mirror of https://github.com/msberends/AMR.git
(v1.7.1.9000) ab_class update, unit tests
This commit is contained in:
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@ -32,9 +32,9 @@ on:
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branches:
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- master
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schedule:
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# run a schedule everyday at 3 AM.
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# run a schedule everyday at 1 AM.
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# this is to check that all dependencies are still available (see R/zzz.R)
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- cron: '0 3 * * *'
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- cron: '0 1 * * *'
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name: R-code-check
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@ -98,8 +98,7 @@ jobs:
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- name: Restore cached R packages
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# this step will add the step 'Post Restore cached R packages' on a succesful run
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if: runner.os != 'Windows'
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uses: actions/cache@v1
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uses: actions/cache@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-v4
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@ -50,7 +50,7 @@ jobs:
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- name: Restore cached R packages
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# this step will add the step 'Post Restore cached R packages' on a succesful run
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uses: actions/cache@v1
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uses: actions/cache@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: macOS-latest-r-release-v5-codecovr
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@ -68,20 +68,6 @@ jobs:
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as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
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shell: Rscript {0}
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# - name: Test coverage
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# env:
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# CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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# run: |
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# library(AMR)
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# library(tinytest)
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# library(covr)
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# source_files <- list.files("R", pattern = ".R$", full.names = TRUE)
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# test_files <- list.files("inst/tinytest", full.names = TRUE)
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# cov <- file_coverage(source_files = source_files, test_files = test_files, parent_env = asNamespace("AMR"), line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
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# attr(cov, which = "package") <- list(path = ".") # until https://github.com/r-lib/covr/issues/478 is solved
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# codecov(coverage = cov, quiet = FALSE)
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# shell: Rscript {0}
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- name: Test coverage
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env:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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@ -89,5 +75,6 @@ jobs:
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run: |
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library(AMR)
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library(tinytest)
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covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
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x <- covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
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print(x)
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shell: Rscript {0}
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@ -52,7 +52,7 @@ jobs:
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shell: Rscript {0}
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- name: Cache R packages
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uses: actions/cache@v1
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uses: actions/cache@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 1.7.1
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Date: 2021-06-03
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Version: 1.7.1.9000
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Date: 2021-06-04
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Title: Antimicrobial Resistance Data Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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@ -170,6 +170,7 @@ export(age)
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export(age_groups)
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export(all_antimicrobials)
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export(aminoglycosides)
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export(aminopenicillins)
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export(anti_join_microorganisms)
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export(antimicrobials_equal)
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export(as.ab)
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@ -255,6 +256,8 @@ export(kurtosis)
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export(labels_rsi_count)
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export(left_join_microorganisms)
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export(like)
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export(lincosamides)
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export(lipoglycopeptides)
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export(macrolides)
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export(mdr_cmi2012)
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export(mdr_tb)
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@ -297,12 +300,14 @@ export(oxazolidinones)
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export(p_symbol)
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export(pca)
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export(penicillins)
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export(polymyxins)
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export(proportion_I)
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export(proportion_IR)
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export(proportion_R)
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export(proportion_S)
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export(proportion_SI)
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export(proportion_df)
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export(quinolones)
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export(random_disk)
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export(random_mic)
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export(random_rsi)
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@ -316,9 +321,11 @@ export(scale_y_percent)
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export(semi_join_microorganisms)
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export(set_mo_source)
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export(skewness)
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export(streptogramins)
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export(susceptibility)
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export(tetracyclines)
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export(theme_rsi)
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export(ureidopenicillins)
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importFrom(graphics,arrows)
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importFrom(graphics,axis)
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importFrom(graphics,barplot)
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7
NEWS.md
7
NEWS.md
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@ -1,3 +1,10 @@
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# `AMR` 1.7.1.9000
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## <small>Last updated: 4 June 2021</small>
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### Changed
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* Added more antibiotic class selectors, such as `lincosamides()` and `lipoglycopeptides()`
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# `AMR` 1.7.1
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### Breaking change
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@ -506,7 +506,7 @@ dataset_UTF8_to_ASCII <- function(df) {
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# for eucast_rules() and mdro(), creates markdown output with URLs and names
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create_eucast_ab_documentation <- function() {
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x <- trimws(unique(toupper(unlist(strsplit(eucast_rules_file$then_change_these_antibiotics, ",")))))
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x <- trimws(unique(toupper(unlist(strsplit(EUCAST_RULES_DF$then_change_these_antibiotics, ",")))))
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ab <- character()
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for (val in x) {
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if (val %in% ls(envir = asNamespace("AMR"))) {
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@ -713,9 +713,10 @@ meet_criteria <- function(object,
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return(invisible())
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}
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get_current_data <- function(arg_name, call) {
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# check if retrieved before, then get it from package environment
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if (identical(unique_call_id(entire_session = FALSE), pkg_env$get_current_data.call)) {
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get_current_data <- function(arg_name, call, reuse_equal_call = TRUE) {
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# check if retrieved before, then get it from package environment to improve speed
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if (reuse_equal_call == TRUE &&
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identical(unique_call_id(entire_session = FALSE), pkg_env$get_current_data.call)) {
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return(pkg_env$get_current_data.out)
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}
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@ -735,9 +736,10 @@ get_current_data <- function(arg_name, call) {
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if (getRversion() < "3.2") {
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# R-3.0 and R-3.1 do not have an `x` element in the call stack, rendering this function useless
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# R-3.2 was released in April 2015
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if (is.na(arg_name)) {
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# like in carbapenems() etc.
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warning_("this function can only be used in R >= 3.2", call = call)
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# such as for carbapenems() etc.
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warning_("this function requires R version 3.2 or later - you have ", R.version.string, call = call)
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return(data.frame())
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} else {
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# mimic a default R error, e.g. for example_isolates[which(mo_name() %like% "^ent"), ]
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6
R/ab.R
6
R/ab.R
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@ -325,9 +325,9 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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function(y) {
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for (i in seq_len(length(y))) {
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for (lang in LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED != "en"]) {
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y[i] <- ifelse(tolower(y[i]) %in% tolower(translations_file[, lang, drop = TRUE]),
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translations_file[which(tolower(translations_file[, lang, drop = TRUE]) == tolower(y[i]) &
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!isFALSE(translations_file$fixed)), "pattern"],
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y[i] <- ifelse(tolower(y[i]) %in% tolower(TRANSLATIONS[, lang, drop = TRUE]),
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TRANSLATIONS[which(tolower(TRANSLATIONS[, lang, drop = TRUE]) == tolower(y[i]) &
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!isFALSE(TRANSLATIONS$fixed)), "pattern"],
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y[i])
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}
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}
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@ -25,18 +25,19 @@
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#' Antibiotic Class Selectors
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#'
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#' These functions help to filter and select columns with antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(getRversion() < "3.2", paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
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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, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(getRversion() < "3.2", paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
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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 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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#' @details \strong{\Sexpr{ifelse(getRversion() < "3.2", paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
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#'
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#'
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#' These functions can be used in data set calls for selecting columns and filtering rows, see *Examples*. They support base R, but work more convenient in dplyr functions such as [`select()`][dplyr::select()], [`filter()`][dplyr::filter()] and [`summarise()`][dplyr::summarise()].
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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.) in the [antibiotics] data set. This means that a selector like e.g. [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
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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.) 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.
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#'
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#' The group of betalactams consists of all carbapenems, cephalosporins and penicillins.
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#' @section Full list of supported agents:
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#'
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#' `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 = "")`
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#' @rdname antibiotic_class_selectors
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#' @name antibiotic_class_selectors
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#' @export
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#' # `example_isolates` is a data set available in the AMR package.
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#' # See ?example_isolates.
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#'
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#' # Base R ------------------------------------------------------------------
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#' # base R ------------------------------------------------------------------
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#'
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#' # select columns 'IPM' (imipenem) and 'MEM' (meropenem)
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#' example_isolates[, carbapenems()]
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#' example_isolates %>%
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#' select(mo, ab_class("mycobact"))
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#'
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#'
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#' # get bug/drug combinations for only macrolides in Gram-positives:
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#' example_isolates %>%
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#' filter(mo_is_gram_positive()) %>%
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@ -112,14 +112,12 @@
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#' bug_drug_combinations() %>%
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#' format()
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#'
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#'
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#' data.frame(some_column = "some_value",
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#' J01CA01 = "S") %>% # ATC code of ampicillin
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#' select(penicillins()) # only the 'J01CA01' column will be selected
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#'
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#'
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#' # with dplyr 1.0.0 and higher (that adds 'across()'), this is all equal:
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#' # (though the row names on the first are more correct)
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#' example_isolates[carbapenems() == "R", ]
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#' example_isolates %>% filter(carbapenems() == "R")
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#' example_isolates %>% filter(across(carbapenems(), ~.x == "R"))
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@ -127,138 +125,193 @@
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#' }
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ab_class <- function(ab_class,
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only_rsi_columns = FALSE) {
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ab_selector(ab_class, function_name = "ab_class", only_rsi_columns = only_rsi_columns)
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meet_criteria(ab_class, allow_class = "character", has_length = 1)
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ab_selector(NULL, only_rsi_columns = only_rsi_columns, ab_class = ab_class)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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aminoglycosides <- function(only_rsi_columns = FALSE) {
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ab_selector("aminoglycoside", function_name = "aminoglycosides", only_rsi_columns = only_rsi_columns)
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ab_selector("aminoglycosides", only_rsi_columns = only_rsi_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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aminopenicillins <- function(only_rsi_columns = FALSE) {
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ab_selector("aminopenicillins", only_rsi_columns = only_rsi_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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betalactams <- function(only_rsi_columns = FALSE) {
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ab_selector("carbapenem|cephalosporin|penicillin", function_name = "betalactams", only_rsi_columns = only_rsi_columns)
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ab_selector("betalactams", only_rsi_columns = only_rsi_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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carbapenems <- function(only_rsi_columns = FALSE) {
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ab_selector("carbapenem", function_name = "carbapenems", only_rsi_columns = only_rsi_columns)
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ab_selector("carbapenems", only_rsi_columns = only_rsi_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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cephalosporins <- function(only_rsi_columns = FALSE) {
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ab_selector("cephalosporin", function_name = "cephalosporins", only_rsi_columns = only_rsi_columns)
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ab_selector("cephalosporins", only_rsi_columns = only_rsi_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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cephalosporins_1st <- function(only_rsi_columns = FALSE) {
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ab_selector("cephalosporins.*1", function_name = "cephalosporins_1st", only_rsi_columns = only_rsi_columns)
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ab_selector("cephalosporins_1st", only_rsi_columns = only_rsi_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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cephalosporins_2nd <- function(only_rsi_columns = FALSE) {
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ab_selector("cephalosporins.*2", function_name = "cephalosporins_2nd", only_rsi_columns = only_rsi_columns)
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ab_selector("cephalosporins_2nd", only_rsi_columns = only_rsi_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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cephalosporins_3rd <- function(only_rsi_columns = FALSE) {
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ab_selector("cephalosporins.*3", function_name = "cephalosporins_3rd", only_rsi_columns = only_rsi_columns)
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ab_selector("cephalosporins_3rd", only_rsi_columns = only_rsi_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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cephalosporins_4th <- function(only_rsi_columns = FALSE) {
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ab_selector("cephalosporins.*4", function_name = "cephalosporins_4th", only_rsi_columns = only_rsi_columns)
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ab_selector("cephalosporins_4th", only_rsi_columns = only_rsi_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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cephalosporins_5th <- function(only_rsi_columns = FALSE) {
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ab_selector("cephalosporins.*5", function_name = "cephalosporins_5th", only_rsi_columns = only_rsi_columns)
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ab_selector("cephalosporins_5th", only_rsi_columns = only_rsi_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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fluoroquinolones <- function(only_rsi_columns = FALSE) {
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ab_selector("fluoroquinolone", function_name = "fluoroquinolones", only_rsi_columns = only_rsi_columns)
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ab_selector("fluoroquinolones", only_rsi_columns = only_rsi_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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glycopeptides <- function(only_rsi_columns = FALSE) {
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ab_selector("glycopeptide", function_name = "glycopeptides", only_rsi_columns = only_rsi_columns)
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ab_selector("glycopeptides", only_rsi_columns = only_rsi_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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lincosamides <- function(only_rsi_columns = FALSE) {
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ab_selector("lincosamides", only_rsi_columns = only_rsi_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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lipoglycopeptides <- function(only_rsi_columns = FALSE) {
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ab_selector("lipoglycopeptides", only_rsi_columns = only_rsi_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
|
||||
macrolides <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("macrolide", function_name = "macrolides", only_rsi_columns = only_rsi_columns)
|
||||
ab_selector("macrolides", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
oxazolidinones <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("oxazolidinone", function_name = "oxazolidinones", only_rsi_columns = only_rsi_columns)
|
||||
ab_selector("oxazolidinones", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
penicillins <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("penicillin", function_name = "penicillins", only_rsi_columns = only_rsi_columns)
|
||||
ab_selector("penicillins", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
polymyxins <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("polymyxins", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
streptogramins <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("streptogramins", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
quinolones <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("quinolones", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
tetracyclines <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("tetracycline", function_name = "tetracyclines", only_rsi_columns = only_rsi_columns)
|
||||
ab_selector("tetracyclines", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
ab_selector <- function(ab_class,
|
||||
function_name,
|
||||
only_rsi_columns) {
|
||||
meet_criteria(ab_class, allow_class = "character", has_length = 1, .call_depth = 1)
|
||||
meet_criteria(function_name, allow_class = "character", has_length = 1, .call_depth = 1)
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
ureidopenicillins <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("ureidopenicillins", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
ab_selector <- function(function_name,
|
||||
only_rsi_columns,
|
||||
ab_class = NULL) {
|
||||
meet_criteria(function_name, allow_class = "character", has_length = 1, allow_NULL = TRUE, .call_depth = 1)
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1, .call_depth = 1)
|
||||
meet_criteria(ab_class, allow_class = "character", has_length = 1, allow_NULL = TRUE, .call_depth = 1)
|
||||
|
||||
if (getRversion() < "3.2") {
|
||||
# get_current_data() does not work on R 3.0 and R 3.1.
|
||||
# R 3.2 was released in April 2015.
|
||||
warning_("antibiotic class selectors such as ", function_name,
|
||||
"() require R version 3.2 or later - you have ", R.version.string,
|
||||
call = FALSE)
|
||||
return(NULL)
|
||||
}
|
||||
|
||||
# to improve speed, get_current_data() and get_column_abx() only run once when e.g. in a select or group call
|
||||
vars_df <- get_current_data(arg_name = NA, call = -3)
|
||||
# get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
|
||||
vars_df <- get_current_data(arg_name = NA, call = -3, reuse_equal_call = FALSE)
|
||||
# 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.")
|
||||
message_("No antimicrobial agents found in the data.")
|
||||
return(NULL)
|
||||
}
|
||||
|
||||
ab_reference <- subset(antibiotics,
|
||||
group %like% ab_class |
|
||||
atc_group1 %like% ab_class |
|
||||
atc_group2 %like% ab_class)
|
||||
ab_group <- find_ab_group(ab_class)
|
||||
if (ab_group == "") {
|
||||
ab_group <- paste0("'", ab_class, "'")
|
||||
examples <- ""
|
||||
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)$ab
|
||||
ab_group <- find_ab_group(ab_class)
|
||||
function_name <- "ab_class"
|
||||
examples <- paste0(" (such as ", find_ab_names(ab_class, 2), ")")
|
||||
}
|
||||
|
||||
# get the columns with a group names in the chosen ab class
|
||||
agents <- ab_in_data[names(ab_in_data) %in% ab_reference$ab]
|
||||
agents <- ab_in_data[names(ab_in_data) %in% abx]
|
||||
|
||||
if (message_not_thrown_before(function_name)) {
|
||||
if (length(agents) == 0) {
|
||||
message_("No antimicrobial agents of class ", ab_group, " found", examples, ".")
|
||||
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)
|
||||
|
|
@ -423,28 +476,16 @@ is_all <- function(el1) {
|
|||
|
||||
|
||||
find_ab_group <- function(ab_class) {
|
||||
ab_class[ab_class == "carbapenem|cephalosporin|penicillin"] <- "betalactam"
|
||||
ab_class <- gsub("[^a-zA-Z0-9]", ".*", ab_class)
|
||||
ifelse(ab_class %in% c("aminoglycoside",
|
||||
"betalactam",
|
||||
"carbapenem",
|
||||
"cephalosporin",
|
||||
"fluoroquinolone",
|
||||
"glycopeptide",
|
||||
"macrolide",
|
||||
"oxazolidinone",
|
||||
"tetracycline"),
|
||||
paste0(ab_class, "s"),
|
||||
antibiotics %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 = "/")
|
||||
)
|
||||
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) {
|
||||
|
|
@ -462,6 +503,9 @@ find_ab_names <- function(ab_group, n = 3) {
|
|||
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),
|
||||
|
|
|
|||
|
|
@ -55,7 +55,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
|
|||
#' @param verbose a [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.
|
||||
#' @param version_breakpoints the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either `r vector_or(names(EUCAST_VERSION_BREAKPOINTS), reverse = TRUE)`.
|
||||
#' @param version_expertrules the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either `r vector_or(names(EUCAST_VERSION_EXPERT_RULES), reverse = TRUE)`.
|
||||
#' @param ampc_cephalosporin_resistance a [character] value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to `NA`. Currently only works when `version_expertrules` is `3.2`; '*EUCAST Expert Rules v3.2 on Enterobacterales*' states that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three agents. A value of `NA` (the default) for this argument will remove results for these three agents, while e.g. a value of `"R"` will make the results for these agents resistant. Use `NULL` or `FALSE` to not alter results for these three agents of AmpC de-repressed cephalosporin-resistant mutants. Using `TRUE` is equal to using `"R"`. \cr For *EUCAST Expert Rules* v3.2, this rule applies to: `r vector_and(gsub("[^a-zA-Z ]+", "", unlist(strsplit(eucast_rules_file[which(eucast_rules_file$reference.version == 3.2 & eucast_rules_file$reference.rule %like% "ampc"), "this_value"][1], "|", fixed = TRUE))), quotes = "*")`.
|
||||
#' @param ampc_cephalosporin_resistance a [character] value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to `NA`. Currently only works when `version_expertrules` is `3.2`; '*EUCAST Expert Rules v3.2 on Enterobacterales*' states that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three agents. A value of `NA` (the default) for this argument will remove results for these three agents, while e.g. a value of `"R"` will make the results for these agents resistant. Use `NULL` or `FALSE` to not alter results for these three agents of AmpC de-repressed cephalosporin-resistant mutants. Using `TRUE` is equal to using `"R"`. \cr For *EUCAST Expert Rules* v3.2, this rule applies to: `r vector_and(gsub("[^a-zA-Z ]+", "", unlist(strsplit(EUCAST_RULES_DF[which(EUCAST_RULES_DF$reference.version == 3.2 & EUCAST_RULES_DF$reference.rule %like% "ampc"), "this_value"][1], "|", fixed = TRUE))), quotes = "*")`.
|
||||
#' @param ... column name of an antibiotic, see section *Antibiotics* below
|
||||
#' @param ab any (vector of) text that can be coerced to a valid antibiotic code with [as.ab()]
|
||||
#' @param administration route of administration, either `r vector_or(dosage$administration)`
|
||||
|
|
@ -561,11 +561,11 @@ eucast_rules <- function(x,
|
|||
# Official EUCAST rules ---------------------------------------------------
|
||||
eucast_notification_shown <- FALSE
|
||||
if (!is.null(list(...)$eucast_rules_df)) {
|
||||
# this allows: eucast_rules(x, eucast_rules_df = AMR:::eucast_rules_file %>% filter(is.na(have_these_values)))
|
||||
# this allows: eucast_rules(x, eucast_rules_df = AMR:::EUCAST_RULES_DF %>% filter(is.na(have_these_values)))
|
||||
eucast_rules_df <- list(...)$eucast_rules_df
|
||||
} else {
|
||||
# otherwise internal data file, created in data-raw/_internals.R
|
||||
eucast_rules_df <- eucast_rules_file
|
||||
eucast_rules_df <- EUCAST_RULES_DF
|
||||
}
|
||||
|
||||
# filter on user-set guideline versions ----
|
||||
|
|
|
|||
|
|
@ -386,15 +386,15 @@ scale_rsi_colours <- function(...,
|
|||
}
|
||||
|
||||
names_susceptible <- c("S", "SI", "IS", "S+I", "I+S", "susceptible", "Susceptible",
|
||||
unique(translations_file[which(translations_file$pattern == "Susceptible"),
|
||||
unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Susceptible"),
|
||||
"replacement", drop = TRUE]))
|
||||
names_incr_exposure <- c("I", "intermediate", "increased exposure", "incr. exposure", "Increased exposure", "Incr. exposure",
|
||||
unique(translations_file[which(translations_file$pattern == "Intermediate"),
|
||||
unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Intermediate"),
|
||||
"replacement", drop = TRUE]),
|
||||
unique(translations_file[which(translations_file$pattern == "Incr. exposure"),
|
||||
unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Incr. exposure"),
|
||||
"replacement", drop = TRUE]))
|
||||
names_resistant <- c("R", "IR", "RI", "R+I", "I+R", "resistant", "Resistant",
|
||||
unique(translations_file[which(translations_file$pattern == "Resistant"),
|
||||
unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Resistant"),
|
||||
"replacement", drop = TRUE]))
|
||||
|
||||
susceptible <- rep("#3CAEA3", length(names_susceptible))
|
||||
|
|
|
|||
2
R/mo.R
2
R/mo.R
|
|
@ -469,7 +469,7 @@ exec_as.mo <- function(x,
|
|||
x <- strip_whitespace(x, dyslexia_mode)
|
||||
# translate 'unknown' names back to English
|
||||
if (any(x %like% "unbekannt|onbekend|desconocid|sconosciut|iconnu|desconhecid", na.rm = TRUE)) {
|
||||
trns <- subset(translations_file, pattern %like% "unknown" | affect_mo_name == TRUE)
|
||||
trns <- subset(TRANSLATIONS, pattern %like% "unknown" | affect_mo_name == TRUE)
|
||||
langs <- LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED != "en"]
|
||||
for (l in langs) {
|
||||
for (i in seq_len(nrow(trns))) {
|
||||
|
|
|
|||
BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
|
|
@ -136,7 +136,7 @@ translate_AMR <- function(from,
|
|||
return(from)
|
||||
}
|
||||
|
||||
df_trans <- translations_file # internal data file
|
||||
df_trans <- TRANSLATIONS # internal data file
|
||||
from.bak <- from
|
||||
from_unique <- unique(from)
|
||||
from_unique_translated <- from_unique
|
||||
|
|
|
|||
Binary file not shown.
|
|
@ -34,7 +34,7 @@ old_globalenv <- ls(envir = globalenv())
|
|||
# Save internal data to R/sysdata.rda -------------------------------------
|
||||
|
||||
# See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
|
||||
eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
|
||||
EUCAST_RULES_DF <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
|
||||
skip = 10,
|
||||
sep = "\t",
|
||||
stringsAsFactors = FALSE,
|
||||
|
|
@ -54,7 +54,7 @@ eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
|
|||
select(-sorting_rule)
|
||||
|
||||
# Translations
|
||||
translations_file <- utils::read.delim(file = "data-raw/translations.tsv",
|
||||
TRANSLATIONS <- utils::read.delim(file = "data-raw/translations.tsv",
|
||||
sep = "\t",
|
||||
stringsAsFactors = FALSE,
|
||||
header = TRUE,
|
||||
|
|
@ -68,7 +68,7 @@ translations_file <- utils::read.delim(file = "data-raw/translations.tsv",
|
|||
quote = "")
|
||||
|
||||
# for checking input in `language` argument in e.g. mo_*() and ab_*() functions
|
||||
LANGUAGES_SUPPORTED <- sort(c("en", colnames(translations_file)[nchar(colnames(translations_file)) == 2]))
|
||||
LANGUAGES_SUPPORTED <- sort(c("en", colnames(TRANSLATIONS)[nchar(colnames(TRANSLATIONS)) == 2]))
|
||||
|
||||
# vectors of CoNS and CoPS, improves speed in as.mo()
|
||||
create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
|
||||
|
|
@ -121,6 +121,8 @@ CEPHALOSPORINS <- antibiotics %>% filter(group %like% "cephalosporin") %>% pull(
|
|||
CEPHALOSPORINS_1ST <- antibiotics %>% filter(group %like% "cephalosporin.*1") %>% pull(ab)
|
||||
CEPHALOSPORINS_2ND <- antibiotics %>% filter(group %like% "cephalosporin.*2") %>% pull(ab)
|
||||
CEPHALOSPORINS_3RD <- antibiotics %>% filter(group %like% "cephalosporin.*3") %>% pull(ab)
|
||||
CEPHALOSPORINS_4TH <- antibiotics %>% filter(group %like% "cephalosporin.*4") %>% pull(ab)
|
||||
CEPHALOSPORINS_5TH <- antibiotics %>% filter(group %like% "cephalosporin.*5") %>% pull(ab)
|
||||
CEPHALOSPORINS_EXCEPT_CAZ <- CEPHALOSPORINS[CEPHALOSPORINS != "CAZ"]
|
||||
FLUOROQUINOLONES <- antibiotics %>% filter(atc_group2 %like% "fluoroquinolone") %>% pull(ab)
|
||||
LIPOGLYCOPEPTIDES <- as.ab(c("DAL", "ORI", "TLV")) # dalba/orita/tela
|
||||
|
|
@ -131,6 +133,7 @@ MACROLIDES <- antibiotics %>% filter(atc_group2 %like% "macrolide") %>% pull(ab)
|
|||
OXAZOLIDINONES <- antibiotics %>% filter(group %like% "oxazolidinone") %>% pull(ab)
|
||||
PENICILLINS <- antibiotics %>% filter(group %like% "penicillin") %>% pull(ab)
|
||||
POLYMYXINS <- antibiotics %>% filter(group %like% "polymyxin") %>% pull(ab)
|
||||
QUINOLONES <- antibiotics %>% filter(group %like% "quinolone") %>% pull(ab)
|
||||
STREPTOGRAMINS <- antibiotics %>% filter(atc_group2 %like% "streptogramin") %>% pull(ab)
|
||||
TETRACYCLINES <- antibiotics %>% filter(atc_group2 %like% "tetracycline") %>% pull(ab)
|
||||
TETRACYCLINES_EXCEPT_TGC <- TETRACYCLINES[TETRACYCLINES != "TGC"]
|
||||
|
|
@ -141,8 +144,8 @@ DEFINED_AB_GROUPS <- ls(envir = globalenv())
|
|||
DEFINED_AB_GROUPS <- DEFINED_AB_GROUPS[!DEFINED_AB_GROUPS %in% globalenv_before_ab]
|
||||
|
||||
# Export to package as internal data ----
|
||||
usethis::use_data(eucast_rules_file,
|
||||
translations_file,
|
||||
usethis::use_data(EUCAST_RULES_DF,
|
||||
TRANSLATIONS,
|
||||
LANGUAGES_SUPPORTED,
|
||||
MO_CONS,
|
||||
MO_COPS,
|
||||
|
|
@ -153,6 +156,8 @@ usethis::use_data(eucast_rules_file,
|
|||
CEPHALOSPORINS_1ST,
|
||||
CEPHALOSPORINS_2ND,
|
||||
CEPHALOSPORINS_3RD,
|
||||
CEPHALOSPORINS_4TH,
|
||||
CEPHALOSPORINS_5TH,
|
||||
CEPHALOSPORINS_EXCEPT_CAZ,
|
||||
FLUOROQUINOLONES,
|
||||
LIPOGLYCOPEPTIDES,
|
||||
|
|
@ -163,6 +168,7 @@ usethis::use_data(eucast_rules_file,
|
|||
OXAZOLIDINONES,
|
||||
PENICILLINS,
|
||||
POLYMYXINS,
|
||||
QUINOLONES,
|
||||
STREPTOGRAMINS,
|
||||
TETRACYCLINES,
|
||||
TETRACYCLINES_EXCEPT_TGC,
|
||||
|
|
|
|||
|
|
@ -32,7 +32,7 @@ for (i in seq_len(nrow(antibiotics))) {
|
|||
}
|
||||
|
||||
int_resis <- eucast_rules(int_resis,
|
||||
eucast_rules_df = subset(AMR:::eucast_rules_file,
|
||||
eucast_rules_df = subset(AMR:::EUCAST_RULES_DF,
|
||||
is.na(have_these_values) & reference.version == 3.2),
|
||||
info = FALSE)
|
||||
|
||||
|
|
|
|||
|
|
@ -81,7 +81,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -81,7 +81,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -39,7 +39,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -192,7 +192,7 @@
|
|||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>Data sets for download / own use</h1>
|
||||
|
||||
<h4 class="date">03 June 2021</h4>
|
||||
<h4 class="date">04 June 2021</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>datasets.Rmd</code></div>
|
||||
|
|
|
|||
|
|
@ -81,7 +81,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -81,7 +81,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -42,7 +42,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -400,7 +400,7 @@
|
|||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/options.html">options</a></span><span class="op">(</span>repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/options.html">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>,
|
||||
msberends <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
<p>After this, you can install and update this <code>AMR</code> package like any official release (using <code><a href="https://rdrr.io/r/utils/install.packages.html">install.packages("AMR")</a></code> or in RStudio via <em>Tools</em> > <em>Check of Package Updates…</em>).</p>
|
||||
<p>After this, you can install and update this <code>AMR</code> package like any official release (e.g., using <code><a href="https://rdrr.io/r/utils/install.packages.html">install.packages("AMR")</a></code> or in RStudio via <em>Tools</em> > <em>Check for Package Updates…</em>).</p>
|
||||
</li>
|
||||
</ol>
|
||||
<p>You can also download the latest build from our repository: <a href="https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz" class="uri">https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz</a></p>
|
||||
|
|
|
|||
|
|
@ -81,7 +81,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -236,9 +236,26 @@
|
|||
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
||||
</div>
|
||||
|
||||
<div id="amr-1719000" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.7.1.9000">
|
||||
<a href="#amr-1719000" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9000</h1>
|
||||
<div id="last-updated-4-june-2021" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#last-updated-4-june-2021" class="anchor"></a><small>Last updated: 4 June 2021</small>
|
||||
</h2>
|
||||
<div id="changed" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changed" class="anchor"></a>Changed</h3>
|
||||
<ul>
|
||||
<li>Added more antibiotic class selectors, such as <code><a href="../reference/antibiotic_class_selectors.html">lincosamides()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">lipoglycopeptides()</a></code>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="amr-171" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.7.1">
|
||||
<a href="#amr-171" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1</h1>
|
||||
<a href="#amr-171" class="anchor"></a><small> 2021-06-03 </small><code>AMR</code> 1.7.1</h1>
|
||||
<div id="breaking-change" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#breaking-change" class="anchor"></a>Breaking change</h3>
|
||||
|
|
@ -289,9 +306,9 @@
|
|||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed" class="section level3">
|
||||
<div id="changed-1" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changed" class="anchor"></a>Changed</h3>
|
||||
<a href="#changed-1" class="anchor"></a>Changed</h3>
|
||||
<ul>
|
||||
<li>
|
||||
<code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> now supports grouping using the <code>dplyr</code> package</li>
|
||||
|
|
@ -427,9 +444,9 @@
|
|||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-1" class="section level3">
|
||||
<div id="changed-2" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changed-1" class="anchor"></a>Changed</h3>
|
||||
<a href="#changed-2" class="anchor"></a>Changed</h3>
|
||||
<ul>
|
||||
<li>Updated the bacterial taxonomy to 3 March 2021 (using <a href="https://lpsn.dsmz.de">LPSN</a>)
|
||||
<ul>
|
||||
|
|
@ -506,9 +523,9 @@
|
|||
<li><p>Functions <code><a href="../reference/random.html">random_mic()</a></code>, <code><a href="../reference/random.html">random_disk()</a></code> and <code><a href="../reference/random.html">random_rsi()</a></code> for random value generation. The functions <code><a href="../reference/random.html">random_mic()</a></code> and <code><a href="../reference/random.html">random_disk()</a></code> take microorganism names and antibiotic names as input to make generation more realistic.</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-2" class="section level3">
|
||||
<div id="changed-3" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changed-2" class="anchor"></a>Changed</h3>
|
||||
<a href="#changed-3" class="anchor"></a>Changed</h3>
|
||||
<ul>
|
||||
<li><p>New argument <code>ampc_cephalosporin_resistance</code> in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> to correct for AmpC de-repressed cephalosporin-resistant mutants</p></li>
|
||||
<li>
|
||||
|
|
@ -623,9 +640,9 @@
|
|||
<li><p>Support for skimming classes <code><rsi></code>, <code><mic></code>, <code><disk></code> and <code><mo></code> with the <code>skimr</code> package</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-3" class="section level3">
|
||||
<div id="changed-4" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changed-3" class="anchor"></a>Changed</h3>
|
||||
<a href="#changed-4" class="anchor"></a>Changed</h3>
|
||||
<ul>
|
||||
<li><p>Although advertised that this package should work under R 3.0.0, we still had a dependency on R 3.6.0. This is fixed, meaning that our package should now work under R 3.0.0.</p></li>
|
||||
<li>
|
||||
|
|
@ -728,9 +745,9 @@
|
|||
<li><p>Added argument <code>conserve_capped_values</code> to <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for interpreting MIC values - it makes sure that values starting with “<” (but not “<=”) will always return “S” and values starting with “>” (but not “>=”) will always return “R”. The default behaviour of <code><a href="../reference/as.rsi.html">as.rsi()</a></code> has not changed, so you need to specifically do <code><a href="../reference/as.rsi.html">as.rsi(..., conserve_capped_values = TRUE)</a></code>.</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-4" class="section level3">
|
||||
<div id="changed-5" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changed-4" class="anchor"></a>Changed</h3>
|
||||
<a href="#changed-5" class="anchor"></a>Changed</h3>
|
||||
<ul>
|
||||
<li>
|
||||
<p>Big speed improvement for using any function on microorganism codes from earlier package versions (prior to <code>AMR</code> v1.2.0), such as <code><a href="../reference/as.mo.html">as.mo()</a></code>, <code><a href="../reference/mo_property.html">mo_name()</a></code>, <code><a href="../reference/first_isolate.html">first_isolate()</a></code>, <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, <code><a href="../reference/mdro.html">mdro()</a></code>, etc.</p>
|
||||
|
|
@ -803,9 +820,9 @@
|
|||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-5" class="section level3">
|
||||
<div id="changed-6" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changed-5" class="anchor"></a>Changed</h3>
|
||||
<a href="#changed-6" class="anchor"></a>Changed</h3>
|
||||
<ul>
|
||||
<li>Taxonomy:
|
||||
<ul>
|
||||
|
|
@ -857,9 +874,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||
<li>Plotting biplots for principal component analysis using the new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-6" class="section level3">
|
||||
<div id="changed-7" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changed-6" class="anchor"></a>Changed</h3>
|
||||
<a href="#changed-7" class="anchor"></a>Changed</h3>
|
||||
<ul>
|
||||
<li>Improvements for the algorithm used by <code><a href="../reference/as.mo.html">as.mo()</a></code> (and consequently all <code>mo_*</code> functions, that use <code><a href="../reference/as.mo.html">as.mo()</a></code> internally):
|
||||
<ul>
|
||||
|
|
@ -890,9 +907,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||
<div id="amr-101" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.0.1">
|
||||
<a href="#amr-101" class="anchor"></a><small> 2020-02-23 </small><code>AMR</code> 1.0.1</h1>
|
||||
<div id="changed-7" class="section level3">
|
||||
<div id="changed-8" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changed-7" class="anchor"></a>Changed</h3>
|
||||
<a href="#changed-8" class="anchor"></a>Changed</h3>
|
||||
<ul>
|
||||
<li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li>
|
||||
<li>
|
||||
|
|
@ -1198,9 +1215,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-8" class="section level3">
|
||||
<div id="changed-9" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changed-8" class="anchor"></a>Changed</h3>
|
||||
<a href="#changed-9" class="anchor"></a>Changed</h3>
|
||||
<ul>
|
||||
<li>Many algorithm improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code> (of which some led to additions to the <code>microorganisms</code> data set). Many thanks to all contributors that helped improving the algorithms.
|
||||
<ul>
|
||||
|
|
@ -1310,9 +1327,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||
<li><p>Function <code><a href="../reference/mo_property.html">mo_synonyms()</a></code> to get all previously accepted taxonomic names of a microorganism</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-9" class="section level4">
|
||||
<div id="changed-10" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-9" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-10" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Column names of output <code><a href="../reference/count.html">count_df()</a></code> and <code>portion_df()</code> are now lowercase</li>
|
||||
<li>Fixed bug in translation of microorganism names</li>
|
||||
|
|
@ -1358,9 +1375,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||
<li>Added guidelines of the WHO to determine multi-drug resistance (MDR) for TB (<code><a href="../reference/mdro.html">mdr_tb()</a></code>) and added a new vignette about MDR. Read this tutorial <a href="https://msberends.gitlab.io/AMR/articles/MDR.html">here on our website</a>.</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-10" class="section level4">
|
||||
<div id="changed-11" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-10" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-11" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Fixed a critical bug in <code><a href="../reference/first_isolate.html">first_isolate()</a></code> where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1.</li>
|
||||
<li>Fixed a bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> where antibiotics from WHONET software would not be recognised</li>
|
||||
|
|
@ -1444,9 +1461,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||
<div id="amr-061" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="0.6.1">
|
||||
<a href="#amr-061" class="anchor"></a><small> 2019-03-29 </small><code>AMR</code> 0.6.1</h1>
|
||||
<div id="changed-11" class="section level4">
|
||||
<div id="changed-12" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-11" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-12" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Fixed a critical bug when using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> with <code>verbose = TRUE</code>
|
||||
</li>
|
||||
|
|
@ -1563,9 +1580,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||
<li><p>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a>.</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-12" class="section level4">
|
||||
<div id="changed-13" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-12" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-13" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Function <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:
|
||||
<ul>
|
||||
|
|
@ -1721,9 +1738,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||
<li>Functions <code>mo_authors</code> and <code>mo_year</code> to get specific values about the scientific reference of a taxonomic entry</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-13" class="section level4">
|
||||
<div id="changed-14" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-13" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-14" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li><p>Functions <code>MDRO</code>, <code>BRMO</code>, <code>MRGN</code> and <code>EUCAST_exceptional_phenotypes</code> were renamed to <code>mdro</code>, <code>brmo</code>, <code>mrgn</code> and <code>eucast_exceptional_phenotypes</code></p></li>
|
||||
<li><p><code>EUCAST_rules</code> was renamed to <code>eucast_rules</code>, the old function still exists as a deprecated function</p></li>
|
||||
|
|
@ -1911,9 +1928,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||
<li><p>Renamed <code>septic_patients$sex</code> to <code>septic_patients$gender</code></p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-14" class="section level4">
|
||||
<div id="changed-15" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-14" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-15" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li><p>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</p></li>
|
||||
<li>
|
||||
|
|
@ -2052,9 +2069,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-15" class="section level4">
|
||||
<div id="changed-16" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-15" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-16" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Improvements for forecasting with <code>resistance_predict</code> and added more examples</li>
|
||||
<li>More antibiotics added as arguments for EUCAST rules</li>
|
||||
|
|
@ -2137,9 +2154,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||
<li>New print format for <code>tibble</code>s and <code>data.table</code>s</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-16" class="section level4">
|
||||
<div id="changed-17" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-16" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-17" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Fixed <code>rsi</code> class for vectors that contain only invalid antimicrobial interpretations</li>
|
||||
<li>Renamed dataset <code>ablist</code> to <code>antibiotics</code>
|
||||
|
|
|
|||
|
|
@ -12,7 +12,7 @@ articles:
|
|||
datasets: datasets.html
|
||||
resistance_predict: resistance_predict.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
last_built: 2021-06-03T13:04Z
|
||||
last_built: 2021-06-04T19:07Z
|
||||
urls:
|
||||
reference: https://msberends.github.io/AMR//reference
|
||||
article: https://msberends.github.io/AMR//articles
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
|
|
@ -82,7 +82,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -321,6 +321,8 @@
|
|||
<li><p><code>cephalosporins_1st</code><br />(cefacetrile, cefadroxil, cefaloridine, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, cephalexin, cephalothin, cephapirin, cephradine)</p></li>
|
||||
<li><p><code>cephalosporins_2nd</code><br />(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil, loracarbef)</p></li>
|
||||
<li><p><code>cephalosporins_3rd</code><br />(cadazolid, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, latamoxef)</p></li>
|
||||
<li><p><code>cephalosporins_4th</code><br />(cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol (Cefcatacol), cefoselis, cefozopran, cefpirome, cefquinome)</p></li>
|
||||
<li><p><code>cephalosporins_5th</code><br />(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam)</p></li>
|
||||
<li><p><code>cephalosporins_except_caz</code><br />(cadazolid, cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol (Cefcatacol), cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef, loracarbef)</p></li>
|
||||
<li><p><code>fluoroquinolones</code><br />(ciprofloxacin, enoxacin, fleroxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, lomefloxacin, moxifloxacin, norfloxacin, ofloxacin, pazufloxacin, pefloxacin, prulifloxacin, rufloxacin, sparfloxacin, temafloxacin, trovafloxacin)</p></li>
|
||||
<li><p><code>glycopeptides</code><br />(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, vancomycin-macromethod)</p></li>
|
||||
|
|
@ -331,6 +333,7 @@
|
|||
<li><p><code>oxazolidinones</code><br />(cycloserine, linezolid, tedizolid, thiacetazone)</p></li>
|
||||
<li><p><code>penicillins</code><br />(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam (Amdinocillin), metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin, ticarcillin/clavulanic acid)</p></li>
|
||||
<li><p><code>polymyxins</code><br />(colistin, polymyxin B, polymyxin B/polysorbate 80)</p></li>
|
||||
<li><p><code>quinolones</code><br />(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, trovafloxacin)</p></li>
|
||||
<li><p><code>streptogramins</code><br />(pristinamycin, quinupristin/dalfopristin)</p></li>
|
||||
<li><p><code>tetracyclines</code><br />(chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline, tigecycline)</p></li>
|
||||
<li><p><code>tetracyclines_except_tgc</code><br />(chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline)</p></li>
|
||||
|
|
|
|||
|
|
@ -81,7 +81,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -526,7 +526,7 @@
|
|||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="antibiotic_class_selectors.html">ab_class()</a></code> <code><a href="antibiotic_class_selectors.html">aminoglycosides()</a></code> <code><a href="antibiotic_class_selectors.html">betalactams()</a></code> <code><a href="antibiotic_class_selectors.html">carbapenems()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_1st()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_2nd()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_3rd()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_4th()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_5th()</a></code> <code><a href="antibiotic_class_selectors.html">fluoroquinolones()</a></code> <code><a href="antibiotic_class_selectors.html">glycopeptides()</a></code> <code><a href="antibiotic_class_selectors.html">macrolides()</a></code> <code><a href="antibiotic_class_selectors.html">oxazolidinones()</a></code> <code><a href="antibiotic_class_selectors.html">penicillins()</a></code> <code><a href="antibiotic_class_selectors.html">tetracyclines()</a></code> </p>
|
||||
<p><code><a href="antibiotic_class_selectors.html">ab_class()</a></code> <code><a href="antibiotic_class_selectors.html">aminoglycosides()</a></code> <code><a href="antibiotic_class_selectors.html">aminopenicillins()</a></code> <code><a href="antibiotic_class_selectors.html">betalactams()</a></code> <code><a href="antibiotic_class_selectors.html">carbapenems()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_1st()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_2nd()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_3rd()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_4th()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_5th()</a></code> <code><a href="antibiotic_class_selectors.html">fluoroquinolones()</a></code> <code><a href="antibiotic_class_selectors.html">glycopeptides()</a></code> <code><a href="antibiotic_class_selectors.html">lincosamides()</a></code> <code><a href="antibiotic_class_selectors.html">lipoglycopeptides()</a></code> <code><a href="antibiotic_class_selectors.html">macrolides()</a></code> <code><a href="antibiotic_class_selectors.html">oxazolidinones()</a></code> <code><a href="antibiotic_class_selectors.html">penicillins()</a></code> <code><a href="antibiotic_class_selectors.html">polymyxins()</a></code> <code><a href="antibiotic_class_selectors.html">streptogramins()</a></code> <code><a href="antibiotic_class_selectors.html">quinolones()</a></code> <code><a href="antibiotic_class_selectors.html">tetracyclines()</a></code> <code><a href="antibiotic_class_selectors.html">ureidopenicillins()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Antibiotic Class Selectors</p></td>
|
||||
</tr><tr>
|
||||
|
|
|
|||
|
|
@ -81,7 +81,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -23,9 +23,14 @@
|
|||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
if (getRversion() < "3.2") {
|
||||
expect_warning(example_isolates[, aminoglycosides(), drop = FALSE])
|
||||
}
|
||||
if (getRversion() >= "3.2") {
|
||||
# antibiotic class selectors require at least R-3.2
|
||||
expect_true(ncol(example_isolates[, ab_class("antimyco"), drop = FALSE]) < ncol(example_isolates))
|
||||
expect_true(ncol(example_isolates[, aminoglycosides(), drop = FALSE]) < ncol(example_isolates))
|
||||
expect_true(ncol(example_isolates[, aminopenicillins(), drop = FALSE]) < ncol(example_isolates))
|
||||
expect_true(ncol(example_isolates[, betalactams(), drop = FALSE]) < ncol(example_isolates))
|
||||
expect_true(ncol(example_isolates[, carbapenems(), drop = FALSE]) < ncol(example_isolates))
|
||||
expect_true(ncol(example_isolates[, cephalosporins(), drop = FALSE]) < ncol(example_isolates))
|
||||
|
|
@ -36,10 +41,16 @@ if (getRversion() >= "3.2") {
|
|||
expect_true(ncol(example_isolates[, cephalosporins_5th(), drop = FALSE]) < ncol(example_isolates))
|
||||
expect_true(ncol(example_isolates[, fluoroquinolones(), drop = FALSE]) < ncol(example_isolates))
|
||||
expect_true(ncol(example_isolates[, glycopeptides(), drop = FALSE]) < ncol(example_isolates))
|
||||
expect_true(ncol(example_isolates[, lincosamides(), drop = FALSE]) < ncol(example_isolates))
|
||||
expect_true(ncol(example_isolates[, lipoglycopeptides(), drop = FALSE]) < ncol(example_isolates))
|
||||
expect_true(ncol(example_isolates[, macrolides(), drop = FALSE]) < ncol(example_isolates))
|
||||
expect_true(ncol(example_isolates[, oxazolidinones(), drop = FALSE]) < ncol(example_isolates))
|
||||
expect_true(ncol(example_isolates[, penicillins(), drop = FALSE]) < ncol(example_isolates))
|
||||
expect_true(ncol(example_isolates[, polymyxins(), drop = FALSE]) < ncol(example_isolates))
|
||||
expect_true(ncol(example_isolates[, streptogramins(), drop = FALSE]) < ncol(example_isolates))
|
||||
expect_true(ncol(example_isolates[, quinolones(), drop = FALSE]) < ncol(example_isolates))
|
||||
expect_true(ncol(example_isolates[, tetracyclines(), drop = FALSE]) < ncol(example_isolates))
|
||||
expect_true(ncol(example_isolates[, ureidopenicillins(), drop = FALSE]) < ncol(example_isolates))
|
||||
|
||||
# Examples:
|
||||
|
||||
|
|
|
|||
|
|
@ -28,3 +28,9 @@ expect_inherits(b, "bug_drug_combinations")
|
|||
expect_stdout(suppressMessages(print(b)))
|
||||
expect_true(is.data.frame(format(b)))
|
||||
expect_true(is.data.frame(format(b, combine_IR = TRUE, add_ab_group = FALSE)))
|
||||
if (AMR:::pkg_is_available("dplyr")) {
|
||||
expect_true(example_isolates %>%
|
||||
group_by(hospital_id) %>%
|
||||
bug_drug_combinations(FUN = mo_gramstain) %>%
|
||||
is.data.frame())
|
||||
}
|
||||
|
|
|
|||
|
|
@ -24,14 +24,14 @@
|
|||
# ==================================================================== #
|
||||
|
||||
# thoroughly check input table
|
||||
expect_equal(colnames(AMR:::eucast_rules_file),
|
||||
expect_equal(colnames(AMR:::EUCAST_RULES_DF),
|
||||
c("if_mo_property", "like.is.one_of", "this_value",
|
||||
"and_these_antibiotics", "have_these_values",
|
||||
"then_change_these_antibiotics", "to_value",
|
||||
"reference.rule", "reference.rule_group",
|
||||
"reference.version",
|
||||
"note"))
|
||||
MOs_mentioned <- unique(AMR:::eucast_rules_file$this_value)
|
||||
MOs_mentioned <- unique(AMR:::EUCAST_RULES_DF$this_value)
|
||||
MOs_mentioned <- sort(AMR:::trimws(unlist(strsplit(MOs_mentioned[!AMR:::is_valid_regex(MOs_mentioned)], ",", fixed = TRUE))))
|
||||
MOs_test <- suppressWarnings(suppressMessages(mo_name(MOs_mentioned)))
|
||||
expect_true(length(MOs_mentioned[MOs_test != MOs_mentioned]) == 0)
|
||||
|
|
|
|||
|
|
@ -4,6 +4,7 @@
|
|||
\alias{antibiotic_class_selectors}
|
||||
\alias{ab_class}
|
||||
\alias{aminoglycosides}
|
||||
\alias{aminopenicillins}
|
||||
\alias{betalactams}
|
||||
\alias{carbapenems}
|
||||
\alias{cephalosporins}
|
||||
|
|
@ -14,16 +15,24 @@
|
|||
\alias{cephalosporins_5th}
|
||||
\alias{fluoroquinolones}
|
||||
\alias{glycopeptides}
|
||||
\alias{lincosamides}
|
||||
\alias{lipoglycopeptides}
|
||||
\alias{macrolides}
|
||||
\alias{oxazolidinones}
|
||||
\alias{penicillins}
|
||||
\alias{polymyxins}
|
||||
\alias{streptogramins}
|
||||
\alias{quinolones}
|
||||
\alias{tetracyclines}
|
||||
\alias{ureidopenicillins}
|
||||
\title{Antibiotic Class Selectors}
|
||||
\usage{
|
||||
ab_class(ab_class, only_rsi_columns = FALSE)
|
||||
|
||||
aminoglycosides(only_rsi_columns = FALSE)
|
||||
|
||||
aminopenicillins(only_rsi_columns = FALSE)
|
||||
|
||||
betalactams(only_rsi_columns = FALSE)
|
||||
|
||||
carbapenems(only_rsi_columns = FALSE)
|
||||
|
|
@ -44,13 +53,25 @@ fluoroquinolones(only_rsi_columns = FALSE)
|
|||
|
||||
glycopeptides(only_rsi_columns = FALSE)
|
||||
|
||||
lincosamides(only_rsi_columns = FALSE)
|
||||
|
||||
lipoglycopeptides(only_rsi_columns = FALSE)
|
||||
|
||||
macrolides(only_rsi_columns = FALSE)
|
||||
|
||||
oxazolidinones(only_rsi_columns = FALSE)
|
||||
|
||||
penicillins(only_rsi_columns = FALSE)
|
||||
|
||||
polymyxins(only_rsi_columns = FALSE)
|
||||
|
||||
streptogramins(only_rsi_columns = FALSE)
|
||||
|
||||
quinolones(only_rsi_columns = FALSE)
|
||||
|
||||
tetracyclines(only_rsi_columns = FALSE)
|
||||
|
||||
ureidopenicillins(only_rsi_columns = FALSE)
|
||||
}
|
||||
\arguments{
|
||||
\item{ab_class}{an antimicrobial class, such as \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched (case-insensitive) for this value.}
|
||||
|
|
@ -58,17 +79,43 @@ tetracyclines(only_rsi_columns = FALSE)
|
|||
\item{only_rsi_columns}{a \link{logical} to indicate whether only columns of class \verb{<rsi>} must be selected (defaults to \code{FALSE}), see \code{\link[=as.rsi]{as.rsi()}}}
|
||||
}
|
||||
\description{
|
||||
These functions help to filter and select columns with antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(getRversion() < "3.2", paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
|
||||
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. \strong{\Sexpr{ifelse(getRversion() < "3.2", paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
|
||||
}
|
||||
\details{
|
||||
\strong{\Sexpr{ifelse(getRversion() < "3.2", paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
|
||||
|
||||
These functions can be used in data set calls for selecting columns and filtering rows, see \emph{Examples}. They support base R, but work more convenient in dplyr functions such as \code{\link[dplyr:select]{select()}}, \code{\link[dplyr:filter]{filter()}} and \code{\link[dplyr:summarise]{summarise()}}.
|
||||
|
||||
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 \link{antibiotics} data set. This means that a selector like e.g. \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
|
||||
|
||||
The group of betalactams consists of all carbapenems, cephalosporins and penicillins.
|
||||
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 \link{antibiotics} data set. This means that a selector such as \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. Use the \code{\link[=ab_class]{ab_class()}} function to filter/select on a manually defined antibiotic class.
|
||||
}
|
||||
\section{Full list of supported agents}{
|
||||
|
||||
\itemize{
|
||||
\item \code{aminoglycosides()} can select amikacin (AMK), amikacin/fosfomycin (AKF), amphotericin B-high (AMH), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB) and tobramycin-high (TOH)
|
||||
\item \code{aminopenicillins()} can select amoxicillin (AMX) and ampicillin (AMP)
|
||||
\item \code{betalactams()} can select amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), cadazolid (CDZ), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefaloridine (RID), cefamandole (MAN), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (Cefcatacol) (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), cefuroxime (CXM), cefuroxime axetil (CXA), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (Amdinocillin) (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), methicillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), phenethicillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC)
|
||||
\item \code{carbapenems()} can select biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA) and tebipenem (TBP)
|
||||
\item \code{cephalosporins()} can select cadazolid (CDZ), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefaloridine (RID), cefamandole (MAN), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (Cefcatacol) (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), cefuroxime (CXM), cefuroxime axetil (CXA), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP), cephradine (CED), latamoxef (LTM) and loracarbef (LOR)
|
||||
\item \code{cephalosporins_1st()} can select cefacetrile (CAC), cefadroxil (CFR), cefaloridine (RID), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP) and cephradine (CED)
|
||||
\item \code{cephalosporins_2nd()} can select cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening (FOX1), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA) and loracarbef (LOR)
|
||||
\item \code{cephalosporins_3rd()} can select cadazolid (CDZ), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO) and latamoxef (LTM)
|
||||
\item \code{cephalosporins_4th()} can select cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetecol (Cefcatacol) (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO) and cefquinome (CEQ)
|
||||
\item \code{cephalosporins_5th()} can select ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI) and ceftolozane/tazobactam (CZT)
|
||||
\item \code{fluoroquinolones()} can select ciprofloxacin (CIP), enoxacin (ENX), fleroxacin (FLE), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), levofloxacin (LVX), lomefloxacin (LOM), moxifloxacin (MFX), norfloxacin (NOR), ofloxacin (OFX), pazufloxacin (PAZ), pefloxacin (PEF), prulifloxacin (PRU), rufloxacin (RFL), sparfloxacin (SPX), temafloxacin (TMX) and trovafloxacin (TVA)
|
||||
\item \code{glycopeptides()} can select avoparcin (AVO), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN) and vancomycin-macromethod (VAM)
|
||||
\item \code{lincosamides()} can select clindamycin (CLI), lincomycin (LIN) and pirlimycin (PRL)
|
||||
\item \code{lipoglycopeptides()} can select dalbavancin (DAL), oritavancin (ORI) and telavancin (TLV)
|
||||
\item \code{macrolides()} can select azithromycin (AZM), clarithromycin (CLR), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), josamycin (JOS), midecamycin (MID), miocamycin (MCM), oleandomycin (OLE), rokitamycin (ROK), roxithromycin (RXT), spiramycin (SPI), telithromycin (TLT) and troleandomycin (TRL)
|
||||
\item \code{oxazolidinones()} can select cycloserine (CYC), linezolid (LNZ), tedizolid (TZD) and thiacetazone (THA)
|
||||
\item \code{penicillins()} can select amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), carbenicillin (CRB), carindacillin (CRN), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (Amdinocillin) (MEC), metampicillin (MTM), methicillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), phenethicillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC)
|
||||
\item \code{polymyxins()} can select colistin (COL), polymyxin B (PLB) and polymyxin B/polysorbate 80 (POP)
|
||||
\item \code{streptogramins()} can select pristinamycin (PRI) and quinupristin/dalfopristin (QDA)
|
||||
\item \code{quinolones()} can select besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA)
|
||||
\item \code{tetracyclines()} can select chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), tetracycline (TCY) and tigecycline (TGC)
|
||||
\item \code{ureidopenicillins()} can select azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP) and piperacillin/tazobactam (TZP)
|
||||
}
|
||||
}
|
||||
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
|
|
@ -91,7 +138,7 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
|
|||
# `example_isolates` is a data set available in the AMR package.
|
||||
# See ?example_isolates.
|
||||
|
||||
# Base R ------------------------------------------------------------------
|
||||
# base R ------------------------------------------------------------------
|
||||
|
||||
# select columns 'IPM' (imipenem) and 'MEM' (meropenem)
|
||||
example_isolates[, carbapenems()]
|
||||
|
|
@ -149,7 +196,6 @@ if (require("dplyr")) {
|
|||
example_isolates \%>\%
|
||||
select(mo, ab_class("mycobact"))
|
||||
|
||||
|
||||
# get bug/drug combinations for only macrolides in Gram-positives:
|
||||
example_isolates \%>\%
|
||||
filter(mo_is_gram_positive()) \%>\%
|
||||
|
|
@ -157,14 +203,12 @@ if (require("dplyr")) {
|
|||
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:
|
||||
# (though the row names on the first are more correct)
|
||||
example_isolates[carbapenems() == "R", ]
|
||||
example_isolates \%>\% filter(carbapenems() == "R")
|
||||
example_isolates \%>\% filter(across(carbapenems(), ~.x == "R"))
|
||||
|
|
|
|||
|
|
@ -76,6 +76,8 @@ It is possible to define antibiotic groups instead of single antibiotics for the
|
|||
\item \code{cephalosporins_1st}\cr(cefacetrile, cefadroxil, cefaloridine, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, cephalexin, cephalothin, cephapirin, cephradine)
|
||||
\item \code{cephalosporins_2nd}\cr(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil, loracarbef)
|
||||
\item \code{cephalosporins_3rd}\cr(cadazolid, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, latamoxef)
|
||||
\item \code{cephalosporins_4th}\cr(cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol (Cefcatacol), cefoselis, cefozopran, cefpirome, cefquinome)
|
||||
\item \code{cephalosporins_5th}\cr(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam)
|
||||
\item \code{cephalosporins_except_caz}\cr(cadazolid, cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol (Cefcatacol), cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef, loracarbef)
|
||||
\item \code{fluoroquinolones}\cr(ciprofloxacin, enoxacin, fleroxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, lomefloxacin, moxifloxacin, norfloxacin, ofloxacin, pazufloxacin, pefloxacin, prulifloxacin, rufloxacin, sparfloxacin, temafloxacin, trovafloxacin)
|
||||
\item \code{glycopeptides}\cr(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, vancomycin-macromethod)
|
||||
|
|
@ -86,6 +88,7 @@ It is possible to define antibiotic groups instead of single antibiotics for the
|
|||
\item \code{oxazolidinones}\cr(cycloserine, linezolid, tedizolid, thiacetazone)
|
||||
\item \code{penicillins}\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam (Amdinocillin), metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin, ticarcillin/clavulanic acid)
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\item \code{polymyxins}\cr(colistin, polymyxin B, polymyxin B/polysorbate 80)
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\item \code{quinolones}\cr(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, trovafloxacin)
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\item \code{streptogramins}\cr(pristinamycin, quinupristin/dalfopristin)
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\item \code{tetracyclines}\cr(chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline, tigecycline)
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\item \code{tetracyclines_except_tgc}\cr(chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline)
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Reference in New Issue