only_rsi_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
lincosamides <- function(only_rsi_columns = FALSE) {
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector("lincosamides", only_rsi_columns = only_rsi_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
lipoglycopeptides <- function(only_rsi_columns = FALSE) {
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector("lipoglycopeptides", only_rsi_columns = only_rsi_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
macrolides <- function(only_rsi_columns = FALSE) {
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector("macrolides", only_rsi_columns = only_rsi_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
oxazolidinones <- function(only_rsi_columns = FALSE) {
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector("oxazolidinones", only_rsi_columns = only_rsi_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
penicillins <- function(only_rsi_columns = FALSE) {
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector("penicillins", only_rsi_columns = only_rsi_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
polymyxins <- function(only_rsi_columns = FALSE) {
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector("polymyxins", only_rsi_columns = only_rsi_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
streptogramins <- function(only_rsi_columns = FALSE) {
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector("streptogramins", only_rsi_columns = only_rsi_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
quinolones <- function(only_rsi_columns = FALSE) {
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector("quinolones", only_rsi_columns = only_rsi_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
tetracyclines <- function(only_rsi_columns = FALSE) {
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector("tetracyclines", only_rsi_columns = only_rsi_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
ureidopenicillins <- function(only_rsi_columns = FALSE) {
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
ab_selector("ureidopenicillins", only_rsi_columns = only_rsi_columns)
}
ab_selector <- function(function_name,
only_rsi_columns,
ab_class = NULL) {
# 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
vars_df <- get_current_data(arg_name = NA, call = -3)
# to improve speed, get_column_abx() will only run once when e.g. in a select or group call
ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE)
if (length(ab_in_data) == 0) {
message_("No antimicrobial agents found in the data.")
return(NULL)
}
if (is.null(ab_class)) {
# their upper case equivalent are vectors with class <ab>, created in data-raw/_internals.R
abx <- get(toupper(function_name), envir = asNamespace("AMR"))
ab_group <- function_name
examples <- paste0(" (such as ", vector_or(ab_name(sample(abx, size = min(2, length(abx)), replace = FALSE),
tolower = TRUE,
language = NULL),
quotes = FALSE), ")")
} else {
# this for the 'manual' ab_class() function
abx <- subset(AB_lookup,
group %like% ab_class |
atc_group1 %like% ab_class |
atc_group2 %like% ab_class)$ab
ab_group <- find_ab_group(ab_class)
function_name <- "ab_class"
examples <- paste0(" (such as ", find_ab_names(ab_class, 2), ")")
}
# get the columns with a group names in the chosen ab class
agents <- ab_in_data[names(ab_in_data) %in% abx]
if (message_not_thrown_before(paste0(function_name, ".", paste(pkg_env$get_column_abx.out, collapse = "|")))) {
if (length(agents) == 0) {
message_("No antimicrobial agents of class '", ab_group, "' found", examples, ".")
} else {
agents_formatted <- paste0("'", font_bold(agents, collapse = NULL), "'")
agents_names <- ab_name(names(agents), tolower = TRUE, language = NULL)
need_name <- generalise_antibiotic_name(agents) != generalise_antibiotic_name(agents_names)
agents_formatted[need_name] <- paste0(agents_formatted[need_name], " (", agents_names[need_name], ")")
message_("For `", function_name, "(",
ifelse(function_name == "ab_class",
paste0("\"", ab_class, "\""),
""),
")` using ",
ifelse(length(agents) == 1, "column ", "columns "),
vector_and(agents_formatted, quotes = FALSE, sort = FALSE))
}
remember_thrown_message(paste0(function_name, ".", paste(pkg_env$get_column_abx.out, collapse = "|")))
}
if (!is.null(attributes(vars_df)$type) &&
attributes(vars_df)$type %in% c("dplyr_cur_data_all", "base_R") &&
!any(as.character(sys.calls()) %like% paste0("(across|if_any|if_all)\\((c\\()?[a-z(), ]*", function_name))) {
structure(unname(agents),
class = c("ab_selector", "character"))
} else {
# don't return with "ab_selector" class if method is a dplyr selector,
# dplyr::select() will complain:
# > Subscript has the wrong type `ab_selector`.
# > It must be numeric or character.
unname(agents)
}
}
#' @method c ab_selector
#' @export
#' @noRd
c.ab_selector <- function(...) {
structure(unlist(lapply(list(...), as.character)),
class = c("ab_selector", "character"))
}
all_any_ab_selector <- function(type, ..., na.rm = TRUE) {
cols_ab <- c(...)
result <- cols_ab[toupper(cols_ab) %in% c("R", "S", "I")]
if (length(result) == 0) {
message_("Filtering ", type, " of columns ", vector_and(font_bold(cols_ab, collapse = NULL), quotes = "'"), ' to contain value "R", "S" or "I"')
result <- c("R", "S", "I")
}
cols_ab <- cols_ab[!cols_ab %in% result]
df <- get_current_data(arg_name = NA, call = -3)
if (type == "all") {
scope_fn <- all
} else {
scope_fn <- any
}
x_transposed <- as.list(as.data.frame(t(df[, cols_ab, drop = FALSE]), stringsAsFactors = FALSE))
vapply(FUN.VALUE = logical(1),
X = x_transposed,
FUN = function(y) scope_fn(y %in% result, na.rm = na.rm),
USE.NAMES = FALSE)
}
#' @method all ab_selector
#' @export
#' @noRd
all.ab_selector <- function(..., na.rm = FALSE) {
# this is all() for
all_any_ab_selector("all", ..., na.rm = na.rm)
}
#' @method any ab_selector
#' @export
#' @noRd
any.ab_selector <- function(..., na.rm = FALSE) {
all_any_ab_selector("any", ..., na.rm = na.rm)
}
#' @method all ab_selector_any_all
#' @export
#' @noRd
all.ab_selector_any_all <- function(..., na.rm = FALSE) {
# this is all() on a logical vector from `==.ab_selector` or `!=.ab_selector`
# e.g., example_isolates %>% filter(all(carbapenems() == "R"))
# so just return the vector as is, only correcting for na.rm
out <- unclass(c(...))
if (na.rm == TRUE) {
out <- out[!is.na(out)]
}
out
}
#' @method any ab_selector_any_all
#' @export
#' @noRd
any.ab_selector_any_all <- function(..., na.rm = FALSE) {
# this is any() on a logical vector from `==.ab_selector` or `!=.ab_selector`
# e.g., example_isolates %>% filter(any(carbapenems() == "R"))
# so just return the vector as is, only correcting for na.rm
out <- unclass(c(...))
if (na.rm == TRUE) {
out <- out[!is.na(out)]
}
out
}
#' @method == ab_selector
#' @export
#' @noRd
`==.ab_selector` <- function(e1, e2) {
calls <- as.character(match.call())
fn_name <- calls[2]
# keep only the ... in c(...)
fn_name <- gsub("^(c\\()(.*)(\\))$", "\\2", fn_name)
if (is_any(fn_name)) {
type <- "any"
} else if (is_all(fn_name)) {
type <- "all"
} else {
type <- "all"
if (length(e1) > 1) {
message_("Assuming a filter on ", type, " ", length(e1), " ", gsub("[\\(\\)]", "", fn_name),
". Wrap around `all()` or `any()` to prevent this note.")
}
}
structure(all_any_ab_selector(type = type, e1, e2),
class = c("ab_selector_any_all", "logical"))
}
#' @method != ab_selector
#' @export
#' @noRd
`!=.ab_selector` <- function(e1, e2) {
calls <- as.character(match.call())
fn_name <- calls[2]
# keep only the ... in c(...)
fn_name <- gsub("^(c\\()(.*)(\\))$", "\\2", fn_name)
if (is_any(fn_name)) {
type <- "any"
} else if (is_all(fn_name)) {
type <- "all"
} else {
type <- "all"
if (length(e1) > 1) {
message_("Assuming a filter on ", type, " ", length(e1), " ", gsub("[\\(\\)]", "", fn_name),
". Wrap around `all()` or `any()` to prevent this note.")
}
}
# this is `!=`, so turn around the values
rsi <- c("R", "S", "I")
e2 <- rsi[rsi != e2]
structure(all_any_ab_selector(type = type, e1, e2),
class = c("ab_selector_any_all", "logical"))
}
is_any <- function(el1) {
syscall <- paste0(trimws(deparse(sys.calls()[[1]])), collapse = " ")
el1 <- gsub("(.*),.*", "\\1", el1)
syscall %like% paste0("[^_a-zA-Z0-9]any\\(", "(c\\()?", el1)
}
is_all <- function(el1) {
syscall <- paste0(trimws(deparse(sys.calls()[[1]])), collapse = " ")
el1 <- gsub("(.*),.*", "\\1", el1)
syscall %like% paste0("[^_a-zA-Z0-9]all\\(", "(c\\()?", el1)
}
find_ab_group <- function(ab_class) {
ab_class <- gsub("[^a-zA-Z0-9]", ".*", ab_class)
AB_lookup %pm>%
subset(group %like% ab_class |
atc_group1 %like% ab_class |
atc_group2 %like% ab_class) %pm>%
pm_pull(group) %pm>%
unique() %pm>%
tolower() %pm>%
sort() %pm>%
paste(collapse = "/")
}
find_ab_names <- function(ab_group, n = 3) {
ab_group <- gsub("[^a-zA-Z|0-9]", ".*", ab_group)
# try popular first, they have DDDs
drugs <- antibiotics[which((!is.na(antibiotics$iv_ddd) | !is.na(antibiotics$oral_ddd)) &
antibiotics$name %unlike% " " &
antibiotics$group %like% ab_group &
antibiotics$ab %unlike% "[0-9]$"), ]$name
if (length(drugs) < n) {
# now try it all
drugs <- antibiotics[which((antibiotics$group %like% ab_group |
antibiotics$atc_group1 %like% ab_group |
antibiotics$atc_group2 %like% ab_group) &
antibiotics$ab %unlike% "[0-9]$"), ]$name
}
if (length(drugs) == 0) {
return("??")
}
vector_or(ab_name(sample(drugs, size = min(n, length(drugs)), replace = FALSE),
tolower = TRUE,
language = NULL),
quotes = FALSE)
}