(v1.7.1.9004) more extensive unit tests

.github/workflows/check.yaml

@@ -23,6 +23,8 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
+# This GitHub Actions file runs without ANY dependency, so works on all versions of R since R-3.0.
+
 on:
   push:
     branches:
@@ -32,9 +34,9 @@ on:
     branches:
       - master
   schedule:
-    # run a schedule everyday at 3 AM.
+    # run a schedule everyday at 1 AM.
     # this is to check that all dependencies are still available (see R/zzz.R)
-    - cron:  '0 3 * * *'
+    - cron:  '0 1 * * *'
 
 name: R-code-check
 
@@ -55,25 +57,33 @@ jobs:
           - {os: windows-latest, r: 'devel',   allowfail: true}
           - {os: ubuntu-20.04,   r: 'devel',   allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           
-          # these are the current release of R
-          - {os: macOS-latest,   r: 'release', allowfail: false}
-          - {os: windows-latest, r: 'release', allowfail: false}
-          - {os: ubuntu-20.04,   r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          
-          # these are the previous release of R
-          - {os: macOS-latest,   r: 'oldrel',  allowfail: false}
-          - {os: windows-latest, r: 'oldrel',  allowfail: false}
-          - {os: ubuntu-20.04,   r: 'oldrel',  allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          
-          # test against all released versions of R >= 3.0, we support them all!
+          # test all systems against all released versions of R >= 3.0, we support them all!
+          - {os: macOS-latest,   r: '4.1',     allowfail: false}
+          - {os: windows-latest, r: '4.1',     allowfail: false}
           - {os: ubuntu-20.04,   r: '4.1',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: macOS-latest,   r: '4.0',     allowfail: false}
+          - {os: windows-latest, r: '4.0',     allowfail: false}
           - {os: ubuntu-20.04,   r: '4.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: macOS-latest,   r: '3.6',     allowfail: false}
+          - {os: windows-latest, r: '3.6',     allowfail: false}
           - {os: ubuntu-20.04,   r: '3.6',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: macOS-latest,   r: '3.5',     allowfail: false}
+          - {os: windows-latest, r: '3.5',     allowfail: false}
           - {os: ubuntu-20.04,   r: '3.5',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: macOS-latest,   r: '3.4',     allowfail: false}
+          - {os: windows-latest, r: '3.4',     allowfail: false}
           - {os: ubuntu-20.04,   r: '3.4',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: macOS-latest,   r: '3.3',     allowfail: false}
+          - {os: windows-latest, r: '3.3',     allowfail: false}
           - {os: ubuntu-20.04,   r: '3.3',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: macOS-latest,   r: '3.2',     allowfail: false}
+          - {os: windows-latest, r: '3.2',     allowfail: false}
           - {os: ubuntu-20.04,   r: '3.2',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: macOS-latest,   r: '3.1',     allowfail: false}
+          - {os: windows-latest, r: '3.1',     allowfail: false}
           - {os: ubuntu-20.04,   r: '3.1',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: macOS-latest,   r: '3.0',     allowfail: false}
+          - {os: windows-latest, r: '3.0',     allowfail: false}
           - {os: ubuntu-20.04,   r: '3.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:
@@ -96,13 +106,18 @@ jobs:
         run: |
           sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev
 
+      - name: Query dependencies
+        # this will change once a week, so it will cache dependency updates
+        run: |
+          writeLines(paste(format(Sys.Date(), "week %V %Y"), sprintf("R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/week-R-version")
+        shell: Rscript {0}
+        
       - name: Restore cached R packages
         # this step will add the step 'Post Restore cached R packages' on a succesful run
-        if: runner.os != 'Windows'
-        uses: actions/cache@v1
+        uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-v4
+          key: ${{ matrix.config.os }}-${{ hashFiles('.github/week-R-version') }}-v4
 
       - name: Unpack AMR and install R dependencies
         if: always()
@@ -156,5 +171,5 @@ jobs:
         if: always()
         uses: actions/upload-artifact@v2
         with:
-          name: artifacts-${{ matrix.config.os }}-r${{ matrix.config.r }}
+          name: artifacts-r-${{ matrix.config.r }}-${{ matrix.config.os }}
           path: AMR.Rcheck

.github/workflows/codecovr.yaml

@@ -48,12 +48,18 @@ jobs:
           
       - uses: r-lib/actions/setup-pandoc@master
 
+      - name: Query dependencies
+        # this will change once a week, so it will cache dependency updates
+        run: |
+          writeLines(paste(format(Sys.Date(), "week %V %Y"), sprintf("R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/week-R-version")
+        shell: Rscript {0}
+        
       - name: Restore cached R packages
         # this step will add the step 'Post Restore cached R packages' on a succesful run
-        uses: actions/cache@v1
+        uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: macOS-latest-r-release-v5-codecovr
+          key: ${{ matrix.config.os }}-${{ hashFiles('.github/week-R-version') }}-v4
 
       - name: Unpack AMR and install R dependencies
         run: |
@@ -68,26 +74,14 @@ jobs:
           as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
         shell: Rscript {0}
 
-      # - name: Test coverage
-      #   env:
-      #     CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-      #   run: |
-      #     library(AMR)
-      #     library(tinytest)
-      #     library(covr)
-      #     source_files <- list.files("R", pattern = ".R$", full.names = TRUE)
-      #     test_files <- list.files("inst/tinytest", full.names = TRUE)
-      #     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"))
-      #     attr(cov, which = "package") <- list(path = ".") # until https://github.com/r-lib/covr/issues/478 is solved
-      #     codecov(coverage = cov, quiet = FALSE)
-      #   shell: Rscript {0}
-      
       - name: Test coverage
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
           R_RUN_TINYTEST: true
         run: |
+          install.packages("covr", repos = "https://cran.rstudio.com/")
           library(AMR)
           library(tinytest)
-          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"))
+          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"))
+          print(x)
         shell: Rscript {0}

.github/workflows/lintr.yaml

@@ -52,7 +52,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Cache R packages
-        uses: actions/cache@v1
+        uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.7.1
-Date: 2021-06-03
+Version: 1.7.1.9004
+Date: 2021-06-15
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 
@@ -59,7 +59,7 @@ Suggests:
     tinytest,
     xml2
 VignetteBuilder: knitr,rmarkdown
-URL: https://msberends.github.io/AMR/, https://github.com/msberends/AMR
+URL: https://github.com/msberends/AMR, https://msberends.github.io/AMR
 BugReports: https://github.com/msberends/AMR/issues
 License: GPL-2 | file LICENSE
 Encoding: UTF-8

NAMESPACE

@@ -170,6 +170,7 @@ export(age)
 export(age_groups)
 export(all_antimicrobials)
 export(aminoglycosides)
+export(aminopenicillins)
 export(anti_join_microorganisms)
 export(antimicrobials_equal)
 export(as.ab)
@@ -255,6 +256,8 @@ export(kurtosis)
 export(labels_rsi_count)
 export(left_join_microorganisms)
 export(like)
+export(lincosamides)
+export(lipoglycopeptides)
 export(macrolides)
 export(mdr_cmi2012)
 export(mdr_tb)
@@ -297,12 +300,14 @@ export(oxazolidinones)
 export(p_symbol)
 export(pca)
 export(penicillins)
+export(polymyxins)
 export(proportion_I)
 export(proportion_IR)
 export(proportion_R)
 export(proportion_S)
 export(proportion_SI)
 export(proportion_df)
+export(quinolones)
 export(random_disk)
 export(random_mic)
 export(random_rsi)
@@ -316,9 +321,11 @@ export(scale_y_percent)
 export(semi_join_microorganisms)
 export(set_mo_source)
 export(skewness)
+export(streptogramins)
 export(susceptibility)
 export(tetracyclines)
 export(theme_rsi)
+export(ureidopenicillins)
 importFrom(graphics,arrows)
 importFrom(graphics,axis)
 importFrom(graphics,barplot)

NEWS.md

@@ -1,7 +1,17 @@
+# `AMR` 1.7.1.9004
+## <small>Last updated: 15 June 2021</small>
+
+### Changed
+* Added more antibiotic class selectors: `aminopenicillins()`, `lincosamides()`, `lipoglycopeptides()`, `polymyxins()`, `quinolones()`, `streptogramins()` and `ureidopenicillins()`
+* Added `ggplot2::autoplot()` generic for classes `<mic>`, `<disk>`, `<rsi>` and `<resistance_predict>`
+* Fix to prevent introducing `NA`s for old MO codes when running `as.mo()` on them
+* Added more informative error messages when any of the `proportion_*()` and `count_*()` functions fail
+* Fix for using antibiotic selectors multiple times in one call (e.g., using in `dplyr::filter()` and immediately after in `dplyr::select()`)
+
+
 # `AMR` 1.7.1
 
 ### Breaking change
-* Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using `as.rsi()`)
 * All antibiotic class selectors (such as `carbapenems()`, `aminoglycosides()`) can now be used for filtering as well, making all their accompanying `filter_*()` functions redundant (such as `filter_carbapenems()`, `filter_aminoglycosides()`). These functions are now deprecated and will be removed in a next release. Examples of how the selectors can be used for filtering:
   ```r
   # select columns with results for carbapenems
@@ -21,6 +31,7 @@
   ```
 
 ### New
+* Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using `as.rsi()`)
 * Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()`
 * Function `italicise_taxonomy()` to make taxonomic names within a string italic, with support for markdown and ANSI
 * Support for all four methods to determine first isolates as summarised by Hindler *et al.* (doi: [10.1086/511864](https://doi.org/10.1086/511864)): isolate-based, patient-based, episode-based and phenotype-based. The last method is now the default.

R/aa_helper_functions.R

@@ -506,7 +506,7 @@ dataset_UTF8_to_ASCII <- function(df) {
 
 # for eucast_rules() and mdro(), creates markdown output with URLs and names
 create_eucast_ab_documentation <- function() {
-  x <- trimws(unique(toupper(unlist(strsplit(eucast_rules_file$then_change_these_antibiotics, ",")))))
+  x <- trimws(unique(toupper(unlist(strsplit(EUCAST_RULES_DF$then_change_these_antibiotics, ",")))))
   ab <- character()
   for (val in x) {
     if (val %in% ls(envir = asNamespace("AMR"))) {
@@ -713,9 +713,10 @@ meet_criteria <- function(object,
   return(invisible())
 }
 
-get_current_data <- function(arg_name, call) {
-  # check if retrieved before, then get it from package environment
-  if (identical(unique_call_id(entire_session = FALSE), pkg_env$get_current_data.call)) {
+get_current_data <- function(arg_name, call, reuse_from_1st_call = TRUE) {
+  # check if retrieved before, then get it from package environment to improve speed
+  if (reuse_from_1st_call == TRUE &&
+      identical(unique_call_id(entire_session = FALSE), pkg_env$get_current_data.call)) {
     return(pkg_env$get_current_data.out)
   }
   
@@ -735,9 +736,10 @@ get_current_data <- function(arg_name, call) {
 
   if (getRversion() < "3.2") {
     # R-3.0 and R-3.1 do not have an `x` element in the call stack, rendering this function useless
+    # R-3.2 was released in April 2015
     if (is.na(arg_name)) {
-      # like in carbapenems() etc.
-      warning_("this function can only be used in R >= 3.2", call = call)
+      # such as for carbapenems() etc.
+      warning_("this function requires R version 3.2 or later - you have ", R.version.string, call = call)
       return(data.frame())
     } else {
       # mimic a default R error, e.g. for example_isolates[which(mo_name() %like% "^ent"), ] 

R/ab.R

@@ -325,9 +325,9 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
                                    function(y) {
                                      for (i in seq_len(length(y))) {
                                        for (lang in LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED != "en"]) {
-                                         y[i] <- ifelse(tolower(y[i]) %in% tolower(translations_file[, lang, drop = TRUE]),
-                                                        translations_file[which(tolower(translations_file[, lang, drop = TRUE]) == tolower(y[i]) &
-                                                                                  !isFALSE(translations_file$fixed)), "pattern"],
+                                         y[i] <- ifelse(tolower(y[i]) %in% tolower(TRANSLATIONS[, lang, drop = TRUE]),
+                                                        TRANSLATIONS[which(tolower(TRANSLATIONS[, lang, drop = TRUE]) == tolower(y[i]) &
+                                                                                  !isFALSE(TRANSLATIONS$fixed)), "pattern"],
                                                         y[i])
                                        }
                                      }

R/ab_class_selectors.R

@@ -25,18 +25,19 @@
 
 #' Antibiotic Class Selectors
 #' 
-#' 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, "."), "")}}
 #' @inheritSection lifecycle Stable Lifecycle
 #' @param ab_class an antimicrobial class, such as `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value.
 #' @param only_rsi_columns a [logical] to indicate whether only columns of class `<rsi>` must be selected (defaults to `FALSE`), see [as.rsi()]
 #' @details \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 *Examples*. They support base R, but work more convenient in dplyr functions such as [`select()`][dplyr::select()], [`filter()`][dplyr::filter()] and [`summarise()`][dplyr::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 [antibiotics] data set. This means that a selector like e.g. [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
+#' 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.
 #' 
-#' The group of betalactams consists of all carbapenems, cephalosporins and penicillins.
+#' @section Full list of supported agents:
+#' 
+#' `r paste0("* ", sapply(c("AMINOGLYCOSIDES", "AMINOPENICILLINS", "BETALACTAMS", "CARBAPENEMS", "CEPHALOSPORINS", "CEPHALOSPORINS_1ST", "CEPHALOSPORINS_2ND", "CEPHALOSPORINS_3RD", "CEPHALOSPORINS_4TH", "CEPHALOSPORINS_5TH", "FLUOROQUINOLONES", "GLYCOPEPTIDES", "LINCOSAMIDES", "LIPOGLYCOPEPTIDES", "MACROLIDES", "OXAZOLIDINONES", "PENICILLINS", "POLYMYXINS", "STREPTOGRAMINS", "QUINOLONES", "TETRACYCLINES", "UREIDOPENICILLINS"), function(x) paste0("``", tolower(x), "()`` can select ", vector_and(paste0(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), " (", eval(parse(text = x), envir = asNamespace("AMR")), ")"), quotes = FALSE))), "\n", collapse = "")`
 #' @rdname antibiotic_class_selectors
 #' @name antibiotic_class_selectors
 #' @export
@@ -46,7 +47,7 @@
 #' # `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()]
@@ -104,7 +105,6 @@
 #'   example_isolates %>% 
 #'     select(mo, ab_class("mycobact"))
 #'     
-#'     
 #'   # get bug/drug combinations for only macrolides in Gram-positives:
 #'   example_isolates %>% 
 #'     filter(mo_is_gram_positive()) %>% 
@@ -112,14 +112,12 @@
 #'     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"))
@@ -127,138 +125,193 @@
 #' }
 ab_class <- function(ab_class, 
                      only_rsi_columns = FALSE) {
-  ab_selector(ab_class, function_name = "ab_class", only_rsi_columns = only_rsi_columns)
+  meet_criteria(ab_class, allow_class = "character", has_length = 1)
+  ab_selector(NULL, only_rsi_columns = only_rsi_columns, ab_class = ab_class)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 aminoglycosides <- function(only_rsi_columns = FALSE) {
-  ab_selector("aminoglycoside", function_name = "aminoglycosides", only_rsi_columns = only_rsi_columns)
+  ab_selector("aminoglycosides", only_rsi_columns = only_rsi_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+aminopenicillins <- function(only_rsi_columns = FALSE) {
+  ab_selector("aminopenicillins", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 betalactams <- function(only_rsi_columns = FALSE) {
-  ab_selector("carbapenem|cephalosporin|penicillin", function_name = "betalactams", only_rsi_columns = only_rsi_columns)
+  ab_selector("betalactams", only_rsi_columns = only_rsi_columns)
 }
+
 #' @rdname antibiotic_class_selectors
 #' @export
 carbapenems <- function(only_rsi_columns = FALSE) {
-  ab_selector("carbapenem", function_name = "carbapenems", only_rsi_columns = only_rsi_columns)
+  ab_selector("carbapenems", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 cephalosporins <- function(only_rsi_columns = FALSE) {
-  ab_selector("cephalosporin", function_name = "cephalosporins", only_rsi_columns = only_rsi_columns)
+  ab_selector("cephalosporins", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 cephalosporins_1st <- function(only_rsi_columns = FALSE) {
-  ab_selector("cephalosporins.*1", function_name = "cephalosporins_1st", only_rsi_columns = only_rsi_columns)
+  ab_selector("cephalosporins_1st", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 cephalosporins_2nd <- function(only_rsi_columns = FALSE) {
-  ab_selector("cephalosporins.*2", function_name = "cephalosporins_2nd", only_rsi_columns = only_rsi_columns)
+  ab_selector("cephalosporins_2nd", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 cephalosporins_3rd <- function(only_rsi_columns = FALSE) {
-  ab_selector("cephalosporins.*3", function_name = "cephalosporins_3rd", only_rsi_columns = only_rsi_columns)
+  ab_selector("cephalosporins_3rd", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 cephalosporins_4th <- function(only_rsi_columns = FALSE) {
-  ab_selector("cephalosporins.*4", function_name = "cephalosporins_4th", only_rsi_columns = only_rsi_columns)
+  ab_selector("cephalosporins_4th", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 cephalosporins_5th <- function(only_rsi_columns = FALSE) {
-  ab_selector("cephalosporins.*5", function_name = "cephalosporins_5th", only_rsi_columns = only_rsi_columns)
+  ab_selector("cephalosporins_5th", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 fluoroquinolones <- function(only_rsi_columns = FALSE) {
-  ab_selector("fluoroquinolone", function_name = "fluoroquinolones", only_rsi_columns = only_rsi_columns)
+  ab_selector("fluoroquinolones", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 glycopeptides <- function(only_rsi_columns = FALSE) {
-  ab_selector("glycopeptide", function_name = "glycopeptides", only_rsi_columns = only_rsi_columns)
+  ab_selector("glycopeptides", only_rsi_columns = only_rsi_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+lincosamides <- function(only_rsi_columns = FALSE) {
+  ab_selector("lincosamides", only_rsi_columns = only_rsi_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+lipoglycopeptides <- function(only_rsi_columns = FALSE) {
+  ab_selector("lipoglycopeptides", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @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_from_1st_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),

R/amr.R

@@ -61,7 +61,7 @@
 #' Matthijs S. Berends \cr
 #' m.s.berends \[at\] umcg \[dot\] nl \cr
 #' University of Groningen
-#' Department of Medical Microbiology and Infection Prevention
+#' Department of Medical Microbiology and Infection Prevention \cr
 #' University Medical Center Groningen \cr
 #' Post Office Box 30001 \cr
 #' 9700 RB Groningen \cr

R/count.R

@@ -82,6 +82,12 @@
 #'               n1 = count_all(CIP),  # the actual total; sum of all three
 #'               n2 = n_rsi(CIP),      # same - analogous to n_distinct
 #'               total = n())          # NOT the number of tested isolates!
+#'               
+#'   # Number of available isolates for a whole antibiotic class
+#'   # (i.e., in this data set columns GEN, TOB, AMK, KAN)
+#'   example_isolates %>%
+#'     group_by(hospital_id) %>%
+#'     summarise(across(aminoglycosides(), n_rsi))
 #'  
 #'   # Count co-resistance between amoxicillin/clav acid and gentamicin,
 #'   # so we can see that combination therapy does a lot more than mono therapy.
@@ -108,81 +114,97 @@
 #' }
 #' }
 count_resistant <- function(..., only_all_tested = FALSE) {
-  rsi_calc(...,
-           ab_result = "R",
-           only_all_tested = only_all_tested,
-           only_count = TRUE)
+  tryCatch(
+    rsi_calc(...,
+             ab_result = "R",
+             only_all_tested = only_all_tested,
+             only_count = TRUE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname count
 #' @export
 count_susceptible <- function(..., only_all_tested = FALSE) {
-  rsi_calc(...,
-           ab_result = c("S", "I"),
-           only_all_tested = only_all_tested,
-           only_count = TRUE)
+  tryCatch(
+    rsi_calc(...,
+             ab_result = c("S", "I"),
+             only_all_tested = only_all_tested,
+             only_count = TRUE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname count
 #' @export
 count_R <- function(..., only_all_tested = FALSE) {
-  rsi_calc(...,
-           ab_result = "R",
-           only_all_tested = only_all_tested,
-           only_count = TRUE)
+  tryCatch(
+    rsi_calc(...,
+             ab_result = "R",
+             only_all_tested = only_all_tested,
+             only_count = TRUE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname count
 #' @export
 count_IR <- function(..., only_all_tested = FALSE) {
-  if (message_not_thrown_before("count_IR")) {
-    warning_("Using count_IR() is discouraged; use count_resistant() instead to not consider \"I\" being resistant.", call = FALSE)
+  if (message_not_thrown_before("count_IR", entire_session = TRUE)) {
+    message_("Using `count_IR()` is discouraged; use `count_resistant()` instead to not consider \"I\" being resistant. This note will be shown once for this session.", as_note = FALSE)
     remember_thrown_message("count_IR")
   }
-  rsi_calc(...,
-           ab_result = c("I", "R"),
-           only_all_tested = only_all_tested,
-           only_count = TRUE)
+  tryCatch(
+    rsi_calc(...,
+             ab_result = c("I", "R"),
+             only_all_tested = only_all_tested,
+             only_count = TRUE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname count
 #' @export
 count_I <- function(..., only_all_tested = FALSE) {
-  rsi_calc(...,
-           ab_result = "I",
-           only_all_tested = only_all_tested,
-           only_count = TRUE)
+  tryCatch(
+    rsi_calc(...,
+             ab_result = "I",
+             only_all_tested = only_all_tested,
+             only_count = TRUE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname count
 #' @export
 count_SI <- function(..., only_all_tested = FALSE) {
-  rsi_calc(...,
-           ab_result = c("S", "I"),
-           only_all_tested = only_all_tested,
-           only_count = TRUE)
+  tryCatch(
+    rsi_calc(...,
+             ab_result = c("S", "I"),
+             only_all_tested = only_all_tested,
+             only_count = TRUE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname count
 #' @export
 count_S <- function(..., only_all_tested = FALSE) {
-  if (message_not_thrown_before("count_S")) {
-    warning_("Using count_S() is discouraged; use count_susceptible() instead to also consider \"I\" being susceptible.", call = FALSE)
+  if (message_not_thrown_before("count_S", entire_session = TRUE)) {
+    message_("Using `count_S()` is discouraged; use `count_susceptible()` instead to also consider \"I\" being susceptible. This note will be shown once for this session.", as_note = FALSE)
     remember_thrown_message("count_S")
   }
-  rsi_calc(...,
-           ab_result = "S",
-           only_all_tested = only_all_tested,
-           only_count = TRUE)
+  tryCatch(
+    rsi_calc(...,
+             ab_result = "S",
+             only_all_tested = only_all_tested,
+             only_count = TRUE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname count
 #' @export
 count_all <- function(..., only_all_tested = FALSE) {
-  rsi_calc(...,
-           ab_result = c("S", "I", "R"),
-           only_all_tested = only_all_tested,
-           only_count = TRUE)
+  tryCatch(
+    rsi_calc(...,
+             ab_result = c("S", "I", "R"),
+             only_all_tested = only_all_tested,
+             only_count = TRUE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname count
@@ -196,11 +218,13 @@ count_df <- function(data,
                      language = get_locale(),
                      combine_SI = TRUE,
                      combine_IR = FALSE) {
-  rsi_calc_df(type = "count",
-              data = data,
-              translate_ab = translate_ab,
-              language = language,
-              combine_SI = combine_SI,
-              combine_IR = combine_IR,
-              combine_SI_missing = missing(combine_SI))
+  tryCatch(
+    rsi_calc_df(type = "count",
+                data = data,
+                translate_ab = translate_ab,
+                language = language,
+                combine_SI = combine_SI,
+                combine_IR = combine_IR,
+                combine_SI_missing = missing(combine_SI)),
+    error = function(e) stop_(e$message, call = -5))
 }

R/deprecated.R

@@ -62,7 +62,7 @@ filter_first_weighted_isolate <- function(x = NULL,
   if (is_null_or_grouped_tbl(x)) {
     # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
     # is also fix for using a grouped df as input (a dot as first argument)
-    x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
+    x <- tryCatch(get_current_data(arg_name = "x", call = -2, reuse_from_1st_call = FALSE), error = function(e) x)
   }
   meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
   meet_criteria(col_date, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
@@ -104,7 +104,7 @@ key_antibiotics <- function(x = NULL,
   if (is_null_or_grouped_tbl(x)) {
     # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
     # is also fix for using a grouped df as input (a dot as first argument)
-    x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
+    x <- tryCatch(get_current_data(arg_name = "x", call = -2, reuse_from_1st_call = FALSE), error = function(e) x)
   }
 
   key_antimicrobials(x = x, 
@@ -170,7 +170,7 @@ filter_ab_class <- function(x,
   if (missing(x) || is_null_or_grouped_tbl(x)) {
     # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
     # is also fix for using a grouped df as input (a dot as first argument)
-    x <- get_current_data(arg_name = "x", call = -2 - .call_depth)
+    x <- get_current_data(arg_name = "x", call = -2 - .call_depth, reuse_from_1st_call = FALSE)
     .x_name <- "your_data"
   }
   meet_criteria(x, allow_class = "data.frame", .call_depth = .call_depth)

R/eucast_rules.R

@@ -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 ----

R/first_isolate.R

@@ -207,7 +207,7 @@ first_isolate <- function(x = NULL,
   if (is_null_or_grouped_tbl(x)) {
     # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
     # is also fix for using a grouped df as input (a dot as first argument)
-    x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
+    x <- tryCatch(get_current_data(arg_name = "x", call = -2, reuse_from_1st_call = FALSE), error = function(e) x)
   }
   meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
   meet_criteria(col_date, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
@@ -618,7 +618,7 @@ filter_first_isolate <- function(x = NULL,
   if (is_null_or_grouped_tbl(x)) {
     # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
     # is also fix for using a grouped df as input (a dot as first argument)
-    x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
+    x <- tryCatch(get_current_data(arg_name = "x", call = -2, reuse_from_1st_call = FALSE), error = function(e) x)
   }
   meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
   meet_criteria(col_date, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))

R/ggplot_rsi.R

@@ -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))

R/key_antimicrobials.R

@@ -130,7 +130,7 @@ key_antimicrobials <- function(x = NULL,
   if (is_null_or_grouped_tbl(x)) {
     # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
     # is also fix for using a grouped df as input (a dot as first argument)
-    x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
+    x <- tryCatch(get_current_data(arg_name = "x", call = -2, reuse_from_1st_call = FALSE), error = function(e) x)
   }
   meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
   meet_criteria(col_mo, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE, is_in = colnames(x))
@@ -232,7 +232,7 @@ all_antimicrobials <- function(x = NULL,
   if (is_null_or_grouped_tbl(x)) {
     # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
     # is also fix for using a grouped df as input (a dot as first argument)
-    x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
+    x <- tryCatch(get_current_data(arg_name = "x", call = -2, reuse_from_1st_call = FALSE), error = function(e) x)
   }
   meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
   meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)

R/mdro.R

@@ -170,7 +170,7 @@ mdro <- function(x = NULL,
   if (is_null_or_grouped_tbl(x)) {
     # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
     # is also fix for using a grouped df as input (a dot as first argument)
-    x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
+    x <- tryCatch(get_current_data(arg_name = "x", call = -2, reuse_from_1st_call = FALSE), error = function(e) x)
   }
   meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
   meet_criteria(guideline, allow_class = c("list", "character"), allow_NULL = TRUE)

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))) {
@@ -1664,16 +1664,25 @@ pillar_shaft.mo <- function(x, ...) {
   out[is.na(x)] <- font_na("  NA")
   out[x == "UNKNOWN"] <- font_na("  UNKNOWN")
   
-  if (!all(x[!is.na(x)] %in% MO_lookup$mo)) {
+  df <- tryCatch(get_current_data(arg_name = "x",
+                                  call = 0,
+                                  reuse_from_1st_call = FALSE),
+                 error = function(e) NULL)
+  if (!is.null(df)) {
+    mo_cols <- vapply(FUN.VALUE = logical(1), df, is.mo)
+  } else {
+    mo_cols <- NULL
+  }
+  
+  if (!all(x[!is.na(x)] %in% MO_lookup$mo) | 
+      (!is.null(df) && !all(unlist(df[, which(mo_cols), drop = FALSE]) %in% MO_lookup$mo))) {
     # markup old mo codes
     out[!x %in% MO_lookup$mo] <- font_italic(font_na(x[!x %in% MO_lookup$mo], 
                                                      collapse = NULL),
                                              collapse = NULL)
-    # throw a warning with the affected column name
-    mo <- tryCatch(search_type_in_df(get_current_data(arg_name = "x", call = 0), type = "mo", info = FALSE),
-                   error = function(e) NULL)
-    if (!is.null(mo)) {
-      col <- paste0("Column '", mo, "'")
+    # throw a warning with the affected column name(s)
+    if (!is.null(mo_cols)) {
+      col <- paste0("Column ", vector_or(colnames(df)[mo_cols], quotes = TRUE, sort = FALSE))
     } else {
       col <- "The data"
     }
@@ -1681,7 +1690,7 @@ pillar_shaft.mo <- function(x, ...) {
              "Please update your MO codes with `as.mo()`.",
              call = FALSE)
   }
-
+  
   # make it always fit exactly
   max_char <- max(nchar(x))
   if (is.na(max_char)) {
@@ -2039,12 +2048,12 @@ parse_and_convert <- function(x) {
         x <- as.data.frame(x, stringsAsFactors = FALSE)[[1]]
       }
     }
-    x[is.null(x)] <- NA
-    parsed <- iconv(x, to = "UTF-8")
+    parsed <- iconv(as.character(x), to = "UTF-8")
     parsed[is.na(parsed) & !is.na(x)] <- iconv(x[is.na(parsed) & !is.na(x)], from = "Latin1", to = "ASCII//TRANSLIT")
     parsed <- gsub('"', "", parsed, fixed = TRUE)
     parsed <- gsub(" +", " ", parsed, perl = TRUE)
     parsed <- trimws(parsed)
+    parsed
   }, error = function(e) stop(e$message, call. = FALSE)) # this will also be thrown when running `as.mo(no_existing_object)`
   parsed
 }

R/mo_property.R

@@ -747,7 +747,9 @@ mo_validate <- function(x, property, language, ...) {
 find_mo_col <- function(fn) {
   # this function tries to find an mo column in the data the function was called in,
   # which is useful when functions are used within dplyr verbs
-  df <- get_current_data(arg_name = "x", call = -3) # will return an error if not found
+  df <- get_current_data(arg_name = "x", 
+                         call = -3,
+                         reuse_from_1st_call = FALSE) # will return an error if not found
   mo <- NULL
   try({
     mo <- suppressMessages(search_type_in_df(df, "mo"))

R/plot.R

@@ -287,6 +287,11 @@ ggplot.mic <- function(data,
     ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
 }
 
+#' @method autoplot mic
+#' @rdname plot
+# will be exported using s3_register() in R/zzz.R
+autoplot.mic <- ggplot.mic
+
 #' @method plot disk
 #' @export
 #' @importFrom graphics barplot axis mtext legend
@@ -506,6 +511,11 @@ ggplot.disk <- function(data,
     ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
 }
 
+#' @method autoplot disk
+#' @rdname plot
+# will be exported using s3_register() in R/zzz.R
+autoplot.disk <- ggplot.disk
+
 #' @method plot rsi
 #' @export
 #' @importFrom graphics plot text axis
@@ -657,6 +667,11 @@ ggplot.rsi <- function(data,
     ggplot2::theme(legend.position = "none")
 }
 
+#' @method autoplot rsi
+#' @rdname plot
+# will be exported using s3_register() in R/zzz.R
+autoplot.rsi <- ggplot.rsi
+
 plot_prepare_table <- function(x, expand) {
   x <- x[!is.na(x)]
   stop_if(length(x) == 0, "no observations to plot", call = FALSE)

R/proportion.R

@@ -167,12 +167,14 @@ resistance <- function(...,
                        minimum = 30,
                        as_percent = FALSE,
                        only_all_tested = FALSE) {
-  rsi_calc(...,
-           ab_result = "R",
-           minimum = minimum,
-           as_percent = as_percent,
-           only_all_tested = only_all_tested,
-           only_count = FALSE)
+  tryCatch(
+    rsi_calc(...,
+             ab_result = "R",
+             minimum = minimum,
+             as_percent = as_percent,
+             only_all_tested = only_all_tested,
+             only_count = FALSE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname proportion
@@ -181,12 +183,14 @@ susceptibility <- function(...,
                            minimum = 30,
                            as_percent = FALSE,
                            only_all_tested = FALSE) {
-  rsi_calc(...,
-           ab_result = c("S", "I"),
-           minimum = minimum,
-           as_percent = as_percent,
-           only_all_tested = only_all_tested,
-           only_count = FALSE)
+  tryCatch(
+    rsi_calc(...,
+             ab_result = c("S", "I"),
+             minimum = minimum,
+             as_percent = as_percent,
+             only_all_tested = only_all_tested,
+             only_count = FALSE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname proportion
@@ -195,12 +199,14 @@ proportion_R <- function(...,
                          minimum = 30,
                          as_percent = FALSE,
                          only_all_tested = FALSE) {
-  rsi_calc(...,
-           ab_result = "R",
-           minimum = minimum,
-           as_percent = as_percent,
-           only_all_tested = only_all_tested,
-           only_count = FALSE)
+  tryCatch(
+    rsi_calc(...,
+             ab_result = "R",
+             minimum = minimum,
+             as_percent = as_percent,
+             only_all_tested = only_all_tested,
+             only_count = FALSE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname proportion
@@ -209,12 +215,14 @@ proportion_IR <- function(...,
                           minimum = 30,
                           as_percent = FALSE,
                           only_all_tested = FALSE) {
-  rsi_calc(...,
-           ab_result = c("I", "R"),
-           minimum = minimum,
-           as_percent = as_percent,
-           only_all_tested = only_all_tested,
-           only_count = FALSE)
+  tryCatch(
+    rsi_calc(...,
+             ab_result = c("I", "R"),
+             minimum = minimum,
+             as_percent = as_percent,
+             only_all_tested = only_all_tested,
+             only_count = FALSE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname proportion
@@ -223,12 +231,14 @@ proportion_I <- function(...,
                          minimum = 30,
                          as_percent = FALSE,
                          only_all_tested = FALSE) {
-  rsi_calc(...,
-           ab_result = "I",
-           minimum = minimum,
-           as_percent = as_percent,
-           only_all_tested = only_all_tested,
-           only_count = FALSE)
+  tryCatch(
+    rsi_calc(...,
+             ab_result = "I",
+             minimum = minimum,
+             as_percent = as_percent,
+             only_all_tested = only_all_tested,
+             only_count = FALSE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname proportion
@@ -237,12 +247,14 @@ proportion_SI <- function(...,
                           minimum = 30,
                           as_percent = FALSE,
                           only_all_tested = FALSE) {
-  rsi_calc(...,
-           ab_result = c("S", "I"),
-           minimum = minimum,
-           as_percent = as_percent,
-           only_all_tested = only_all_tested,
-           only_count = FALSE)
+  tryCatch(
+    rsi_calc(...,
+             ab_result = c("S", "I"),
+             minimum = minimum,
+             as_percent = as_percent,
+             only_all_tested = only_all_tested,
+             only_count = FALSE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname proportion
@@ -251,12 +263,14 @@ proportion_S <- function(...,
                          minimum = 30,
                          as_percent = FALSE,
                          only_all_tested = FALSE) {
-  rsi_calc(...,
-           ab_result = "S",
-           minimum = minimum,
-           as_percent = as_percent,
-           only_all_tested = only_all_tested,
-           only_count = FALSE)
+  tryCatch(
+    rsi_calc(...,
+             ab_result = "S",
+             minimum = minimum,
+             as_percent = as_percent,
+             only_all_tested = only_all_tested,
+             only_count = FALSE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname proportion
@@ -268,13 +282,15 @@ proportion_df <- function(data,
                           as_percent = FALSE,
                           combine_SI = TRUE,
                           combine_IR = FALSE) {
-  rsi_calc_df(type = "proportion",
-              data = data,
-              translate_ab = translate_ab,
-              language = language,
-              minimum = minimum,
-              as_percent = as_percent,
-              combine_SI = combine_SI,
-              combine_IR = combine_IR,
-              combine_SI_missing = missing(combine_SI))
+  tryCatch(
+    rsi_calc_df(type = "proportion",
+                data = data,
+                translate_ab = translate_ab,
+                language = language,
+                minimum = minimum,
+                as_percent = as_percent,
+                combine_SI = combine_SI,
+                combine_IR = combine_IR,
+                combine_SI_missing = missing(combine_SI)),
+    error = function(e) stop_(e$message, call = -5))
 }

R/resistance_predict.R

@@ -143,7 +143,7 @@ resistance_predict <- function(x,
   meet_criteria(info, allow_class = "logical", has_length = 1)
   
   stop_if(is.null(model), 'choose a regression model with the `model` argument, e.g. resistance_predict(..., model = "binomial")')
-
+  
   dots <- unlist(list(...))
   if (length(dots) != 0) {
     # backwards compatibility with old arguments
@@ -321,7 +321,7 @@ plot.resistance_predict <- function(x, main = paste("Resistance Prediction of",
   } else {
     ylab <- "%IR"
   }
-
+  
   plot(x = x$year,
        y = x$value,
        ylim = c(0, 1),
@@ -351,20 +351,6 @@ plot.resistance_predict <- function(x, main = paste("Resistance Prediction of",
          col = "grey40")
 }
 
-
-#' @method ggplot resistance_predict
-#' @rdname resistance_predict
-# will be exported using s3_register() in R/zzz.R
-ggplot.resistance_predict <- function(x,
-                               main = paste("Resistance Prediction of", x_name),
-                               ribbon = TRUE,
-                               ...) {
-  x_name <- paste0(ab_name(attributes(x)$ab), " (", attributes(x)$ab, ")")
-  meet_criteria(main, allow_class = "character", has_length = 1)
-  meet_criteria(ribbon, allow_class = "logical", has_length = 1)
-  ggplot_rsi_predict(x = x, main = main, ribbon = ribbon, ...)
-}
-
 #' @rdname resistance_predict
 #' @export
 ggplot_rsi_predict <- function(x,
@@ -407,3 +393,21 @@ ggplot_rsi_predict <- function(x,
                         colour = "grey40")
   p
 }
+
+#' @method ggplot resistance_predict
+#' @rdname resistance_predict
+# will be exported using s3_register() in R/zzz.R
+ggplot.resistance_predict <- function(x,
+                                      main = paste("Resistance Prediction of", x_name),
+                                      ribbon = TRUE,
+                                      ...) {
+  x_name <- paste0(ab_name(attributes(x)$ab), " (", attributes(x)$ab, ")")
+  meet_criteria(main, allow_class = "character", has_length = 1)
+  meet_criteria(ribbon, allow_class = "logical", has_length = 1)
+  ggplot_rsi_predict(x = x, main = main, ribbon = ribbon, ...)
+}
+
+#' @method autoplot resistance_predict
+#' @rdname resistance_predict
+# will be exported using s3_register() in R/zzz.R
+autoplot.resistance_predict <- ggplot.resistance_predict

R/rsi.R

@@ -349,7 +349,7 @@ as.rsi.mic <- function(x,
   
   # for dplyr's across()
   cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
-  if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", 0)), error = function(e) FALSE)) {
+  if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", call = 0, reuse_from_1st_call = FALSE)), error = function(e) FALSE)) {
     # try to get current column, which will only be available when in across()
     ab <- tryCatch(cur_column_dplyr(),
                    error = function(e) ab)
@@ -438,7 +438,7 @@ as.rsi.disk <- function(x,
   
   # for dplyr's across()
   cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
-  if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", 0)), error = function(e) FALSE)) {
+  if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", call = 0, reuse_from_1st_call = FALSE)), error = function(e) FALSE)) {
     # try to get current column, which will only be available when in across()
     ab <- tryCatch(cur_column_dplyr(),
                    error = function(e) ab)
@@ -448,7 +448,7 @@ as.rsi.disk <- function(x,
   mo_var_found <- ""
   if (is.null(mo)) {
     tryCatch({
-      df <- get_current_data(arg_name = "mo", call = -3) # will return an error if not found
+      df <- get_current_data(arg_name = "mo", call = -3, reuse_from_1st_call = FALSE) # will return an error if not found
       mo <- NULL
       try({
         mo <- suppressMessages(search_type_in_df(df, "mo"))

R/translate.R

@@ -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

R/zzz.R

@@ -65,6 +65,10 @@ if (utf8_supported && !is_latex) {
   s3_register("ggplot2::ggplot", "mic")
   s3_register("ggplot2::ggplot", "disk")
   s3_register("ggplot2::ggplot", "resistance_predict")
+  s3_register("ggplot2::autoplot", "rsi")
+  s3_register("ggplot2::autoplot", "mic")
+  s3_register("ggplot2::autoplot", "disk")
+  s3_register("ggplot2::autoplot", "resistance_predict")
   
   # if mo source exists, fire it up (see mo_source())
   try({

data-raw/_install_deps.R

@@ -26,7 +26,6 @@
 # some old R instances have trouble installing tinytest, so we ship it too
 install.packages("data-raw/tinytest_1.2.4.10.tar.gz")
 install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
-install.packages("covr", repos = "https://cran.rstudio.com/")
 
 pkg_suggests <- gsub("[^a-zA-Z0-9]+", "", unlist(strsplit(packageDescription("AMR", fields = "Suggests"), ", ?")))
 cat("Packages listed in Suggests:", paste(pkg_suggests, collapse = ", "), "\n")

data-raw/_internals.R

@@ -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,

data-raw/exploratory_data_analysis_test.R

@@ -0,0 +1,28 @@
+library(dplyr)
+example_isolates %>% 
+  select(mo, where(is.rsi)) %>% 
+  tidyr::pivot_longer(cols = where(is.rsi)) %>% 
+  # remove intrisic R
+  filter(!paste(mo, name) %in% AMR:::INTRINSIC_R) %>% 
+  mutate(name = as.ab(name),
+         value = ifelse(value == "R", 1, 0),
+         class = ab_group(name)) %>% 
+  group_by(mo, class) %>% 
+  summarise(n = n(),
+            res = mean(value, na.rm = TRUE)) %>% 
+  filter(n > 30, !is.na(res))
+
+
+
+df <- example_isolates
+search_mo <- "B_ESCHR_COLI"
+intrinsic_res <- INTRINSIC_R[INTRINSIC_R %like% search_mo]
+intrinsic_res <- gsub(".* (.*)", "\\1", intrinsic_res)
+
+x <- df %>%
+  select(mo, where(is.rsi)) %>% 
+  filter(mo == search_mo) %>%
+  # at least 30 results available
+  select(function(x) sum(!is.na(x)) >= 30) %>% 
+  # remove intrisic R
+  select(!matches(paste(intrinsic_res, collapse = "|")))

data-raw/reproduction_of_intrinsic_resistant.R

@@ -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)
 

docs/404.html

@@ -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">1.7.1.9004</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -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">1.7.1.9004</span>
       </span>
     </div>
 

docs/articles/datasets.html

@@ -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">1.7.1.9004</span>
       </span>
     </div>
 
@@ -187,12 +187,12 @@
 
       
 
-      </header><script src="datasets_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
+      </header><script src="datasets_files/header-attrs-2.7/header-attrs.js"></script><div class="row">
   <div class="col-md-9 contents">
     <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">15 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>

docs/articles/index.html

@@ -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">1.7.1.9004</span>
       </span>
     </div>
 

docs/authors.html

@@ -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">1.7.1.9004</span>
       </span>
     </div>
 

docs/index.html

@@ -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">1.7.1.9004</span>
       </span>
     </div>
 
@@ -213,7 +213,7 @@
 <a href="#with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side" class="anchor"></a>With <code>AMR</code> (for R), there’s always a knowledgeable microbiologist by your side!</h5>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span>
-<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
+<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/AMR">AMR</a></span><span class="op">)</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
 
 <span class="va">example_isolates</span> <span class="op">%&gt;%</span>
@@ -223,9 +223,9 @@
 <span class="co">#&gt; ℹ Using column 'mo' as input for `mo_is_gram_negative()`</span>
 <span class="co">#&gt; ℹ Using column 'mo' as input for `mo_is_intrinsic_resistant()`</span>
 <span class="co">#&gt; ℹ Determining intrinsic resistance based on 'EUCAST Expert Rules' and 'EUCAST Intrinsic</span>
-<span class="co">#&gt;   Resistance and Unusual Phenotypes' v3.2 (2020)</span>
+<span class="co">#&gt;    Resistance and Unusual Phenotypes' v3.2 (2020)</span>
 <span class="co">#&gt; ℹ For `aminoglycosides()` using columns: 'AMK' (amikacin), 'GEN' (gentamicin), 'KAN'</span>
-<span class="co">#&gt;   (kanamycin) and 'TOB' (tobramycin)</span>
+<span class="co">#&gt;    (kanamycin) and 'TOB' (tobramycin)</span>
 <span class="co">#&gt; ℹ For `carbapenems()` using columns: 'IPM' (imipenem) and 'MEM' (meropenem)</span></code></pre></div>
 <p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p>
 <table class="table">
@@ -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> &gt; <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> &gt; <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>

docs/news/index.html

@@ -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">1.7.1.9004</span>
       </span>
     </div>
 
@@ -236,14 +236,35 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
+    <div id="amr-1719004" class="section level1">
+<h1 class="page-header" data-toc-text="1.7.1.9004">
+<a href="#amr-1719004" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9004</h1>
+<div id="last-updated-15-june-2021" class="section level2">
+<h2 class="hasAnchor">
+<a href="#last-updated-15-june-2021" class="anchor"></a><small>Last updated: 15 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: <code><a href="../reference/antibiotic_class_selectors.html">aminopenicillins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">lincosamides()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">lipoglycopeptides()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">polymyxins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">quinolones()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">streptogramins()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">ureidopenicillins()</a></code>
+</li>
+<li>Added <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html">ggplot2::autoplot()</a></code> generic for classes <code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code>, <code>&lt;rsi&gt;</code> and <code>&lt;resistance_predict&gt;</code>
+</li>
+<li>Fix to prevent introducing <code>NA</code>s for old MO codes when running <code><a href="../reference/as.mo.html">as.mo()</a></code> on them</li>
+<li>Added more informative error messages when any of the <code>proportion_*()</code> and <code>count_*()</code> functions fail</li>
+<li>Fix for using antibiotic selectors multiple times in one call (e.g., using in <code><a href="https://dplyr.tidyverse.org/reference/filter.html">dplyr::filter()</a></code> and immediately after in <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</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>
 <ul>
-<li><p>Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>)</p></li>
 <li>
 <p>All antibiotic class selectors (such as <code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>) can now be used for filtering as well, making all their accompanying <code>filter_*()</code> functions redundant (such as <code><a href="../reference/AMR-deprecated.html">filter_carbapenems()</a></code>, <code><a href="../reference/AMR-deprecated.html">filter_aminoglycosides()</a></code>). These functions are now deprecated and will be removed in a next release. Examples of how the selectors can be used for filtering:</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
@@ -269,6 +290,7 @@
 <h3 class="hasAnchor">
 <a href="#new" class="anchor"></a>New</h3>
 <ul>
+<li>Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>)</li>
 <li>Function <code><a href="../reference/custom_eucast_rules.html">custom_eucast_rules()</a></code> that brings support for custom AMR rules in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>
 </li>
 <li>Function <code><a href="../reference/italicise_taxonomy.html">italicise_taxonomy()</a></code> to make taxonomic names within a string italic, with support for markdown and ANSI</li>
@@ -289,9 +311,9 @@
 </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 +449,9 @@
 </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>
@@ -481,7 +503,7 @@
 <a href="#other-1" class="anchor"></a>Other</h3>
 <ul>
 <li>Big documentation updates</li>
-<li>Loading the package (i.e., <code><a href="https://msberends.github.io/AMR/">library(AMR)</a></code>) now is ~50 times faster than before, in costs of package size (which increased by ~3 MB)</li>
+<li>Loading the package (i.e., <code><a href="https://github.com/msberends/AMR">library(AMR)</a></code>) now is ~50 times faster than before, in costs of package size (which increased by ~3 MB)</li>
 </ul>
 </div>
 </div>
@@ -506,9 +528,9 @@
 <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>
@@ -612,7 +634,7 @@
 <p>Curious about which enterococci are actually intrinsic resistant to vancomycin?</p>
 <div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
-<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
+<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/AMR">AMR</a></span><span class="op">)</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
 <span class="va">intrinsic_resistant</span> <span class="op">%&gt;%</span>
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="va">antibiotic</span> <span class="op">==</span> <span class="st">"Vancomycin"</span>, <span class="va">microorganism</span> <span class="op">%like%</span> <span class="st">"Enterococcus"</span><span class="op">)</span> <span class="op">%&gt;%</span> 
@@ -623,9 +645,9 @@
 <li><p>Support for skimming classes <code>&lt;rsi&gt;</code>, <code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code> and <code>&lt;mo&gt;</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 +750,9 @@
 <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 “&lt;” (but not “&lt;=”) will always return “S” and values starting with “&gt;” (but not “&gt;=”) 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 +825,9 @@
 </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 +879,9 @@ 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 +912,9 @@ 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 +1220,9 @@ 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 +1332,9 @@ 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 +1380,9 @@ 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 +1466,9 @@ 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 +1585,9 @@ 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 +1743,9 @@ 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 +1933,9 @@ 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 +2074,9 @@ 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 +2159,9 @@ 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>

docs/pkgdown.yml

@@ -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: 2021-06-15T08:50Z
 urls:
   reference: https://msberends.github.io/AMR//reference
   article: https://msberends.github.io/AMR//articles

docs/reference/AMR.html

@@ -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">1.7.1.9002</span>
       </span>
     </div>
 
@@ -286,7 +286,7 @@
 <p>Matthijs S. Berends <br />
 m.s.berends [at] umcg [dot] nl <br />
 University of Groningen
-Department of Medical Microbiology and Infection Prevention
+Department of Medical Microbiology and Infection Prevention <br />
 University Medical Center Groningen <br />
 Post Office Box 30001 <br />
 9700 RB Groningen <br />

docs/reference/count.html

@@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
       </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">1.7.1.9002</span>
       </span>
     </div>
 
@@ -409,6 +409,12 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
               n1 <span class='op'>=</span> <span class='fu'>count_all</span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span>,  <span class='co'># the actual total; sum of all three</span>
               n2 <span class='op'>=</span> <span class='fu'>n_rsi</span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span>,      <span class='co'># same - analogous to n_distinct</span>
               total <span class='op'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/context.html'>n</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>          <span class='co'># NOT the number of tested isolates!</span>
+              
+  <span class='co'># Number of available isolates for a whole antibiotic class</span>
+  <span class='co'># (i.e., in this data set columns GEN, TOB, AMK, KAN)</span>
+  <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
+    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
+    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'><a href='antibiotic_class_selectors.html'>aminoglycosides</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>n_rsi</span><span class='op'>)</span><span class='op'>)</span>
  
   <span class='co'># Count co-resistance between amoxicillin/clav acid and gentamicin,</span>
   <span class='co'># so we can see that combination therapy does a lot more than mono therapy.</span>

docs/reference/custom_eucast_rules.html

@@ -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">1.7.1.9001</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>

docs/reference/index.html

@@ -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">1.7.1.9004</span>
       </span>
     </div>
 
@@ -508,7 +508,7 @@
       </tr><tr>
         
         <td>
-          <p><code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;rsi&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;rsi&gt;</i>)</a></code> </p>
+          <p><code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;rsi&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;rsi&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;rsi&gt;</i>)</a></code> </p>
         </td>
         <td><p>Plotting for Classes <code>rsi</code>, <code>mic</code> and <code>disk</code></p></td>
       </tr><tr>
@@ -526,13 +526,13 @@
       </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>
         
         <td>
-          <p><code><a href="resistance_predict.html">resistance_predict()</a></code> <code><a href="resistance_predict.html">rsi_predict()</a></code> <code><a href="resistance_predict.html">plot(<i>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">ggplot(<i>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_predict()</a></code> </p>
+          <p><code><a href="resistance_predict.html">resistance_predict()</a></code> <code><a href="resistance_predict.html">rsi_predict()</a></code> <code><a href="resistance_predict.html">plot(<i>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_predict()</a></code> <code><a href="resistance_predict.html">ggplot(<i>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">autoplot(<i>&lt;resistance_predict&gt;</i>)</a></code> </p>
         </td>
         <td><p>Predict antimicrobial resistance</p></td>
       </tr><tr>

docs/reference/plot.html

@@ -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">1.7.1.9002</span>
       </span>
     </div>
 
@@ -258,7 +258,23 @@
 <span class='op'>)</span>
 
 <span class='co'># S3 method for mic</span>
-<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span>
+<span class='fu'>ggplot</span><span class='op'>(</span>
+  <span class='va'>data</span>,
+  mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
+  title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"MIC values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
+  ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
+  xlab <span class='op'>=</span> <span class='st'>"Minimum Inhibitory Concentration (mg/L)"</span>,
+  mo <span class='op'>=</span> <span class='cn'>NULL</span>,
+  ab <span class='op'>=</span> <span class='cn'>NULL</span>,
+  guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>,
+  colours_RSI <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='st'>"#ED553B"</span>, <span class='st'>"#3CAEA3"</span>, <span class='st'>"#F6D55C"</span><span class='op'>)</span>,
+  language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
+  expand <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  <span class='va'>...</span>
+<span class='op'>)</span>
+
+<span class='co'># S3 method for mic</span>
+<span class='fu'>autoplot</span><span class='op'>(</span>
   <span class='va'>data</span>,
   mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
   title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"MIC values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
@@ -289,7 +305,23 @@
 <span class='op'>)</span>
 
 <span class='co'># S3 method for disk</span>
-<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span>
+<span class='fu'>ggplot</span><span class='op'>(</span>
+  <span class='va'>data</span>,
+  mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
+  title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Disk zones of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
+  ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
+  xlab <span class='op'>=</span> <span class='st'>"Disk diffusion diameter (mm)"</span>,
+  mo <span class='op'>=</span> <span class='cn'>NULL</span>,
+  ab <span class='op'>=</span> <span class='cn'>NULL</span>,
+  guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>,
+  colours_RSI <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='st'>"#ED553B"</span>, <span class='st'>"#3CAEA3"</span>, <span class='st'>"#F6D55C"</span><span class='op'>)</span>,
+  language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
+  expand <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  <span class='va'>...</span>
+<span class='op'>)</span>
+
+<span class='co'># S3 method for disk</span>
+<span class='fu'>autoplot</span><span class='op'>(</span>
   <span class='va'>data</span>,
   mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
   title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Disk zones of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
@@ -314,7 +346,19 @@
 <span class='op'>)</span>
 
 <span class='co'># S3 method for rsi</span>
-<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span>
+<span class='fu'>ggplot</span><span class='op'>(</span>
+  <span class='va'>data</span>,
+  mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
+  title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
+  xlab <span class='op'>=</span> <span class='st'>"Antimicrobial Interpretation"</span>,
+  ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
+  colours_RSI <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='st'>"#ED553B"</span>, <span class='st'>"#3CAEA3"</span>, <span class='st'>"#F6D55C"</span><span class='op'>)</span>,
+  language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
+  <span class='va'>...</span>
+<span class='op'>)</span>
+
+<span class='co'># S3 method for rsi</span>
+<span class='fu'>autoplot</span><span class='op'>(</span>
   <span class='va'>data</span>,
   mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
   title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,

docs/reference/resistance_predict.html

@@ -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">1.7.1.9002</span>
       </span>
     </div>
 
@@ -275,10 +275,18 @@
 <span class='co'># S3 method for resistance_predict</span>
 <span class='fu'><a href='plot.html'>plot</a></span><span class='op'>(</span><span class='va'>x</span>, main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Prediction of"</span>, <span class='va'>x_name</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
 
+<span class='fu'>ggplot_rsi_predict</span><span class='op'>(</span>
+  <span class='va'>x</span>,
+  main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Prediction of"</span>, <span class='va'>x_name</span><span class='op'>)</span>,
+  ribbon <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  <span class='va'>...</span>
+<span class='op'>)</span>
+
 <span class='co'># S3 method for resistance_predict</span>
 <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>x</span>, main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Prediction of"</span>, <span class='va'>x_name</span><span class='op'>)</span>, ribbon <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span>
 
-<span class='fu'>ggplot_rsi_predict</span><span class='op'>(</span>
+<span class='co'># S3 method for resistance_predict</span>
+<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/autoplot.html'>autoplot</a></span><span class='op'>(</span>
   <span class='va'>x</span>,
   main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Prediction of"</span>, <span class='va'>x_name</span><span class='op'>)</span>,
   ribbon <span class='op'>=</span> <span class='cn'>TRUE</span>,

docs/survey.html

@@ -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">1.7.1.9004</span>
       </span>
     </div>
 

index.md

@@ -31,9 +31,9 @@ example_isolates %>%
 #> ℹ Using column 'mo' as input for `mo_is_gram_negative()`
 #> ℹ Using column 'mo' as input for `mo_is_intrinsic_resistant()`
 #> ℹ Determining intrinsic resistance based on 'EUCAST Expert Rules' and 'EUCAST Intrinsic
-#>   Resistance and Unusual Phenotypes' v3.2 (2020)
+#>    Resistance and Unusual Phenotypes' v3.2 (2020)
 #> ℹ For `aminoglycosides()` using columns: 'AMK' (amikacin), 'GEN' (gentamicin), 'KAN'
-#>   (kanamycin) and 'TOB' (tobramycin)
+#>    (kanamycin) and 'TOB' (tobramycin)
 #> ℹ For `carbapenems()` using columns: 'IPM' (imipenem) and 'MEM' (meropenem)
 ```
 

inst/tinytest/test-ab_class_selectors.R

@@ -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:
   

inst/tinytest/test-bug_drug_combinations.R

@@ -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())
+}

inst/tinytest/test-eucast_rules.R

@@ -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)

inst/tinytest/test-zzz.R

@@ -24,7 +24,7 @@
 # ==================================================================== #
 
 # Check if these function still exist in the package (all are in Suggests field)
-# Since GitHub Action runs every night, we will get emailed when a dependency fails based on this unit test
+# Since GitHub Actions runs every night, we will get emailed when a dependency fails based on this unit test
 # functions used by import_fn()
 import_functions <- c(
   "anti_join" = "dplyr",
@@ -53,14 +53,23 @@ call_functions <- c(
   # skimr
   "inline_hist" = "skimr",
   "sfl" = "skimr",
-  # set_mo_source
+  # readxl
   "read_excel" = "readxl",
-  # ggplot_rsi
+  # ggplot2
+  "aes" = "ggplot2",
   "aes_string" = "ggplot2",
+  "arrow" = "ggplot2",
+  "autoplot" = "ggplot2",
   "element_blank" = "ggplot2",
   "element_line" = "ggplot2",
   "element_text" = "ggplot2",
+  "expand_limits" = "ggplot2",
   "facet_wrap" = "ggplot2",
+  "geom_errorbar" = "ggplot2",
+  "geom_path" = "ggplot2",
+  "geom_point" = "ggplot2",
+  "geom_ribbon" = "ggplot2",
+  "geom_segment" = "ggplot2",
   "geom_text" = "ggplot2",
   "ggplot" = "ggplot2",
   "labs" = "ggplot2",
@@ -70,31 +79,9 @@ call_functions <- c(
   "scale_y_continuous" = "ggplot2",
   "theme" = "ggplot2",
   "theme_minimal" = "ggplot2",
-  # ggplot_pca
-  "aes" = "ggplot2",
-  "arrow" = "ggplot2",
-  "element_blank" = "ggplot2",
-  "element_line" = "ggplot2",
-  "element_text" = "ggplot2",
-  "expand_limits" = "ggplot2",
-  "geom_path" = "ggplot2",
-  "geom_point" = "ggplot2",
-  "geom_segment" = "ggplot2",
-  "geom_text" = "ggplot2",
-  "ggplot" = "ggplot2",
-  "labs" = "ggplot2",
-  "theme" = "ggplot2",
-  "theme_minimal" = "ggplot2",
   "unit" = "ggplot2",
   "xlab" = "ggplot2",
-  "ylab" = "ggplot2",
-  # resistance_predict
-  "aes" = "ggplot2",
-  "geom_errorbar" = "ggplot2",
-  "geom_point" = "ggplot2",
-  "geom_ribbon" = "ggplot2",
-  "ggplot" = "ggplot2",
-  "labs" = "ggplot2"
+  "ylab" = "ggplot2"
 )
 
 import_functions <- c(import_functions, call_functions)

man/AMR.Rd

@@ -50,7 +50,7 @@ For suggestions, comments or questions, please contact us at:
 Matthijs S. Berends \cr
 m.s.berends [at] umcg [dot] nl \cr
 University of Groningen
-Department of Medical Microbiology and Infection Prevention
+Department of Medical Microbiology and Infection Prevention \cr
 University Medical Center Groningen \cr
 Post Office Box 30001 \cr
 9700 RB Groningen \cr

man/antibiotic_class_selectors.Rd

@@ -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"))

man/count.Rd

@@ -167,6 +167,12 @@ if (require("dplyr")) {
               n1 = count_all(CIP),  # the actual total; sum of all three
               n2 = n_rsi(CIP),      # same - analogous to n_distinct
               total = n())          # NOT the number of tested isolates!
+              
+  # Number of available isolates for a whole antibiotic class
+  # (i.e., in this data set columns GEN, TOB, AMK, KAN)
+  example_isolates \%>\%
+    group_by(hospital_id) \%>\%
+    summarise(across(aminoglycosides(), n_rsi))
  
   # Count co-resistance between amoxicillin/clav acid and gentamicin,
   # so we can see that combination therapy does a lot more than mono therapy.

man/custom_eucast_rules.Rd

@@ -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)
 \item \code{polymyxins}\cr(colistin, polymyxin B, polymyxin B/polysorbate 80)
+\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)
 \item \code{streptogramins}\cr(pristinamycin, quinupristin/dalfopristin)
 \item \code{tetracyclines}\cr(chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline, tigecycline)
 \item \code{tetracyclines_except_tgc}\cr(chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline)

man/plot.Rd

@@ -4,10 +4,13 @@
 \alias{plot}
 \alias{plot.mic}
 \alias{ggplot.mic}
+\alias{autoplot.mic}
 \alias{plot.disk}
 \alias{ggplot.disk}
+\alias{autoplot.disk}
 \alias{plot.rsi}
 \alias{ggplot.rsi}
+\alias{autoplot.rsi}
 \title{Plotting for Classes \code{rsi}, \code{mic} and \code{disk}}
 \usage{
 \method{plot}{mic}(
@@ -39,6 +42,21 @@
   ...
 )
 
+\method{autoplot}{mic}(
+  data,
+  mapping = NULL,
+  title = paste("MIC values of", deparse(substitute(data))),
+  ylab = "Frequency",
+  xlab = "Minimum Inhibitory Concentration (mg/L)",
+  mo = NULL,
+  ab = NULL,
+  guideline = "EUCAST",
+  colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
+  language = get_locale(),
+  expand = TRUE,
+  ...
+)
+
 \method{plot}{disk}(
   x,
   main = paste("Disk zones of", deparse(substitute(x))),
@@ -68,6 +86,21 @@
   ...
 )
 
+\method{autoplot}{disk}(
+  data,
+  mapping = NULL,
+  title = paste("Disk zones of", deparse(substitute(data))),
+  ylab = "Frequency",
+  xlab = "Disk diffusion diameter (mm)",
+  mo = NULL,
+  ab = NULL,
+  guideline = "EUCAST",
+  colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
+  language = get_locale(),
+  expand = TRUE,
+  ...
+)
+
 \method{plot}{rsi}(
   x,
   ylab = "Percentage",
@@ -86,6 +119,17 @@
   language = get_locale(),
   ...
 )
+
+\method{autoplot}{rsi}(
+  data,
+  mapping = NULL,
+  title = paste("Resistance Overview of", deparse(substitute(data))),
+  xlab = "Antimicrobial Interpretation",
+  ylab = "Frequency",
+  colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
+  language = get_locale(),
+  ...
+)
 }
 \arguments{
 \item{x, data}{MIC values created with \code{\link[=as.mic]{as.mic()}} or disk diffusion values created with \code{\link[=as.disk]{as.disk()}}}

man/resistance_predict.Rd

@@ -4,8 +4,9 @@
 \alias{resistance_predict}
 \alias{rsi_predict}
 \alias{plot.resistance_predict}
-\alias{ggplot.resistance_predict}
 \alias{ggplot_rsi_predict}
+\alias{ggplot.resistance_predict}
+\alias{autoplot.resistance_predict}
 \title{Predict antimicrobial resistance}
 \usage{
 resistance_predict(
@@ -40,9 +41,16 @@ rsi_predict(
 
 \method{plot}{resistance_predict}(x, main = paste("Resistance Prediction of", x_name), ...)
 
+ggplot_rsi_predict(
+  x,
+  main = paste("Resistance Prediction of", x_name),
+  ribbon = TRUE,
+  ...
+)
+
 \method{ggplot}{resistance_predict}(x, main = paste("Resistance Prediction of", x_name), ribbon = TRUE, ...)
 
-ggplot_rsi_predict(
+\method{autoplot}{resistance_predict}(
   x,
   main = paste("Resistance Prediction of", x_name),
   ribbon = TRUE,