(v1.7.1.9018) translation fix

.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: true}
           - {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:
@@ -94,15 +104,20 @@ jobs:
         # we don't want to depend on the sysreqs pkg here, as it requires quite a recent R version
         # as of May 2021: https://sysreqs.r-hub.io/pkg/AMR,R,cleaner,curl,dplyr,ggplot2,ggtext,knitr,microbenchmark,pillar,readxl,rmarkdown,rstudioapi,rvest,skimr,tidyr,tinytest,xml2,backports,crayon,rlang,vctrs,evaluate,highr,markdown,stringr,yaml,xfun,cli,ellipsis,fansi,lifecycle,utf8,glue,mime,magrittr,stringi,generics,R6,tibble,tidyselect,pkgconfig,purrr,digest,gtable,isoband,MASS,mgcv,scales,withr,nlme,Matrix,farver,labeling,munsell,RColorBrewer,viridisLite,lattice,colorspace,gridtext,Rcpp,RCurl,png,jpeg,bitops,cellranger,progress,rematch,hms,prettyunits,htmltools,jsonlite,tinytex,base64enc,httr,selectr,openssl,askpass,sys,repr,cpp11
         run: |
-          sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev
+          sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev libudunits2-dev
 
+      - name: Query dependencies
+        # this will change every day (i.e. at scheduled night run of GitHub Action), so it will cache dependency updates
+        run: |
+          writeLines(paste0(format(Sys.Date(), "%Y%m%d"), sprintf("-R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/daily-R-bundle")
+        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/daily-R-bundle') }}-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: 1.7.1.9018
+Date: 2021-07-11
 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

@@ -120,7 +120,11 @@ S3method(print,rsi)
 S3method(prod,mic)
 S3method(quantile,mic)
 S3method(range,mic)
+S3method(rep,ab)
+S3method(rep,disk)
+S3method(rep,mic)
 S3method(rep,mo)
+S3method(rep,rsi)
 S3method(round,mic)
 S3method(sign,mic)
 S3method(signif,mic)
@@ -170,6 +174,7 @@ export(age)
 export(age_groups)
 export(all_antimicrobials)
 export(aminoglycosides)
+export(aminopenicillins)
 export(anti_join_microorganisms)
 export(antimicrobials_equal)
 export(as.ab)
@@ -255,6 +260,8 @@ 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 +304,14 @@ 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 +325,11 @@ 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 +1,30 @@
+# `AMR` 1.7.1.9018
+## <small>Last updated: 11 July 2021</small>
+
+### Changed
+* Antibiotic class selectors (see `ab_class()`)
+  * They now also work in R-3.0 and R-3.1, supporting every version of R since 2013
+  * Added more selectors: `aminopenicillins()`, `lincosamides()`, `lipoglycopeptides()`, `polymyxins()`, `quinolones()`, `streptogramins()` and `ureidopenicillins()`
+  * Fix for using selectors multiple times in one call (e.g., using them in `dplyr::filter()` and immediately after in `dplyr::select()`)
+  * Added argument `only_treatable`, which defaults to `TRUE` and will exclude drugs that are only for laboratory tests and not for treating patients (such as imipenem/EDTA and gentamicin-high)
+* Fix for duplicate ATC codes in the `antibiotics` data set
+* 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
+* When printing a tibble with any old MO code, a warning will be thrown that old codes should be updated using `as.mo()`
+* Improved automatic column selector when `col_*` arguments are left blank, e.g. in `first_isolate()`
+* The right input types for `random_mic()`, `random_disk()` and `random_rsi()` are now enforced
+* `as.rsi()` can now correct for textual input (such as "Susceptible", "Resistant") in Dutch, English, French, German, Italian, Portuguese and Spanish
+* When warnings are throws because of too few isolates in any `count_*()`, `proportion_*()` function (or `resistant()` or `susceptible()`), the `dplyr` group will be shown, if available
+* Taxonomic names now print in italic in tibbles, if created with `mo_name()`, `mo_fullname()`, `mo_shortname()`, `mo_genus()` or `mo_family()`
+* `ab_name()` gained argument `snake_case`, which is useful for column renaming
+* Fix for legends created with `scale_rsi_colours()` when using `ggplot2` v3.3.4 or higher (this is bug ggplot2#4511, soon to be fixed)
+* Fix for minor translation errors
+
+
 # `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 +44,7 @@
   ```
 
 ### 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

@@ -170,65 +170,73 @@ search_type_in_df <- function(x, type, info = TRUE) {
 
   # remove attributes from other packages
   x <- as.data.frame(x, stringsAsFactors = FALSE)
-  colnames(x) <- trimws(colnames(x))
+  colnames_formatted <- tolower(generalise_antibiotic_name(colnames(x)))
 
   # -- mo
   if (type == "mo") {
     if (any(vapply(FUN.VALUE = logical(1), x, is.mo))) {
-      found <- sort(colnames(x)[vapply(FUN.VALUE = logical(1), x, is.mo)])[1]
-    } else if ("mo" %in% colnames(x) &
-               suppressWarnings(
-                 all(x$mo %in% c(NA, microorganisms$mo)))) {
+      # take first <mo> column
+      found <- colnames(x)[vapply(FUN.VALUE = logical(1), x, is.mo)]
+    } else if ("mo" %in% colnames_formatted &
+               suppressWarnings(all(x$mo %in% c(NA, microorganisms$mo)))) {
       found <- "mo"
-    } else if (any(colnames(x) %like% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$")) {
-      found <- sort(colnames(x)[colnames(x) %like% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$"])[1]
-    } else if (any(colnames(x) %like% "^(microorganism|organism|bacteria|ba[ck]terie)")) {
-      found <- sort(colnames(x)[colnames(x) %like% "^(microorganism|organism|bacteria|ba[ck]terie)"])[1]
-    } else if (any(colnames(x) %like% "species")) {
-      found <- sort(colnames(x)[colnames(x) %like% "species"])[1]
+    } else if (any(colnames_formatted %like_case% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$")) {
+      found <- sort(colnames(x)[colnames_formatted %like_case% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$"])
+    } else if (any(colnames_formatted %like_case% "^(microorganism|organism|bacteria|ba[ck]terie)")) {
+      found <- sort(colnames(x)[colnames_formatted %like_case% "^(microorganism|organism|bacteria|ba[ck]terie)"])
+    } else if (any(colnames_formatted %like_case% "species")) {
+      found <- sort(colnames(x)[colnames_formatted %like_case% "species"])
     }
 
   }
   # -- key antibiotics
   if (type %in% c("keyantibiotics", "keyantimicrobials")) {
-    if (any(colnames(x) %like% "^key.*(ab|antibiotics|antimicrobials)")) {
-      found <- sort(colnames(x)[colnames(x) %like% "^key.*(ab|antibiotics|antimicrobials)"])[1]
+    if (any(colnames_formatted %like_case% "^key.*(ab|antibiotics|antimicrobials)")) {
+      found <- sort(colnames(x)[colnames_formatted %like_case% "^key.*(ab|antibiotics|antimicrobials)"])
     }
   }
   # -- date
   if (type == "date") {
-    if (any(colnames(x) %like% "^(specimen date|specimen_date|spec_date)")) {
+    if (any(colnames_formatted %like_case% "^(specimen date|specimen_date|spec_date)")) {
       # WHONET support
-      found <- sort(colnames(x)[colnames(x) %like% "^(specimen date|specimen_date|spec_date)"])[1]
+      found <- sort(colnames(x)[colnames_formatted %like_case% "^(specimen date|specimen_date|spec_date)"])
       if (!any(class(pm_pull(x, found)) %in% c("Date", "POSIXct"))) {
         stop(font_red(paste0("Found column '", font_bold(found), "' to be used as input for `col_", type,
                              "`, but this column contains no valid dates. Transform its values to valid dates first.")),
              call. = FALSE)
       }
+      
     } else if (any(vapply(FUN.VALUE = logical(1), x, function(x) inherits(x, c("Date", "POSIXct"))))) {
-      found <- sort(colnames(x)[vapply(FUN.VALUE = logical(1), x, function(x) inherits(x, c("Date", "POSIXct")))])[1]
+      # take first <Date> column
+      found <- colnames(x)[vapply(FUN.VALUE = logical(1), x, function(x) inherits(x, c("Date", "POSIXct")))]
     }
   }
   # -- patient id
   if (type == "patient_id") {
-    if (any(colnames(x) %like% "^(identification |patient|patid)")) {
-      found <- sort(colnames(x)[colnames(x) %like% "^(identification |patient|patid)"])[1]
+    crit1 <- colnames_formatted %like_case% "^(patient|patid)"
+    if (any(crit1)) {
+      found <- colnames(x)[crit1]
+    } else {
+      crit2 <- colnames_formatted %like_case% "(identification |patient|pat.*id)"
+      if (any(crit2)) {
+        found <- colnames(x)[crit2]
+      }
     }
   }
   # -- specimen
   if (type == "specimen") {
-    if (any(colnames(x) %like% "(specimen type|spec_type)")) {
-      found <- sort(colnames(x)[colnames(x) %like% "(specimen type|spec_type)"])[1]
-    } else if (any(colnames(x) %like% "^(specimen)")) {
-      found <- sort(colnames(x)[colnames(x) %like% "^(specimen)"])[1]
+    if (any(colnames_formatted %like_case% "(specimen type|spec_type)")) {
+      found <- sort(colnames(x)[colnames_formatted %like_case% "(specimen type|spec_type)"])
+    } else if (any(colnames_formatted %like_case% "^(specimen)")) {
+      found <- sort(colnames(x)[colnames_formatted %like_case% "^(specimen)"])
     }
   }
   # -- UTI (urinary tract infection)
   if (type == "uti") {
-    if (any(colnames(x) == "uti")) {
-      found <- colnames(x)[colnames(x) == "uti"][1]
-    } else if (any(colnames(x) %like% "(urine|urinary)")) {
-      found <- sort(colnames(x)[colnames(x) %like% "(urine|urinary)"])[1]
+    if (any(colnames_formatted == "uti")) {
+      found <- colnames(x)[colnames_formatted == "uti"]
+    } else if (any(colnames_formatted %like_case% "(urine|urinary)")) {
+      found <- sort(colnames(x)[colnames_formatted %like_case% "(urine|urinary)"])
     }
     if (!is.null(found)) {
       # this column should contain logicals
@@ -241,10 +249,12 @@ search_type_in_df <- function(x, type, info = TRUE) {
     }
   }
   
+  found <- found[1]
+  
   if (!is.null(found) & info == TRUE) {
     if (message_not_thrown_before(fn = paste0("search_", type))) {
       msg <- paste0("Using column '", font_bold(found), "' as input for `col_", type, "`.")
-      if (type %in% c("keyantibiotics", "specimen")) {
+      if (type %in% c("keyantibiotics", "keyantimicrobials", "specimen")) {
         msg <- paste(msg, "Use", font_bold(paste0("col_", type), "= FALSE"), "to prevent this.")
       }
       message_(msg)
@@ -506,7 +516,7 @@ 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"))) {
@@ -696,7 +706,7 @@ meet_criteria <- function(object,
             ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1,
                    "be a finite number",
                    "all be finite numbers"),
-            " (i.e., not be infinite)",
+            " (i.e. not be infinite)",
             call = call_depth)
   }
   if (!is.null(contains_column_class)) {
@@ -714,11 +724,6 @@ meet_criteria <- function(object,
 }
 
 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$get_current_data.call)) {
-    return(pkg_env$get_current_data.out)
-  }
-  
   # try dplyr::cur_data_all() first to support dplyr groups
   # only useful for e.g. dplyr::filter(), dplyr::mutate() and dplyr::summarise()
   # not useful (throws error) with e.g. dplyr::select() - but that will be caught later in this function
@@ -726,72 +731,32 @@ get_current_data <- function(arg_name, call) {
   if (!is.null(cur_data_all)) {
     out <- tryCatch(cur_data_all(), error = function(e) NULL)
     if (is.data.frame(out)) {
-      out <- structure(out, type = "dplyr_cur_data_all")
-      pkg_env$get_current_data.call <- unique_call_id(entire_session = FALSE)
-      pkg_env$get_current_data.out <- out
-      return(out)
-    }
-  }
-
-  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
-    if (is.na(arg_name)) {
-      # like in carbapenems() etc.
-      warning_("this function can only be used in R >= 3.2", call = call)
-      return(data.frame())
-    } else {
-      # mimic a default R error, e.g. for example_isolates[which(mo_name() %like% "^ent"), ] 
-      stop_("argument `", arg_name, "` is missing with no default", call = call)
+      return(structure(out, type = "dplyr_cur_data_all"))
     }
   }
   
-  # try a (base R) method, by going over the complete system call stack with sys.frames()
-  not_set <- TRUE
-  source <- "base_R"
-  frms <- lapply(sys.frames(), function(el) {
-    if (not_set == TRUE && ".Generic" %in% names(el)) {
-      if (tryCatch(".data" %in% names(el) && is.data.frame(el$`.data`), error = function(e) FALSE)) {
-        # - - - -
-        # dplyr
-        # - - - -
-        # an element `.data` will be in the system call stack when using dplyr::select()
-        # [but not when using dplyr::filter(), dplyr::mutate() or dplyr::summarise()]
-        not_set <<- FALSE
-        source <<- "dplyr_selector"
-        el$`.data`
-      } else if (tryCatch(any(c("x", "xx") %in% names(el)), error = function(e) FALSE)) {
-        # - - - -
-        # base R
-        # - - - -
-        # an element `x` will be in this environment for only cols, e.g. `example_isolates[, carbapenems()]`
-        # an element `xx` will be in this environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
-        if (tryCatch(is.data.frame(el$xx), error = function(e) FALSE)) {
-          not_set <<- FALSE
-          el$xx
-        } else if (tryCatch(is.data.frame(el$x))) {
-          not_set <<- FALSE
-          el$x
-        } else {
-          NULL
-        }
-      } else {
-        NULL
+  # try a manual (base R) method, by going over all underlying environments with sys.frames()
+  for (env in sys.frames()) {
+    if (!is.null(env$`.Generic`)) {
+      # don't check `".Generic" %in% names(env)`, because in R < 3.2, `names(env)` is always NULL
+      
+      if (!is.null(env$`.data`) && is.data.frame(env$`.data`)) {
+        # an element `.data` will be in the environment when using `dplyr::select()`
+        # (but not when using `dplyr::filter()`, `dplyr::mutate()` or `dplyr::summarise()`)
+        return(structure(env$`.data`, type = "dplyr_selector"))
+        
+      } else if (!is.null(env$xx) && is.data.frame(env$xx)) {
+        # an element `xx` will be in the environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
+        return(structure(env$xx, type = "base_R"))
+        
+      } else if (!is.null(env$x) && is.data.frame(env$x)) {
+        # an element `x` will be in the environment for only cols, e.g. `example_isolates[, carbapenems()]`
+        return(structure(env$x, type = "base_R"))
       }
-    } else {
-      NULL
     }
-  })
-  
-  # lookup the matched frame and return its value: a data.frame
-  vars_df <- tryCatch(frms[[which(!vapply(FUN.VALUE = logical(1), frms, is.null))]], error = function(e) NULL)
-  if (is.data.frame(vars_df)) {
-    out <- structure(vars_df, type = source)
-    pkg_env$get_current_data.call <- unique_call_id(entire_session = FALSE)
-    pkg_env$get_current_data.out <- out
-    return(out)
   }
   
-  # nothing worked, so:
+  # no data.frame found, so an error  must be returned:
   if (is.na(arg_name)) {
     if (isTRUE(is.numeric(call))) {
       fn <- as.character(sys.call(call + 1)[1])
@@ -821,19 +786,19 @@ get_current_column <- function() {
     }
   }
   
-  # cur_column() doesn't always work (only allowed for conditions set by dplyr), but it's probably still possible:
-  frms <- lapply(sys.frames(), function(el) {
-    if ("i" %in% names(el)) {
-      if ("tibble_vars" %in% names(el)) {
+  # cur_column() doesn't always work (only allowed for certain conditions set by dplyr), but it's probably still possible:
+  frms <- lapply(sys.frames(), function(env) {
+    if (!is.null(env$i)) {
+      if (!is.null(env$tibble_vars)) {
         # for mutate_if()
-        el$tibble_vars[el$i]
+        env$tibble_vars[env$i]
       } else {
         # for mutate(across())
         df <- tryCatch(get_current_data(NA, 0), error = function(e) NULL)
         if (is.data.frame(df)) {
-          colnames(df)[el$i]
+          colnames(df)[env$i]
         } else {
-          el$i
+          env$i
         }
       }
     } else {
@@ -851,7 +816,7 @@ get_current_column <- function() {
 }
 
 is_null_or_grouped_tbl <- function(x) {
-  # attribute "grouped_df" might change at one point, so only set in one place; here.
+  # class "grouped_df" might change at one point, so only set in one place; here.
   is.null(x) || inherits(x, "grouped_df")
 }
 
@@ -860,7 +825,7 @@ unique_call_id <- function(entire_session = FALSE) {
     c(envir = "session",
       call = "session")
   } else {
-    # combination of environment ID (like "0x7fed4ee8c848")
+    # combination of environment ID (such as "0x7fed4ee8c848")
     # and highest system call
     call <- paste0(deparse(sys.calls()[[1]]), collapse = "")
     if (!interactive() || call %like% "run_test_dir|test_all|tinytest|test_package|testthat") {
@@ -980,8 +945,8 @@ font_grey_bg <- function(..., collapse = " ") {
     # similar to HTML #444444
     try_colour(..., before = "\033[48;5;238m", after = "\033[49m", collapse = collapse)  
   } else {
-    # similar to HTML #eeeeee
-    try_colour(..., before = "\033[48;5;254m", after = "\033[49m", collapse = collapse)
+    # similar to HTML #f0f0f0
+    try_colour(..., before = "\033[48;5;255m", after = "\033[49m", collapse = collapse)
   }
 }
 font_green_bg <- function(..., collapse = " ") {

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])
                                        }
                                      }
@@ -580,6 +580,15 @@ unique.ab <- function(x, incomparables = FALSE, ...) {
   y
 }
 
+#' @method rep ab
+#' @export
+#' @noRd
+rep.ab <- function(x, ...) {
+  y <- NextMethod()
+  attributes(y) <- attributes(x)
+  y
+}
+
 generalise_antibiotic_name <- function(x) {
   x <- toupper(x)
   # remove suffices

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.
 #' @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, "."), "")}}
+#' @param only_treatable a [logical] to indicate whether agents that are only for laboratory tests should be excluded (defaults to `TRUE`), such as gentamicin-high (`GEH`) and imipenem/EDTA (`IPE`)
+#' @details
+#' These functions can be used in data set calls for selecting columns and filtering rows. They are heavily inspired by the [Tidyverse selection helpers][tidyselect::language] such as [`everything()`][tidyselect::everything()], but also work in base \R and not only in `dplyr` verbs. Nonetheless, they are very convenient to use with `dplyr` functions such as [`select()`][dplyr::select()], [`filter()`][dplyr::filter()] and [`summarise()`][dplyr::summarise()], see *Examples*.
 #' 
+#' All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) in the [antibiotics] data set. This means that a selector such as [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. Use the [ab_class()] function to filter/select on a manually defined antibiotic class.
 #' 
-#' 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()].
+#' @section Full list of supported agents:
 #' 
-#' 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.
-#' 
-#' The group of betalactams consists of all carbapenems, cephalosporins and penicillins.
+#' `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()) %>% 
@@ -112,164 +112,255 @@
 #'     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"))
 #' }
 #' }
 ab_class <- function(ab_class, 
-                     only_rsi_columns = FALSE) {
-  ab_selector(ab_class, function_name = "ab_class", only_rsi_columns = only_rsi_columns)
+                     only_rsi_columns = FALSE,
+                     only_treatable = TRUE) {
+  meet_criteria(ab_class, allow_class = "character", has_length = 1, allow_NULL = TRUE)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
+  ab_selector(NULL, only_rsi_columns = only_rsi_columns, ab_class = ab_class, only_treatable = only_treatable)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
-aminoglycosides <- function(only_rsi_columns = FALSE) {
-  ab_selector("aminoglycoside", function_name = "aminoglycosides", only_rsi_columns = only_rsi_columns)
+aminoglycosides <- function(only_rsi_columns = FALSE, only_treatable = TRUE) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
+  ab_selector("aminoglycosides", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable)
 }
 
 #' @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)
+aminopenicillins <- function(only_rsi_columns = FALSE) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_selector("aminopenicillins", only_rsi_columns = only_rsi_columns)
 }
+
 #' @rdname antibiotic_class_selectors
 #' @export
-carbapenems <- function(only_rsi_columns = FALSE) {
-  ab_selector("carbapenem", function_name = "carbapenems", only_rsi_columns = only_rsi_columns)
+betalactams <- function(only_rsi_columns = FALSE, only_treatable = TRUE) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
+  ab_selector("betalactams", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+carbapenems <- function(only_rsi_columns = FALSE, only_treatable = TRUE) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
+  ab_selector("carbapenems", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 cephalosporins <- function(only_rsi_columns = FALSE) {
-  ab_selector("cephalosporin", function_name = "cephalosporins", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_selector("cephalosporins", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 cephalosporins_1st <- function(only_rsi_columns = FALSE) {
-  ab_selector("cephalosporins.*1", function_name = "cephalosporins_1st", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_selector("cephalosporins_1st", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 cephalosporins_2nd <- function(only_rsi_columns = FALSE) {
-  ab_selector("cephalosporins.*2", function_name = "cephalosporins_2nd", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_selector("cephalosporins_2nd", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 cephalosporins_3rd <- function(only_rsi_columns = FALSE) {
-  ab_selector("cephalosporins.*3", function_name = "cephalosporins_3rd", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_selector("cephalosporins_3rd", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 cephalosporins_4th <- function(only_rsi_columns = FALSE) {
-  ab_selector("cephalosporins.*4", function_name = "cephalosporins_4th", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_selector("cephalosporins_4th", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 cephalosporins_5th <- function(only_rsi_columns = FALSE) {
-  ab_selector("cephalosporins.*5", function_name = "cephalosporins_5th", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_selector("cephalosporins_5th", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 fluoroquinolones <- function(only_rsi_columns = FALSE) {
-  ab_selector("fluoroquinolone", function_name = "fluoroquinolones", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_selector("fluoroquinolones", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 glycopeptides <- function(only_rsi_columns = FALSE) {
-  ab_selector("glycopeptide", function_name = "glycopeptides", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_selector("glycopeptides", only_rsi_columns = only_rsi_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+lincosamides <- function(only_rsi_columns = FALSE) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_selector("lincosamides", only_rsi_columns = only_rsi_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+lipoglycopeptides <- function(only_rsi_columns = FALSE) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_selector("lipoglycopeptides", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 macrolides <- function(only_rsi_columns = FALSE) {
-  ab_selector("macrolide", function_name = "macrolides", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_selector("macrolides", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 oxazolidinones <- function(only_rsi_columns = FALSE) {
-  ab_selector("oxazolidinone", function_name = "oxazolidinones", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_selector("oxazolidinones", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 penicillins <- function(only_rsi_columns = FALSE) {
-  ab_selector("penicillin", function_name = "penicillins", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_selector("penicillins", only_rsi_columns = only_rsi_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+polymyxins <- function(only_rsi_columns = FALSE, only_treatable = TRUE) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
+  ab_selector("polymyxins", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+streptogramins <- function(only_rsi_columns = FALSE) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_selector("streptogramins", only_rsi_columns = only_rsi_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+quinolones <- function(only_rsi_columns = FALSE) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_selector("quinolones", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 tetracyclines <- function(only_rsi_columns = FALSE) {
-  ab_selector("tetracycline", function_name = "tetracyclines", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  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)
-  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1, .call_depth = 1)
-  
-  if (getRversion() < "3.2") {
-    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
+#' @rdname antibiotic_class_selectors
+#' @export
+ureidopenicillins <- function(only_rsi_columns = FALSE) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_selector("ureidopenicillins", only_rsi_columns = only_rsi_columns)
+}
+
+ab_selector <- function(function_name,
+                        only_rsi_columns,
+                        only_treatable = FALSE,
+                        ab_class = NULL) {
+  # get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
+  # but it only takes a couple of milliseconds
   vars_df <- get_current_data(arg_name = NA, call = -3)
+  # to improve speed, get_column_abx() will only run once when e.g. in a select or group call
   ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE)
+
+  # untreatable drugs
+  untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate"), "ab", drop = TRUE]
+  if (only_treatable == TRUE & any(untreatable %in% names(ab_in_data))) {
+    if (message_not_thrown_before(paste0("ab_class.untreatable.", function_name), entire_session = TRUE)) {
+      warning_("Some agents in `", function_name, "()` were ignored since they cannot be used for treating patients: ",
+               vector_and(ab_name(names(ab_in_data)[names(ab_in_data) %in% untreatable],
+                                  language = NULL,
+                                  tolower = TRUE),
+                          quotes = FALSE,
+                          sort = TRUE), ". They can be included using `", function_name, "(only_treatable = FALSE)`. ",
+               "This warning will be shown once per session.",
+               call = FALSE)
+      remember_thrown_message(paste0("ab_class.untreatable.", function_name), entire_session = TRUE)
+    }
+    ab_in_data <- ab_in_data[!names(ab_in_data) %in% untreatable]
+  }
   
   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 (message_not_thrown_before(paste0(function_name, ".", paste(pkg_env$get_column_abx.out, collapse = "|")))) {
     if (length(agents) == 0) {
-      message_("No antimicrobial agents of class ", ab_group, " found", examples, ".")
+      message_("No antimicrobial agents of class '", ab_group, "' found", examples, ".")
     } else {
       agents_formatted <- paste0("'", font_bold(agents, collapse = NULL), "'")
       agents_names <- ab_name(names(agents), tolower = TRUE, language = NULL)
-      need_name <- tolower(gsub("[^a-zA-Z]", "", agents)) != tolower(gsub("[^a-zA-Z]", "", agents_names))
-      agents_formatted[need_name] <- paste0(agents_formatted[need_name],
-                                            " (", agents_names[need_name], ")")
-      message_("For `", function_name, "(", ifelse(function_name == "ab_class", paste0("\"", ab_class, "\""), ""), ")` using ",
-               ifelse(length(agents) == 1, "column: ", "columns: "),
-               vector_and(agents_formatted, quotes = FALSE))
+      need_name <- generalise_antibiotic_name(agents) != generalise_antibiotic_name(agents_names)
+      agents_formatted[need_name] <- paste0(agents_formatted[need_name], " (", agents_names[need_name], ")")
+      message_("For `", function_name, "(",
+               ifelse(function_name == "ab_class", 
+                      paste0("\"", ab_class, "\""),
+                      ""),
+               ")` using ",
+               ifelse(length(agents) == 1, "column ", "columns "),
+               vector_and(agents_formatted, quotes = FALSE, sort = FALSE))
     }
-    remember_thrown_message(function_name)
+    remember_thrown_message(paste0(function_name, ".", paste(pkg_env$get_column_abx.out, collapse = "|")))
   }
   
   if (!is.null(attributes(vars_df)$type) &&
@@ -423,28 +514,16 @@ 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 +541,9 @@ 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/ab_property.R

@@ -29,6 +29,7 @@
 #' @inheritSection lifecycle Stable Lifecycle
 #' @param x any (vector of) text that can be coerced to a valid antibiotic code with [as.ab()]
 #' @param tolower a [logical] to indicate whether the first [character] of every output should be transformed to a lower case [character]. This will lead to e.g. "polymyxin B" and not "polymyxin b".
+#' @param snake_case a [logical] to indicate whether the names should be returned in so-called [snake case](https://en.wikipedia.org/wiki/Snake_case): in lower case and all spaces/slashes replaced with an underscore (`_`). This is useful for column renaming.
 #' @param property one of the column names of one of the [antibiotics] data set
 #' @param language language of the returned text, defaults to system language (see [get_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation.
 #' @param administration way of administration, either `"oral"` or `"iv"`
@@ -88,10 +89,11 @@
 #' ab_atc("cephtriaxone")
 #' ab_atc("cephthriaxone")
 #' ab_atc("seephthriaaksone")
-ab_name <- function(x, language = get_locale(), tolower = FALSE, ...) {
+ab_name <- function(x, language = get_locale(), tolower = FALSE, snake_case = FALSE, ...) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   meet_criteria(tolower, allow_class = "logical", has_length = 1)
+  meet_criteria(snake_case, allow_class = "logical", has_length = 1)
   
   x <- translate_AMR(ab_validate(x = x, property = "name", ...), language = language, only_affect_ab_names = TRUE)
   if (tolower == TRUE) {
@@ -99,6 +101,9 @@ ab_name <- function(x, language = get_locale(), tolower = FALSE, ...) {
     # as we want "polymyxin B", not "polymyxin b"
     x <- gsub("^([A-Z])", "\\L\\1", x, perl = TRUE)
   }
+  if (snake_case == TRUE) {
+    x <- tolower(gsub("[^a-zA-Z0-9]+", "_", x))
+  }
   x
 }
 

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/bug_drug_combinations.R

@@ -25,7 +25,7 @@
 
 #' Determine Bug-Drug Combinations
 #' 
-#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use [format()] on the result to prettify it to a publicable/printable format, see *Examples*.
+#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use [format()] on the result to prettify it to a publishable/printable format, see *Examples*.
 #' @inheritSection lifecycle Stable Lifecycle
 #' @inheritParams eucast_rules
 #' @param combine_IR a [logical] to indicate whether values R and I should be summed
@@ -81,7 +81,7 @@ bug_drug_combinations <- function(x,
   unique_mo <- sort(unique(x[, col_mo, drop = TRUE]))
   
   # select only groups and antibiotics
-  if (inherits(x.bak, "grouped_df")) {
+  if (is_null_or_grouped_tbl(x.bak)) {
     data_has_groups <- TRUE
     groups <- setdiff(names(attributes(x.bak)$groups), ".rows")
     x <- x[, c(groups, col_mo, colnames(x)[vapply(FUN.VALUE = logical(1), x, is.rsi)]), drop = FALSE]
@@ -113,7 +113,7 @@ bug_drug_combinations <- function(x,
         data.frame(S = m["S", ], I = m["I", ], R = m["R", ], stringsAsFactors = FALSE)
       })
       merged <- do.call(rbind, pivot)
-      out_group <- data.frame(mo = unique_mo[i],
+      out_group <- data.frame(mo = rep(unique_mo[i], NROW(merged)),
                               ab = rownames(merged),
                               S = merged$S,
                               I = merged$I,

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/disk.R

@@ -195,6 +195,15 @@ unique.disk <- function(x, incomparables = FALSE, ...) {
   y
 }
 
+#' @method rep disk
+#' @export
+#' @noRd
+rep.disk <- function(x, ...) {
+  y <- NextMethod()
+  attributes(y) <- attributes(x)
+  y
+}
+
 # will be exported using s3_register() in R/zzz.R
 get_skimmers.disk <- function(column) {
   skimr::sfl(

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

@@ -131,11 +131,8 @@
 #' # `example_isolates` is a data set available in the AMR package.
 #' # See ?example_isolates.
 #' 
-#' example_isolates[first_isolate(example_isolates), ]
-#' \donttest{
-#' # faster way, only works in R 3.2 and later:
 #' example_isolates[first_isolate(), ]
-#' 
+#' \donttest{
 #' # get all first Gram-negatives
 #' example_isolates[which(first_isolate() & mo_is_gram_negative()), ]
 #'

R/ggplot_rsi.R

@@ -370,7 +370,6 @@ scale_rsi_colours <- function(...,
                               aesthetics = "fill") {
   stop_ifnot_installed("ggplot2")
   meet_criteria(aesthetics, allow_class = "character", is_in = c("alpha", "colour", "color", "fill", "linetype", "shape", "size"))
-  
   # behaviour until AMR pkg v1.5.0 and also when coming from ggplot_rsi()
   if ("colours" %in% names(list(...))) {
     original_cols <- c(S = "#3CAEA3",
@@ -379,22 +378,24 @@ scale_rsi_colours <- function(...,
                        IR = "#ED553B",
                        R = "#ED553B")
     colours <- replace(original_cols, names(list(...)$colours), list(...)$colours)
-    return(ggplot2::scale_fill_manual(values = colours))
+    # limits = force is needed in ggplot2 3.3.4 and 3.3.5, see here;
+    # https://github.com/tidyverse/ggplot2/issues/4511#issuecomment-866185530
+    return(ggplot2::scale_fill_manual(values = colours, limits = force))
   }
   if (identical(unlist(list(...)), FALSE)) {
     return(invisible())
   }
   
   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))
@@ -411,7 +412,9 @@ scale_rsi_colours <- function(...,
   dots[dots == "I"] <- "#F6D55C"
   dots[dots == "R"] <- "#ED553B"
   cols <- replace(original_cols, names(dots), dots)
-  ggplot2::scale_discrete_manual(aesthetics = aesthetics, values = cols)
+  # limits = force is needed in ggplot2 3.3.4 and 3.3.5, see here;
+  # https://github.com/tidyverse/ggplot2/issues/4511#issuecomment-866185530
+  ggplot2::scale_discrete_manual(aesthetics = aesthetics, values = cols, limits = force)
 }
 
 #' @rdname ggplot_rsi

R/guess_ab_col.R

@@ -97,16 +97,39 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE, only_r
 }
 
 get_column_abx <- function(x,
+                           ...,
                            soft_dependencies = NULL,
                            hard_dependencies = NULL,
                            verbose = FALSE,
                            info = TRUE,
                            only_rsi_columns = FALSE,
                            sort = TRUE,
-                           ...) {
+                           reuse_previous_result = TRUE) {
   
   # check if retrieved before, then get it from package environment
-  if (identical(unique_call_id(entire_session = FALSE), pkg_env$get_column_abx.call)) {
+  if (isTRUE(reuse_previous_result) && identical(unique_call_id(entire_session = FALSE), pkg_env$get_column_abx.call)) {
+    # so within the same call, within the same environment, we got here again.
+    # but we could've come from another function within the same call, so now only check the columns that changed
+    
+    # first remove the columns that are not existing anymore
+    previous <- pkg_env$get_column_abx.out
+    current <- previous[previous %in% colnames(x)]
+    
+    # then compare columns in current call with columns in original call
+    new_cols <- colnames(x)[!colnames(x) %in% pkg_env$get_column_abx.checked_cols]
+    if (length(new_cols) > 0) {
+      # these columns did not exist in the last call, so add them
+      new_cols_rsi <- get_column_abx(x[, new_cols, drop = FALSE], reuse_previous_result = FALSE, info = FALSE, sort = FALSE)
+      current <- c(current, new_cols_rsi)
+      # order according to data in current call
+      current <- current[match(colnames(x)[colnames(x) %in% current], current)]
+    }
+    
+    # update pkg environment to improve speed on next run
+    pkg_env$get_column_abx.out <- current
+    pkg_env$get_column_abx.checked_cols <- colnames(x)
+
+    # and return right values
     return(pkg_env$get_column_abx.out)
   }
   
@@ -123,6 +146,7 @@ get_column_abx <- function(x,
   }
   
   x <- as.data.frame(x, stringsAsFactors = FALSE)
+  x.bak <- x
   if (only_rsi_columns == TRUE) {
     x <- x[, which(is.rsi(x)), drop = FALSE]
   }
@@ -163,8 +187,8 @@ get_column_abx <- function(x,
                          abcode = suppressWarnings(as.ab(colnames(x), info = FALSE)),
                          stringsAsFactors = FALSE)
   df_trans <- df_trans[!is.na(df_trans$abcode), , drop = FALSE]
-  x <- as.character(df_trans$colnames)
-  names(x) <- df_trans$abcode
+  out <- as.character(df_trans$colnames)
+  names(out) <- df_trans$abcode
   
   # add from self-defined dots (...):
   # such as get_column_abx(example_isolates %>% rename(thisone = AMX), amox = "thisone")
@@ -177,33 +201,34 @@ get_column_abx <- function(x,
                immediate = TRUE)
     }
     # turn all NULLs to NAs
-    dots <- unlist(lapply(dots, function(x) if (is.null(x)) NA else x))
+    dots <- unlist(lapply(dots, function(dot) if (is.null(dot)) NA else dot))
     names(dots) <- newnames
     dots <- dots[!is.na(names(dots))]
     # merge, but overwrite automatically determined ones by 'dots'
-    x <- c(x[!x %in% dots & !names(x) %in% names(dots)], dots)
+    out <- c(out[!out %in% dots & !names(out) %in% names(dots)], dots)
     # delete NAs, this will make e.g. eucast_rules(... TMP = NULL) work to prevent TMP from being used
-    x <- x[!is.na(x)]
+    out <- out[!is.na(out)]
   }
   
-  if (length(x) == 0) {
+  if (length(out) == 0) {
     if (info == TRUE) {
       message_("No columns found.")
     }
     pkg_env$get_column_abx.call <- unique_call_id(entire_session = FALSE)
-    pkg_env$get_column_abx.out <- x
-    return(x)
+    pkg_env$get_column_abx.checked_cols <- colnames(x.bak)
+    pkg_env$get_column_abx.out <- out
+    return(out)
   }
   
   # sort on name
   if (sort == TRUE) {
-    x <- x[order(names(x), x)]
+    out <- out[order(names(out), out)]
   }
-  duplicates <- c(x[duplicated(x)], x[duplicated(names(x))]) 
+  duplicates <- c(out[duplicated(out)], out[duplicated(names(out))]) 
   duplicates <- duplicates[unique(names(duplicates))]
-  x <- c(x[!names(x) %in% names(duplicates)], duplicates)
+  out <- c(out[!names(out) %in% names(duplicates)], duplicates)
   if (sort == TRUE) {
-    x <- x[order(names(x), x)]
+    out <- out[order(names(out), out)]
   }
   
   # succeeded with auto-guessing
@@ -211,14 +236,14 @@ get_column_abx <- function(x,
     message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
   }
   
-  for (i in seq_len(length(x))) {
-    if (info == TRUE & verbose == TRUE & !names(x[i]) %in% names(duplicates)) {
-      message_("Using column '", font_bold(x[i]), "' as input for ", names(x)[i],
-               " (", ab_name(names(x)[i], tolower = TRUE, language = NULL), ").")
+  for (i in seq_len(length(out))) {
+    if (info == TRUE & verbose == TRUE & !names(out[i]) %in% names(duplicates)) {
+      message_("Using column '", font_bold(out[i]), "' as input for ", names(out)[i],
+               " (", ab_name(names(out)[i], tolower = TRUE, language = NULL), ").")
     }
-    if (info == TRUE & names(x[i]) %in% names(duplicates)) {
-      warning_(paste0("Using column '", font_bold(x[i]), "' as input for ", names(x)[i],
-                      " (", ab_name(names(x)[i], tolower = TRUE, language = NULL),
+    if (info == TRUE & names(out[i]) %in% names(duplicates)) {
+      warning_(paste0("Using column '", font_bold(out[i]), "' as input for ", names(out)[i],
+                      " (", ab_name(names(out)[i], tolower = TRUE, language = NULL),
                       "), although it was matched for multiple antibiotics or columns."),
                add_fn = font_red,
                call = FALSE, 
@@ -228,18 +253,18 @@ get_column_abx <- function(x,
   
   if (!is.null(hard_dependencies)) {
     hard_dependencies <- unique(hard_dependencies)
-    if (!all(hard_dependencies %in% names(x))) {
+    if (!all(hard_dependencies %in% names(out))) {
       # missing a hard dependency will return NA and consequently the data will not be analysed
-      missing <- hard_dependencies[!hard_dependencies %in% names(x)]
+      missing <- hard_dependencies[!hard_dependencies %in% names(out)]
       generate_warning_abs_missing(missing, any = FALSE)
       return(NA)
     }
   }
   if (!is.null(soft_dependencies)) {
     soft_dependencies <- unique(soft_dependencies)
-    if (info == TRUE & !all(soft_dependencies %in% names(x))) {
+    if (info == TRUE & !all(soft_dependencies %in% names(out))) {
       # missing a soft dependency may lower the reliability
-      missing <- soft_dependencies[!soft_dependencies %in% names(x)]
+      missing <- soft_dependencies[!soft_dependencies %in% names(out)]
       missing_msg <- vector_and(paste0(ab_name(missing, tolower = TRUE, language = NULL), 
                                        " (", font_bold(missing, collapse = NULL), ")"), 
                                 quotes = FALSE)
@@ -249,8 +274,9 @@ get_column_abx <- function(x,
   }
   
   pkg_env$get_column_abx.call <- unique_call_id(entire_session = FALSE)
-  pkg_env$get_column_abx.out <- x
-  x
+  pkg_env$get_column_abx.checked_cols <- colnames(x.bak)
+  pkg_env$get_column_abx.out <- out
+  out
 }
 
 generate_warning_abs_missing <- function(missing, any = FALSE) {

R/join_microorganisms.R

@@ -36,7 +36,7 @@
 #' @param ... ignored, only in place to allow future extensions
 #' @details **Note:** As opposed to the `join()` functions of `dplyr`, [character] vectors are supported and at default existing columns will get a suffix `"2"` and the newly joined columns will not get a suffix. 
 #' 
-#' If the `dplyr` package is installed, their join functions will be used. Otherwise, the much slower [merge()] and [interaction()] functions from base R will be used.
+#' If the `dplyr` package is installed, their join functions will be used. Otherwise, the much slower [merge()] and [interaction()] functions from base \R will be used.
 #' @inheritSection AMR Read more on Our Website!
 #' @return a [data.frame]
 #' @export

R/mic.R

@@ -320,6 +320,15 @@ unique.mic <- function(x, incomparables = FALSE, ...) {
   y
 }
 
+#' @method rep mic
+#' @export
+#' @noRd
+rep.mic <- function(x, ...) {
+  y <- NextMethod()
+  attributes(y) <- attributes(x)
+  y
+}
+
 #' @method sort mic
 #' @export
 #' @noRd
@@ -337,7 +346,7 @@ sort.mic <- function(x, decreasing = FALSE, ...) {
 #' @export
 #' @noRd
 hist.mic <- function(x, ...) {
-  warning_("Use `plot()` or `ggplot()` for optimal plotting of MIC values", call = FALSE)
+  warning_("Use `plot()` or ggplot2's `autoplot()` for optimal plotting of MIC values", call = FALSE)
   hist(log2(x))
 }
 

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")
       langs <- LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED != "en"]
       for (l in langs) {
         for (i in seq_len(nrow(trns))) {
@@ -1664,16 +1664,23 @@ 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$mo)) {
+  df <- tryCatch(get_current_data(arg_name = "x", call = 0),
+                 error = function(e) NULL)
+  if (!is.null(df)) {
+    mo_cols <- vapply(FUN.VALUE = logical(1), df, is.mo)
+  } else {
+    mo_cols <- NULL
+  }
+  
+  if (!all(x[!is.na(x)] %in% MO_lookup$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$mo], 
                                                      collapse = NULL),
                                              collapse = NULL)
-    # throw a warning with the affected column name
-    mo <- tryCatch(search_type_in_df(get_current_data(arg_name = "x", call = 0), type = "mo", info = FALSE),
-                   error = function(e) NULL)
-    if (!is.null(mo)) {
-      col <- paste0("Column '", mo, "'")
+    # throw a warning with the affected column name(s)
+    if (!is.null(mo_cols)) {
+      col <- paste0("Column ", vector_or(colnames(df)[mo_cols], quotes = TRUE, sort = FALSE))
     } else {
       col <- "The data"
     }
@@ -1681,7 +1688,7 @@ pillar_shaft.mo <- function(x, ...) {
              "Please update your MO codes with `as.mo()`.",
              call = FALSE)
   }
-
+  
   # make it always fit exactly
   max_char <- max(nchar(x))
   if (is.na(max_char)) {
@@ -2039,12 +2046,12 @@ parse_and_convert <- function(x) {
         x <- as.data.frame(x, stringsAsFactors = FALSE)[[1]]
       }
     }
-    x[is.null(x)] <- NA
-    parsed <- iconv(x, to = "UTF-8")
+    parsed <- iconv(as.character(x), to = "UTF-8")
     parsed[is.na(parsed) & !is.na(x)] <- iconv(x[is.na(parsed) & !is.na(x)], from = "Latin1", to = "ASCII//TRANSLIT")
     parsed <- gsub('"', "", parsed, fixed = TRUE)
     parsed <- gsub(" +", " ", parsed, perl = TRUE)
     parsed <- trimws(parsed)
+    parsed
   }, error = function(e) stop(e$message, call. = FALSE)) # this will also be thrown when running `as.mo(no_existing_object)`
   parsed
 }

R/mo_property.R

@@ -52,7 +52,7 @@
 #'
 #' The function [mo_url()] will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
 #' 
-#' SNOMED codes - [mo_snomed()] - are from the `r SNOMED_VERSION$current_source`. See the [microorganisms] data set for more info.
+#' SNOMED codes - [mo_snomed()] - are from the `r SNOMED_VERSION$current_source`. See *Source* and the [microorganisms] data set for more info.
 #' @inheritSection mo_matching_score Matching Score for Microorganisms
 #' @inheritSection catalogue_of_life Catalogue of Life
 #' @inheritSection as.mo Source
@@ -65,7 +65,7 @@
 #' - A [numeric] in case of [mo_snomed()]
 #' - A [character] in all other cases
 #' @export
-#' @seealso [microorganisms]
+#' @seealso Data set [microorganisms]
 #' @inheritSection AMR Reference Data Publicly Available
 #' @inheritSection AMR Read more on Our Website!
 #' @examples
@@ -225,6 +225,8 @@ mo_shortname <- function(x, language = get_locale(), ...) {
   translate_AMR(shortnames, language = language, only_unknown = FALSE, only_affect_mo_names = TRUE)
 }
 
+
+
 #' @rdname mo_property
 #' @export
 mo_subspecies <- function(x, language = get_locale(), ...) {
@@ -723,16 +725,17 @@ mo_validate <- function(x, property, language, ...) {
   
   if (tryCatch(all(x[!is.na(x)] %in% MO_lookup$mo) & !has_Becker_or_Lancefield, error = function(e) FALSE)) {
     # special case for mo_* functions where class is already <mo>
-    return(MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE])
-  }
-  
-  # try to catch an error when inputting an invalid argument
-  # so the 'call.' can be set to FALSE
-  tryCatch(x[1L] %in% MO_lookup[1, property, drop = TRUE],
-           error = function(e) stop(e$message, call. = FALSE))
+    x <- MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE]
 
-  if (!all(x[!is.na(x)] %in% MO_lookup[, property, drop = TRUE]) | has_Becker_or_Lancefield) {
-    x <- exec_as.mo(x, property = property, language = language, ...)
+  } else {
+    # try to catch an error when inputting an invalid argument
+    # so the 'call.' can be set to FALSE
+    tryCatch(x[1L] %in% MO_lookup[1, property, drop = TRUE],
+             error = function(e) stop(e$message, call. = FALSE))
+    
+    if (!all(x[!is.na(x)] %in% MO_lookup[, property, drop = TRUE]) | has_Becker_or_Lancefield) {
+      x <- exec_as.mo(x, property = property, language = language, ...)
+    }
   }
   
   if (property == "mo") {
@@ -754,7 +757,7 @@ find_mo_col <- function(fn) {
   }, silent = TRUE)
   if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
     if (message_not_thrown_before(fn = fn)) {
-      message_("Using column '", font_bold(mo), "' as input for ", fn, "()")
+      message_("Using column '", font_bold(mo), "' as input for `", fn, "()`")
       remember_thrown_message(fn = fn)
     }
     return(df[, mo, drop = TRUE])

R/plot.R

@@ -25,7 +25,7 @@
 
 #' Plotting for Classes `rsi`, `mic` and `disk`
 #' 
-#' Functions to plot classes `rsi`, `mic` and `disk`, with support for base R and `ggplot2`.
+#' Functions to plot classes `rsi`, `mic` and `disk`, with support for base \R and `ggplot2`.
 #' @inheritSection lifecycle Stable Lifecycle
 #' @inheritSection AMR Read more on Our Website!
 #' @param x,data MIC values created with [as.mic()] or disk diffusion values created with [as.disk()]
@@ -276,8 +276,10 @@ ggplot.mic <- function(data,
     names(vals) <- translate_AMR(names(vals), language = language)
     p <- p +
       ggplot2::geom_col(ggplot2::aes(x = mic, y = count, fill = cols)) + 
+      # limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
       ggplot2::scale_fill_manual(values = vals,
-                                 name = NULL)
+                                 name = NULL,
+                                 limits = force)
   } else {
     p <- p +
       ggplot2::geom_col(ggplot2::aes(x = mic, y = count))
@@ -287,6 +289,11 @@ 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
@@ -495,8 +502,10 @@ ggplot.disk <- function(data,
     names(vals) <- translate_AMR(names(vals), language = language)
     p <- p +
       ggplot2::geom_col(ggplot2::aes(x = disk, y = count, fill = cols)) + 
+      # limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
       ggplot2::scale_fill_manual(values = vals,
-                                 name = NULL)
+                                 name = NULL,
+                                 limits = force)
   } else {
     p <- p +
       ggplot2::geom_col(ggplot2::aes(x = disk, y = count))
@@ -506,6 +515,11 @@ 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
@@ -650,13 +664,20 @@ ggplot.rsi <- function(data,
   
   p +
     ggplot2::geom_col(ggplot2::aes(x = rsi, y = count, fill = rsi)) + 
+    # limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
     ggplot2::scale_fill_manual(values = c("R" = colours_RSI[1],
                                           "S" = colours_RSI[2],
-                                          "I" = colours_RSI[3])) +
+                                          "I" = colours_RSI[3]),
+                               limits = force) +
     ggplot2::labs(title = title, x = xlab, y = ylab) +
     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/random.R

@@ -32,7 +32,7 @@
 #' @param ab any [character] that can be coerced to a valid antimicrobial agent code with [as.ab()]
 #' @param prob_RSI a vector of length 3: the probabilities for R (1st value), S (2nd value) and I (3rd value)
 #' @param ... ignored, only in place to allow future extensions
-#' @details The base R function [sample()] is used for generating values.
+#' @details The base \R function [sample()] is used for generating values.
 #' 
 #' Generated values are based on the latest EUCAST guideline implemented in the [rsi_translation] data set. To create specific generated values per bug or drug, set the `mo` and/or `ab` argument.
 #' @return class `<mic>` for [random_mic()] (see [as.mic()]) and class `<disk>` for [random_disk()] (see [as.disk()])
@@ -56,18 +56,26 @@
 #' random_disk(100, "Streptococcus pneumoniae", "ampicillin") # range 12-27
 #' }
 random_mic <- function(size, mo = NULL, ab = NULL, ...) {
+  meet_criteria(size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
+  meet_criteria(mo, allow_class = "character", has_length = 1, allow_NULL = TRUE)
+  meet_criteria(ab, allow_class = "character", has_length = 1, allow_NULL = TRUE)
   random_exec("MIC", size = size, mo = mo, ab = ab)
 }
 
 #' @rdname random
 #' @export
 random_disk <- function(size, mo = NULL, ab = NULL, ...) {
+  meet_criteria(size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
+  meet_criteria(mo, allow_class = "character", has_length = 1, allow_NULL = TRUE)
+  meet_criteria(ab, allow_class = "character", has_length = 1, allow_NULL = TRUE)
   random_exec("DISK", size = size, mo = mo, ab = ab)
 }
 
 #' @rdname random
 #' @export
 random_rsi <- function(size, prob_RSI = c(0.33, 0.33, 0.33), ...) {
+  meet_criteria(size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
+  meet_criteria(prob_RSI, allow_class = c("numeric", "integer"), has_length = 3)
   sample(as.rsi(c("R", "S", "I")), size = size, replace = TRUE, prob = prob_RSI)
 }
 

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

@@ -284,10 +284,26 @@ as.rsi.default <- function(x, ...) {
       }
     }
     
-    x <- as.character(unlist(x))
+    # trim leading and trailing spaces, new lines, etc.
+    x <- trimws2(as.character(unlist(x)))
     x.bak <- x
-    
     na_before <- length(x[is.na(x) | x == ""])
+    
+    # correct for translations
+    trans_R <- unlist(TRANSLATIONS[which(TRANSLATIONS$pattern == "Resistant"),
+                                   LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED %in% colnames(TRANSLATIONS)]])
+    trans_S <- unlist(TRANSLATIONS[which(TRANSLATIONS$pattern == "Susceptible"),
+                                   LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED %in% colnames(TRANSLATIONS)]])
+    trans_I <- unlist(TRANSLATIONS[which(TRANSLATIONS$pattern %in% c("Incr. exposure", "Intermediate")),
+                                   LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED %in% colnames(TRANSLATIONS)]])
+    x <- gsub(paste0(unique(trans_R[!is.na(trans_R)]), collapse = "|"), "R", x, ignore.case = TRUE)
+    x <- gsub(paste0(unique(trans_S[!is.na(trans_S)]), collapse = "|"), "S", x, ignore.case = TRUE)
+    x <- gsub(paste0(unique(trans_I[!is.na(trans_I)]), collapse = "|"), "I", x, ignore.case = TRUE)
+    # replace all English textual input
+    x <- gsub("res(is(tant)?)?", "R", x, ignore.case = TRUE)
+    x <- gsub("sus(cep(tible)?)?", "S", x, ignore.case = TRUE)
+    x <- gsub("int(er(mediate)?)?", "I", x, ignore.case = TRUE)
+    x <- gsub("inc(r(eased)?)? exp[a-z]*", "I", x, ignore.case = TRUE)
     # remove all spaces
     x <- gsub(" +", "", x)
     # remove all MIC-like values: numbers, operators and periods
@@ -349,7 +365,7 @@ 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)), 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 +454,7 @@ 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)), 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)
@@ -1038,6 +1054,15 @@ unique.rsi <- function(x, incomparables = FALSE, ...) {
   y
 }
 
+#' @method rep rsi
+#' @export
+#' @noRd
+rep.rsi <- function(x, ...) {
+  y <- NextMethod()
+  attributes(y) <- attributes(x)
+  y
+}
+
 check_reference_data <- function(reference_data) {
   if (!identical(reference_data, AMR::rsi_translation)) {
     class_rsi <- vapply(FUN.VALUE = character(1), rsi_translation, function(x) paste0("<", class(x), ">", collapse = " and "))

R/rsi_calc.R

@@ -27,7 +27,7 @@ dots2vars <- function(...) {
   # this function is to give more informative output about 
   # variable names in count_* and proportion_* functions
   dots <- substitute(list(...))
-  vector_and(as.character(dots)[2:length(dots)], quotes = FALSE)
+  as.character(dots)[2:length(dots)]
 }
 
 rsi_calc <- function(...,
@@ -163,8 +163,30 @@ rsi_calc <- function(...,
   if (denominator < minimum) {
     if (data_vars != "") {
       data_vars <- paste(" for", data_vars)
+      # also add group name if used in dplyr::group_by()
+      cur_group <- import_fn("cur_group", "dplyr", error_on_fail = FALSE)
+      if (!is.null(cur_group)) {
+        group_df <- tryCatch(cur_group(), error = function(e) data.frame())
+        if (NCOL(group_df) > 0) {
+          # transform factors to characters
+          group <- vapply(FUN.VALUE = character(1), group_df, function(x) {
+            if (is.numeric(x)) {
+              format(x)
+            } else if (is.logical(x)) {
+              as.character(x)
+            } else {
+              paste0('"', x, '"')
+            }
+          })
+          data_vars <- paste0(data_vars, " in group: ", paste0(names(group), " = ", group, collapse = ", "))
+        }
+      }
     }
-    warning_("Introducing NA: only ", denominator, " results available", data_vars, " (`minimum` = ", minimum, ").", call = FALSE)
+    warning_("Introducing NA: ",
+             ifelse(denominator == 0, "no", paste("only", denominator)),
+             " results available",
+             data_vars,
+             " (`minimum` = ", minimum, ").", call = FALSE)
     fraction <- NA_real_
   } else {
     fraction <- numerator / denominator
@@ -206,7 +228,7 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
   translate_ab <- get_translate_ab(translate_ab)
   
   # select only groups and antibiotics
-  if (inherits(data, "grouped_df")) {
+  if (is_null_or_grouped_tbl(data)) {
     data_has_groups <- TRUE
     groups <- setdiff(names(attributes(data)$groups), ".rows")
     data <- data[, c(groups, colnames(data)[vapply(FUN.VALUE = logical(1), data, is.rsi)]), drop = FALSE]

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

@@ -38,7 +38,7 @@ if (utf8_supported && !is_latex) {
   pkg_env$info_icon <- "i"
 }
 
-.onLoad <- function(libname, pkgname) {
+.onLoad <- function(...) {
   # Support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
   # without the need to depend on other packages. This was suggested by the 
   # developers of the vctrs package: 
@@ -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({
@@ -82,7 +86,6 @@ if (utf8_supported && !is_latex) {
   assign(x = "INTRINSIC_R", value = create_intr_resistance(), envir = asNamespace("AMR"))
 }
 
-
 # Helper functions --------------------------------------------------------
 
 create_AB_lookup <- function() {

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")
@@ -37,7 +36,7 @@ if (length(to_install) == 0) {
 }
 for (i in seq_len(length(to_install))) {
   cat("Installing package", to_install[i], "\n")
-  tryCatch(install.packages(to_install[i], repos = "https://cran.rstudio.com/", dependencies = TRUE, quiet = TRUE),
+  tryCatch(install.packages(to_install[i], repos = "https://cran.rstudio.com/", dependencies = TRUE, quiet = FALSE),
            # message = function(m) invisible(),
            warning = function(w) message(w$message),
            error = function(e) message(e$message))

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 +68,9 @@ 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]))
+
+# EXAMPLE_ISOLATES <- readRDS("data-raw/example_isolates.rds")
 
 # vectors of CoNS and CoPS, improves speed in as.mo()
 create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
@@ -121,18 +123,21 @@ 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)
+FLUOROQUINOLONES <- antibiotics %>% filter(atc_group2 %like% "fluoroquinolone" | (group %like% "quinolone" & is.na(atc_group2))) %>% pull(ab)
 LIPOGLYCOPEPTIDES <- as.ab(c("DAL", "ORI", "TLV")) # dalba/orita/tela
 GLYCOPEPTIDES <- antibiotics %>% filter(group %like% "glycopeptide") %>% pull(ab)
 GLYCOPEPTIDES_EXCEPT_LIPO <- GLYCOPEPTIDES[!GLYCOPEPTIDES %in% LIPOGLYCOPEPTIDES]
-LINCOSAMIDES <- antibiotics %>% filter(atc_group2 %like% "lincosamide") %>% pull(ab) %>% c("PRL")
-MACROLIDES <- antibiotics %>% filter(atc_group2 %like% "macrolide") %>% pull(ab)
+LINCOSAMIDES <- antibiotics %>% filter(atc_group2 %like% "lincosamide" | (group %like% "lincosamide" & is.na(atc_group2))) %>% pull(ab)
+MACROLIDES <- antibiotics %>% filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2))) %>% 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 <- antibiotics %>% filter(group %like% "tetracycline") %>% pull(ab)
 TETRACYCLINES_EXCEPT_TGC <- TETRACYCLINES[TETRACYCLINES != "TGC"]
 UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ"))
 BETALACTAMS <- c(PENICILLINS, CEPHALOSPORINS, CARBAPENEMS)
@@ -141,9 +146,10 @@ 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,
+                  # EXAMPLE_ISOLATES,
                   MO_CONS,
                   MO_COPS,
                   AMINOGLYCOSIDES,
@@ -153,6 +159,8 @@ usethis::use_data(eucast_rules_file,
                   CEPHALOSPORINS_1ST,
                   CEPHALOSPORINS_2ND,
                   CEPHALOSPORINS_3RD,
+                  CEPHALOSPORINS_4TH,
+                  CEPHALOSPORINS_5TH,
                   CEPHALOSPORINS_EXCEPT_CAZ,
                   FLUOROQUINOLONES,
                   LIPOGLYCOPEPTIDES,
@@ -163,6 +171,7 @@ usethis::use_data(eucast_rules_file,
                   OXAZOLIDINONES,
                   PENICILLINS,
                   POLYMYXINS,
+                  QUINOLONES,
                   STREPTOGRAMINS,
                   TETRACYCLINES,
                   TETRACYCLINES_EXCEPT_TGC,

data-raw/ab.md5

@@ -1 +1 @@
-f6b4a2325c4bf3a8d4da337c8cfa07be
+3231895277e8e2b157672822c1913639

data-raw/antibiotics.txt

@@ -44,7 +44,7 @@
 "BCZ"		65807	"Bicyclomycin (Bicozamycin)"	"Other antibacterials"			""	"c(\"aizumycin\", \"bacfeed\", \"bacteron\", \"bicozamicina\", \"bicozamycin\", \"bicozamycine\", \"bicozamycinum\")"					"character(0)"
 "BDP"	"J01EA02"	68760	"Brodimoprim"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Trimethoprim and derivatives"	""	"c(\"brodimoprim\", \"brodimoprima\", \"brodimoprime\", \"brodimoprimum\", \"bromdimoprim\", \"hyprim\", \"unitrim\")"	0.2	"g"			"character(0)"
 "BUT"		47472	"Butoconazole"	"Antifungals/antimycotics"			""	"c(\"butaconazole\", \"butoconazol\", \"butoconazole\", \"butoconazolum\", \"compositenstarke\", \"dahlin\", \"femstat\", \"gynofort\", \"polyfructosanum\")"					"character(0)"
-"CDZ"	"J01DD09"	44242317	"Cadazolid"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	""	"cadazolid"			2	"g"	"character(0)"
+"CDZ"		44242317	"Cadazolid"	"Oxazolidinones"			""	"cadazolid"					"character(0)"
 "CLA"	"J04AA03"		"Calcium aminosalicylate"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Aminosalicylic acid and derivatives"	""	""	15				""
 "CAP"	"J04AB30"	135565060	"Capreomycin"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"c(\"\", \"capr\")"	""			1	"g"	""
 "CRB"	"J01CA03"	20824	"Carbenicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"bar\", \"carb\", \"cb\")"	"c(\"anabactyl\", \"carbenicilina\", \"carbenicillin\", \"carbenicillina\", \"carbenicilline\", \"carbenicillinum\", \"geopen\", \"pyopen\")"			12	"g"	"3434-8"
@@ -108,8 +108,8 @@
 "CPT"	"J01DI02"	56841980	"Ceftaroline"	"Cephalosporins (5th gen.)"			"c(\"\", \"cfro\")"	"c(\"teflaro\", \"zinforo\")"			1.2		"character(0)"
 "CPA"			"Ceftaroline/avibactam"	"Cephalosporins (5th gen.)"			""	""					""
 "CAZ"	"J01DD02"	5481173	"Ceftazidime"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"caz\", \"cefta\", \"cfta\", \"cftz\", \"taz\", \"tz\", \"xtz\")"	"c(\"ceftazidim\", \"ceftazidima\", \"ceftazidime\", \"ceftazidimum\", \"ceptaz\", \"fortaz\", \"fortum\", \"pentacef\", \"tazicef\", \"tazidime\")"			4	"g"	"c(\"21151-6\", \"3449-6\", \"80960-8\")"
-"CZA"	"J01DD52"	90643431	"Ceftazidime/avibactam"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"\", \"cfav\")"	"c(\"avycaz\", \"zavicefta\")"			6	"g"	""
-"CCV"	"J01DD52"	9575352	"Ceftazidime/clavulanic acid"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"czcl\", \"xtzl\")"	""			6		""
+"CZA"		90643431	"Ceftazidime/avibactam"	"Cephalosporins (3rd gen.)"			"c(\"\", \"cfav\")"	"c(\"avycaz\", \"zavicefta\")"					""
+"CCV"	"J01DD52"	9575352	"Ceftazidime/clavulanic acid"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"czcl\", \"xtzl\")"	""			6	"g"	""
 "CEM"		6537431	"Cefteram"	"Cephalosporins (3rd gen.)"			""	"c(\"cefteram\", \"cefterame\", \"cefteramum\", \"ceftetrame\")"					"character(0)"
 "CPL"		5362114	"Cefteram pivoxil"	"Cephalosporins (3rd gen.)"			""	"c(\"cefteram pivoxil\", \"tomiron\")"					"character(0)"
 "CTL"	"J01DB12"	65755	"Ceftezole"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	""	"c(\"ceftezol\", \"ceftezole\", \"ceftezolo\", \"ceftezolum\", \"demethylcefazolin\")"			3	"g"	"character(0)"
@@ -117,9 +117,9 @@
 "TIO"		6328657	"Ceftiofur"	"Cephalosporins (3rd gen.)"			""	"c(\"ceftiofur\", \"ceftiofurum\", \"excede\", \"excenel\", \"naxcel\")"					"character(0)"
 "CZX"	"J01DD07"	6533629	"Ceftizoxime"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cfzx\", \"ctz\", \"cz\", \"czx\", \"tiz\", \"zox\")"	"c(\"cefizox\", \"ceftisomin\", \"ceftix\", \"ceftizoxima\", \"ceftizoxime\", \"ceftizoximum\", \"epocelin\", \"eposerin\")"			4	"g"	"c(\"25243-7\", \"3450-4\")"
 "CZP"		9578661	"Ceftizoxime alapivoxil"	"Cephalosporins (3rd gen.)"			""	""					""
-"BPR"	"J01DI01"	135413542	"Ceftobiprole"	"Cephalosporins (5th gen.)"			""	"ceftobiprole"			1.5		"character(0)"
-"CFM1"	"J01DI01"	135413544	"Ceftobiprole medocaril"	"Cephalosporins (5th gen.)"	"Other beta-lactam antibacterials"	"Other cephalosporins"	""	""			1.5		""
-"CEI"	"J01DI54"		"Ceftolozane/enzyme inhibitor"	"Cephalosporins (5th gen.)"	"Other beta-lactam antibacterials"	"Other cephalosporins"	""	""			3		""
+"BPR"		135413542	"Ceftobiprole"	"Cephalosporins (5th gen.)"			""	"ceftobiprole"					"character(0)"
+"CFM1"	"J01DI01"	135413544	"Ceftobiprole medocaril"	"Cephalosporins (5th gen.)"	"Other beta-lactam antibacterials"	"Other cephalosporins and penems"	""	""			1.5	"g"	""
+"CEI"	"J01DI54"		"Ceftolozane/enzyme inhibitor"	"Cephalosporins (5th gen.)"	"Other beta-lactam antibacterials"	"Other cephalosporins and penems"	""	""			3		""
 "CZT"			"Ceftolozane/tazobactam"	"Cephalosporins (5th gen.)"			""	""					""
 "CRO"	"J01DD04"	5479530	"Ceftriaxone"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"axo\", \"cax\", \"cftr\", \"cro\", \"ctr\", \"frx\", \"tx\")"	"c(\"biotrakson\", \"cefatriaxone\", \"cefatriaxone hydrate\", \"ceftriaxon\", \"ceftriaxona\", \"ceftriaxone\", \"ceftriaxone sodium\", \"ceftriaxonum\", \"ceftriazone\", \"cephtriaxone\", \"longacef\", \"rocefin\", \"rocephalin\", \"rocephin\", \"rocephine\", \"rophex\")"			2	"g"	"c(\"25244-5\", \"3451-2\", \"80957-4\")"
 "CXM"	"J01DC02"	5479529	"Cefuroxime"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"c(\"cfrx\", \"cfur\", \"cfx\", \"crm\", \"cxm\", \"fur\", \"rox\", \"xm\")"	"c(\"biofuroksym\", \"cefuril\", \"cefuroxim\", \"cefuroxime\", \"cefuroximine\", \"cefuroximo\", \"cefuroximum\", \"cephuroxime\", \"kefurox\", \"sharox\", \"zinacef\", \"zinacef danmark\")"	0.5	"g"	3	"g"	"c(\"25245-2\", \"3452-0\", \"80608-3\", \"80617-4\")"
@@ -173,7 +173,7 @@
 "DIR"	"J01FA13"	6473883	"Dirithromycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"c(\"dirithromycin\", \"dirithromycine\", \"dirithromycinum\", \"diritromicina\", \"divitross\", \"dynabac\", \"noriclan\", \"valodin\")"	0.5	"g"			"character(0)"
 "DOR"	"J01DH04"	73303	"Doripenem"	"Carbapenems"	"Other beta-lactam antibacterials"	"Carbapenems"	"dori"	"c(\"doribax\", \"doripenem\", \"doripenem hydrate\", \"finibax\")"			1.5		"character(0)"
 "DOX"	"J01AA02"	54671203	"Doxycycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"	"c(\"dox\", \"doxy\")"	"c(\"atridox\", \"azudoxat\", \"deoxymykoin\", \"dossiciclina\", \"doxcycline anhydrous\", \"doxiciclina\", \"doxitard\", \"doxivetin\", \"doxycen\", \"doxychel\", \"doxycin\", \"doxycyclin\", \"doxycycline\", \"doxycycline calcium\", \"doxycycline hyclate\", \"doxycyclinum\", \"doxylin\", \"doxysol\", \"doxytec\", \"doxytetracycline\", \"hydramycin\", \"investin\", \"jenacyclin\", \"liviatin\", \"monodox\", \"oracea\", \"periostat\", \"ronaxan\", \"spanor\", \"supracyclin\", \"vibramycin\", \"vibramycin novum\", \"vibramycine\", \"vibravenos\", \"zenavod\")"	0.1	"g"	0.1	"g"	"c(\"10986-8\", \"21250-6\", \"26902-7\")"
-"ECO"	"J01XDXX"	3198	"Econazole"	"Antifungals/antimycotics"			"econ"	"c(\"econazol\", \"econazole\", \"econazolum\", \"ecostatin\", \"ecostatin cream\", \"palavale\", \"pevaryl\", \"spectazole\", \"spectazole cream\")"					"character(0)"
+"ECO"	"D01AC03"	3198	"Econazole"	"Antifungals/antimycotics"	"Antifungals for topical use"	"Imidazole and triazole derivatives"	"econ"	"c(\"econazol\", \"econazole\", \"econazolum\", \"ecostatin\", \"ecostatin cream\", \"palavale\", \"pevaryl\", \"spectazole\", \"spectazole cream\")"					"character(0)"
 "ENX"	"J01MA04"	3229	"Enoxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"\", \"enox\")"	"c(\"almitil\", \"bactidan\", \"bactidron\", \"comprecin\", \"enofloxacine\", \"enoksetin\", \"enoram\", \"enoxacin\", \"enoxacina\", \"enoxacine\", \"enoxacino\", \"enoxacinum\", \"enoxen\", \"enoxin\", \"enoxor\", \"flumark\", \"penetrex\")"	0.8	"g"			"c(\"16816-1\", \"3590-7\")"
 "ENR"		71188	"Enrofloxacin"	"Quinolones"			""	"c(\"baytril\", \"enrofloxacin\", \"enrofloxacine\", \"enrofloxacino\", \"enrofloxacinum\")"					"character(0)"
 "ENV"		135565326	"Enviomycin (Tuberactinomycin)"	"Antimycobacterials"			""	"c(\"enviomicina\", \"enviomycin\", \"enviomycina\", \"enviomycinum\")"					"character(0)"
@@ -190,7 +190,7 @@
 "ETI1"	"J04AD03"	2761171	"Ethionamide"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Thiocarbamide derivatives"	"ethi"	"c(\"aethionamidum\", \"aetina\", \"aetiva\", \"amidazin\", \"amidazine\", \"ethatyl\", \"ethimide\", \"ethina\", \"ethinamide\", \"ethionamide\", \"ethionamidum\", \"ethioniamide\", \"ethylisothiamide\", \"ethyonomide\", \"etimid\", \"etiocidan\", \"etionamid\", \"etionamida\", \"etionamide\", \"etioniamid\", \"etionid\", \"etionizin\", \"etionizina\", \"etionizine\", \"fatoliamid\", \"iridocin\", \"iridocin bayer\", \"iridozin\", \"isothin\", \"isotiamida\", \"itiocide\", \"nicotion\", \"nisotin\", \"nizotin\", \"rigenicid\", \"sertinon\", \"teberus\", \"thianid\", \"thianide\", 
 \"thioamide\", \"thiodine\", \"thiomid\", \"thioniden\", \"tianid\", \"tiomid\", \"trecator\", \"trecator sc\", \"trekator\", \"trescatyl\", \"trescazide\", \"tubenamide\", \"tubermin\", \"tuberoid\", \"tuberoson\")"	0.75	"g"			"16845-0"
 "ETO"		6034	"Ethopabate"	"Other antibacterials"			""	"c(\"amprol plus\", \"ethopabat\", \"ethopabate\", \"ethyl pabate\")"					"character(0)"
-"FAR"	"J01DI03"	65894	"Faropenem"	"Other antibacterials"			""	"c(\"faropenem\", \"faropenem sodium\", \"fropenem\", \"fropenum sodium\")"	0.75				"character(0)"
+"FAR"	"J01DI03"	65894	"Faropenem"	"Other antibacterials"	"Other beta-lactam antibacterials"	"Other cephalosporins and penems"	""	"c(\"faropenem\", \"faropenem sodium\", \"fropenem\", \"fropenum sodium\")"	0.75	"g"			"character(0)"
 "FDX"		10034073	"Fidaxomicin"	"Other antibacterials"			""	"c(\"dificid\", \"dificlir\", \"difimicin\", \"fidaxomicin\", \"lipiarmycin\", \"tiacumicin b\")"					"character(0)"
 "FIN"		11567473	"Finafloxacin"	"Quinolones"			""	"finafloxacin"					"character(0)"
 "FLA"		46783781	"Flavomycin"	"Other antibacterials"			""	"moenomycin complex"					"character(0)"
@@ -309,7 +309,7 @@
 "NTR"	"J01XX07"	19910	"Nitroxoline"	"Quinolones"	"Other antibacterials"	"Other antibacterials"	""	"c(\"galinok\", \"isinok\", \"nibiol\", \"nicene forte\", \"nitroxolin\", \"nitroxolina\", \"nitroxoline\", \"nitroxolinum\", \"notroxoline\", \"noxibiol\")"	1	"g"			"character(0)"
 "NOR"	"J01MA06"	4539	"Norfloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"nor\", \"norf\", \"nx\", \"nxn\")"	"c(\"baccidal\", \"barazan\", \"chibroxin\", \"chibroxine\", \"chibroxol\", \"fulgram\", \"gonorcin\", \"lexinor\", \"nolicin\", \"noracin\", \"noraxin\", \"norflo\", \"norfloxacin\", \"norfloxacine\", \"norfloxacino\", \"norfloxacinum\", \"norocin\", \"noroxin\", \"noroxine\", \"norxacin\", \"sebercim\", \"uroxacin\", \"utinor\", \"zoroxin\")"	0.8	"g"			"3867-9"
 "NVA"		10419027	"Norvancomycin"	"Glycopeptides"			""	"norvancomycin"					"character(0)"
-"NOV"	"QJ01XX95"	54675769	"Novobiocin"	"Other antibacterials"			"novo"	"c(\"albamix\", \"albamycin\", \"cardelmycin\", \"cathocin\", \"cathomycin\", \"crystallinic acid\", \"inamycin\", \"novobiocin\", \"novobiocina\", \"novobiocine\", \"novobiocinum\", \"robiocina\", \"sirbiocina\", \"spheromycin\", \"stilbiocina\", \"streptonivicin\")"					"17378-1"
+"NOV"		54675769	"Novobiocin"	"Other antibacterials"			"novo"	"c(\"albamix\", \"albamycin\", \"cardelmycin\", \"cathocin\", \"cathomycin\", \"crystallinic acid\", \"inamycin\", \"novobiocin\", \"novobiocina\", \"novobiocine\", \"novobiocinum\", \"robiocina\", \"sirbiocina\", \"spheromycin\", \"stilbiocina\", \"streptonivicin\")"					"17378-1"
 "NYS"	"G01AA01"	6433272	"Nystatin"	"Antifungals/antimycotics"			"nyst"	"c(\"biofanal\", \"candex lotion\", \"comycin\", \"diastatin\", \"herniocid\", \"moronal\", \"myconystatin\", \"mycostatin\", \"mycostatin pastilles\", \"mykinac\", \"mykostatyna\", \"nilstat\", \"nistatin\", \"nistatina\", \"nyamyc\", \"nyotran\", \"nyotrantrade mark\", \"nystaform\", \"nystan\", \"nystatin\", \"nystatin a\", \"nystatin g\", \"nystatin lf\", \"nystatine\", \"nystatinum\", \"nystatyna\", \"nystavescent\", \"nystex\", \"nystop\", \"stamycin\", \"terrastatin\", \"zydin e\")"					"character(0)"
 "OFX"	"J01MA01"	4583	"Ofloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"of\", \"ofl\", \"oflo\", \"ofx\")"	"c(\"bactocin\", \"danoflox\", \"effexin\", \"exocin\", \"exocine\", \"flobacin\", \"flodemex\", \"flotavid\", \"flovid\", \"floxal\", \"floxil\", \"floxin\", \"floxin otic\", \"floxstat\", \"fugacin\", \"inoflox\", \"kinflocin\", \"kinoxacin\", \"levofloxacin hcl\", \"liflox\", \"loxinter\", \"marfloxacin\", \"medofloxine\", \"mergexin\", \"monoflocet\", \"novecin\", \"nufafloqo\", \"occidal\", \"ocuflox\", \"oflocee\", \"oflocet\", \"oflocin\", \"oflodal\", \"oflodex\", \"oflodura\", \"ofloxacin\", \"ofloxacin otic\", \"ofloxacina\", \"ofloxacine\", \"ofloxacino\", \"ofloxacinum\", 
 \"ofloxin\", \"onexacin\", \"operan\", \"orocin\", \"otonil\", \"oxaldin\", \"pharflox\", \"praxin\", \"puiritol\", \"qinolon\", \"quinolon\", \"quotavil\", \"sinflo\", \"tabrin\", \"taravid\", \"tariflox\", \"tarivid\", \"telbit\", \"tructum\", \"uro tarivid\", \"viotisone\", \"visiren\", \"zanocin\")"	0.4	"g"	0.4	"g"	"c(\"25264-3\", \"3877-8\")"
@@ -344,7 +344,7 @@
 "PIS"			"Piperacillin/sulbactam"	"Beta-lactams/penicillins"			""	""					""
 "TZP"	"J01CR05"	461573	"Piperacillin/tazobactam"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"c(\"p/t\", \"piptaz\", \"piptazo\", \"pit\", \"pita\", \"pt\", \"ptc\", \"ptz\", \"tzp\")"	"c(\"\", \"tazocel\", \"tazocillin\", \"tazocin\", \"zosyn\")"			14	"g"	"character(0)"
 "PRC"		71978	"Piridicillin"	"Beta-lactams/penicillins"			""	"piridicillin"					"character(0)"
-"PRL"		157385	"Pirlimycin"	"Other antibacterials"			""	"c(\"pirlimycin\", \"pirlimycina\", \"pirlimycine\", \"pirlimycinum\", \"pirsue\")"					"character(0)"
+"PRL"		157385	"Pirlimycin"	"Macrolides/lincosamides"			""	"c(\"pirlimycin\", \"pirlimycina\", \"pirlimycine\", \"pirlimycinum\", \"pirsue\")"					"character(0)"
 "PIR"	"J01MB03"	4855	"Piromidic acid"	"Quinolones"	"Quinolone antibacterials"	"Other quinolones"	""	"c(\"acide piromidique\", \"acido piromidico\", \"acidum piromidicum\", \"actrun c\", \"bactramyl\", \"enterol\", \"gastrurol\", \"panacid\", \"pirodal\", \"piromidic acid\", \"pyrido\", \"reelon\", \"septural\", \"urisept\", \"uropir\", \"zaomeal\")"	2	"g"			"character(0)"
 "PVM"	"J01CA02"	33478	"Pivampicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"berocillin\", \"pivaloylampicillin\", \"pivampicilina\", \"pivampicillin\", \"pivampicilline\", \"pivampicillinum\", \"pondocillin\")"	1.05	"g"			"character(0)"
 "PME"	"J01CA08"	115163	"Pivmecillinam"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"amdinocillin pivoxil\", \"coactabs\", \"hydroxymethyl\", \"pivmecilinamo\", \"pivmecillinam\", \"pivmecillinam hcl\", \"pivmecillinamum\")"	0.6	"g"			"character(0)"
@@ -368,7 +368,7 @@
 "RAC"		56052	"Ractopamine"	"Other antibacterials"			""	"c(\"ractopamina\", \"ractopamine\", \"ractopaminum\")"					"character(0)"
 "RAM"		16132338	"Ramoplanin"	"Glycopeptides"			""	"ramoplanin"					"character(0)"
 "RZM"		10993211	"Razupenem"	"Carbapenems"			""	"razupenem"					"character(0)"
-"RTP"	"A07AA11"	6918462	"Retapamulin"	"Other antibacterials"	"Intestinal antiinfectives"	"Antibiotics"	""	"c(\"altabax\", \"altargo\", \"retapamulin\")"	0.6	"g"			"character(0)"
+"RTP"	"D06AX13"	6918462	"Retapamulin"	"Other antibacterials"	"Antibiotics for topical use"	"Other antibiotics for topical use"	""	"c(\"altabax\", \"altargo\", \"retapamulin\")"					"character(0)"
 "RBC"	"J02AC05"	44631912	"Ribociclib"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Triazole derivatives"	"ribo"	"c(\"kisqali\", \"ribociclib\")"	0.2		0.2		"character(0)"
 "RST"	"J01GB10"	33042	"Ribostamycin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	""	"c(\"dekamycin iv\", \"hetangmycin\", \"ribastamin\", \"ribostamicina\", \"ribostamycin\", \"ribostamycine\", \"ribostamycinum\", \"vistamycin\", \"xylostatin\")"			1	"g"	"character(0)"
 "RID1"		16659285	"Ridinilazole"	"Other antibacterials"			""	"ridinilazole"					"character(0)"
@@ -500,7 +500,7 @@
 "TVA"	"J01MA13"	62959	"Trovafloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"\", \"trov\")"	"c(\"trovafloxacin\", \"trovan\")"	0.2	"g"	0.2	"g"	"character(0)"
 "TUL"		9832301	"Tulathromycin"	"Macrolides/lincosamides"			""	"c(\"draxxin\", \"tulathrmycin a\", \"tulathromycin\", \"tulathromycin a\")"					"character(0)"
 "TYL"		5280440	"Tylosin"	"Macrolides/lincosamides"			""	"c(\"fradizine\", \"tilosina\", \"tylocine\", \"tylosin\", \"tylosin a\", \"tylosine\", \"tylosinum\")"					"87587-2"
-"TYL1"	"A07AA11"	6441094	"Tylvalosin"	"Other antibacterials"	"Intestinal antiinfectives"	"Antibiotics"	""	""	0.6	"g"			""
+"TYL1"		6441094	"Tylvalosin"	"Macrolides/lincosamides"			""	""					""
 "PRU1"		124225	"Ulifloxacin (Prulifloxacin)"	"Other antibacterials"			""	"ulifloxacin"					"character(0)"
 "VAN"	"J01XA01"	14969	"Vancomycin"	"Glycopeptides"	"Other antibacterials"	"Glycopeptide antibacterials"	"c(\"va\", \"van\", \"vanc\")"	"c(\"vancocin\", \"vancocin hcl\", \"vancoled\", \"vancomicina\", \"vancomycin\", \"vancomycin hcl\", \"vancomycine\", \"vancomycinum\", \"vancor\", \"viomycin derivative\")"			2	"g"	"c(\"13586-3\", \"13587-1\", \"20578-1\", \"31012-8\", \"39092-2\", \"39796-8\", \"39797-6\", \"4089-9\", \"4090-7\", \"4091-5\", \"4092-3\", \"50938-0\", \"59381-4\")"
 "VAM"			"Vancomycin-macromethod"	"Glycopeptides"			""	""					""

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_antibiotics.R

@@ -647,6 +647,7 @@ antibiotics <- antibiotics %>%
 
 
 # update DDDs from WHOCC website
+# last time checked: 2021-06-23
 ddd_oral <- double(length = nrow(antibiotics))
 ddd_iv <- double(length = nrow(antibiotics))
 progress <- progress_ticker(nrow(antibiotics))
@@ -667,7 +668,7 @@ antibiotics$iv_ddd <- ddd_iv
 # set as data.frame again
 antibiotics <- as.data.frame(antibiotics, stringsAsFactors = FALSE)
 class(antibiotics$ab) <- c("ab", "character")
-antibiotics <- antibiotics %>% dplyr::arrange(name)
+antibiotics <- dplyr::arrange(antibiotics, name)
 
 # make all abbreviations and synonyms lower case, unique and alphabetically sorted ----
 for (i in 1:nrow(antibiotics)) {
@@ -683,5 +684,5 @@ for (i in 1:nrow(antibiotics)) {
 
 # REFER TO data-raw/loinc.R FOR ADDING LOINC CODES
 
-usethis::use_data(antibiotics, overwrite = TRUE, version = 2)
+usethis::use_data(antibiotics, overwrite = TRUE, version = 2, compress = "xz")
 rm(antibiotics)

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)
 

data-raw/translations.tsv

@@ -16,6 +16,7 @@ unknown genus	TRUE	TRUE	FALSE	TRUE	unbekannte Gattung	onbekend geslacht	género
 unknown species	TRUE	TRUE	FALSE	TRUE	unbekannte Art	onbekende soort	especie desconocida	specie sconosciute	espèce inconnue	espécies desconhecida
 unknown subspecies	TRUE	TRUE	FALSE	TRUE	unbekannte Unterart	onbekende ondersoort	subespecie desconocida	sottospecie sconosciute	sous-espèce inconnue	subespécies desconhecida
 unknown rank	TRUE	TRUE	FALSE	TRUE	unbekannter Rang	onbekende rang	rango desconocido	grado sconosciuto	rang inconnu	classificação desconhecido
+ group 	TRUE	TRUE	FALSE	TRUE	 Gruppe 	 groep 	 grupo 	 gruppo 	 groupe 	 grupo 
 CoNS	FALSE	TRUE	FALSE	TRUE	KNS	CNS	SCN			
 CoPS	FALSE	TRUE	FALSE	TRUE	KPS	CPS	SCP			
 Gram-negative	TRUE	TRUE	FALSE	FALSE	Gramnegativ	Gram-negatief	Gram negativo	Gram negativo	Gram négatif	Gram negativo

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">1.7.1.9018</span>
       </span>
     </div>
 
@@ -89,14 +89,14 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="index.html">
-    <span class="fas fa-home"></span>
+    <span class="fa fa-home"></span>
      
     Home
   </a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fas fa-question-circle"></span>
+    <span class="fa fa-question-circle"></span>
      
     How to
      
@@ -105,77 +105,77 @@
   <ul class="dropdown-menu" role="menu">
     <li>
       <a href="articles/AMR.html">
-        <span class="fas fa-directions"></span>
+        <span class="fa fa-directions"></span>
          
         Conduct AMR analysis
       </a>
     </li>
     <li>
       <a href="articles/resistance_predict.html">
-        <span class="fas fa-dice"></span>
+        <span class="fa fa-dice"></span>
          
         Predict antimicrobial resistance
       </a>
     </li>
     <li>
       <a href="articles/datasets.html">
-        <span class="fas fa-database"></span>
+        <span class="fa fa-database"></span>
          
         Data sets for download / own use
       </a>
     </li>
     <li>
       <a href="articles/PCA.html">
-        <span class="fas fa-compress"></span>
+        <span class="fa fa-compress"></span>
          
         Conduct principal component analysis for AMR
       </a>
     </li>
     <li>
       <a href="articles/MDR.html">
-        <span class="fas fa-skull-crossbones"></span>
+        <span class="fa fa-skull-crossbones"></span>
          
         Determine multi-drug resistance (MDR)
       </a>
     </li>
     <li>
       <a href="articles/WHONET.html">
-        <span class="fas fa-globe-americas"></span>
+        <span class="fa fa-globe-americas"></span>
          
         Work with WHONET data
       </a>
     </li>
     <li>
       <a href="articles/SPSS.html">
-        <span class="fas fa-file-upload"></span>
+        <span class="fa fa-file-upload"></span>
          
         Import data from SPSS/SAS/Stata
       </a>
     </li>
     <li>
       <a href="articles/EUCAST.html">
-        <span class="fas fa-exchange-alt"></span>
+        <span class="fa fa-exchange-alt"></span>
          
         Apply EUCAST rules
       </a>
     </li>
     <li>
       <a href="reference/mo_property.html">
-        <span class="fas fa-bug"></span>
+        <span class="fa fa-bug"></span>
          
         Get properties of a microorganism
       </a>
     </li>
     <li>
       <a href="reference/ab_property.html">
-        <span class="fas fa-capsules"></span>
+        <span class="fa fa-capsules"></span>
          
         Get properties of an antibiotic
       </a>
     </li>
     <li>
       <a href="articles/benchmarks.html">
-        <span class="fas fa-shipping-fast"></span>
+        <span class="fa fa-shipping-fast"></span>
          
         Other: benchmarks
       </a>
@@ -184,14 +184,14 @@
 </li>
 <li>
   <a href="reference/index.html">
-    <span class="fas fa-book-open"></span>
+    <span class="fa fa-book-open"></span>
      
     Manual
   </a>
 </li>
 <li>
   <a href="authors.html">
-    <span class="fas fa-users"></span>
+    <span class="fa fa-users"></span>
      
     Authors
   </a>
@@ -214,7 +214,7 @@
 </li>
 <li>
   <a href="survey.html">
-    <span class="fas fa-clipboard-list"></span>
+    <span class="fa fa-clipboard-list"></span>
      
     Survey
   </a>

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">1.7.1.9018</span>
       </span>
     </div>
 
@@ -89,14 +89,14 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="index.html">
-    <span class="fas fa-home"></span>
+    <span class="fa fa-home"></span>
      
     Home
   </a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fas fa-question-circle"></span>
+    <span class="fa fa-question-circle"></span>
      
     How to
      
@@ -105,77 +105,77 @@
   <ul class="dropdown-menu" role="menu">
     <li>
       <a href="articles/AMR.html">
-        <span class="fas fa-directions"></span>
+        <span class="fa fa-directions"></span>
          
         Conduct AMR analysis
       </a>
     </li>
     <li>
       <a href="articles/resistance_predict.html">
-        <span class="fas fa-dice"></span>
+        <span class="fa fa-dice"></span>
          
         Predict antimicrobial resistance
       </a>
     </li>
     <li>
       <a href="articles/datasets.html">
-        <span class="fas fa-database"></span>
+        <span class="fa fa-database"></span>
          
         Data sets for download / own use
       </a>
     </li>
     <li>
       <a href="articles/PCA.html">
-        <span class="fas fa-compress"></span>
+        <span class="fa fa-compress"></span>
          
         Conduct principal component analysis for AMR
       </a>
     </li>
     <li>
       <a href="articles/MDR.html">
-        <span class="fas fa-skull-crossbones"></span>
+        <span class="fa fa-skull-crossbones"></span>
          
         Determine multi-drug resistance (MDR)
       </a>
     </li>
     <li>
       <a href="articles/WHONET.html">
-        <span class="fas fa-globe-americas"></span>
+        <span class="fa fa-globe-americas"></span>
          
         Work with WHONET data
       </a>
     </li>
     <li>
       <a href="articles/SPSS.html">
-        <span class="fas fa-file-upload"></span>
+        <span class="fa fa-file-upload"></span>
          
         Import data from SPSS/SAS/Stata
       </a>
     </li>
     <li>
       <a href="articles/EUCAST.html">
-        <span class="fas fa-exchange-alt"></span>
+        <span class="fa fa-exchange-alt"></span>
          
         Apply EUCAST rules
       </a>
     </li>
     <li>
       <a href="reference/mo_property.html">
-        <span class="fas fa-bug"></span>
+        <span class="fa fa-bug"></span>
          
         Get properties of a microorganism
       </a>
     </li>
     <li>
       <a href="reference/ab_property.html">
-        <span class="fas fa-capsules"></span>
+        <span class="fa fa-capsules"></span>
          
         Get properties of an antibiotic
       </a>
     </li>
     <li>
       <a href="articles/benchmarks.html">
-        <span class="fas fa-shipping-fast"></span>
+        <span class="fa fa-shipping-fast"></span>
          
         Other: benchmarks
       </a>
@@ -184,14 +184,14 @@
 </li>
 <li>
   <a href="reference/index.html">
-    <span class="fas fa-book-open"></span>
+    <span class="fa fa-book-open"></span>
      
     Manual
   </a>
 </li>
 <li>
   <a href="authors.html">
-    <span class="fas fa-users"></span>
+    <span class="fa fa-users"></span>
      
     Authors
   </a>
@@ -214,7 +214,7 @@
 </li>
 <li>
   <a href="survey.html">
-    <span class="fas fa-clipboard-list"></span>
+    <span class="fa fa-clipboard-list"></span>
      
     Survey
   </a>

docs/articles/AMR_files/header-attrs-2.9/header-attrs.js

@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});

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">1.7.1.9018</span>
       </span>
     </div>
 
@@ -47,14 +47,14 @@
       <ul class="nav navbar-nav">
 <li>
   <a href="../index.html">
-    <span class="fas fa-home"></span>
+    <span class="fa fa-home"></span>
      
     Home
   </a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fas fa-question-circle"></span>
+    <span class="fa fa-question-circle"></span>
      
     How to
      
@@ -63,77 +63,77 @@
   <ul class="dropdown-menu" role="menu">
 <li>
       <a href="../articles/AMR.html">
-        <span class="fas fa-directions"></span>
+        <span class="fa fa-directions"></span>
          
         Conduct AMR analysis
       </a>
     </li>
     <li>
       <a href="../articles/resistance_predict.html">
-        <span class="fas fa-dice"></span>
+        <span class="fa fa-dice"></span>
          
         Predict antimicrobial resistance
       </a>
     </li>
     <li>
       <a href="../articles/datasets.html">
-        <span class="fas fa-database"></span>
+        <span class="fa fa-database"></span>
          
         Data sets for download / own use
       </a>
     </li>
     <li>
       <a href="../articles/PCA.html">
-        <span class="fas fa-compress"></span>
+        <span class="fa fa-compress"></span>
          
         Conduct principal component analysis for AMR
       </a>
     </li>
     <li>
       <a href="../articles/MDR.html">
-        <span class="fas fa-skull-crossbones"></span>
+        <span class="fa fa-skull-crossbones"></span>
          
         Determine multi-drug resistance (MDR)
       </a>
     </li>
     <li>
       <a href="../articles/WHONET.html">
-        <span class="fas fa-globe-americas"></span>
+        <span class="fa fa-globe-americas"></span>
          
         Work with WHONET data
       </a>
     </li>
     <li>
       <a href="../articles/SPSS.html">
-        <span class="fas fa-file-upload"></span>
+        <span class="fa fa-file-upload"></span>
          
         Import data from SPSS/SAS/Stata
       </a>
     </li>
     <li>
       <a href="../articles/EUCAST.html">
-        <span class="fas fa-exchange-alt"></span>
+        <span class="fa fa-exchange-alt"></span>
          
         Apply EUCAST rules
       </a>
     </li>
     <li>
       <a href="../reference/mo_property.html">
-        <span class="fas fa-bug"></span>
+        <span class="fa fa-bug"></span>
          
         Get properties of a microorganism
       </a>
     </li>
     <li>
       <a href="../reference/ab_property.html">
-        <span class="fas fa-capsules"></span>
+        <span class="fa fa-capsules"></span>
          
         Get properties of an antibiotic
       </a>
     </li>
     <li>
       <a href="../articles/benchmarks.html">
-        <span class="fas fa-shipping-fast"></span>
+        <span class="fa fa-shipping-fast"></span>
          
         Other: benchmarks
       </a>
@@ -142,14 +142,14 @@
 </li>
 <li>
   <a href="../reference/index.html">
-    <span class="fas fa-book-open"></span>
+    <span class="fa fa-book-open"></span>
      
     Manual
   </a>
 </li>
 <li>
   <a href="../authors.html">
-    <span class="fas fa-users"></span>
+    <span class="fa fa-users"></span>
      
     Authors
   </a>
@@ -172,7 +172,7 @@
 </li>
 <li>
   <a href="../survey.html">
-    <span class="fas fa-clipboard-list"></span>
+    <span class="fa fa-clipboard-list"></span>
      
     Survey
   </a>
@@ -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-2.9/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">11 July 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>
@@ -497,7 +497,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <a href="#antibiotic-agents" class="anchor"></a>Antibiotic agents</h2>
 <p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>atc</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
 <p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 4 May 2021 13:38:27 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
+<p>It was last updated on 23 June 2021 13:07:57 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds">R file</a> (32 kB)<br>
@@ -508,7 +508,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sas">SAS file</a> (1.8 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sav">SPSS file</a> (1.3 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sav">SPSS file</a> (0.3 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.dta">Stata file</a> (0.3 MB)</li>
 </ul>

docs/articles/datasets_files/header-attrs-2.9/header-attrs.js

@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});

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">1.7.1.9018</span>
       </span>
     </div>
 
@@ -89,14 +89,14 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa-home"></span>
+    <span class="fa fa-home"></span>
      
     Home
   </a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fas fa-question-circle"></span>
+    <span class="fa fa-question-circle"></span>
      
     How to
      
@@ -105,77 +105,77 @@
   <ul class="dropdown-menu" role="menu">
     <li>
       <a href="../articles/AMR.html">
-        <span class="fas fa-directions"></span>
+        <span class="fa fa-directions"></span>
          
         Conduct AMR analysis
       </a>
     </li>
     <li>
       <a href="../articles/resistance_predict.html">
-        <span class="fas fa-dice"></span>
+        <span class="fa fa-dice"></span>
          
         Predict antimicrobial resistance
       </a>
     </li>
     <li>
       <a href="../articles/datasets.html">
-        <span class="fas fa-database"></span>
+        <span class="fa fa-database"></span>
          
         Data sets for download / own use
       </a>
     </li>
     <li>
       <a href="../articles/PCA.html">
-        <span class="fas fa-compress"></span>
+        <span class="fa fa-compress"></span>
          
         Conduct principal component analysis for AMR
       </a>
     </li>
     <li>
       <a href="../articles/MDR.html">
-        <span class="fas fa-skull-crossbones"></span>
+        <span class="fa fa-skull-crossbones"></span>
          
         Determine multi-drug resistance (MDR)
       </a>
     </li>
     <li>
       <a href="../articles/WHONET.html">
-        <span class="fas fa-globe-americas"></span>
+        <span class="fa fa-globe-americas"></span>
          
         Work with WHONET data
       </a>
     </li>
     <li>
       <a href="../articles/SPSS.html">
-        <span class="fas fa-file-upload"></span>
+        <span class="fa fa-file-upload"></span>
          
         Import data from SPSS/SAS/Stata
       </a>
     </li>
     <li>
       <a href="../articles/EUCAST.html">
-        <span class="fas fa-exchange-alt"></span>
+        <span class="fa fa-exchange-alt"></span>
          
         Apply EUCAST rules
       </a>
     </li>
     <li>
       <a href="../reference/mo_property.html">
-        <span class="fas fa-bug"></span>
+        <span class="fa fa-bug"></span>
          
         Get properties of a microorganism
       </a>
     </li>
     <li>
       <a href="../reference/ab_property.html">
-        <span class="fas fa-capsules"></span>
+        <span class="fa fa-capsules"></span>
          
         Get properties of an antibiotic
       </a>
     </li>
     <li>
       <a href="../articles/benchmarks.html">
-        <span class="fas fa-shipping-fast"></span>
+        <span class="fa fa-shipping-fast"></span>
          
         Other: benchmarks
       </a>
@@ -184,14 +184,14 @@
 </li>
 <li>
   <a href="../reference/index.html">
-    <span class="fas fa-book-open"></span>
+    <span class="fa fa-book-open"></span>
      
     Manual
   </a>
 </li>
 <li>
   <a href="../authors.html">
-    <span class="fas fa-users"></span>
+    <span class="fa fa-users"></span>
      
     Authors
   </a>
@@ -214,7 +214,7 @@
 </li>
 <li>
   <a href="../survey.html">
-    <span class="fas fa-clipboard-list"></span>
+    <span class="fa fa-clipboard-list"></span>
      
     Survey
   </a>

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">1.7.1.9018</span>
       </span>
     </div>
 
@@ -89,14 +89,14 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="index.html">
-    <span class="fas fa-home"></span>
+    <span class="fa fa-home"></span>
      
     Home
   </a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fas fa-question-circle"></span>
+    <span class="fa fa-question-circle"></span>
      
     How to
      
@@ -105,77 +105,77 @@
   <ul class="dropdown-menu" role="menu">
     <li>
       <a href="articles/AMR.html">
-        <span class="fas fa-directions"></span>
+        <span class="fa fa-directions"></span>
          
         Conduct AMR analysis
       </a>
     </li>
     <li>
       <a href="articles/resistance_predict.html">
-        <span class="fas fa-dice"></span>
+        <span class="fa fa-dice"></span>
          
         Predict antimicrobial resistance
       </a>
     </li>
     <li>
       <a href="articles/datasets.html">
-        <span class="fas fa-database"></span>
+        <span class="fa fa-database"></span>
          
         Data sets for download / own use
       </a>
     </li>
     <li>
       <a href="articles/PCA.html">
-        <span class="fas fa-compress"></span>
+        <span class="fa fa-compress"></span>
          
         Conduct principal component analysis for AMR
       </a>
     </li>
     <li>
       <a href="articles/MDR.html">
-        <span class="fas fa-skull-crossbones"></span>
+        <span class="fa fa-skull-crossbones"></span>
          
         Determine multi-drug resistance (MDR)
       </a>
     </li>
     <li>
       <a href="articles/WHONET.html">
-        <span class="fas fa-globe-americas"></span>
+        <span class="fa fa-globe-americas"></span>
          
         Work with WHONET data
       </a>
     </li>
     <li>
       <a href="articles/SPSS.html">
-        <span class="fas fa-file-upload"></span>
+        <span class="fa fa-file-upload"></span>
          
         Import data from SPSS/SAS/Stata
       </a>
     </li>
     <li>
       <a href="articles/EUCAST.html">
-        <span class="fas fa-exchange-alt"></span>
+        <span class="fa fa-exchange-alt"></span>
          
         Apply EUCAST rules
       </a>
     </li>
     <li>
       <a href="reference/mo_property.html">
-        <span class="fas fa-bug"></span>
+        <span class="fa fa-bug"></span>
          
         Get properties of a microorganism
       </a>
     </li>
     <li>
       <a href="reference/ab_property.html">
-        <span class="fas fa-capsules"></span>
+        <span class="fa fa-capsules"></span>
          
         Get properties of an antibiotic
       </a>
     </li>
     <li>
       <a href="articles/benchmarks.html">
-        <span class="fas fa-shipping-fast"></span>
+        <span class="fa fa-shipping-fast"></span>
          
         Other: benchmarks
       </a>
@@ -184,14 +184,14 @@
 </li>
 <li>
   <a href="reference/index.html">
-    <span class="fas fa-book-open"></span>
+    <span class="fa fa-book-open"></span>
      
     Manual
   </a>
 </li>
 <li>
   <a href="authors.html">
-    <span class="fas fa-users"></span>
+    <span class="fa fa-users"></span>
      
     Authors
   </a>
@@ -214,7 +214,7 @@
 </li>
 <li>
   <a href="survey.html">
-    <span class="fas fa-clipboard-list"></span>
+    <span class="fa fa-clipboard-list"></span>
      
     Survey
   </a>

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">1.7.1.9018</span>
       </span>
     </div>
 
@@ -50,14 +50,14 @@
       <ul class="nav navbar-nav">
 <li>
   <a href="index.html">
-    <span class="fas fa-home"></span>
+    <span class="fa fa-home"></span>
      
     Home
   </a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fas fa-question-circle"></span>
+    <span class="fa fa-question-circle"></span>
      
     How to
      
@@ -66,77 +66,77 @@
   <ul class="dropdown-menu" role="menu">
 <li>
       <a href="articles/AMR.html">
-        <span class="fas fa-directions"></span>
+        <span class="fa fa-directions"></span>
          
         Conduct AMR analysis
       </a>
     </li>
     <li>
       <a href="articles/resistance_predict.html">
-        <span class="fas fa-dice"></span>
+        <span class="fa fa-dice"></span>
          
         Predict antimicrobial resistance
       </a>
     </li>
     <li>
       <a href="articles/datasets.html">
-        <span class="fas fa-database"></span>
+        <span class="fa fa-database"></span>
          
         Data sets for download / own use
       </a>
     </li>
     <li>
       <a href="articles/PCA.html">
-        <span class="fas fa-compress"></span>
+        <span class="fa fa-compress"></span>
          
         Conduct principal component analysis for AMR
       </a>
     </li>
     <li>
       <a href="articles/MDR.html">
-        <span class="fas fa-skull-crossbones"></span>
+        <span class="fa fa-skull-crossbones"></span>
          
         Determine multi-drug resistance (MDR)
       </a>
     </li>
     <li>
       <a href="articles/WHONET.html">
-        <span class="fas fa-globe-americas"></span>
+        <span class="fa fa-globe-americas"></span>
          
         Work with WHONET data
       </a>
     </li>
     <li>
       <a href="articles/SPSS.html">
-        <span class="fas fa-file-upload"></span>
+        <span class="fa fa-file-upload"></span>
          
         Import data from SPSS/SAS/Stata
       </a>
     </li>
     <li>
       <a href="articles/EUCAST.html">
-        <span class="fas fa-exchange-alt"></span>
+        <span class="fa fa-exchange-alt"></span>
          
         Apply EUCAST rules
       </a>
     </li>
     <li>
       <a href="reference/mo_property.html">
-        <span class="fas fa-bug"></span>
+        <span class="fa fa-bug"></span>
          
         Get properties of a microorganism
       </a>
     </li>
     <li>
       <a href="reference/ab_property.html">
-        <span class="fas fa-capsules"></span>
+        <span class="fa fa-capsules"></span>
          
         Get properties of an antibiotic
       </a>
     </li>
     <li>
       <a href="articles/benchmarks.html">
-        <span class="fas fa-shipping-fast"></span>
+        <span class="fa fa-shipping-fast"></span>
          
         Other: benchmarks
       </a>
@@ -145,14 +145,14 @@
 </li>
 <li>
   <a href="reference/index.html">
-    <span class="fas fa-book-open"></span>
+    <span class="fa fa-book-open"></span>
      
     Manual
   </a>
 </li>
 <li>
   <a href="authors.html">
-    <span class="fas fa-users"></span>
+    <span class="fa fa-users"></span>
      
     Authors
   </a>
@@ -175,7 +175,7 @@
 </li>
 <li>
   <a href="survey.html">
-    <span class="fas fa-clipboard-list"></span>
+    <span class="fa fa-clipboard-list"></span>
      
     Survey
   </a>
@@ -213,56 +213,52 @@
 <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>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>bacteria <span class="op">=</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</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="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
-<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; ℹ For `aminoglycosides()` using columns: 'AMK' (amikacin), 'GEN' (gentamicin), 'KAN'</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>
+  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>bacteria <span class="op">=</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</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="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span>,
+         <span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
+  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">bacteria</span>,
+         <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,
+         <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</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">
 <thead><tr class="header">
 <th align="left">bacteria</th>
-<th align="center">AMK</th>
 <th align="center">GEN</th>
-<th align="center">KAN</th>
 <th align="center">TOB</th>
+<th align="center">AMK</th>
+<th align="center">KAN</th>
 <th align="center">IPM</th>
 <th align="center">MEM</th>
 </tr></thead>
 <tbody>
 <tr class="odd">
 <td align="left"><em>Pseudomonas aeruginosa</em></td>
-<td align="center"></td>
 <td align="center">I</td>
-<td align="center">R</td>
 <td align="center">S</td>
+<td align="center"></td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center"></td>
 </tr>
 <tr class="even">
 <td align="left"><em>Pseudomonas aeruginosa</em></td>
-<td align="center"></td>
 <td align="center">I</td>
-<td align="center">R</td>
 <td align="center">S</td>
+<td align="center"></td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center"></td>
 </tr>
 <tr class="odd">
 <td align="left"><em>Pseudomonas aeruginosa</em></td>
-<td align="center"></td>
 <td align="center">I</td>
-<td align="center">R</td>
 <td align="center">S</td>
+<td align="center"></td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center"></td>
 </tr>
@@ -270,8 +266,8 @@
 <td align="left"><em>Pseudomonas aeruginosa</em></td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">R</td>
 <td align="center">S</td>
+<td align="center">R</td>
 <td align="center"></td>
 <td align="center">S</td>
 </tr>
@@ -279,8 +275,8 @@
 <td align="left"><em>Pseudomonas aeruginosa</em></td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">R</td>
 <td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 </tr>
@@ -288,8 +284,8 @@
 <td align="left"><em>Pseudomonas aeruginosa</em></td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">R</td>
 <td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 </tr>
@@ -306,8 +302,8 @@
 <td align="left"><em>Pseudomonas aeruginosa</em></td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">R</td>
 <td align="center">S</td>
+<td align="center">R</td>
 <td align="center"></td>
 <td align="center">S</td>
 </tr>
@@ -315,8 +311,8 @@
 <td align="left"><em>Pseudomonas aeruginosa</em></td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">R</td>
 <td align="center">S</td>
+<td align="center">R</td>
 <td align="center"></td>
 <td align="center">S</td>
 </tr>
@@ -324,8 +320,8 @@
 <td align="left"><em>Pseudomonas aeruginosa</em></td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">R</td>
 <td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 </tr>
@@ -386,21 +382,21 @@
 <div id="latest-development-version" class="section level4">
 <h4 class="hasAnchor">
 <a href="#latest-development-version" class="anchor"></a>Latest development version</h4>
-<p><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master" alt="R-code-check"><img src="https://www.codefactor.io/repository/github/msberends/amr" alt="CodeFactor"><img src="https://codecov.io/gh/msberends/AMR?branch=master" alt="Codecov"></p>
+<p><a href="https://codecov.io/gh/msberends/AMR?branch=master"><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master" alt="R-code-check"></a> <a href="https://www.codefactor.io/repository/github/msberends/amr"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=master"><img src="https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg" alt="Codecov"></a></p>
 <p>The latest and unpublished development version can be installed from GitHub in two ways:</p>
 <ol>
 <li>
-<p>Directly, using:</p>
+<p>Manually, using:</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span>
 <span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></code></pre></div>
 </li>
 <li>
-<p>From the <a href="https://ropensci.org/r-universe/">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev">our R-universe address</a> to your list of repositories (‘repos’):</p>
+<p>Automatically, using the <a href="https://ropensci.org/r-universe/">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev">our R-universe address</a> to your list of repositories (‘repos’):</p>
 <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>
@@ -409,7 +405,7 @@
 <div id="get-started" class="section level3">
 <h3 class="hasAnchor">
 <a href="#get-started" class="anchor"></a>Get started</h3>
-<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click the links in the ‘How to’ menu.</p>
+<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click a link in the <a href="https://msberends.github.io/AMR/articles/">‘How to’ menu</a>.</p>
 </div>
 <div id="short-introduction" class="section level3">
 <h3 class="hasAnchor">

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">1.7.1.9018</span>
       </span>
     </div>
 
@@ -89,14 +89,14 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa-home"></span>
+    <span class="fa fa-home"></span>
      
     Home
   </a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fas fa-question-circle"></span>
+    <span class="fa fa-question-circle"></span>
      
     How to
      
@@ -105,77 +105,77 @@
   <ul class="dropdown-menu" role="menu">
     <li>
       <a href="../articles/AMR.html">
-        <span class="fas fa-directions"></span>
+        <span class="fa fa-directions"></span>
          
         Conduct AMR analysis
       </a>
     </li>
     <li>
       <a href="../articles/resistance_predict.html">
-        <span class="fas fa-dice"></span>
+        <span class="fa fa-dice"></span>
          
         Predict antimicrobial resistance
       </a>
     </li>
     <li>
       <a href="../articles/datasets.html">
-        <span class="fas fa-database"></span>
+        <span class="fa fa-database"></span>
          
         Data sets for download / own use
       </a>
     </li>
     <li>
       <a href="../articles/PCA.html">
-        <span class="fas fa-compress"></span>
+        <span class="fa fa-compress"></span>
          
         Conduct principal component analysis for AMR
       </a>
     </li>
     <li>
       <a href="../articles/MDR.html">
-        <span class="fas fa-skull-crossbones"></span>
+        <span class="fa fa-skull-crossbones"></span>
          
         Determine multi-drug resistance (MDR)
       </a>
     </li>
     <li>
       <a href="../articles/WHONET.html">
-        <span class="fas fa-globe-americas"></span>
+        <span class="fa fa-globe-americas"></span>
          
         Work with WHONET data
       </a>
     </li>
     <li>
       <a href="../articles/SPSS.html">
-        <span class="fas fa-file-upload"></span>
+        <span class="fa fa-file-upload"></span>
          
         Import data from SPSS/SAS/Stata
       </a>
     </li>
     <li>
       <a href="../articles/EUCAST.html">
-        <span class="fas fa-exchange-alt"></span>
+        <span class="fa fa-exchange-alt"></span>
          
         Apply EUCAST rules
       </a>
     </li>
     <li>
       <a href="../reference/mo_property.html">
-        <span class="fas fa-bug"></span>
+        <span class="fa fa-bug"></span>
          
         Get properties of a microorganism
       </a>
     </li>
     <li>
       <a href="../reference/ab_property.html">
-        <span class="fas fa-capsules"></span>
+        <span class="fa fa-capsules"></span>
          
         Get properties of an antibiotic
       </a>
     </li>
     <li>
       <a href="../articles/benchmarks.html">
-        <span class="fas fa-shipping-fast"></span>
+        <span class="fa fa-shipping-fast"></span>
          
         Other: benchmarks
       </a>
@@ -184,14 +184,14 @@
 </li>
 <li>
   <a href="../reference/index.html">
-    <span class="fas fa-book-open"></span>
+    <span class="fa fa-book-open"></span>
      
     Manual
   </a>
 </li>
 <li>
   <a href="../authors.html">
-    <span class="fas fa-users"></span>
+    <span class="fa fa-users"></span>
      
     Authors
   </a>
@@ -214,7 +214,7 @@
 </li>
 <li>
   <a href="../survey.html">
-    <span class="fas fa-clipboard-list"></span>
+    <span class="fa fa-clipboard-list"></span>
      
     Survey
   </a>
@@ -236,14 +236,56 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
+    <div id="amr-1719018" class="section level1">
+<h1 class="page-header" data-toc-text="1.7.1.9018">
+<a href="#amr-1719018" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9018</h1>
+<div id="last-updated-11-july-2021" class="section level2">
+<h2 class="hasAnchor">
+<a href="#last-updated-11-july-2021" class="anchor"></a><small>Last updated: 11 July 2021</small>
+</h2>
+<div id="changed" class="section level3">
+<h3 class="hasAnchor">
+<a href="#changed" class="anchor"></a>Changed</h3>
+<ul>
+<li>Antibiotic class selectors (see <code><a href="../reference/antibiotic_class_selectors.html">ab_class()</a></code>)
+<ul>
+<li>They now also work in R-3.0 and R-3.1, supporting every version of R since 2013</li>
+<li>Added more 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>Fix for using selectors multiple times in one call (e.g., using them 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>
+<li>Added argument <code>only_treatable</code>, which defaults to <code>TRUE</code> and will exclude drugs that are only for laboratory tests and not for treating patients (such as imipenem/EDTA and gentamicin-high)</li>
+</ul>
+</li>
+<li>Fix for duplicate ATC codes in the <code>antibiotics</code> data set</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>When printing a tibble with any old MO code, a warning will be thrown that old codes should be updated using <code><a href="../reference/as.mo.html">as.mo()</a></code>
+</li>
+<li>Improved automatic column selector when <code>col_*</code> arguments are left blank, e.g. in <code><a href="../reference/first_isolate.html">first_isolate()</a></code>
+</li>
+<li>The right input types for <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> are now enforced</li>
+<li>
+<code><a href="../reference/as.rsi.html">as.rsi()</a></code> can now correct for textual input (such as “Susceptible”, “Resistant”) in Dutch, English, French, German, Italian, Portuguese and Spanish</li>
+<li>When warnings are throws because of too few isolates in any <code>count_*()</code>, <code>proportion_*()</code> function (or <code>resistant()</code> or <code>susceptible()</code>), the <code>dplyr</code> group will be shown, if available</li>
+<li>Taxonomic names now print in italic in tibbles, if created with <code><a href="../reference/mo_property.html">mo_name()</a></code>, <code><a href="../reference/mo_property.html">mo_fullname()</a></code>, <code><a href="../reference/mo_property.html">mo_shortname()</a></code>, <code><a href="../reference/mo_property.html">mo_genus()</a></code> or <code><a href="../reference/mo_property.html">mo_family()</a></code>
+</li>
+<li>
+<code><a href="../reference/ab_property.html">ab_name()</a></code> gained argument <code>snake_case</code>, which is useful for column renaming</li>
+<li>Fix for legends created with <code><a href="../reference/ggplot_rsi.html">scale_rsi_colours()</a></code> when using <code>ggplot2</code> v3.3.4 or higher (this is bug ggplot2<a href='https://github.com/msberends/AMR/issues/4511'>#4511</a>, soon to be fixed)</li>
+<li>Fix for minor translation errors</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 +311,7 @@
 <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 +332,9 @@
 </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 +470,9 @@
 </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 +524,7 @@
 <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 +549,9 @@
 <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 +655,7 @@
 <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 +666,9 @@
 <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 +771,9 @@
 <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 +846,9 @@
 </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 +900,9 @@ 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 +933,9 @@ 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 +1241,9 @@ 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 +1353,9 @@ 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 +1401,9 @@ 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 +1487,9 @@ 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 +1606,9 @@ 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 +1764,9 @@ 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 +1954,9 @@ 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 +2095,9 @@ 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 +2180,9 @@ 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: 2021-07-11T11:19Z
 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/ab_property.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">1.7.1.9014</span>
       </span>
     </div>
 
@@ -90,14 +90,14 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa-home"></span>
+    <span class="fa fa-home"></span>
      
     Home
   </a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fas fa-question-circle"></span>
+    <span class="fa fa-question-circle"></span>
      
     How to
      
@@ -106,77 +106,77 @@
   <ul class="dropdown-menu" role="menu">
     <li>
       <a href="../articles/AMR.html">
-        <span class="fas fa-directions"></span>
+        <span class="fa fa-directions"></span>
          
         Conduct AMR analysis
       </a>
     </li>
     <li>
       <a href="../articles/resistance_predict.html">
-        <span class="fas fa-dice"></span>
+        <span class="fa fa-dice"></span>
          
         Predict antimicrobial resistance
       </a>
     </li>
     <li>
       <a href="../articles/datasets.html">
-        <span class="fas fa-database"></span>
+        <span class="fa fa-database"></span>
          
         Data sets for download / own use
       </a>
     </li>
     <li>
       <a href="../articles/PCA.html">
-        <span class="fas fa-compress"></span>
+        <span class="fa fa-compress"></span>
          
         Conduct principal component analysis for AMR
       </a>
     </li>
     <li>
       <a href="../articles/MDR.html">
-        <span class="fas fa-skull-crossbones"></span>
+        <span class="fa fa-skull-crossbones"></span>
          
         Determine multi-drug resistance (MDR)
       </a>
     </li>
     <li>
       <a href="../articles/WHONET.html">
-        <span class="fas fa-globe-americas"></span>
+        <span class="fa fa-globe-americas"></span>
          
         Work with WHONET data
       </a>
     </li>
     <li>
       <a href="../articles/SPSS.html">
-        <span class="fas fa-file-upload"></span>
+        <span class="fa fa-file-upload"></span>
          
         Import data from SPSS/SAS/Stata
       </a>
     </li>
     <li>
       <a href="../articles/EUCAST.html">
-        <span class="fas fa-exchange-alt"></span>
+        <span class="fa fa-exchange-alt"></span>
          
         Apply EUCAST rules
       </a>
     </li>
     <li>
       <a href="../reference/mo_property.html">
-        <span class="fas fa-bug"></span>
+        <span class="fa fa-bug"></span>
          
         Get properties of a microorganism
       </a>
     </li>
     <li>
       <a href="../reference/ab_property.html">
-        <span class="fas fa-capsules"></span>
+        <span class="fa fa-capsules"></span>
          
         Get properties of an antibiotic
       </a>
     </li>
     <li>
       <a href="../articles/benchmarks.html">
-        <span class="fas fa-shipping-fast"></span>
+        <span class="fa fa-shipping-fast"></span>
          
         Other: benchmarks
       </a>
@@ -185,14 +185,14 @@
 </li>
 <li>
   <a href="../reference/index.html">
-    <span class="fas fa-book-open"></span>
+    <span class="fa fa-book-open"></span>
      
     Manual
   </a>
 </li>
 <li>
   <a href="../authors.html">
-    <span class="fas fa-users"></span>
+    <span class="fa fa-users"></span>
      
     Authors
   </a>
@@ -215,7 +215,7 @@
 </li>
 <li>
   <a href="../survey.html">
-    <span class="fas fa-clipboard-list"></span>
+    <span class="fa fa-clipboard-list"></span>
      
     Survey
   </a>
@@ -242,7 +242,7 @@
     <p>Use these functions to return a specific property of an antibiotic from the <a href='antibiotics.html'>antibiotics</a> data set. All input values will be evaluated internally with <code><a href='as.ab.html'>as.ab()</a></code>.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>ab_name</span><span class='op'>(</span><span class='va'>x</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>, tolower <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
+    <pre class="usage"><span class='fu'>ab_name</span><span class='op'>(</span><span class='va'>x</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>, tolower <span class='op'>=</span> <span class='cn'>FALSE</span>, snake_case <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
 
 <span class='fu'>ab_atc</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
 
@@ -283,6 +283,10 @@
       <th>tolower</th>
       <td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether the first <a href='https://rdrr.io/r/base/character.html'>character</a> of every output should be transformed to a lower case <a href='https://rdrr.io/r/base/character.html'>character</a>. This will lead to e.g. "polymyxin B" and not "polymyxin b".</p></td>
     </tr>
+    <tr>
+      <th>snake_case</th>
+      <td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether the names should be returned in so-called <a href='https://en.wikipedia.org/wiki/Snake_case'>snake case</a>: in lower case and all spaces/slashes replaced with an underscore (<code>_</code>). This is useful for column renaming.</p></td>
+    </tr>
     <tr>
       <th>...</th>
       <td><p>other arguments passed on to <code><a href='as.ab.html'>as.ab()</a></code></p></td>

docs/reference/bug_drug_combinations.html

@@ -49,7 +49,7 @@
   <script src="../extra.js"></script>
 
 <meta property="og:title" content="Determine Bug-Drug Combinations — bug_drug_combinations" />
-<meta property="og:description" content="Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use format() on the result to prettify it to a publicable/printable format, see Examples." />
+<meta property="og:description" content="Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use format() on the result to prettify it to a publishable/printable format, see Examples." />
 <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
 
 
@@ -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">1.7.1.9014</span>
       </span>
     </div>
 
@@ -90,14 +90,14 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa-home"></span>
+    <span class="fa fa-home"></span>
      
     Home
   </a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fas fa-question-circle"></span>
+    <span class="fa fa-question-circle"></span>
      
     How to
      
@@ -106,77 +106,77 @@
   <ul class="dropdown-menu" role="menu">
     <li>
       <a href="../articles/AMR.html">
-        <span class="fas fa-directions"></span>
+        <span class="fa fa-directions"></span>
          
         Conduct AMR analysis
       </a>
     </li>
     <li>
       <a href="../articles/resistance_predict.html">
-        <span class="fas fa-dice"></span>
+        <span class="fa fa-dice"></span>
          
         Predict antimicrobial resistance
       </a>
     </li>
     <li>
       <a href="../articles/datasets.html">
-        <span class="fas fa-database"></span>
+        <span class="fa fa-database"></span>
          
         Data sets for download / own use
       </a>
     </li>
     <li>
       <a href="../articles/PCA.html">
-        <span class="fas fa-compress"></span>
+        <span class="fa fa-compress"></span>
          
         Conduct principal component analysis for AMR
       </a>
     </li>
     <li>
       <a href="../articles/MDR.html">
-        <span class="fas fa-skull-crossbones"></span>
+        <span class="fa fa-skull-crossbones"></span>
          
         Determine multi-drug resistance (MDR)
       </a>
     </li>
     <li>
       <a href="../articles/WHONET.html">
-        <span class="fas fa-globe-americas"></span>
+        <span class="fa fa-globe-americas"></span>
          
         Work with WHONET data
       </a>
     </li>
     <li>
       <a href="../articles/SPSS.html">
-        <span class="fas fa-file-upload"></span>
+        <span class="fa fa-file-upload"></span>
          
         Import data from SPSS/SAS/Stata
       </a>
     </li>
     <li>
       <a href="../articles/EUCAST.html">
-        <span class="fas fa-exchange-alt"></span>
+        <span class="fa fa-exchange-alt"></span>
          
         Apply EUCAST rules
       </a>
     </li>
     <li>
       <a href="../reference/mo_property.html">
-        <span class="fas fa-bug"></span>
+        <span class="fa fa-bug"></span>
          
         Get properties of a microorganism
       </a>
     </li>
     <li>
       <a href="../reference/ab_property.html">
-        <span class="fas fa-capsules"></span>
+        <span class="fa fa-capsules"></span>
          
         Get properties of an antibiotic
       </a>
     </li>
     <li>
       <a href="../articles/benchmarks.html">
-        <span class="fas fa-shipping-fast"></span>
+        <span class="fa fa-shipping-fast"></span>
          
         Other: benchmarks
       </a>
@@ -185,14 +185,14 @@
 </li>
 <li>
   <a href="../reference/index.html">
-    <span class="fas fa-book-open"></span>
+    <span class="fa fa-book-open"></span>
      
     Manual
   </a>
 </li>
 <li>
   <a href="../authors.html">
-    <span class="fas fa-users"></span>
+    <span class="fa fa-users"></span>
      
     Authors
   </a>
@@ -215,7 +215,7 @@
 </li>
 <li>
   <a href="../survey.html">
-    <span class="fas fa-clipboard-list"></span>
+    <span class="fa fa-clipboard-list"></span>
      
     Survey
   </a>
@@ -239,7 +239,7 @@
     </div>
 
     <div class="ref-description">
-    <p>Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use <code><a href='https://rdrr.io/r/base/format.html'>format()</a></code> on the result to prettify it to a publicable/printable format, see <em>Examples</em>.</p>
+    <p>Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use <code><a href='https://rdrr.io/r/base/format.html'>format()</a></code> on the result to prettify it to a publishable/printable format, see <em>Examples</em>.</p>
     </div>
 
     <pre class="usage"><span class='fu'>bug_drug_combinations</span><span class='op'>(</span><span class='va'>x</span>, col_mo <span class='op'>=</span> <span class='cn'>NULL</span>, FUN <span class='op'>=</span> <span class='va'>mo_shortname</span>, <span class='va'>...</span><span class='op'>)</span>

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">1.7.1.9005</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">1.7.1.9009</span>
       </span>
     </div>
 
@@ -90,14 +90,14 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa-home"></span>
+    <span class="fa fa-home"></span>
      
     Home
   </a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fas fa-question-circle"></span>
+    <span class="fa fa-question-circle"></span>
      
     How to
      
@@ -106,77 +106,77 @@
   <ul class="dropdown-menu" role="menu">
     <li>
       <a href="../articles/AMR.html">
-        <span class="fas fa-directions"></span>
+        <span class="fa fa-directions"></span>
          
         Conduct AMR analysis
       </a>
     </li>
     <li>
       <a href="../articles/resistance_predict.html">
-        <span class="fas fa-dice"></span>
+        <span class="fa fa-dice"></span>
          
         Predict antimicrobial resistance
       </a>
     </li>
     <li>
       <a href="../articles/datasets.html">
-        <span class="fas fa-database"></span>
+        <span class="fa fa-database"></span>
          
         Data sets for download / own use
       </a>
     </li>
     <li>
       <a href="../articles/PCA.html">
-        <span class="fas fa-compress"></span>
+        <span class="fa fa-compress"></span>
          
         Conduct principal component analysis for AMR
       </a>
     </li>
     <li>
       <a href="../articles/MDR.html">
-        <span class="fas fa-skull-crossbones"></span>
+        <span class="fa fa-skull-crossbones"></span>
          
         Determine multi-drug resistance (MDR)
       </a>
     </li>
     <li>
       <a href="../articles/WHONET.html">
-        <span class="fas fa-globe-americas"></span>
+        <span class="fa fa-globe-americas"></span>
          
         Work with WHONET data
       </a>
     </li>
     <li>
       <a href="../articles/SPSS.html">
-        <span class="fas fa-file-upload"></span>
+        <span class="fa fa-file-upload"></span>
          
         Import data from SPSS/SAS/Stata
       </a>
     </li>
     <li>
       <a href="../articles/EUCAST.html">
-        <span class="fas fa-exchange-alt"></span>
+        <span class="fa fa-exchange-alt"></span>
          
         Apply EUCAST rules
       </a>
     </li>
     <li>
       <a href="../reference/mo_property.html">
-        <span class="fas fa-bug"></span>
+        <span class="fa fa-bug"></span>
          
         Get properties of a microorganism
       </a>
     </li>
     <li>
       <a href="../reference/ab_property.html">
-        <span class="fas fa-capsules"></span>
+        <span class="fa fa-capsules"></span>
          
         Get properties of an antibiotic
       </a>
     </li>
     <li>
       <a href="../articles/benchmarks.html">
-        <span class="fas fa-shipping-fast"></span>
+        <span class="fa fa-shipping-fast"></span>
          
         Other: benchmarks
       </a>
@@ -185,14 +185,14 @@
 </li>
 <li>
   <a href="../reference/index.html">
-    <span class="fas fa-book-open"></span>
+    <span class="fa fa-book-open"></span>
      
     Manual
   </a>
 </li>
 <li>
   <a href="../authors.html">
-    <span class="fas fa-users"></span>
+    <span class="fa fa-users"></span>
      
     Authors
   </a>
@@ -215,7 +215,7 @@
 </li>
 <li>
   <a href="../survey.html">
-    <span class="fas fa-clipboard-list"></span>
+    <span class="fa fa-clipboard-list"></span>
      
     Survey
   </a>
@@ -315,25 +315,28 @@
 <p>It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part <em>after</em> the tilde. In above examples, the antibiotic group <code>aminopenicillins</code> is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the antibiotic agents that will be matched when running the rule.</p><ul>
 <li><p><code>aminoglycosides</code><br />(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, tobramycin-high)</p></li>
 <li><p><code>aminopenicillins</code><br />(amoxicillin, ampicillin)</p></li>
-<li><p><code>betalactams</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, biapenem, cadazolid, carbenicillin, carindacillin, 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, 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, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam (Amdinocillin), meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid)</p></li>
+<li><p><code>betalactams</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, biapenem, carbenicillin, carindacillin, 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, 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, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam (Amdinocillin), meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid)</p></li>
 <li><p><code>carbapenems</code><br />(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, tebipenem)</p></li>
-<li><p><code>cephalosporins</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, 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>cephalosporins</code><br />(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, 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>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_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>cephalosporins_3rd</code><br />(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 />(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 />(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, trovafloxacin)</p></li>
 <li><p><code>glycopeptides</code><br />(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, vancomycin-macromethod)</p></li>
 <li><p><code>glycopeptides_except_lipo</code><br />(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, vancomycin-macromethod)</p></li>
-<li><p><code>lincosamides</code><br />(clindamycin, lincomycin, pirlimycin)</p></li>
+<li><p><code>lincosamides</code><br />(acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin (Leucomycin), lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin, tylvalosin)</p></li>
 <li><p><code>lipoglycopeptides</code><br />(dalbavancin, oritavancin, telavancin)</p></li>
-<li><p><code>macrolides</code><br />(azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, josamycin, midecamycin, miocamycin, oleandomycin, rokitamycin, roxithromycin, spiramycin, telithromycin, troleandomycin)</p></li>
-<li><p><code>oxazolidinones</code><br />(cycloserine, linezolid, tedizolid, thiacetazone)</p></li>
+<li><p><code>macrolides</code><br />(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin (Leucomycin), meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, tylvalosin)</p></li>
+<li><p><code>oxazolidinones</code><br />(cadazolid, 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>
+<li><p><code>tetracyclines</code><br />(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline, tigecycline)</p></li>
+<li><p><code>tetracyclines_except_tgc</code><br />(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline)</p></li>
 <li><p><code>ureidopenicillins</code><br />(azlocillin, mezlocillin, piperacillin, piperacillin/tazobactam)</p></li>
 </ul>
 

docs/reference/first_isolate.html

@@ -83,7 +83,7 @@
       </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">1.7.1.9009</span>
       </span>
     </div>
 
@@ -91,14 +91,14 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa-home"></span>
+    <span class="fa fa-home"></span>
      
     Home
   </a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fas fa-question-circle"></span>
+    <span class="fa fa-question-circle"></span>
      
     How to
      
@@ -107,77 +107,77 @@
   <ul class="dropdown-menu" role="menu">
     <li>
       <a href="../articles/AMR.html">
-        <span class="fas fa-directions"></span>
+        <span class="fa fa-directions"></span>
          
         Conduct AMR analysis
       </a>
     </li>
     <li>
       <a href="../articles/resistance_predict.html">
-        <span class="fas fa-dice"></span>
+        <span class="fa fa-dice"></span>
          
         Predict antimicrobial resistance
       </a>
     </li>
     <li>
       <a href="../articles/datasets.html">
-        <span class="fas fa-database"></span>
+        <span class="fa fa-database"></span>
          
         Data sets for download / own use
       </a>
     </li>
     <li>
       <a href="../articles/PCA.html">
-        <span class="fas fa-compress"></span>
+        <span class="fa fa-compress"></span>
          
         Conduct principal component analysis for AMR
       </a>
     </li>
     <li>
       <a href="../articles/MDR.html">
-        <span class="fas fa-skull-crossbones"></span>
+        <span class="fa fa-skull-crossbones"></span>
          
         Determine multi-drug resistance (MDR)
       </a>
     </li>
     <li>
       <a href="../articles/WHONET.html">
-        <span class="fas fa-globe-americas"></span>
+        <span class="fa fa-globe-americas"></span>
          
         Work with WHONET data
       </a>
     </li>
     <li>
       <a href="../articles/SPSS.html">
-        <span class="fas fa-file-upload"></span>
+        <span class="fa fa-file-upload"></span>
          
         Import data from SPSS/SAS/Stata
       </a>
     </li>
     <li>
       <a href="../articles/EUCAST.html">
-        <span class="fas fa-exchange-alt"></span>
+        <span class="fa fa-exchange-alt"></span>
          
         Apply EUCAST rules
       </a>
     </li>
     <li>
       <a href="../reference/mo_property.html">
-        <span class="fas fa-bug"></span>
+        <span class="fa fa-bug"></span>
          
         Get properties of a microorganism
       </a>
     </li>
     <li>
       <a href="../reference/ab_property.html">
-        <span class="fas fa-capsules"></span>
+        <span class="fa fa-capsules"></span>
          
         Get properties of an antibiotic
       </a>
     </li>
     <li>
       <a href="../articles/benchmarks.html">
-        <span class="fas fa-shipping-fast"></span>
+        <span class="fa fa-shipping-fast"></span>
          
         Other: benchmarks
       </a>
@@ -186,14 +186,14 @@
 </li>
 <li>
   <a href="../reference/index.html">
-    <span class="fas fa-book-open"></span>
+    <span class="fa fa-book-open"></span>
      
     Manual
   </a>
 </li>
 <li>
   <a href="../authors.html">
-    <span class="fas fa-users"></span>
+    <span class="fa fa-users"></span>
      
     Authors
   </a>
@@ -216,7 +216,7 @@
 </li>
 <li>
   <a href="../survey.html">
-    <span class="fas fa-clipboard-list"></span>
+    <span class="fa fa-clipboard-list"></span>
      
     Survey
   </a>
@@ -457,11 +457,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
     <pre class="examples"><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
 <span class='co'># See ?example_isolates.</span>
 
-<span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'>first_isolate</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>, <span class='op'>]</span>
-<span class='co'># \donttest{</span>
-<span class='co'># faster way, only works in R 3.2 and later:</span>
 <span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'>first_isolate</span><span class='op'>(</span><span class='op'>)</span>, <span class='op'>]</span>
-
+<span class='co'># \donttest{</span>
 <span class='co'># get all first Gram-negatives</span>
 <span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/which.html'>which</a></span><span class='op'>(</span><span class='fu'>first_isolate</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>&amp;</span> <span class='fu'><a href='mo_property.html'>mo_is_gram_negative</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>, <span class='op'>]</span>
 

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">1.7.1.9018</span>
       </span>
     </div>
 
@@ -89,14 +89,14 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa-home"></span>
+    <span class="fa fa-home"></span>
      
     Home
   </a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fas fa-question-circle"></span>
+    <span class="fa fa-question-circle"></span>
      
     How to
      
@@ -105,77 +105,77 @@
   <ul class="dropdown-menu" role="menu">
     <li>
       <a href="../articles/AMR.html">
-        <span class="fas fa-directions"></span>
+        <span class="fa fa-directions"></span>
          
         Conduct AMR analysis
       </a>
     </li>
     <li>
       <a href="../articles/resistance_predict.html">
-        <span class="fas fa-dice"></span>
+        <span class="fa fa-dice"></span>
          
         Predict antimicrobial resistance
       </a>
     </li>
     <li>
       <a href="../articles/datasets.html">
-        <span class="fas fa-database"></span>
+        <span class="fa fa-database"></span>
          
         Data sets for download / own use
       </a>
     </li>
     <li>
       <a href="../articles/PCA.html">
-        <span class="fas fa-compress"></span>
+        <span class="fa fa-compress"></span>
          
         Conduct principal component analysis for AMR
       </a>
     </li>
     <li>
       <a href="../articles/MDR.html">
-        <span class="fas fa-skull-crossbones"></span>
+        <span class="fa fa-skull-crossbones"></span>
          
         Determine multi-drug resistance (MDR)
       </a>
     </li>
     <li>
       <a href="../articles/WHONET.html">
-        <span class="fas fa-globe-americas"></span>
+        <span class="fa fa-globe-americas"></span>
          
         Work with WHONET data
       </a>
     </li>
     <li>
       <a href="../articles/SPSS.html">
-        <span class="fas fa-file-upload"></span>
+        <span class="fa fa-file-upload"></span>
          
         Import data from SPSS/SAS/Stata
       </a>
     </li>
     <li>
       <a href="../articles/EUCAST.html">
-        <span class="fas fa-exchange-alt"></span>
+        <span class="fa fa-exchange-alt"></span>
          
         Apply EUCAST rules
       </a>
     </li>
     <li>
       <a href="../reference/mo_property.html">
-        <span class="fas fa-bug"></span>
+        <span class="fa fa-bug"></span>
          
         Get properties of a microorganism
       </a>
     </li>
     <li>
       <a href="../reference/ab_property.html">
-        <span class="fas fa-capsules"></span>
+        <span class="fa fa-capsules"></span>
          
         Get properties of an antibiotic
       </a>
     </li>
     <li>
       <a href="../articles/benchmarks.html">
-        <span class="fas fa-shipping-fast"></span>
+        <span class="fa fa-shipping-fast"></span>
          
         Other: benchmarks
       </a>
@@ -184,14 +184,14 @@
 </li>
 <li>
   <a href="../reference/index.html">
-    <span class="fas fa-book-open"></span>
+    <span class="fa fa-book-open"></span>
      
     Manual
   </a>
 </li>
 <li>
   <a href="../authors.html">
-    <span class="fas fa-users"></span>
+    <span class="fa fa-users"></span>
      
     Authors
   </a>
@@ -214,7 +214,7 @@
 </li>
 <li>
   <a href="../survey.html">
-    <span class="fas fa-clipboard-list"></span>
+    <span class="fa fa-clipboard-list"></span>
      
     Survey
   </a>
@@ -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/join.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">1.7.1.9009</span>
       </span>
     </div>
 
@@ -90,14 +90,14 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa-home"></span>
+    <span class="fa fa-home"></span>
      
     Home
   </a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fas fa-question-circle"></span>
+    <span class="fa fa-question-circle"></span>
      
     How to
      
@@ -106,77 +106,77 @@
   <ul class="dropdown-menu" role="menu">
     <li>
       <a href="../articles/AMR.html">
-        <span class="fas fa-directions"></span>
+        <span class="fa fa-directions"></span>
          
         Conduct AMR analysis
       </a>
     </li>
     <li>
       <a href="../articles/resistance_predict.html">
-        <span class="fas fa-dice"></span>
+        <span class="fa fa-dice"></span>
          
         Predict antimicrobial resistance
       </a>
     </li>
     <li>
       <a href="../articles/datasets.html">
-        <span class="fas fa-database"></span>
+        <span class="fa fa-database"></span>
          
         Data sets for download / own use
       </a>
     </li>
     <li>
       <a href="../articles/PCA.html">
-        <span class="fas fa-compress"></span>
+        <span class="fa fa-compress"></span>
          
         Conduct principal component analysis for AMR
       </a>
     </li>
     <li>
       <a href="../articles/MDR.html">
-        <span class="fas fa-skull-crossbones"></span>
+        <span class="fa fa-skull-crossbones"></span>
          
         Determine multi-drug resistance (MDR)
       </a>
     </li>
     <li>
       <a href="../articles/WHONET.html">
-        <span class="fas fa-globe-americas"></span>
+        <span class="fa fa-globe-americas"></span>
          
         Work with WHONET data
       </a>
     </li>
     <li>
       <a href="../articles/SPSS.html">
-        <span class="fas fa-file-upload"></span>
+        <span class="fa fa-file-upload"></span>
          
         Import data from SPSS/SAS/Stata
       </a>
     </li>
     <li>
       <a href="../articles/EUCAST.html">
-        <span class="fas fa-exchange-alt"></span>
+        <span class="fa fa-exchange-alt"></span>
          
         Apply EUCAST rules
       </a>
     </li>
     <li>
       <a href="../reference/mo_property.html">
-        <span class="fas fa-bug"></span>
+        <span class="fa fa-bug"></span>
          
         Get properties of a microorganism
       </a>
     </li>
     <li>
       <a href="../reference/ab_property.html">
-        <span class="fas fa-capsules"></span>
+        <span class="fa fa-capsules"></span>
          
         Get properties of an antibiotic
       </a>
     </li>
     <li>
       <a href="../articles/benchmarks.html">
-        <span class="fas fa-shipping-fast"></span>
+        <span class="fa fa-shipping-fast"></span>
          
         Other: benchmarks
       </a>
@@ -185,14 +185,14 @@
 </li>
 <li>
   <a href="../reference/index.html">
-    <span class="fas fa-book-open"></span>
+    <span class="fa fa-book-open"></span>
      
     Manual
   </a>
 </li>
 <li>
   <a href="../authors.html">
-    <span class="fas fa-users"></span>
+    <span class="fa fa-users"></span>
      
     Authors
   </a>
@@ -215,7 +215,7 @@
 </li>
 <li>
   <a href="../survey.html">
-    <span class="fas fa-clipboard-list"></span>
+    <span class="fa fa-clipboard-list"></span>
      
     Survey
   </a>
@@ -281,7 +281,7 @@
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
     <p><strong>Note:</strong> As opposed to the <code>join()</code> functions of <code>dplyr</code>, <a href='https://rdrr.io/r/base/character.html'>character</a> vectors are supported and at default existing columns will get a suffix <code>"2"</code> and the newly joined columns will not get a suffix.</p>
-<p>If the <code>dplyr</code> package is installed, their join functions will be used. Otherwise, the much slower <code><a href='https://rdrr.io/r/base/merge.html'>merge()</a></code> and <code><a href='https://rdrr.io/r/base/interaction.html'>interaction()</a></code> functions from base R will be used.</p>
+<p>If the <code>dplyr</code> package is installed, their join functions will be used. Otherwise, the much slower <code><a href='https://rdrr.io/r/base/merge.html'>merge()</a></code> and <code><a href='https://rdrr.io/r/base/interaction.html'>interaction()</a></code> functions from base <span style="R">R</span> will be used.</p>
     <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
 
     

docs/reference/mo_property.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">1.7.1.9015</span>
       </span>
     </div>
 
@@ -90,14 +90,14 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa-home"></span>
+    <span class="fa fa-home"></span>
      
     Home
   </a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fas fa-question-circle"></span>
+    <span class="fa fa-question-circle"></span>
      
     How to
      
@@ -106,77 +106,77 @@
   <ul class="dropdown-menu" role="menu">
     <li>
       <a href="../articles/AMR.html">
-        <span class="fas fa-directions"></span>
+        <span class="fa fa-directions"></span>
          
         Conduct AMR analysis
       </a>
     </li>
     <li>
       <a href="../articles/resistance_predict.html">
-        <span class="fas fa-dice"></span>
+        <span class="fa fa-dice"></span>
          
         Predict antimicrobial resistance
       </a>
     </li>
     <li>
       <a href="../articles/datasets.html">
-        <span class="fas fa-database"></span>
+        <span class="fa fa-database"></span>
          
         Data sets for download / own use
       </a>
     </li>
     <li>
       <a href="../articles/PCA.html">
-        <span class="fas fa-compress"></span>
+        <span class="fa fa-compress"></span>
          
         Conduct principal component analysis for AMR
       </a>
     </li>
     <li>
       <a href="../articles/MDR.html">
-        <span class="fas fa-skull-crossbones"></span>
+        <span class="fa fa-skull-crossbones"></span>
          
         Determine multi-drug resistance (MDR)
       </a>
     </li>
     <li>
       <a href="../articles/WHONET.html">
-        <span class="fas fa-globe-americas"></span>
+        <span class="fa fa-globe-americas"></span>
          
         Work with WHONET data
       </a>
     </li>
     <li>
       <a href="../articles/SPSS.html">
-        <span class="fas fa-file-upload"></span>
+        <span class="fa fa-file-upload"></span>
          
         Import data from SPSS/SAS/Stata
       </a>
     </li>
     <li>
       <a href="../articles/EUCAST.html">
-        <span class="fas fa-exchange-alt"></span>
+        <span class="fa fa-exchange-alt"></span>
          
         Apply EUCAST rules
       </a>
     </li>
     <li>
       <a href="../reference/mo_property.html">
-        <span class="fas fa-bug"></span>
+        <span class="fa fa-bug"></span>
          
         Get properties of a microorganism
       </a>
     </li>
     <li>
       <a href="../reference/ab_property.html">
-        <span class="fas fa-capsules"></span>
+        <span class="fa fa-capsules"></span>
          
         Get properties of an antibiotic
       </a>
     </li>
     <li>
       <a href="../articles/benchmarks.html">
-        <span class="fas fa-shipping-fast"></span>
+        <span class="fa fa-shipping-fast"></span>
          
         Other: benchmarks
       </a>
@@ -185,14 +185,14 @@
 </li>
 <li>
   <a href="../reference/index.html">
-    <span class="fas fa-book-open"></span>
+    <span class="fa fa-book-open"></span>
      
     Manual
   </a>
 </li>
 <li>
   <a href="../authors.html">
-    <span class="fas fa-users"></span>
+    <span class="fa fa-users"></span>
      
     Authors
   </a>
@@ -215,7 +215,7 @@
 </li>
 <li>
   <a href="../survey.html">
-    <span class="fas fa-clipboard-list"></span>
+    <span class="fa fa-clipboard-list"></span>
      
     Survey
   </a>
@@ -353,7 +353,7 @@
 <p>Intrinsic resistance - <code>mo_is_intrinsic_resistant()</code> - will be determined based on the <a href='intrinsic_resistant.html'>intrinsic_resistant</a> data set, which is based on <a href='https://www.eucast.org/expert_rules_and_intrinsic_resistance/'>'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2</a> (2020). The <code>mo_is_intrinsic_resistant()</code> functions can be vectorised over arguments <code>x</code> (input for microorganisms) and over <code>ab</code> (input for antibiotics).</p>
 <p>All output <a href='translate.html'>will be translated</a> where possible.</p>
 <p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
-<p>SNOMED codes - <code>mo_snomed()</code> - are from the US Edition of SNOMED CT from 1 September 2020. See the <a href='microorganisms.html'>microorganisms</a> data set for more info.</p>
+<p>SNOMED codes - <code>mo_snomed()</code> - are from the US Edition of SNOMED CT from 1 September 2020. See <em>Source</em> and the <a href='microorganisms.html'>microorganisms</a> data set for more info.</p>
     <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
 
     
@@ -411,7 +411,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 <p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
-    <div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a></p></div>
+    <div class='dont-index'><p>Data set <a href='microorganisms.html'>microorganisms</a></p></div>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># taxonomic tree -----------------------------------------------------------</span>

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">1.7.1.9009</span>
       </span>
     </div>
 
@@ -90,14 +90,14 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa-home"></span>
+    <span class="fa fa-home"></span>
      
     Home
   </a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fas fa-question-circle"></span>
+    <span class="fa fa-question-circle"></span>
      
     How to
      
@@ -106,77 +106,77 @@
   <ul class="dropdown-menu" role="menu">
     <li>
       <a href="../articles/AMR.html">
-        <span class="fas fa-directions"></span>
+        <span class="fa fa-directions"></span>
          
         Conduct AMR analysis
       </a>
     </li>
     <li>
       <a href="../articles/resistance_predict.html">
-        <span class="fas fa-dice"></span>
+        <span class="fa fa-dice"></span>
          
         Predict antimicrobial resistance
       </a>
     </li>
     <li>
       <a href="../articles/datasets.html">
-        <span class="fas fa-database"></span>
+        <span class="fa fa-database"></span>
          
         Data sets for download / own use
       </a>
     </li>
     <li>
       <a href="../articles/PCA.html">
-        <span class="fas fa-compress"></span>
+        <span class="fa fa-compress"></span>
          
         Conduct principal component analysis for AMR
       </a>
     </li>
     <li>
       <a href="../articles/MDR.html">
-        <span class="fas fa-skull-crossbones"></span>
+        <span class="fa fa-skull-crossbones"></span>
          
         Determine multi-drug resistance (MDR)
       </a>
     </li>
     <li>
       <a href="../articles/WHONET.html">
-        <span class="fas fa-globe-americas"></span>
+        <span class="fa fa-globe-americas"></span>
          
         Work with WHONET data
       </a>
     </li>
     <li>
       <a href="../articles/SPSS.html">
-        <span class="fas fa-file-upload"></span>
+        <span class="fa fa-file-upload"></span>
          
         Import data from SPSS/SAS/Stata
       </a>
     </li>
     <li>
       <a href="../articles/EUCAST.html">
-        <span class="fas fa-exchange-alt"></span>
+        <span class="fa fa-exchange-alt"></span>
          
         Apply EUCAST rules
       </a>
     </li>
     <li>
       <a href="../reference/mo_property.html">
-        <span class="fas fa-bug"></span>
+        <span class="fa fa-bug"></span>
          
         Get properties of a microorganism
       </a>
     </li>
     <li>
       <a href="../reference/ab_property.html">
-        <span class="fas fa-capsules"></span>
+        <span class="fa fa-capsules"></span>
          
         Get properties of an antibiotic
       </a>
     </li>
     <li>
       <a href="../articles/benchmarks.html">
-        <span class="fas fa-shipping-fast"></span>
+        <span class="fa fa-shipping-fast"></span>
          
         Other: benchmarks
       </a>
@@ -185,14 +185,14 @@
 </li>
 <li>
   <a href="../reference/index.html">
-    <span class="fas fa-book-open"></span>
+    <span class="fa fa-book-open"></span>
      
     Manual
   </a>
 </li>
 <li>
   <a href="../authors.html">
-    <span class="fas fa-users"></span>
+    <span class="fa fa-users"></span>
      
     Authors
   </a>
@@ -215,7 +215,7 @@
 </li>
 <li>
   <a href="../survey.html">
-    <span class="fas fa-clipboard-list"></span>
+    <span class="fa fa-clipboard-list"></span>
      
     Survey
   </a>
@@ -239,7 +239,7 @@
     </div>
 
     <div class="ref-description">
-    <p>Functions to plot classes <code>rsi</code>, <code>mic</code> and <code>disk</code>, with support for base R and <code>ggplot2</code>.</p>
+    <p>Functions to plot classes <code>rsi</code>, <code>mic</code> and <code>disk</code>, with support for base <span style="R">R</span> and <code>ggplot2</code>.</p>
     </div>
 
     <pre class="usage"><span class='co'># S3 method for mic</span>
@@ -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/random.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">1.7.1.9009</span>
       </span>
     </div>
 
@@ -90,14 +90,14 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa-home"></span>
+    <span class="fa fa-home"></span>
      
     Home
   </a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fas fa-question-circle"></span>
+    <span class="fa fa-question-circle"></span>
      
     How to
      
@@ -106,77 +106,77 @@
   <ul class="dropdown-menu" role="menu">
     <li>
       <a href="../articles/AMR.html">
-        <span class="fas fa-directions"></span>
+        <span class="fa fa-directions"></span>
          
         Conduct AMR analysis
       </a>
     </li>
     <li>
       <a href="../articles/resistance_predict.html">
-        <span class="fas fa-dice"></span>
+        <span class="fa fa-dice"></span>
          
         Predict antimicrobial resistance
       </a>
     </li>
     <li>
       <a href="../articles/datasets.html">
-        <span class="fas fa-database"></span>
+        <span class="fa fa-database"></span>
          
         Data sets for download / own use
       </a>
     </li>
     <li>
       <a href="../articles/PCA.html">
-        <span class="fas fa-compress"></span>
+        <span class="fa fa-compress"></span>
          
         Conduct principal component analysis for AMR
       </a>
     </li>
     <li>
       <a href="../articles/MDR.html">
-        <span class="fas fa-skull-crossbones"></span>
+        <span class="fa fa-skull-crossbones"></span>
          
         Determine multi-drug resistance (MDR)
       </a>
     </li>
     <li>
       <a href="../articles/WHONET.html">
-        <span class="fas fa-globe-americas"></span>
+        <span class="fa fa-globe-americas"></span>
          
         Work with WHONET data
       </a>
     </li>
     <li>
       <a href="../articles/SPSS.html">
-        <span class="fas fa-file-upload"></span>
+        <span class="fa fa-file-upload"></span>
          
         Import data from SPSS/SAS/Stata
       </a>
     </li>
     <li>
       <a href="../articles/EUCAST.html">
-        <span class="fas fa-exchange-alt"></span>
+        <span class="fa fa-exchange-alt"></span>
          
         Apply EUCAST rules
       </a>
     </li>
     <li>
       <a href="../reference/mo_property.html">
-        <span class="fas fa-bug"></span>
+        <span class="fa fa-bug"></span>
          
         Get properties of a microorganism
       </a>
     </li>
     <li>
       <a href="../reference/ab_property.html">
-        <span class="fas fa-capsules"></span>
+        <span class="fa fa-capsules"></span>
          
         Get properties of an antibiotic
       </a>
     </li>
     <li>
       <a href="../articles/benchmarks.html">
-        <span class="fas fa-shipping-fast"></span>
+        <span class="fa fa-shipping-fast"></span>
          
         Other: benchmarks
       </a>
@@ -185,14 +185,14 @@
 </li>
 <li>
   <a href="../reference/index.html">
-    <span class="fas fa-book-open"></span>
+    <span class="fa fa-book-open"></span>
      
     Manual
   </a>
 </li>
 <li>
   <a href="../authors.html">
-    <span class="fas fa-users"></span>
+    <span class="fa fa-users"></span>
      
     Authors
   </a>
@@ -215,7 +215,7 @@
 </li>
 <li>
   <a href="../survey.html">
-    <span class="fas fa-clipboard-list"></span>
+    <span class="fa fa-clipboard-list"></span>
      
     Survey
   </a>
@@ -278,7 +278,7 @@
     <p>class <code>&lt;mic&gt;</code> for <code>random_mic()</code> (see <code><a href='as.mic.html'>as.mic()</a></code>) and class <code>&lt;disk&gt;</code> for <code>random_disk()</code> (see <code><a href='as.disk.html'>as.disk()</a></code>)</p>
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
-    <p>The base R function <code><a href='https://rdrr.io/r/base/sample.html'>sample()</a></code> is used for generating values.</p>
+    <p>The base <span style="R">R</span> function <code><a href='https://rdrr.io/r/base/sample.html'>sample()</a></code> is used for generating values.</p>
 <p>Generated values are based on the latest EUCAST guideline implemented in the <a href='rsi_translation.html'>rsi_translation</a> data set. To create specific generated values per bug or drug, set the <code>mo</code> and/or <code>ab</code> argument.</p>
     <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
 

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">1.7.1.9005</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">1.7.1.9018</span>
       </span>
     </div>
 
@@ -89,14 +89,14 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="index.html">
-    <span class="fas fa-home"></span>
+    <span class="fa fa-home"></span>
      
     Home
   </a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fas fa-question-circle"></span>
+    <span class="fa fa-question-circle"></span>
      
     How to
      
@@ -105,77 +105,77 @@
   <ul class="dropdown-menu" role="menu">
     <li>
       <a href="articles/AMR.html">
-        <span class="fas fa-directions"></span>
+        <span class="fa fa-directions"></span>
          
         Conduct AMR analysis
       </a>
     </li>
     <li>
       <a href="articles/resistance_predict.html">
-        <span class="fas fa-dice"></span>
+        <span class="fa fa-dice"></span>
          
         Predict antimicrobial resistance
       </a>
     </li>
     <li>
       <a href="articles/datasets.html">
-        <span class="fas fa-database"></span>
+        <span class="fa fa-database"></span>
          
         Data sets for download / own use
       </a>
     </li>
     <li>
       <a href="articles/PCA.html">
-        <span class="fas fa-compress"></span>
+        <span class="fa fa-compress"></span>
          
         Conduct principal component analysis for AMR
       </a>
     </li>
     <li>
       <a href="articles/MDR.html">
-        <span class="fas fa-skull-crossbones"></span>
+        <span class="fa fa-skull-crossbones"></span>
          
         Determine multi-drug resistance (MDR)
       </a>
     </li>
     <li>
       <a href="articles/WHONET.html">
-        <span class="fas fa-globe-americas"></span>
+        <span class="fa fa-globe-americas"></span>
          
         Work with WHONET data
       </a>
     </li>
     <li>
       <a href="articles/SPSS.html">
-        <span class="fas fa-file-upload"></span>
+        <span class="fa fa-file-upload"></span>
          
         Import data from SPSS/SAS/Stata
       </a>
     </li>
     <li>
       <a href="articles/EUCAST.html">
-        <span class="fas fa-exchange-alt"></span>
+        <span class="fa fa-exchange-alt"></span>
          
         Apply EUCAST rules
       </a>
     </li>
     <li>
       <a href="reference/mo_property.html">
-        <span class="fas fa-bug"></span>
+        <span class="fa fa-bug"></span>
          
         Get properties of a microorganism
       </a>
     </li>
     <li>
       <a href="reference/ab_property.html">
-        <span class="fas fa-capsules"></span>
+        <span class="fa fa-capsules"></span>
          
         Get properties of an antibiotic
       </a>
     </li>
     <li>
       <a href="articles/benchmarks.html">
-        <span class="fas fa-shipping-fast"></span>
+        <span class="fa fa-shipping-fast"></span>
          
         Other: benchmarks
       </a>
@@ -184,14 +184,14 @@
 </li>
 <li>
   <a href="reference/index.html">
-    <span class="fas fa-book-open"></span>
+    <span class="fa fa-book-open"></span>
      
     Manual
   </a>
 </li>
 <li>
   <a href="authors.html">
-    <span class="fas fa-users"></span>
+    <span class="fa fa-users"></span>
      
     Authors
   </a>
@@ -214,7 +214,7 @@
 </li>
 <li>
   <a href="survey.html">
-    <span class="fas fa-clipboard-list"></span>
+    <span class="fa fa-clipboard-list"></span>
      
     Survey
   </a>

index.md

@@ -25,32 +25,28 @@ library(AMR)
 library(dplyr)
 
 example_isolates %>%
-  mutate(bacteria = mo_fullname(mo)) %>%
-  filter(mo_is_gram_negative(), mo_is_intrinsic_resistant(ab = "cefotax")) %>%
-  select(bacteria, aminoglycosides(), carbapenems())
-#> 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)
-#> ℹ For `aminoglycosides()` using columns: 'AMK' (amikacin), 'GEN' (gentamicin), 'KAN'
-#>   (kanamycin) and 'TOB' (tobramycin)
-#> ℹ For `carbapenems()` using columns: 'IPM' (imipenem) and 'MEM' (meropenem)
+  mutate(bacteria = mo_fullname()) %>%
+  filter(mo_is_gram_negative(),
+         mo_is_intrinsic_resistant(ab = "cefotax")) %>%
+  select(bacteria,
+         aminoglycosides(),
+         carbapenems())
 ```
 
 With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (`mo_is_gram_negative()` and `mo_is_intrinsic_resistant()`) and a column selection on two antibiotic groups (`aminoglycosides()` and `carbapenems()`), the reference data about [all microorganisms](./reference/microorganisms.html) and [all antibiotics](./reference/antibiotics.html) in the `AMR` package make sure you get what you meant:
 
-|bacteria                       | AMK | GEN | KAN | TOB | IPM | MEM |
+|bacteria                       | GEN | TOB | AMK | KAN | IPM | MEM |
 |:------------------------------|:---:|:---:|:---:|:---:|:---:|:---:|
-|*Pseudomonas aeruginosa*       |     |  I  |  R  |  S  |  S  |     |
-|*Pseudomonas aeruginosa*       |     |  I  |  R  |  S  |  S  |     |
-|*Pseudomonas aeruginosa*       |     |  I  |  R  |  S  |  S  |     |
-|*Pseudomonas aeruginosa*       |  S  |  S  |  R  |  S  |     |  S  |
-|*Pseudomonas aeruginosa*       |  S  |  S  |  R  |  S  |  S  |  S  |
-|*Pseudomonas aeruginosa*       |  S  |  S  |  R  |  S  |  S  |  S  |
+|*Pseudomonas aeruginosa*       |  I  |  S  |     |  R  |  S  |     |
+|*Pseudomonas aeruginosa*       |  I  |  S  |     |  R  |  S  |     |
+|*Pseudomonas aeruginosa*       |  I  |  S  |     |  R  |  S  |     |
+|*Pseudomonas aeruginosa*       |  S  |  S  |  S  |  R  |     |  S  |
+|*Pseudomonas aeruginosa*       |  S  |  S  |  S  |  R  |  S  |  S  |
+|*Pseudomonas aeruginosa*       |  S  |  S  |  S  |  R  |  S  |  S  |
 |*Stenotrophomonas maltophilia* |  R  |  R  |  R  |  R  |  R  |  R  |
-|*Pseudomonas aeruginosa*       |  S  |  S  |  R  |  S  |     |  S  |
-|*Pseudomonas aeruginosa*       |  S  |  S  |  R  |  S  |     |  S  |
-|*Pseudomonas aeruginosa*       |  S  |  S  |  R  |  S  |  S  |  S  |
+|*Pseudomonas aeruginosa*       |  S  |  S  |  S  |  R  |     |  S  |
+|*Pseudomonas aeruginosa*       |  S  |  S  |  S  |  R  |     |  S  |
+|*Pseudomonas aeruginosa*       |  S  |  S  |  S  |  R  |  S  |  S  |
 
 A base R equivalent would be, giving the exact same results:
 
@@ -114,30 +110,33 @@ It will be downloaded and installed automatically. For RStudio, click on the men
 
 #### Latest development version
 
-![R-code-check](https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master)
-![[CodeFactor](https://www.codefactor.io/repository/github/msberends/amr/badge)](https://www.codefactor.io/repository/github/msberends/amr)
-![[Codecov](https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg)](https://codecov.io/gh/msberends/AMR?branch=master)
+[![R-code-check](https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master)](https://codecov.io/gh/msberends/AMR?branch=master)
+[![CodeFactor](https://www.codefactor.io/repository/github/msberends/amr/badge)](https://www.codefactor.io/repository/github/msberends/amr)
+[![Codecov](https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg)](https://codecov.io/gh/msberends/AMR?branch=master)
 
 The latest and unpublished development version can be installed from GitHub in two ways:
 
-1. Directly, using:
+1. Manually, using:
+
    ```r
    install.packages("remotes") # if you haven't already
    remotes::install_github("msberends/AMR")
    ```
    
-2. From the [rOpenSci R-universe platform](https://ropensci.org/r-universe/), by adding [our R-universe address](https://msberends.r-universe.dev) to your list of repositories ('repos'):
+2. Automatically, using the [rOpenSci R-universe platform](https://ropensci.org/r-universe/), by adding [our R-universe address](https://msberends.r-universe.dev) to your list of repositories ('repos'):
+
    ```r
    options(repos = c(getOption("repos"),
                      msberends = "https://msberends.r-universe.dev"))
    ```
+   
    After this, you can install and update this `AMR` package like any official release (e.g., using `install.packages("AMR")` or in RStudio via *Tools* > *Check for Package Updates...*).
 
 You can also download the latest build from our repository: <https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz>
 
 ### Get started
 
-To find out how to conduct AMR data analysis, please [continue reading here to get started](./articles/AMR.html) or click the links in the 'How to' menu.
+To find out how to conduct AMR data analysis, please [continue reading here to get started](./articles/AMR.html) or click a link in the ['How to' menu](https://msberends.github.io/AMR/articles/).
 
 ### Short introduction
 

inst/tinytest/test-ab_class_selectors.R

@@ -23,41 +23,48 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-if (getRversion() >= "3.2") {
-  # antibiotic class selectors require at least R-3.2
-  expect_true(ncol(example_isolates[, aminoglycosides(), 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))
-  expect_true(ncol(example_isolates[, cephalosporins_1st(), drop = FALSE]) < ncol(example_isolates))
-  expect_true(ncol(example_isolates[, cephalosporins_2nd(), drop = FALSE]) < ncol(example_isolates))
-  expect_true(ncol(example_isolates[, cephalosporins_3rd(), drop = FALSE]) < ncol(example_isolates))
-  expect_true(ncol(example_isolates[, cephalosporins_4th(), drop = FALSE]) < ncol(example_isolates))
-  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[, 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[, tetracyclines(), drop = FALSE]) < ncol(example_isolates))
-  
-  # Examples:
-  
-  # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
-  expect_equal(ncol(example_isolates[, c("mo", aminoglycosides())]), 5, tolerance = 0.5)
-  
-  # filter using any() or all()
-  expect_equal(nrow(example_isolates[any(carbapenems() == "R"), ]), 55, tolerance = 0.5)
-  expect_equal(nrow(subset(example_isolates, any(carbapenems() == "R"))), 55, tolerance = 0.5)
-  
-  # filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
-  expect_equal(nrow(example_isolates[any(carbapenems()), ]), 962, tolerance = 0.5)
-  expect_equal(nrow(example_isolates[all(carbapenems()), ]), 756, tolerance = 0.5)
-  
-  # filter with multiple antibiotic selectors using c()
-  expect_equal(nrow(example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]), 26, tolerance = 0.5)
-  
-  # filter + select in one go: get penicillins in carbapenems-resistant strains
-  expect_equal(nrow(example_isolates[any(carbapenems() == "R"), penicillins()]), 55, tolerance = 0.5)
-  expect_equal(ncol(example_isolates[any(carbapenems() == "R"), penicillins()]), 7, tolerance = 0.5)
-}
+# antibiotic class selectors
+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))
+expect_true(ncol(example_isolates[, cephalosporins_1st(), drop = FALSE]) < ncol(example_isolates))
+expect_true(ncol(example_isolates[, cephalosporins_2nd(), drop = FALSE]) < ncol(example_isolates))
+expect_true(ncol(example_isolates[, cephalosporins_3rd(), drop = FALSE]) < ncol(example_isolates))
+expect_true(ncol(example_isolates[, cephalosporins_4th(), drop = FALSE]) < ncol(example_isolates))
+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:
+
+# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
+expect_equal(ncol(example_isolates[, c("mo", aminoglycosides())]), 5, tolerance = 0.5)
+
+# filter using any() or all()
+expect_equal(nrow(example_isolates[any(carbapenems() == "R"), ]), 55, tolerance = 0.5)
+expect_equal(nrow(subset(example_isolates, any(carbapenems() == "R"))), 55, tolerance = 0.5)
+
+# filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
+expect_equal(nrow(example_isolates[any(carbapenems()), ]), 962, tolerance = 0.5)
+expect_equal(nrow(example_isolates[all(carbapenems()), ]), 756, tolerance = 0.5)
+
+# filter with multiple antibiotic selectors using c()
+expect_equal(nrow(example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]), 26, tolerance = 0.5)
+
+# filter + select in one go: get penicillins in carbapenems-resistant strains
+expect_equal(nrow(example_isolates[any(carbapenems() == "R"), penicillins()]), 55, tolerance = 0.5)
+expect_equal(ncol(example_isolates[any(carbapenems() == "R"), penicillins()]), 7, tolerance = 0.5)
+

inst/tinytest/test-ab_property.R

@@ -24,7 +24,8 @@
 # ==================================================================== #
 
 expect_identical(ab_name("AMX", language = NULL), "Amoxicillin")
-expect_identical(as.character(ab_atc("AMX")), "J01CA04")
+expect_identical(ab_name("AMX", language = NULL, snake_case = TRUE), "amoxicillin")
+expect_identical(ab_atc("AMX"), "J01CA04")
 expect_identical(ab_cid("AMX"), as.integer(33613))
 
 expect_inherits(ab_tradenames("AMX"), "character")

inst/tinytest/test-atc_online.R

@@ -30,5 +30,4 @@ if (AMR:::pkg_is_available("curl", also_load = FALSE) &&
   expect_true(length(atc_online_groups(ab_atc("AMX"))) >= 1)
   expect_equal(atc_online_ddd(ab_atc("AMX"), administration = "O"), 1.5)
   expect_equal(atc_online_ddd(ab_atc("AMX"), administration = "P"), 3)
-  expect_warning(atc_online_ddd(ab_atc("Novobiocin"), administration = "P"))
 }

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-data.R

@@ -29,8 +29,10 @@ expect_true(AMR:::check_dataset_integrity()) # in misc.R
 expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
 expect_identical(class(microorganisms$mo), c("mo", "character"))
 expect_identical(nrow(antibiotics), length(unique(antibiotics$ab)))
+expect_true(all(is.na(antibiotics$atc[duplicated(antibiotics$atc)])))
 expect_identical(class(antibiotics$ab), c("ab", "character"))
 
+
 # check cross table reference
 expect_true(all(microorganisms.codes$mo %in% microorganisms$mo))
 expect_true(all(example_isolates$mo %in% microorganisms$mo))

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-get_locale.R

@@ -23,9 +23,7 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-expect_identical(mo_genus("B_GRAMP", language = "pt"),
-                 "(Gram positivos desconhecidos)")
-
+expect_identical(mo_genus("B_GRAMP", language = "pt"), "(Gram positivos desconhecidos)")
 expect_identical(mo_fullname("CoNS", "en"), "Coagulase-negative Staphylococcus (CoNS)")
 expect_identical(mo_fullname("CoNS", "de"), "Koagulase-negative Staphylococcus (KNS)")
 expect_identical(mo_fullname("CoNS", "nl"), "Coagulase-negatieve Staphylococcus (CNS)")

inst/tinytest/test-mo.R

@@ -240,8 +240,8 @@ x <- as.mo("S. aur")
 expect_stdout(print(mo_uncertainties()))
 
 # Salmonella (City) are all actually Salmonella enterica spp (City)
-expect_equal(suppressMessages(mo_name(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"))),
-             c("Salmonella enterica", "Salmonella enterica", "Salmonella"))
+expect_equal(suppressMessages(as.mo(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"))),
+             as.mo(c("Salmonella enterica", "Salmonella enterica", "Salmonella")))
 
 # no virusses
 expect_equal(as.character(as.mo("Virus")), NA_character_)

inst/tinytest/test-mo_property.R

@@ -29,11 +29,19 @@ expect_equal(mo_phylum("Escherichia coli"), "Proteobacteria")
 expect_equal(mo_class("Escherichia coli"), "Gammaproteobacteria")
 expect_equal(mo_order("Escherichia coli"), "Enterobacterales")
 expect_equal(mo_family("Escherichia coli"), "Enterobacteriaceae")
+expect_equal(mo_fullname("Escherichia coli"), "Escherichia coli")
 expect_equal(mo_genus("Escherichia coli"), "Escherichia")
+expect_equal(mo_name("Escherichia coli"), "Escherichia coli")
+expect_equal(mo_shortname("Escherichia coli"), "E. coli")
+expect_equal(mo_shortname("Escherichia"), "Escherichia")
+expect_equal(mo_shortname("Staphylococcus aureus"), "S. aureus")
+expect_equal(mo_shortname("Staphylococcus aureus", Becker = TRUE), "S. aureus")
+expect_equal(mo_shortname("Staphylococcus aureus", Becker = "all", language = "en"), "CoPS")
+expect_equal(mo_shortname("Streptococcus agalactiae"), "S. agalactiae")
+expect_equal(mo_shortname("Streptococcus agalactiae", Lancefield = TRUE), "GBS")
+
 expect_equal(mo_species("Escherichia coli"), "coli")
 expect_equal(mo_subspecies("Escherichia coli"), "")
-expect_equal(mo_fullname("Escherichia coli"), "Escherichia coli")
-expect_equal(mo_name("Escherichia coli"), "Escherichia coli")
 expect_equal(mo_type("Escherichia coli", language = "en"), "Bacteria")
 expect_equal(mo_gramstain("Escherichia coli", language = "en"), "Gram-negative")
 expect_inherits(mo_taxonomy("Escherichia coli"), "list")
@@ -52,14 +60,6 @@ expect_equal(mo_ref("Escherichia coli"), "Castellani et al., 1919")
 expect_equal(mo_authors("Escherichia coli"), "Castellani et al.")
 expect_equal(mo_year("Escherichia coli"), 1919)
 
-expect_equal(mo_shortname("Escherichia coli"), "E. coli")
-expect_equal(mo_shortname("Escherichia"), "Escherichia")
-expect_equal(mo_shortname("Staphylococcus aureus"), "S. aureus")
-expect_equal(mo_shortname("Staphylococcus aureus", Becker = TRUE), "S. aureus")
-expect_equal(mo_shortname("Staphylococcus aureus", Becker = "all", language = "en"), "CoPS")
-expect_equal(mo_shortname("Streptococcus agalactiae"), "S. agalactiae")
-expect_equal(mo_shortname("Streptococcus agalactiae", Lancefield = TRUE), "GBS")
-
 expect_true(mo_url("Candida albicans") %like% "catalogueoflife.org")
 expect_true(mo_url("Escherichia coli") %like% "lpsn.dsmz.de")
 

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/ab_property.Rd

@@ -17,7 +17,7 @@
 \alias{ab_url}
 \title{Get Properties of an Antibiotic}
 \usage{
-ab_name(x, language = get_locale(), tolower = FALSE, ...)
+ab_name(x, language = get_locale(), tolower = FALSE, snake_case = FALSE, ...)
 
 ab_atc(x, ...)
 
@@ -50,6 +50,8 @@ ab_property(x, property = "name", language = get_locale(), ...)
 
 \item{tolower}{a \link{logical} to indicate whether the first \link{character} of every output should be transformed to a lower case \link{character}. This will lead to e.g. "polymyxin B" and not "polymyxin b".}
 
+\item{snake_case}{a \link{logical} to indicate whether the names should be returned in so-called \href{https://en.wikipedia.org/wiki/Snake_case}{snake case}: in lower case and all spaces/slashes replaced with an underscore (\verb{_}). This is useful for column renaming.}
+
 \item{...}{other arguments passed on to \code{\link[=as.ab]{as.ab()}}}
 
 \item{administration}{way of administration, either \code{"oral"} or \code{"iv"}}