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(v1.7.1.9026) updated DDDs
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@ -27,7 +27,7 @@
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#'
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#' These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group, without the need to define the columns or antibiotic abbreviations. In short, if you have a column name that resembles an antimicrobial agent, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "CZO" and "J01DB04" will all be picked up by [cephalosporins()].
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#' @inheritSection lifecycle Stable Lifecycle
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#' @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.
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#' @param ab_class an antimicrobial class or a part of it, such as `"carba"` and `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value.
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#' @param filter an [expression] to be evaluated in the [antibiotics] data set, such as `name %like% "trim"`
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#' @param only_rsi_columns a [logical] to indicate whether only columns of class `<rsi>` must be selected (defaults to `FALSE`), see [as.rsi()]
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#' @param only_treatable a [logical] to indicate whether agents that are only for laboratory tests should be excluded (defaults to `TRUE`), such as gentamicin-high (`GEH`) and imipenem/EDTA (`IPE`)
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@ -37,7 +37,7 @@
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#'
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#' 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.) according to the [antibiotics] data set. This means that a selector such as [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
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#'
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#' The [ab_class()] function can be used to filter/select on a manually defined antibiotic class. It searches for results in the [antibiotics] data set within the columns `name`, `atc_group1` and `atc_group2`.
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#' The [ab_class()] function can be used to filter/select on a manually defined antibiotic class. It searches for results in the [antibiotics] data set within the columns `group`, `atc_group1` and `atc_group2`.
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#'
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#' The [ab_selector()] function can be used to internally filter the [antibiotics] data set on any results, see *Examples*. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.
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#'
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@ -88,6 +88,10 @@
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#' # and erythromycin is not a penicillin:
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#' example_isolates[, penicillins() & administrable_per_os()]
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#'
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#' # ab_selector() applies a filter in the `antibiotics` data set and is thus very
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#' # flexible. For instance, to select antibiotic columns with an oral DDD of at
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#' # least 1 gram:
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#' example_isolates[, ab_selector(oral_ddd > 1 & oral_units == "g")]
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#'
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#' # dplyr -------------------------------------------------------------------
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#' \donttest{
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@ -159,7 +163,7 @@ ab_class <- function(ab_class,
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meet_criteria(ab_class, allow_class = "character", has_length = 1, allow_NULL = TRUE)
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
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ab_select_exec(NULL, only_rsi_columns = only_rsi_columns, ab_class = ab_class, only_treatable = only_treatable)
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ab_select_exec(NULL, only_rsi_columns = only_rsi_columns, ab_class_args = ab_class, only_treatable = only_treatable)
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}
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#' @rdname antibiotic_class_selectors
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@ -455,7 +459,7 @@ ureidopenicillins <- function(only_rsi_columns = FALSE, ...) {
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ab_select_exec <- function(function_name,
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only_rsi_columns = FALSE,
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only_treatable = FALSE,
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ab_class = NULL) {
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ab_class_args = NULL) {
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# get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
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# but it only takes a couple of milliseconds
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vars_df <- get_current_data(arg_name = NA, call = -3)
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@ -483,7 +487,7 @@ ab_select_exec <- function(function_name,
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return(NULL)
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}
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if (is.null(ab_class)) {
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if (is.null(ab_class_args)) {
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# their upper case equivalent are vectors with class <ab>, created in data-raw/_internals.R
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# carbapenems() gets its codes from AMR:::AB_CARBAPENEMS
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abx <- get(paste0("AB_", toupper(function_name)), envir = asNamespace("AMR"))
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@ -495,12 +499,12 @@ ab_select_exec <- function(function_name,
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} else {
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# this for the 'manual' ab_class() function
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abx <- subset(AB_lookup,
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group %like% ab_class |
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atc_group1 %like% ab_class |
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atc_group2 %like% ab_class)$ab
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ab_group <- find_ab_group(ab_class)
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group %like% ab_class_args |
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atc_group1 %like% ab_class_args |
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atc_group2 %like% ab_class_args)$ab
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ab_group <- find_ab_group(ab_class_args)
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function_name <- "ab_class"
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examples <- paste0(" (such as ", find_ab_names(ab_class, 2), ")")
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examples <- paste0(" (such as ", find_ab_names(ab_class_args, 2), ")")
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}
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# get the columns with a group names in the chosen ab class
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@ -509,7 +513,8 @@ ab_select_exec <- function(function_name,
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message_agent_names(function_name = function_name,
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agents = agents,
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ab_group = ab_group,
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examples = examples)
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examples = examples,
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ab_class_args = ab_class_args)
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structure(unname(agents),
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class = c("ab_selector", "character"))
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@ -666,12 +671,12 @@ is_all <- function(el1) {
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syscall %like% paste0("[^_a-zA-Z0-9]all\\(", "(c\\()?", el1)
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}
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find_ab_group <- function(ab_class) {
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ab_class <- gsub("[^a-zA-Z0-9]", ".*", ab_class)
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find_ab_group <- function(ab_class_args) {
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ab_class_args <- gsub("[^a-zA-Z0-9]", ".*", ab_class_args)
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AB_lookup %pm>%
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subset(group %like% ab_class |
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atc_group1 %like% ab_class |
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atc_group2 %like% ab_class) %pm>%
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subset(group %like% ab_class_args |
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atc_group1 %like% ab_class_args |
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atc_group2 %like% ab_class_args) %pm>%
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pm_pull(group) %pm>%
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unique() %pm>%
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tolower() %pm>%
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@ -703,7 +708,7 @@ find_ab_names <- function(ab_group, n = 3) {
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quotes = FALSE)
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}
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message_agent_names <- function(function_name, agents, ab_group = NULL, examples = "", call = NULL) {
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message_agent_names <- function(function_name, agents, ab_group = NULL, examples = "", ab_class_args = NULL, call = NULL) {
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if (message_not_thrown_before(paste0(function_name, ".", paste(sort(agents), collapse = "|")))) {
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if (length(agents) == 0) {
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if (is.null(ab_group)) {
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@ -722,7 +727,7 @@ message_agent_names <- function(function_name, agents, ab_group = NULL, examples
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agents_formatted[need_name] <- paste0(agents_formatted[need_name], " (", agents_names[need_name], ")")
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message_("For `", function_name, "(",
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ifelse(function_name == "ab_class",
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paste0("\"", ab_class, "\""),
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paste0("\"", ab_class_args, "\""),
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ifelse(!is.null(call),
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paste0(deparse(call), collapse = " "),
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"")),
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@ -283,12 +283,6 @@ ab_ddd <- function(x, administration = "oral", ...) {
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meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1)
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x <- as.ab(x, ...)
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if (any(ab_name(x, language = NULL) %like% "/")) {
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warning_("DDDs of combined products are available for different dose combinations and not (yet) part of the AMR package. ",
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"Please refer to the WHOCC website:\n",
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"www.whocc.no/ddd/list_of_ddds_combined_products/", call = FALSE)
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}
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ddd_prop <- administration
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# old behaviour
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units <- list(...)$units
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@ -301,7 +295,14 @@ ab_ddd <- function(x, administration = "oral", ...) {
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} else {
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ddd_prop <- paste0(ddd_prop, "_ddd")
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}
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ab_validate(x = x, property = ddd_prop)
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out <- ab_validate(x = x, property = ddd_prop)
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if (any(ab_name(x, language = NULL) %like% "/" & is.na(out)) ) {
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warning_("DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package. ",
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"Please refer to the WHOCC website:\n",
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"www.whocc.no/ddd/list_of_ddds_combined_products/", call = FALSE)
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}
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out
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}
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#' @rdname ab_property
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@ -25,9 +25,9 @@
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#' Get ATC Properties from WHOCC Website
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#'
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#' Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic), such as the name, defined daily dose (DDD) or standard unit.
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#' Gets data from the WHOCC website to determine properties of an Anatomical Therapeutic Chemical (ATC) (e.g. an antibiotic), such as the name, defined daily dose (DDD) or standard unit.
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#' @inheritSection lifecycle Stable Lifecycle
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#' @param atc_code a [character] or [character] vector with ATC code(s) of antibiotic(s)
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#' @param atc_code a [character] (vector) with ATC code(s) of antibiotics, will be coerced with [as.ab()] and [ab_atc()] internally if not a valid ATC code
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#' @param property property of an ATC code. Valid values are `"ATC"`, `"Name"`, `"DDD"`, `"U"` (`"unit"`), `"Adm.R"`, `"Note"` and `groups`. For this last option, all hierarchical groups of an ATC code will be returned, see *Examples*.
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#' @param administration type of administration when using `property = "Adm.R"`, see *Details*
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#' @param url url of website of the WHOCC. The sign `%s` can be used as a placeholder for ATC codes.
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@ -68,6 +68,7 @@
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#' if (requireNamespace("curl") && requireNamespace("rvest") && requireNamespace("xml2")) {
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#' # oral DDD (Defined Daily Dose) of amoxicillin
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#' atc_online_property("J01CA04", "DDD", "O")
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#' atc_online_ddd(ab_atc("amox"))
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#'
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#' # parenteral DDD (Defined Daily Dose) of amoxicillin
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#' atc_online_property("J01CA04", "DDD", "P")
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@ -81,7 +82,7 @@ atc_online_property <- function(atc_code,
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url = "https://www.whocc.no/atc_ddd_index/?code=%s&showdescription=no",
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url_vet = "https://www.whocc.no/atcvet/atcvet_index/?code=%s&showdescription=no") {
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meet_criteria(atc_code, allow_class = "character")
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meet_criteria(property, allow_class = "character", has_length = 1, is_in = c("ATC", "Name", "DDD", "U", "Adm.R", "Note", "groups"), ignore.case = TRUE)
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meet_criteria(property, allow_class = "character", has_length = 1, is_in = c("ATC", "Name", "DDD", "U", "unit", "Adm.R", "Note", "groups"), ignore.case = TRUE)
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meet_criteria(administration, allow_class = "character", has_length = 1)
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meet_criteria(url, allow_class = "character", has_length = 1, looks_like = "https?://")
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meet_criteria(url_vet, allow_class = "character", has_length = 1, looks_like = "https?://")
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@ -108,12 +109,11 @@ atc_online_property <- function(atc_code,
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return(rep(NA, length(atc_code)))
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}
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# also allow unit as property
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if (property %like% "unit") {
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property <- "U"
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}
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property <- tolower(property)
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# also allow unit as property
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if (property == "unit") {
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property <- "u"
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}
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if (property == "ddd") {
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returnvalue <- rep(NA_real_, length(atc_code))
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} else if (property == "groups") {
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@ -206,3 +206,10 @@ atc_online_ddd <- function(atc_code, ...) {
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meet_criteria(atc_code, allow_class = "character")
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atc_online_property(atc_code = atc_code, property = "ddd", ...)
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}
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#' @rdname atc_online
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#' @export
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atc_online_ddd_units <- function(atc_code, ...) {
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meet_criteria(atc_code, allow_class = "character")
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atc_online_property(atc_code = atc_code, property = "unit", ...)
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}
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8
R/data.R
8
R/data.R
@ -23,7 +23,7 @@
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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#' Data Sets with `r format(nrow(antibiotics) + nrow(antivirals), big.mark = ",")` Antimicrobials
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#' Data Sets with `r format(nrow(antibiotics) + nrow(antivirals), big.mark = ",")` Antimicrobial Drugs
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#'
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#' Two data sets containing all antibiotics/antimycotics and antivirals. Use [as.ab()] or one of the [`ab_*`][ab_property()] functions to retrieve values from the [antibiotics] data set. Three identifiers are included in this data set: an antibiotic ID (`ab`, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (`atc`) as defined by the WHO, and a Compound ID (`cid`) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.
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#' @format
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@ -37,9 +37,9 @@
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#' - `atc_group2`\cr Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like `"Macrolides"`
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#' - `abbr`\cr List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)
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#' - `synonyms`\cr Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID
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#' - `oral_ddd`\cr Defined Daily Dose (DDD), oral treatment
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#' - `oral_ddd`\cr Defined Daily Dose (DDD), oral treatment, currently available for `r sum(!is.na(antibiotics$oral_ddd))` drugs
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#' - `oral_units`\cr Units of `oral_ddd`
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#' - `iv_ddd`\cr Defined Daily Dose (DDD), parenteral treatment
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#' - `iv_ddd`\cr Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for `r sum(!is.na(antibiotics$iv_ddd))` drugs
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#' - `iv_units`\cr Units of `iv_ddd`
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#' - `loinc`\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use [ab_loinc()] to retrieve them quickly, see [ab_property()].
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#'
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@ -55,7 +55,7 @@
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#' - `iv_units`\cr Units of `iv_ddd`
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#' @details Properties that are based on an ATC code are only available when an ATC is available. These properties are: `atc_group1`, `atc_group2`, `oral_ddd`, `oral_units`, `iv_ddd` and `iv_units`.
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#'
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#' Synonyms (i.e. trade names) are derived from the Compound ID (`cid`) and consequently only available where a CID is available.
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#' Synonyms (i.e. trade names) were derived from the Compound ID (`cid`) and consequently only available where a CID is available.
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#'
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#' ## Direct download
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#' These data sets are available as 'flat files' for use even without \R - you can find the files here:
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