(v1.7.1.9008) unit tests

.github/workflows/check.yaml

@@ -23,6 +23,8 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
+# This GitHub Actions file runs without ANY dependency, so works on all versions of R since R-3.0.
+
 on:
   push:
     branches:
@@ -32,9 +34,9 @@ on:
     branches:
       - master
   schedule:
-    # run a schedule everyday at 3 AM.
+    # run a schedule everyday at 1 AM.
     # this is to check that all dependencies are still available (see R/zzz.R)
-    - cron:  '0 3 * * *'
+    - cron:  '0 1 * * *'
 
 name: R-code-check
 
@@ -55,31 +57,40 @@ 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:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
-
+      R_REPOSITORIES: "https://cran.rstudio.com"
+    
     steps:
       - uses: actions/checkout@v2
 
@@ -95,13 +106,18 @@ jobs:
         run: |
           sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev
 
+      - name: Query dependencies
+        # this will change 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()
@@ -155,5 +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-v4
+          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: 1.7.0
-Date: 2021-05-26
+Version: 1.7.1.9008
+Date: 2021-06-23
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 
@@ -43,7 +43,6 @@ Depends:
     R (>= 3.0.0)
 Suggests:
     cleaner,
-    covr,
     curl,
     dplyr,
     ggplot2,
@@ -60,7 +59,7 @@ Suggests:
     tinytest,
     xml2
 VignetteBuilder: knitr,rmarkdown
-URL: https://msberends.github.io/AMR/, https://github.com/msberends/AMR
+URL: https://github.com/msberends/AMR, https://msberends.github.io/AMR
 BugReports: https://github.com/msberends/AMR/issues
 License: GPL-2 | file LICENSE
 Encoding: UTF-8

NAMESPACE

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

NEWS.md

@@ -1,8 +1,24 @@
-# `AMR` 1.7.0
+# `AMR` 1.7.1.9008
+## <small>Last updated: 23 June 2021</small>
 
+### Changed
+* Antibiotic class selectors (see `ab_class()`)
+  * They now finally 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()`)
+* Fixed 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
+
+
+# `AMR` 1.7.1
 
 ### Breaking change
-* 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.
+* 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
   example_isolates[, carbapenems()]           # base R
@@ -21,6 +37,7 @@
   ```
 
 ### 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.
@@ -35,6 +52,7 @@
 
 
 ### Changed
+* `bug_drug_combinations()` now supports grouping using the `dplyr` package
 * Custom MDRO guidelines (`mdro()`, `custom_mdro_guideline()`):
   * Custom MDRO guidelines can now be combined with other custom MDRO guidelines using `c()`
   * Fix for applying the rules; in previous versions, rows were interpreted according to the last matched rule. Now, rows are interpreted according to the first matched rule
@@ -67,6 +85,7 @@
 * `age()` now vectorises over both `x` and `reference`
 
 ### Other
+* As requested by CRAN administrators: decreased package size by 3 MB in costs of a slower loading time of the package
 * All unit tests are now processed by the `tinytest` package, instead of the `testthat` package. The `testthat` package unfortunately requires tons of dependencies that are also heavy and only usable for recent R versions, disallowing developers to test a package under any R 3.* version. On the contrary, the `tinytest` package is very lightweight and dependency-free.
 
 

R/aa_helper_functions.R

@@ -170,67 +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,
-                                 microorganisms.translation$mo_old)))) {
+      # take first <mo> column
+      found <- colnames(x)[vapply(FUN.VALUE = logical(1), x, is.mo)]
+    } else if ("mo" %in% colnames_formatted &
+               suppressWarnings(all(x$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
@@ -243,10 +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)
@@ -508,7 +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"))) {
@@ -698,7 +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)) {
@@ -716,11 +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
@@ -728,72 +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 (el in sys.frames()) {
+    if (!is.null(el$`.Generic`)) {
+      # don't check `".Generic" %in% names(el)`, because in R < 3.2, `names(el)` is always NULL
+      
+      if (!is.null(el$`.data`) && is.data.frame(el$`.data`)) {
+        # an element `.data` will be in the environment when using `dplyr::select()`
+        # (but not when using `dplyr::filter()`, `dplyr::mutate()` or `dplyr::summarise()`)
+        return(structure(el$`.data`, type = "dplyr_selector"))
+        
+      } else if (!is.null(el$xx) && is.data.frame(el$xx)) {
+        # an element `xx` will be in the environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
+        return(structure(el$xx, type = "base_R"))
+        
+      } else if (!is.null(el$x) && is.data.frame(el$x)) {
+        # an element `x` will be in the environment for only cols, e.g. `example_isolates[, carbapenems()]`
+        return(structure(el$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])
@@ -982,8 +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])
                                        }
                                      }

R/ab_class_selectors.R

@@ -25,18 +25,18 @@
 
 #' 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, "."), "")}}
+#' @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](https://tidyselect.r-lib.org/reference/language.html), 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 +46,7 @@
 #' # `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()]
@@ -73,6 +73,11 @@
 #' \donttest{
 #' if (require("dplyr")) {
 #' 
+#'   # get AMR for all aminoglycosides e.g., per hospital:
+#'   example_isolates %>%
+#'     group_by(hospital_id) %>% 
+#'     summarise(across(aminoglycosides(), resistance))
+#' 
 #'   # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
 #'   example_isolates %>% 
 #'     select(carbapenems())
@@ -99,7 +104,6 @@
 #'   example_isolates %>% 
 #'     select(mo, ab_class("mycobact"))
 #'     
-#'     
 #'   # get bug/drug combinations for only macrolides in Gram-positives:
 #'   example_isolates %>% 
 #'     filter(mo_is_gram_positive()) %>% 
@@ -107,14 +111,12 @@
 #'     bug_drug_combinations() %>%
 #'     format()
 #'     
-#'     
 #'   data.frame(some_column = "some_value",
 #'              J01CA01 = "S") %>%   # ATC code of ampicillin
 #'     select(penicillins())         # only the 'J01CA01' column will be selected
 #'     
 #'     
 #'   # with dplyr 1.0.0 and higher (that adds 'across()'), this is all equal:
-#'   # (though the row names on the first are more correct)
 #'   example_isolates[carbapenems() == "R", ]
 #'   example_isolates %>% filter(carbapenems() == "R")
 #'   example_isolates %>% filter(across(carbapenems(), ~.x == "R"))
@@ -122,147 +124,196 @@
 #' }
 ab_class <- function(ab_class, 
                      only_rsi_columns = FALSE) {
-  ab_selector(ab_class, function_name = "ab_class", only_rsi_columns = only_rsi_columns)
+  meet_criteria(ab_class, allow_class = "character", has_length = 1)
+  ab_selector(NULL, only_rsi_columns = only_rsi_columns, ab_class = ab_class)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 aminoglycosides <- function(only_rsi_columns = FALSE) {
-  ab_selector("aminoglycoside", function_name = "aminoglycosides", only_rsi_columns = only_rsi_columns)
+  ab_selector("aminoglycosides", only_rsi_columns = only_rsi_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+aminopenicillins <- function(only_rsi_columns = FALSE) {
+  ab_selector("aminopenicillins", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 betalactams <- function(only_rsi_columns = FALSE) {
-  ab_selector("carbapenem|cephalosporin|penicillin", function_name = "betalactams", only_rsi_columns = only_rsi_columns)
+  ab_selector("betalactams", only_rsi_columns = only_rsi_columns)
 }
+
 #' @rdname antibiotic_class_selectors
 #' @export
 carbapenems <- function(only_rsi_columns = FALSE) {
-  ab_selector("carbapenem", function_name = "carbapenems", only_rsi_columns = only_rsi_columns)
+  ab_selector("carbapenems", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 cephalosporins <- function(only_rsi_columns = FALSE) {
-  ab_selector("cephalosporin", function_name = "cephalosporins", only_rsi_columns = only_rsi_columns)
+  ab_selector("cephalosporins", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 cephalosporins_1st <- function(only_rsi_columns = FALSE) {
-  ab_selector("cephalosporins.*1", function_name = "cephalosporins_1st", only_rsi_columns = only_rsi_columns)
+  ab_selector("cephalosporins_1st", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 cephalosporins_2nd <- function(only_rsi_columns = FALSE) {
-  ab_selector("cephalosporins.*2", function_name = "cephalosporins_2nd", only_rsi_columns = only_rsi_columns)
+  ab_selector("cephalosporins_2nd", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 cephalosporins_3rd <- function(only_rsi_columns = FALSE) {
-  ab_selector("cephalosporins.*3", function_name = "cephalosporins_3rd", only_rsi_columns = only_rsi_columns)
+  ab_selector("cephalosporins_3rd", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 cephalosporins_4th <- function(only_rsi_columns = FALSE) {
-  ab_selector("cephalosporins.*4", function_name = "cephalosporins_4th", only_rsi_columns = only_rsi_columns)
+  ab_selector("cephalosporins_4th", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 cephalosporins_5th <- function(only_rsi_columns = FALSE) {
-  ab_selector("cephalosporins.*5", function_name = "cephalosporins_5th", only_rsi_columns = only_rsi_columns)
+  ab_selector("cephalosporins_5th", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 fluoroquinolones <- function(only_rsi_columns = FALSE) {
-  ab_selector("fluoroquinolone", function_name = "fluoroquinolones", only_rsi_columns = only_rsi_columns)
+  ab_selector("fluoroquinolones", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 glycopeptides <- function(only_rsi_columns = FALSE) {
-  ab_selector("glycopeptide", function_name = "glycopeptides", only_rsi_columns = only_rsi_columns)
+  ab_selector("glycopeptides", only_rsi_columns = only_rsi_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+lincosamides <- function(only_rsi_columns = FALSE) {
+  ab_selector("lincosamides", only_rsi_columns = only_rsi_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+lipoglycopeptides <- function(only_rsi_columns = FALSE) {
+  ab_selector("lipoglycopeptides", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 macrolides <- function(only_rsi_columns = FALSE) {
-  ab_selector("macrolide", function_name = "macrolides", only_rsi_columns = only_rsi_columns)
+  ab_selector("macrolides", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 oxazolidinones <- function(only_rsi_columns = FALSE) {
-  ab_selector("oxazolidinone", function_name = "oxazolidinones", only_rsi_columns = only_rsi_columns)
+  ab_selector("oxazolidinones", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 penicillins <- function(only_rsi_columns = FALSE) {
-  ab_selector("penicillin", function_name = "penicillins", only_rsi_columns = only_rsi_columns)
+  ab_selector("penicillins", only_rsi_columns = only_rsi_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+polymyxins <- function(only_rsi_columns = FALSE) {
+  ab_selector("polymyxins", only_rsi_columns = only_rsi_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+streptogramins <- function(only_rsi_columns = FALSE) {
+  ab_selector("streptogramins", only_rsi_columns = only_rsi_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+quinolones <- function(only_rsi_columns = FALSE) {
+  ab_selector("quinolones", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
 tetracyclines <- function(only_rsi_columns = FALSE) {
-  ab_selector("tetracycline", function_name = "tetracyclines", only_rsi_columns = only_rsi_columns)
+  ab_selector("tetracyclines", only_rsi_columns = only_rsi_columns)
 }
 
-ab_selector <- function(ab_class,
-                        function_name,
-                        only_rsi_columns) {
-  meet_criteria(ab_class, allow_class = "character", has_length = 1, .call_depth = 1)
-  meet_criteria(function_name, allow_class = "character", has_length = 1, .call_depth = 1)
+#' @rdname antibiotic_class_selectors
+#' @export
+ureidopenicillins <- function(only_rsi_columns = FALSE) {
+  ab_selector("ureidopenicillins", only_rsi_columns = only_rsi_columns)
+}
+
+ab_selector <- function(function_name,
+                        only_rsi_columns,
+                        ab_class = NULL) {
+  meet_criteria(function_name, allow_class = "character", has_length = 1, allow_NULL = TRUE, .call_depth = 1)
   meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1, .call_depth = 1)
-  
-  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
+  meet_criteria(ab_class, allow_class = "character", has_length = 1, allow_NULL = TRUE, .call_depth = 1)
+
+  # get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
   vars_df <- get_current_data(arg_name = NA, call = -3)
+  # to improve speed, get_column_abx() will only run once when e.g. in a select or group call
   ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE)
   
   if (length(ab_in_data) == 0) {
-    message_("No antimicrobial agents found.")
+    message_("No antimicrobial agents found in the data.")
     return(NULL)
   }
   
-  ab_reference <- subset(antibiotics,
-                         group %like% ab_class | 
-                           atc_group1 %like% ab_class | 
-                           atc_group2 %like% ab_class)
-  ab_group <- find_ab_group(ab_class)
-  if (ab_group == "") {
-    ab_group <- paste0("'", ab_class, "'")
-    examples <- ""
+  if (is.null(ab_class)) {
+    # their upper case equivalent are vectors with class <ab>, created in data-raw/_internals.R
+    abx <- get(toupper(function_name), envir = asNamespace("AMR"))  
+    ab_group <- function_name
+    examples <- paste0(" (such as ", vector_or(ab_name(sample(abx, size = min(2, length(abx)), replace = FALSE),
+                                                       tolower = TRUE,
+                                                       language = NULL),
+                                               quotes = FALSE), ")")
   } else {
+    # this for the 'manual' ab_class() function
+    abx <- subset(AB_lookup,
+                  group %like% ab_class |
+                    atc_group1 %like% ab_class |
+                    atc_group2 %like% ab_class)$ab
+    ab_group <- find_ab_group(ab_class)
+    function_name <- "ab_class"
     examples <- paste0(" (such as ", find_ab_names(ab_class, 2), ")")
   }
+
   # get the columns with a group names in the chosen ab class
-  agents <- ab_in_data[names(ab_in_data) %in% ab_reference$ab]
+  agents <- ab_in_data[names(ab_in_data) %in% abx]
     
   if (message_not_thrown_before(function_name)) {
     if (length(agents) == 0) {
-      message_("No antimicrobial agents of class ", ab_group, " found", examples, ".")
+      message_("No antimicrobial agents of class '", ab_group, "' found", examples, ".")
     } else {
       agents_formatted <- paste0("'", font_bold(agents, collapse = NULL), "'")
       agents_names <- ab_name(names(agents), tolower = TRUE, language = NULL)
-      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 ",
+      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))
+               vector_and(agents_formatted, quotes = FALSE, sort = FALSE))
     }
     remember_thrown_message(function_name)
   }
@@ -418,28 +469,16 @@ 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) {
@@ -457,6 +496,9 @@ find_ab_names <- function(ab_group, n = 3) {
                                   antibiotics$atc_group2 %like% ab_group) &
                                  antibiotics$ab %unlike% "[0-9]$"), ]$name
   }
+  if (length(drugs) == 0) {
+    return("??")
+  }
   vector_or(ab_name(sample(drugs, size = min(n, length(drugs)), replace = FALSE),
                     tolower = TRUE,
                     language = NULL),

R/amr.R

@@ -54,14 +54,14 @@
 #' @section Reference Data Publicly Available:
 #' All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this `AMR` package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find [all download links on our website](https://msberends.github.io/AMR/articles/datasets.html), which is automatically updated with every code change.
 #' @section Read more on Our Website!:
-#' On our website <https://msberends.github.io/AMR/> you can find [a comprehensive tutorial](https://msberends.github.io/AMR/articles/AMR.html) about how to conduct AMR data analysis, the [complete documentation of all functions](https://msberends.github.io/AMR/reference/) and [an example analysis using WHONET data](https://msberends.github.io/AMR/articles/WHONET.html). As we would like to better understand the backgrounds and needs of our users, please [participate in our survey](https://msberends.github.io/AMR/survey.html)!
+#' On our website <https://msberends.github.io/AMR/> you can find [a comprehensive tutorial](https://msberends.github.io/AMR/articles/AMR.html) about how to conduct AMR data analysis, the [complete documentation of all functions](https://msberends.github.io/AMR/reference/) and [an example analysis using WHONET data](https://msberends.github.io/AMR/articles/WHONET.html).
 #' @section Contact Us:
 #' 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
+#' 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

@@ -31,7 +31,7 @@
 #' @param combine_IR a [logical] to indicate whether values R and I should be summed
 #' @param add_ab_group a [logical] to indicate where the group of the antimicrobials must be included as a first column
 #' @param remove_intrinsic_resistant [logical] to indicate that rows and columns with 100% resistance for all tested antimicrobials must be removed from the table
-#' @param FUN the function to call on the `mo` column to transform the microorganism IDs, defaults to [mo_shortname()] 
+#' @param FUN the function to call on the `mo` column to transform the microorganism codes, defaults to [mo_shortname()] 
 #' @param translate_ab a [character] of length 1 containing column names of the [antibiotics] data set
 #' @param ... arguments passed on to `FUN`
 #' @inheritParams rsi_df
@@ -74,42 +74,87 @@ bug_drug_combinations <- function(x,
     stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found")
   }
   
-  x_class <- class(x)
+  x.bak <- x
   x <- as.data.frame(x, stringsAsFactors = FALSE)
   x[, col_mo] <- FUN(x[, col_mo, drop = TRUE], ...)
-  x <- x[, c(col_mo, names(which(vapply(FUN.VALUE = logical(1), x, is.rsi)))), drop = FALSE]
   
   unique_mo <- sort(unique(x[, col_mo, drop = TRUE]))
   
-  out <- data.frame(mo = character(0),
-                    ab = character(0),
-                    S = integer(0),
-                    I = integer(0),
-                    R = integer(0),
-                    total = integer(0),
-                    stringsAsFactors = FALSE)
-  
-  for (i in seq_len(length(unique_mo))) {
-    # filter on MO group and only select R/SI columns
-    x_mo_filter <- x[which(x[, col_mo, drop = TRUE] == unique_mo[i]), names(which(vapply(FUN.VALUE = logical(1), x, is.rsi))), drop = FALSE]
-    # turn and merge everything
-    pivot <- lapply(x_mo_filter, function(x) {
-      m <- as.matrix(table(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],
-                            ab = rownames(merged),
-                            S = merged$S,
-                            I = merged$I,
-                            R = merged$R,
-                            total = merged$S + merged$I + merged$R,
-                            stringsAsFactors = FALSE)
-    out <- rbind(out, out_group, stringsAsFactors = FALSE)
+  # select only groups and antibiotics
+  if (inherits(x.bak, "grouped_df")) {
+    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]
+  } else {
+    data_has_groups <- FALSE
+    x <- x[, c(col_mo, names(which(vapply(FUN.VALUE = logical(1), x, is.rsi)))), drop = FALSE]
   }
   
-  set_clean_class(out,
-                  new_class = c("bug_drug_combinations", x_class))
+  run_it <- function(x) {
+    out <- data.frame(mo = character(0),
+                      ab = character(0),
+                      S = integer(0),
+                      I = integer(0),
+                      R = integer(0),
+                      total = integer(0),
+                      stringsAsFactors = FALSE)
+    if (data_has_groups) {
+      group_values <- unique(x[, which(colnames(x) %in% groups), drop = FALSE])
+      rownames(group_values) <- NULL
+      x <- x[, which(!colnames(x) %in% groups), drop = FALSE]
+    }
+    
+    for (i in seq_len(length(unique_mo))) {
+      # filter on MO group and only select R/SI columns
+      x_mo_filter <- x[which(x[, col_mo, drop = TRUE] == unique_mo[i]), names(which(vapply(FUN.VALUE = logical(1), x, is.rsi))), drop = FALSE]
+      # turn and merge everything
+      pivot <- lapply(x_mo_filter, function(x) {
+        m <- as.matrix(table(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],
+                              ab = rownames(merged),
+                              S = merged$S,
+                              I = merged$I,
+                              R = merged$R,
+                              total = merged$S + merged$I + merged$R,
+                              stringsAsFactors = FALSE)
+      if (data_has_groups) {
+        if (nrow(group_values) < nrow(out_group)) {
+          # repeat group_values for the number of rows in out_group
+          repeated <- rep(seq_len(nrow(group_values)),
+                          each = nrow(out_group) / nrow(group_values))
+          group_values <- group_values[repeated, , drop = FALSE]
+        }
+        out_group <- cbind(group_values, out_group)
+      }
+      out <- rbind(out, out_group, stringsAsFactors = FALSE)
+    }
+    out
+  }
+  # based on pm_apply_grouped_function
+  apply_group <- function(.data, fn, groups, drop = FALSE, ...) {
+    grouped <- pm_split_into_groups(.data, groups, drop)
+    res <- do.call(rbind, unname(lapply(grouped, fn, ...)))
+    if (any(groups %in% colnames(res))) {
+      class(res) <- c("grouped_data", class(res))
+      res <- pm_set_groups(res, groups[groups %in% colnames(res)])
+    }
+    res
+  }
+  
+  if (data_has_groups) {
+    out <- apply_group(x, "run_it", groups)
+    rownames(out) <- NULL
+    set_clean_class(out,
+                    new_class = c("grouped", "bug_drug_combinations", "data.frame"))
+  } else {
+    out <- run_it(x)
+    rownames(out) <- NULL
+    set_clean_class(out,
+                    new_class = c("bug_drug_combinations", "data.frame"))
+  }
 }
 
 #' @method format bug_drug_combinations
@@ -137,6 +182,21 @@ format.bug_drug_combinations <- function(x,
   meet_criteria(decimal.mark, allow_class = "character", has_length = 1)
   meet_criteria(big.mark, allow_class = "character", has_length = 1)
   
+  if (inherits(x, "grouped")) {
+    # bug_drug_combinations() has been run on groups, so de-group here
+    warning_("formatting the output of `bug_drug_combinations()` does not support grouped variables, they are ignored", call = FALSE)
+    idx <- split(seq_len(nrow(x)), paste0(x$mo, "%%", x$ab))
+    x <- data.frame(mo = gsub("(.*)%%(.*)", "\\1", names(idx)),
+                    ab = gsub("(.*)%%(.*)", "\\2", names(idx)),
+                    S = sapply(idx, function(i) sum(y$S[i], na.rm = TRUE)), 
+                    I = sapply(idx, function(i) sum(y$I[i], na.rm = TRUE)), 
+                    R = sapply(idx, function(i) sum(y$R[i], na.rm = TRUE)),
+                    total = sapply(idx, function(i) sum(y$S[i], na.rm = TRUE) + 
+                                     sum(y$I[i], na.rm = TRUE) +
+                                     sum(y$R[i], na.rm = TRUE)),
+                    stringsAsFactors = FALSE)
+  }
+  
   x <- as.data.frame(x, stringsAsFactors = FALSE)
   x <- subset(x, total >= minimum)
   
@@ -249,7 +309,9 @@ format.bug_drug_combinations <- function(x,
 print.bug_drug_combinations <- function(x, ...) {
   x_class <- class(x)
   print(set_clean_class(x, 
-                        new_class = x_class[x_class != "bug_drug_combinations"]),
+                        new_class = x_class[!x_class %in% c("bug_drug_combinations", "grouped")]),
         ...)
-  message_("Use 'format()' on this result to get a publishable/printable format.", as_note = FALSE)
+  message_("Use 'format()' on this result to get a publishable/printable format.",
+           ifelse(inherits(x, "grouped"), " Note: The grouping variable(s) will be ignored.", ""),
+           as_note = FALSE)
 }

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/data.R

@@ -239,7 +239,7 @@
 
 #' Data Set for R/SI Interpretation
 #'
-#' Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`) and EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`). Use [as.rsi()] to transform MICs or disks measurements to R/SI values.
+#' Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`). Use [as.rsi()] to transform MICs or disks measurements to R/SI values.
 #' @format A [data.frame] with `r format(nrow(rsi_translation), big.mark = ",")` observations and `r ncol(rsi_translation)` variables:
 #' - `guideline`\cr Name of the guideline
 #' - `method`\cr Either `r vector_or(rsi_translation$method)`

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()), ]
 #'
@@ -472,8 +469,8 @@ first_isolate <- function(x = NULL,
                  as_note = FALSE)
       }
       if (type == "points") {
-        message_("Basing inclusion on all antimicrobial results, using a points threshold of "
-                 , points_threshold,
+        message_("Basing inclusion on all antimicrobial results, using a points threshold of ",
+                 points_threshold,
                  add_fn = font_black,
                  as_note = FALSE)
       }

R/ggplot_rsi.R

@@ -386,15 +386,15 @@ scale_rsi_colours <- function(...,
   }
   
   names_susceptible <- c("S", "SI", "IS", "S+I", "I+S", "susceptible", "Susceptible",
-                         unique(translations_file[which(translations_file$pattern == "Susceptible"),
+                         unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Susceptible"),
                                                   "replacement", drop = TRUE]))
   names_incr_exposure <- c("I", "intermediate", "increased exposure", "incr. exposure", "Increased exposure", "Incr. exposure",
-                           unique(translations_file[which(translations_file$pattern == "Intermediate"),
+                           unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Intermediate"),
                                                     "replacement", drop = TRUE]),
-                           unique(translations_file[which(translations_file$pattern == "Incr. exposure"),
+                           unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Incr. exposure"),
                                                     "replacement", drop = TRUE]))
   names_resistant <- c("R", "IR", "RI", "R+I", "I+R", "resistant", "Resistant",
-                       unique(translations_file[which(translations_file$pattern == "Resistant"), 
+                       unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Resistant"), 
                                                 "replacement", drop = TRUE]))
   
   susceptible <- rep("#3CAEA3", length(names_susceptible))

R/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/key_antimicrobials.R

@@ -140,7 +140,7 @@ key_antimicrobials <- function(x = NULL,
   meet_criteria(antifungal, allow_class = "character", allow_NULL = TRUE)
   meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
   
-  # force regular [data.frame], not a tibble or data.table
+  # force regular data.frame, not a tibble or data.table
   x <- as.data.frame(x, stringsAsFactors = FALSE)
   cols <- get_column_abx(x, info = FALSE, only_rsi_columns = only_rsi_columns)
   
@@ -237,7 +237,7 @@ all_antimicrobials <- function(x = NULL,
   meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
   meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
   
-  # force regular [data.frame], not a tibble or data.table
+  # force regular data.frame, not a tibble or data.table
   x <- as.data.frame(x, stringsAsFactors = FALSE)
   cols <- get_column_abx(x, only_rsi_columns = only_rsi_columns, info = FALSE, sort = FALSE)
   

R/mo.R

@@ -23,9 +23,9 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-#' Transform Input to a Microorganism ID
+#' Transform Input to a Microorganism Code
 #'
-#' Use this function to determine a valid microorganism ID ([`mo`]). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see *Source*). The input can be almost anything: a full name (like `"Staphylococcus aureus"`), an abbreviated name (such as `"S. aureus"`), an abbreviation known in the field (such as `"MRSA"`), or just a genus. See *Examples*.
+#' Use this function to determine a valid microorganism code ([`mo`]). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see *Source*). The input can be almost anything: a full name (like `"Staphylococcus aureus"`), an abbreviated name (such as `"S. aureus"`), an abbreviation known in the field (such as `"MRSA"`), or just a genus. See *Examples*.
 #' @inheritSection lifecycle Stable Lifecycle
 #' @param x a [character] vector or a [data.frame] with one or two columns
 #' @param Becker a [logical] to indicate whether staphylococci should be categorised into coagulase-negative staphylococci ("CoNS") and coagulase-positive staphylococci ("CoPS") instead of their own species, according to Karsten Becker *et al.* (1,2,3).
@@ -46,7 +46,7 @@
 #' @details
 #' ## General Info
 #'
-#' A microorganism ID from this package (class: [`mo`]) is human readable and typically looks like these examples:
+#' A microorganism (MO) code from this package (class: [`mo`]) is human readable and typically looks like these examples:
 #' ```
 #'   Code               Full name
 #'   ---------------    --------------------------------------
@@ -469,7 +469,7 @@ exec_as.mo <- function(x,
     x <- strip_whitespace(x, dyslexia_mode)
     # translate 'unknown' names back to English
     if (any(x %like% "unbekannt|onbekend|desconocid|sconosciut|iconnu|desconhecid", na.rm = TRUE)) {
-      trns <- subset(translations_file, pattern %like% "unknown" | affect_mo_name == TRUE)
+      trns <- subset(TRANSLATIONS, pattern %like% "unknown" | affect_mo_name == TRUE)
       langs <- LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED != "en"]
       for (l in langs) {
         for (i in seq_len(nrow(trns))) {
@@ -1664,16 +1664,23 @@ 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$mo], 
                                                      collapse = NULL),
                                              collapse = NULL)
-    # throw a warning with the affected column name
-    mo <- tryCatch(search_type_in_df(get_current_data(arg_name = "x", call = 0), type = "mo", info = FALSE),
-                   error = function(e) NULL)
-    if (!is.null(mo)) {
-      col <- paste0("Column '", mo, "'")
+    # throw a warning with the affected column name(s)
+    if (!is.null(mo_cols)) {
+      col <- paste0("Column ", vector_or(colnames(df)[mo_cols], quotes = TRUE, sort = FALSE))
     } else {
       col <- "The data"
     }
@@ -1681,7 +1688,7 @@ pillar_shaft.mo <- function(x, ...) {
              "Please update your MO codes with `as.mo()`.",
              call = FALSE)
   }
-
+  
   # make it always fit exactly
   max_char <- max(nchar(x))
   if (is.na(max_char)) {
@@ -1817,8 +1824,7 @@ as.data.frame.mo <- function(x, ...) {
   y <- NextMethod()
   attributes(y) <- attributes(i)
   # must only contain valid MOs
-  return_after_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
-                                                          as.character(microorganisms.translation$mo_old)))
+  return_after_integrity_check(y, "microorganism code", as.character(microorganisms$mo))
 }
 #' @method [[<- mo
 #' @export
@@ -1827,8 +1833,7 @@ as.data.frame.mo <- function(x, ...) {
   y <- NextMethod()
   attributes(y) <- attributes(i)
   # must only contain valid MOs
-  return_after_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
-                                                          as.character(microorganisms.translation$mo_old)))
+  return_after_integrity_check(y, "microorganism code", as.character(microorganisms$mo))
 }
 #' @method c mo
 #' @export
@@ -1837,8 +1842,7 @@ c.mo <- function(...) {
   x <- list(...)[[1L]]
   y <- NextMethod()
   attributes(y) <- attributes(x)
-  return_after_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
-                                                          as.character(microorganisms.translation$mo_old)))
+  return_after_integrity_check(y, "microorganism code", as.character(microorganisms$mo))
 }
 
 #' @method unique mo
@@ -2042,35 +2046,63 @@ 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
 }
 
 replace_old_mo_codes <- function(x, property) {
-  if (any(toupper(x) %in% microorganisms.translation$mo_old, na.rm = TRUE)) {
+  ind <- x %like_case% "^[A-Z]_[A-Z_]+$" & !x %in% MO_lookup$mo
+  if (any(ind)) {
     # get the ones that match
-    matched <- match(toupper(x), microorganisms.translation$mo_old)
-    # and their new codes
-    mo_new <- microorganisms.translation$mo_new[matched]
+    affected <- x[ind]
+    affected_unique <- unique(affected)
+    all_direct_matches <- TRUE
+    # find their new codes, once per code
+    solved_unique <- unlist(lapply(strsplit(affected_unique, ""), 
+                                   function(m) {
+                                     kingdom <- paste0("^", m[1])
+                                     name <- m[3:length(m)]
+                                     name[name == "_"] <- " "
+                                     name <- tolower(paste0(name, ".*", collapse = ""))
+                                     name <- gsub(" .*", " ", name, fixed = TRUE)
+                                     name <- paste0("^", name)
+                                     results <- MO_lookup$mo[MO_lookup$kingdom %like_case% kingdom & 
+                                                               MO_lookup$fullname_lower %like_case% name]
+                                     if (length(results) > 1) {
+                                       all_direct_matches <<- FALSE
+                                     }
+                                     results[1L]
+                                   }), use.names = FALSE)
+    solved <- solved_unique[match(affected, affected_unique)]
     # assign on places where a match was found
-    x[which(!is.na(matched))] <- mo_new[which(!is.na(matched))]
-    n_matched <- length(matched[!is.na(matched)])
-    if (property != "mo") {
-      message_(font_blue(paste0("The input contained ", n_matched,
-                                " old MO code", ifelse(n_matched == 1, "", "s"),
-                                " (from a previous AMR package version). Please update your MO codes with `as.mo()`.")))
+    x[ind] <- solved
+    n_matched <- length(affected[!is.na(affected)])
+    n_unique <- length(affected_unique[!is.na(affected_unique)])
+    if (n_unique < n_matched) {
+      n_unique <- paste0(n_unique, " unique, ")
     } else {
-      message_(font_blue(paste0(n_matched, " old MO code", ifelse(n_matched == 1, "", "s"), 
-                                " (from a previous AMR package version) ", 
-                                ifelse(n_matched == 1, "was", "were"), 
-                                " updated to ", ifelse(n_matched == 1, "a ", ""), 
-                                "currently used MO code", ifelse(n_matched == 1, "", "s"), ".")))
+      n_unique <- ""
+    }
+    if (property != "mo") {
+      warning_(paste0("The input contained ", n_matched,
+                      " old MO code", ifelse(n_matched == 1, "", "s"),
+                      " (", n_unique, "from a previous AMR package version). ",
+                      "Please update your MO codes with `as.mo()` to increase speed."),
+               call = FALSE)
+    } else {
+      warning_(paste0(n_matched, " old MO code", ifelse(n_matched == 1, "", "s"), 
+                      " (", n_unique, "from a previous AMR package version) ", 
+                      ifelse(n_matched == 1, "was", "were"), 
+                      ifelse(all_direct_matches, " updated ", font_bold(" guessed ")),
+                      "to ", ifelse(n_matched == 1, "a ", ""), 
+                      "currently used MO code", ifelse(n_matched == 1, "", "s"), "."),
+               call = FALSE)
     }
   }
   x

R/mo_property.R

@@ -754,7 +754,7 @@ 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/mo_source.R

@@ -275,9 +275,9 @@ check_validity_mo_source <- function(x, refer_to_name = "`reference_df`", stop_o
       return(FALSE)
     }
   }
-  if (!all(x$mo %in% c("", microorganisms$mo, microorganisms.translation$mo_old), na.rm = TRUE)) {
+  if (!all(x$mo %in% c("", microorganisms$mo), na.rm = TRUE)) {
     if (stop_on_error == TRUE) {
-      invalid <- x[which(!x$mo %in% c("", microorganisms$mo, microorganisms.translation$mo_old)), , drop = FALSE]
+      invalid <- x[which(!x$mo %in% c("", microorganisms$mo)), , drop = FALSE]
       if (nrow(invalid) > 1) {
         plural <- "s"
       } else {

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

R/proportion.R

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

R/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

@@ -65,9 +65,9 @@
 #' 
 #' ## Supported Guidelines
 #' 
-#' For interpreting MIC values as well as disk diffusion diameters, currently supported guidelines to be used as input for the `guideline` argument are: `r vector_and(AMR::rsi_translation$guideline, quotes = TRUE, reverse = TRUE)`.
+#' For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`). 
 #' 
-#' Simply using `"CLSI"` or `"EUCAST"` as input will automatically select the latest version of that guideline. You can set your own data set using the `reference_data` argument. The `guideline` argument will then be ignored.
+#' Thus, the `guideline` argument must be set to e.g., ``r paste0('"', subset(rsi_translation, guideline %like% "EUCAST")$guideline[1], '"')`` or ``r paste0('"', subset(rsi_translation, guideline %like% "CLSI")$guideline[1], '"')``. By simply using `"EUCAST"` (the default) or `"CLSI"` as input, the latest version of that guideline will automatically be selected. You can set your own data set using the `reference_data` argument. The `guideline` argument will then be ignored.
 #' 
 #' ## After Interpretation
 #' 
@@ -92,7 +92,7 @@
 #' - **I = Increased exposure, but still susceptible**\cr
 #'   A microorganism is categorised as *Susceptible, Increased exposure* when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
 #'
-#' This AMR package honours this new insight. Use [susceptibility()] (equal to [proportion_SI()]) to determine antimicrobial susceptibility and [count_susceptible()] (equal to [count_SI()]) to count susceptible isolates.
+#' This AMR package honours this (new) insight. Use [susceptibility()] (equal to [proportion_SI()]) to determine antimicrobial susceptibility and [count_susceptible()] (equal to [count_SI()]) to count susceptible isolates.
 #' @return Ordered [factor] with new class `<rsi>`
 #' @aliases rsi
 #' @export
@@ -349,7 +349,7 @@ as.rsi.mic <- function(x,
   
   # for dplyr's across()
   cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
-  if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", 0)), error = function(e) FALSE)) {
+  if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", call = 0)), error = function(e) FALSE)) {
     # try to get current column, which will only be available when in across()
     ab <- tryCatch(cur_column_dplyr(),
                    error = function(e) ab)
@@ -438,7 +438,7 @@ as.rsi.disk <- function(x,
   
   # for dplyr's across()
   cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
-  if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", 0)), error = function(e) FALSE)) {
+  if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", call = 0)), 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)

R/translate.R

@@ -136,7 +136,7 @@ translate_AMR <- function(from,
     return(from)
   }
   
-  df_trans <- translations_file # internal data file
+  df_trans <- TRANSLATIONS # internal data file
   from.bak <- from
   from_unique <- unique(from)
   from_unique_translated <- from_unique

R/zzz.R

@@ -65,6 +65,10 @@ if (utf8_supported && !is_latex) {
   s3_register("ggplot2::ggplot", "mic")
   s3_register("ggplot2::ggplot", "disk")
   s3_register("ggplot2::ggplot", "resistance_predict")
+  s3_register("ggplot2::autoplot", "rsi")
+  s3_register("ggplot2::autoplot", "mic")
+  s3_register("ggplot2::autoplot", "disk")
+  s3_register("ggplot2::autoplot", "resistance_predict")
   
   # if mo source exists, fire it up (see mo_source())
   try({
@@ -72,4 +76,76 @@ if (utf8_supported && !is_latex) {
       invisible(get_mo_source())
     }
   }, silent = TRUE)
+  
+  
+  # reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed
+  assign(x = "AB_lookup", value = create_AB_lookup(), envir = asNamespace("AMR"))
+  assign(x = "MO_lookup", value = create_MO_lookup(), envir = asNamespace("AMR"))
+  assign(x = "MO.old_lookup", value = create_MO.old_lookup(), envir = asNamespace("AMR"))
+  # for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
+  assign(x = "INTRINSIC_R", value = create_intr_resistance(), envir = asNamespace("AMR"))
+}
+
+
+# Helper functions --------------------------------------------------------
+
+create_AB_lookup <- function() {
+  AB_lookup <- AMR::antibiotics
+  AB_lookup$generalised_name <- generalise_antibiotic_name(AB_lookup$name)
+  AB_lookup$generalised_synonyms <- lapply(AB_lookup$synonyms, generalise_antibiotic_name)
+  AB_lookup$generalised_abbreviations <- lapply(AB_lookup$abbreviations, generalise_antibiotic_name)
+  AB_lookup$generalised_loinc <- lapply(AB_lookup$loinc, generalise_antibiotic_name)
+  AB_lookup$generalised_all <- unname(lapply(as.list(as.data.frame(t(AB_lookup[, 
+                                                                               c("ab", "atc", "cid", "name",
+                                                                                 colnames(AB_lookup)[colnames(AB_lookup) %like% "generalised"]),
+                                                                               drop = FALSE]),
+                                                                   stringsAsFactors = FALSE)),
+                                             function(x) {
+                                               x <- generalise_antibiotic_name(unname(unlist(x)))
+                                               x[x != ""]
+                                             }))
+  AB_lookup
+}
+
+create_MO_lookup <- function() {
+  MO_lookup <- AMR::microorganisms
+  
+  MO_lookup$kingdom_index <- NA_real_
+  MO_lookup[which(MO_lookup$kingdom == "Bacteria" | MO_lookup$mo == "UNKNOWN"), "kingdom_index"] <- 1
+  MO_lookup[which(MO_lookup$kingdom == "Fungi"), "kingdom_index"] <- 2
+  MO_lookup[which(MO_lookup$kingdom == "Protozoa"), "kingdom_index"] <- 3
+  MO_lookup[which(MO_lookup$kingdom == "Archaea"), "kingdom_index"] <- 4
+  # all the rest
+  MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5
+  
+  # use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
+  MO_lookup$fullname_lower <- tolower(trimws(paste(MO_lookup$genus, 
+                                                   MO_lookup$species,
+                                                   MO_lookup$subspecies)))
+  ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname, perl = TRUE)
+  MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname"])
+  MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
+  
+  # add a column with only "e coli" like combinations
+  MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower, perl = TRUE)
+  
+  # so arrange data on prevalence first, then kingdom, then full name
+  MO_lookup[order(MO_lookup$prevalence, MO_lookup$kingdom_index, MO_lookup$fullname_lower), ]
+}
+
+create_MO.old_lookup <- function() {
+  MO.old_lookup <- AMR::microorganisms.old
+  MO.old_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", tolower(trimws(MO.old_lookup$fullname))))
+  
+  # add a column with only "e coli"-like combinations
+  MO.old_lookup$g_species <- trimws(gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO.old_lookup$fullname_lower))
+  
+  # so arrange data on prevalence first, then full name
+  MO.old_lookup[order(MO.old_lookup$prevalence, MO.old_lookup$fullname_lower), ]
+}
+
+create_intr_resistance <- function() {
+  # for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
+  paste(AMR::microorganisms[match(AMR::intrinsic_resistant$microorganism, AMR::microorganisms$fullname), "mo", drop = TRUE],
+        AMR::antibiotics[match(AMR::intrinsic_resistant$antibiotic, AMR::antibiotics$name), "ab", drop = TRUE])
 }

README.md

@@ -23,7 +23,13 @@ This is the development source of the `AMR` package for R. Not a developer? Then
 ### How to get this package
 Please see [our website](https://msberends.github.io/AMR/#get-this-package).
 
-Bottom line: `install.packages("AMR", repos = "https://msberends.r-universe.dev")`
+You can install or update the `AMR` package from CRAN using:
+
+```r
+install.packages("AMR")
+```
+
+It will be downloaded and installed automatically. For RStudio, click on the menu *Tools* > *Install Packages...* and then type in "AMR" and press <kbd>Install</kbd>.
 
 ### Copyright
 

cran-comments.md

@@ -1,3 +1 @@
-* This package has been archived on 22 May 2021 because of errors in the dplyr package, causing the skimr package to fail: <https://github.com/tidyverse/dplyr/issues/5881>. This AMR package contains a fix around this error. Perhaps an idea for future development of CRAN to send an automated email to a maintainer with a warning that a package will be archived in due time?
-
-* This package continuously has a tarball size of over 7 MB and an installation size of over 5 MB, which will return a NOTE on R CMD CHECK. This has been the case in the last releases as well. The package size is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package. This was written and explained in a manuscript that was accepted for publication in the Journal of Statistical Software earlier this year. We will add the paper as a vignette after publication in a next version. All data sets were compressed using `compression = "xz"` to make them as small as possible.
+* This package now has a data folder size of ~2.8 MB (this was ~5.6 MB), which will return a NOTE on R CMD CHECK. This package size is needed to provide users reference data for the complete taxonomy of microorganisms - one of the most important features of this package, following 15 previous releases of this package. All data sets were compressed using `compression = "xz"` to make them as small as possible.

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")
 
 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

@@ -31,8 +31,46 @@ devtools::load_all(quiet = TRUE)
 
 old_globalenv <- ls(envir = globalenv())
 
-# Helper functions --------------------------------------------------------
+# Save internal data to R/sysdata.rda -------------------------------------
 
+# See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
+EUCAST_RULES_DF <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
+                                       skip = 10,
+                                       sep = "\t",
+                                       stringsAsFactors = FALSE,
+                                       header = TRUE,
+                                       strip.white = TRUE,
+                                       na = c(NA, "", NULL)) %>% 
+  # take the order of the reference.rule_group column in the original data file
+  mutate(reference.rule_group = factor(reference.rule_group,
+                                       levels = unique(reference.rule_group),
+                                       ordered = TRUE),
+         sorting_rule = ifelse(grepl("^Table", reference.rule, ignore.case = TRUE), 1, 2)) %>% 
+  arrange(reference.rule_group,
+          reference.version,
+          sorting_rule,
+          reference.rule) %>% 
+  mutate(reference.rule_group = as.character(reference.rule_group)) %>% 
+  select(-sorting_rule)
+
+# Translations
+TRANSLATIONS <- utils::read.delim(file = "data-raw/translations.tsv",
+                                       sep = "\t",
+                                       stringsAsFactors = FALSE,
+                                       header = TRUE,
+                                       blank.lines.skip = TRUE,
+                                       fill = TRUE,
+                                       strip.white = TRUE,
+                                       encoding = "UTF-8",
+                                       fileEncoding = "UTF-8",
+                                       na.strings = c(NA, "", NULL),
+                                       allowEscapes = TRUE, # else "\\1" will be imported as "\\\\1"
+                                       quote = "")
+
+# for checking input in `language` argument in e.g. mo_*() and ab_*() functions
+LANGUAGES_SUPPORTED <- sort(c("en", colnames(TRANSLATIONS)[nchar(colnames(TRANSLATIONS)) == 2]))
+
+# vectors of CoNS and CoPS, improves speed in as.mo()
 create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
   # Determination of which staphylococcal species are CoNS/CoPS according to:
   # - Becker et al. 2014, PMID 25278577
@@ -70,124 +108,9 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
              "mo", drop = TRUE]
   }
 }
-
-create_AB_lookup <- function() {
-  AB_lookup <- AMR::antibiotics
-  AB_lookup$generalised_name <- generalise_antibiotic_name(AB_lookup$name)
-  AB_lookup$generalised_synonyms <- lapply(AB_lookup$synonyms, generalise_antibiotic_name)
-  AB_lookup$generalised_abbreviations <- lapply(AB_lookup$abbreviations, generalise_antibiotic_name)
-  AB_lookup$generalised_loinc <- lapply(AB_lookup$loinc, generalise_antibiotic_name)
-  AB_lookup$generalised_all <- unname(lapply(as.list(as.data.frame(t(AB_lookup[, 
-                                                                               c("ab", "atc", "cid", "name",
-                                                                                 colnames(AB_lookup)[colnames(AB_lookup) %like% "generalised"]),
-                                                                               drop = FALSE]),
-                                                                   stringsAsFactors = FALSE)),
-                                             function(x) {
-                                               x <- generalise_antibiotic_name(unname(unlist(x)))
-                                               x[x != ""]
-                                             }))
-  AB_lookup
-}
-
-create_MO_lookup <- function() {
-  MO_lookup <- AMR::microorganisms
-  
-  MO_lookup$kingdom_index <- NA_real_
-  MO_lookup[which(MO_lookup$kingdom == "Bacteria" | MO_lookup$mo == "UNKNOWN"), "kingdom_index"] <- 1
-  MO_lookup[which(MO_lookup$kingdom == "Fungi"), "kingdom_index"] <- 2
-  MO_lookup[which(MO_lookup$kingdom == "Protozoa"), "kingdom_index"] <- 3
-  MO_lookup[which(MO_lookup$kingdom == "Archaea"), "kingdom_index"] <- 4
-  # all the rest
-  MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5
-  
-  # use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
-  MO_lookup$fullname_lower <- tolower(trimws(paste(MO_lookup$genus, 
-                                                   MO_lookup$species,
-                                                   MO_lookup$subspecies)))
-  ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname)
-  MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname"])
-  MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
-  
-  # add a column with only "e coli" like combinations
-  MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower, perl = TRUE)
-  
-  # so arrange data on prevalence first, then kingdom, then full name
-  MO_lookup[order(MO_lookup$prevalence, MO_lookup$kingdom_index, MO_lookup$fullname_lower), ]
-}
-
-create_MO.old_lookup <- function() {
-  MO.old_lookup <- AMR::microorganisms.old
-  MO.old_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", tolower(trimws(MO.old_lookup$fullname))))
-  
-  # add a column with only "e coli"-like combinations
-  MO.old_lookup$g_species <- trimws(gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO.old_lookup$fullname_lower))
-  
-  # so arrange data on prevalence first, then full name
-  MO.old_lookup[order(MO.old_lookup$prevalence, MO.old_lookup$fullname_lower), ]
-}
-
-create_intr_resistance <- function() {
-  # for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
-  paste(AMR::microorganisms[match(AMR::intrinsic_resistant$microorganism, AMR::microorganisms$fullname), "mo", drop = TRUE],
-        AMR::antibiotics[match(AMR::intrinsic_resistant$antibiotic, AMR::antibiotics$name), "ab", drop = TRUE])
-}
-
-
-
-# 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",
-                                       skip = 10,
-                                       sep = "\t",
-                                       stringsAsFactors = FALSE,
-                                       header = TRUE,
-                                       strip.white = TRUE,
-                                       na = c(NA, "", NULL)) %>% 
-  # take the order of the reference.rule_group column in the original data file
-  mutate(reference.rule_group = factor(reference.rule_group,
-                                       levels = unique(reference.rule_group),
-                                       ordered = TRUE),
-         sorting_rule = ifelse(grepl("^Table", reference.rule, ignore.case = TRUE), 1, 2)) %>% 
-  arrange(reference.rule_group,
-          reference.version,
-          sorting_rule,
-          reference.rule) %>% 
-  mutate(reference.rule_group = as.character(reference.rule_group)) %>% 
-  select(-sorting_rule)
-
-# Translations
-translations_file <- utils::read.delim(file = "data-raw/translations.tsv",
-                                       sep = "\t",
-                                       stringsAsFactors = FALSE,
-                                       header = TRUE,
-                                       blank.lines.skip = TRUE,
-                                       fill = TRUE,
-                                       strip.white = TRUE,
-                                       encoding = "UTF-8",
-                                       fileEncoding = "UTF-8",
-                                       na.strings = c(NA, "", NULL),
-                                       allowEscapes = TRUE, # else "\\1" will be imported as "\\\\1"
-                                       quote = "")
-
-# Old microorganism codes
-microorganisms.translation <- readRDS("data-raw/microorganisms.translation.rds")
-
-# for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
-INTRINSIC_R <- create_intr_resistance()
-
-# 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]))
-
-# vectors of CoNS and CoPS, improves speed in as.mo()
 MO_CONS <- create_species_cons_cops("CoNS")
 MO_COPS <- create_species_cons_cops("CoPS")
 
-# reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed
-AB_lookup <- create_AB_lookup()
-MO_lookup <- create_MO_lookup()
-MO.old_lookup <- create_MO.old_lookup()
-
 # antibiotic groups
 # (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv)
 globalenv_before_ab <- c(ls(envir = globalenv()), "globalenv_before_ab")
@@ -198,18 +121,21 @@ 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)
@@ -218,16 +144,11 @@ 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,
-                  microorganisms.translation,
-                  INTRINSIC_R,
+usethis::use_data(EUCAST_RULES_DF, 
+                  TRANSLATIONS,
                   LANGUAGES_SUPPORTED,
                   MO_CONS,
                   MO_COPS,
-                  AB_lookup,
-                  MO_lookup,
-                  MO.old_lookup,
                   AMINOGLYCOSIDES,
                   AMINOPENICILLINS,
                   CARBAPENEMS,
@@ -235,6 +156,8 @@ usethis::use_data(eucast_rules_file,
                   CEPHALOSPORINS_1ST,
                   CEPHALOSPORINS_2ND,
                   CEPHALOSPORINS_3RD,
+                  CEPHALOSPORINS_4TH,
+                  CEPHALOSPORINS_5TH,
                   CEPHALOSPORINS_EXCEPT_CAZ,
                   FLUOROQUINOLONES,
                   LIPOGLYCOPEPTIDES,
@@ -245,6 +168,7 @@ 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/reproduction_of_microorganisms.R

@@ -872,12 +872,12 @@ View(old_new)
 # set new MO codes as names to existing data sets
 rsi_translation$mo <- mo_name(rsi_translation$mo, language = NULL)
 microorganisms.codes$mo <- mo_name(microorganisms.codes$mo, language = NULL)
-microorganisms.translation <- AMR:::microorganisms.translation %>%
-  bind_rows(tibble(mo_old = AMR:::microorganisms.translation$mo_new, mo_new = mo_old)) %>%
-  filter(!mo_old %in% MOs$mo) %>% 
-  mutate(mo_new = mo_name(mo_new, language = NULL)) %>% 
-  bind_rows(old_new %>% select(mo_old, mo_new)) %>% 
-  distinct(mo_old, .keep_all = TRUE)
+# microorganisms.translation <- AMR:::microorganisms.translation %>%
+#   bind_rows(tibble(mo_old = AMR:::microorganisms.translation$mo_new, mo_new = mo_old)) %>%
+#   filter(!mo_old %in% MOs$mo) %>% 
+#   mutate(mo_new = mo_name(mo_new, language = NULL)) %>% 
+#   bind_rows(old_new %>% select(mo_old, mo_new)) %>% 
+#   distinct(mo_old, .keep_all = TRUE)
 
 # arrange the data sets to save
 MOs <- MOs %>% arrange(fullname)
@@ -911,23 +911,23 @@ devtools::load_all(".")
 rsi_translation$mo <- as.mo(rsi_translation$mo)
 microorganisms.codes$mo <- as.mo(microorganisms.codes$mo)
 class(microorganisms.codes$mo) <- c("mo", "character")
-microorganisms.translation <- microorganisms.translation %>%
-  # (to do: add last package version to column pkg_version)
-  left_join(microorganisms.old[, c("fullname", "fullname_new")], # microorganisms.old is now new and loaded
-            by = c("mo_new" = "fullname")) %>%
-  mutate(name = ifelse(!is.na(fullname_new), fullname_new, mo_new)) %>% 
-  left_join(microorganisms[, c("fullname", "mo")],               # as is microorganisms
-            by = c("name" = "fullname")) %>% 
-  select(mo_old, mo_new = mo) %>% 
-  filter(!is.na(mo_old), !is.na(mo_new))
-class(microorganisms.translation$mo_old) <- "character" # no class <mo> since those aren't valid MO codes
-class(microorganisms.translation$mo_new) <- c("mo", "character")
+# microorganisms.translation <- microorganisms.translation %>%
+#   # (to do: add last package version to column pkg_version)
+#   left_join(microorganisms.old[, c("fullname", "fullname_new")], # microorganisms.old is now new and loaded
+#             by = c("mo_new" = "fullname")) %>%
+#   mutate(name = ifelse(!is.na(fullname_new), fullname_new, mo_new)) %>% 
+#   left_join(microorganisms[, c("fullname", "mo")],               # as is microorganisms
+#             by = c("name" = "fullname")) %>% 
+#   select(mo_old, mo_new = mo) %>% 
+#   filter(!is.na(mo_old), !is.na(mo_new))
+# class(microorganisms.translation$mo_old) <- "character" # no class <mo> since those aren't valid MO codes
+# class(microorganisms.translation$mo_new) <- c("mo", "character")
 # save those to the package
 usethis::use_data(rsi_translation, overwrite = TRUE, version = 2)
 usethis::use_data(microorganisms.codes, overwrite = TRUE, version = 2)
-saveRDS(microorganisms.translation, file = "data-raw/microorganisms.translation.rds", version = 2)
+# saveRDS(microorganisms.translation, file = "data-raw/microorganisms.translation.rds", version = 2)
 # to save microorganisms.translation internally to the package
-source("data-raw/_internals.R")
+# source("data-raw/_internals.R")
 
 # load new data sets again
 devtools::load_all(".")
@@ -935,7 +935,7 @@ devtools::load_all(".")
 # and check: these codes should not be missing (will otherwise throw a unit test error):
 AMR::microorganisms.codes %>% filter(!mo %in% MOs$mo)
 AMR::rsi_translation %>% filter(!mo %in% MOs$mo)
-AMR:::microorganisms.translation %>% filter(!mo_new %in% MOs$mo)
+# AMR:::microorganisms.translation %>% filter(!mo_new %in% MOs$mo)
 
 # update the example_isolates data set
 example_isolates$mo <- as.mo(example_isolates$mo)

data-raw/reproduction_of_microorganisms_update.R

@@ -380,37 +380,37 @@ MOs.old <- microorganisms.old %>%
 # Keep old codes for translation ------------------------------------------
 
 # add removed microbial IDs to the internal translation table so old package versions keep working
-MOs.translation <- microorganisms %>% 
-  filter(!mo %in% MOs$mo) %>%
-  select(mo, fullname) %>%
-  left_join(new_synonyms) %>% 
-  left_join(MOs %>% transmute(fullname_new = fullname, mo2 = as.character(mo))) %>% 
-  select(mo_old = mo, mo_new = mo2) %>% 
-  distinct()
-MOs.translation <- AMR:::microorganisms.translation %>% 
-  left_join(MOs.translation %>% select(mo_new_update = mo_new, mo_new = mo_old)) %>% 
-  mutate(mo_new = as.character(ifelse(!is.na(mo_new_update), mo_new_update, mo_new))) %>% 
-  select(-mo_new_update) %>% 
-  bind_rows(
-    # old IDs used in microorganisms.codes must put in here as well
-    microorganisms.codes %>%
-      filter(!mo %in% MOs$mo) %>%
-      transmute(mo_old = mo, fullname = mo_name(mo)) %>%
-      left_join(MOs.old %>%
-                  select(fullname, fullname_new)) %>%
-      left_join(MOs %>%
-                  select(mo_new = mo, fullname_new = fullname)) %>%
-      transmute(mo_old = as.character(mo_old), mo_new)) %>% 
-  arrange(mo_old) %>% 
-  filter(mo_old != mo_new,
-         !mo_old %in% MOs$mo) %>%
-  left_join(., ., 
-            by = c("mo_new" = "mo_old"), 
-            suffix = c("", ".2")) %>%
-  mutate(mo_new = ifelse(!is.na(mo_new.2), mo_new.2, mo_new)) %>% 
-  distinct(mo_old, mo_new) %>% 
-  # clean up
-  df_remove_nonASCII()
+# MOs.translation <- microorganisms %>% 
+#   filter(!mo %in% MOs$mo) %>%
+#   select(mo, fullname) %>%
+#   left_join(new_synonyms) %>% 
+#   left_join(MOs %>% transmute(fullname_new = fullname, mo2 = as.character(mo))) %>% 
+#   select(mo_old = mo, mo_new = mo2) %>% 
+#   distinct()
+# MOs.translation <- AMR:::microorganisms.translation %>% 
+#   left_join(MOs.translation %>% select(mo_new_update = mo_new, mo_new = mo_old)) %>% 
+#   mutate(mo_new = as.character(ifelse(!is.na(mo_new_update), mo_new_update, mo_new))) %>% 
+#   select(-mo_new_update) %>% 
+#   bind_rows(
+#     # old IDs used in microorganisms.codes must put in here as well
+#     microorganisms.codes %>%
+#       filter(!mo %in% MOs$mo) %>%
+#       transmute(mo_old = mo, fullname = mo_name(mo)) %>%
+#       left_join(MOs.old %>%
+#                   select(fullname, fullname_new)) %>%
+#       left_join(MOs %>%
+#                   select(mo_new = mo, fullname_new = fullname)) %>%
+#       transmute(mo_old = as.character(mo_old), mo_new)) %>% 
+#   arrange(mo_old) %>% 
+#   filter(mo_old != mo_new,
+#          !mo_old %in% MOs$mo) %>%
+#   left_join(., ., 
+#             by = c("mo_new" = "mo_old"), 
+#             suffix = c("", ".2")) %>%
+#   mutate(mo_new = ifelse(!is.na(mo_new.2), mo_new.2, mo_new)) %>% 
+#   distinct(mo_old, mo_new) %>% 
+#   # clean up
+#   df_remove_nonASCII()
 
 message("microorganisms new:     ", sum(!MOs$fullname %in% c(microorganisms$fullname, MOs.old$fullname)))
 message("microorganisms renamed: ", sum(!MOs.old$fullname %in% microorganisms.old$fullname))
@@ -424,12 +424,12 @@ class(MOs.translation$mo_new) <- c("mo", "character")
 
 microorganisms <- MOs
 microorganisms.old <- MOs.old
-microorganisms.translation <- MOs.translation
+# microorganisms.translation <- MOs.translation
 
 # on the server, do:
 usethis::use_data(microorganisms, overwrite = TRUE, version = 2, compress = "xz")
 usethis::use_data(microorganisms.old, overwrite = TRUE, version = 2)
-saveRDS(microorganisms.translation, file = "data-raw/microorganisms.translation.rds", version = 2)
+# saveRDS(microorganisms.translation, file = "data-raw/microorganisms.translation.rds", version = 2)
 rm(microorganisms)
 rm(microorganisms.old)
 rm(microorganisms.translation)

data-raw/reproduction_of_rsi_translation.R

@@ -2,10 +2,9 @@ library(dplyr)
 library(readr)
 library(tidyr)
 
-# Installed WHONET 2019 software on Windows (http://www.whonet.org/software.html),
-#    opened C:\WHONET\Codes\WHONETCodes.mdb in MS Access
-#    and exported table 'DRGLST1' to MS Excel
-DRGLST1 <- readxl::read_excel("data-raw/DRGLST1.xlsx", na = c("", "NA", "-"))
+# Installed WHONET software on Windows (http://www.whonet.org/software.html),
+#    imported C:\WHONET\Codes\DRGLST1.txt
+DRGLST1 <- readr::read_tsv("data-raw/DRGLST1.txt", na = c("", "NA", "-"))
 rsi_trans <- DRGLST1 %>%
   # only keep CLSI and EUCAST guidelines:
   filter(GUIDELINES %like% "^(CLSI|EUCST)")
@@ -13,6 +12,9 @@ if (any(is.na(rsi_trans$BREAKPOINT_TYPE)) | !"Human" %in% rsi_trans$BREAKPOINT_T
   stop("Check column BREAKPOINT_TYPE - something is WRONG!")
 }
 rsi_trans <- rsi_trans %>% 
+  ##### If looking for adding a specific guideline, do it here!
+  # filter(GUIDELINES == "CLSI20") %>% 
+  #####
   filter(BREAKPOINT_TYPE == "Human") %>% 
   mutate(DISK_S = ifelse(as.double(DISK_S) > 50, 50, DISK_S),
          MIC_R = ifelse(as.double(MIC_R) %in% c(1025, 129, 513), as.double(MIC_R) - 1, MIC_R)) %>%
@@ -50,7 +52,7 @@ rsi_trans <- bind_rows(tbl_mic, tbl_disk) %>%
   select(-ends_with("_mic"), -ends_with("_disk"))
 
 # add extra CLSI general guidelines
-clsi_general <- read_tsv("data-raw/DRGLST.txt") %>%
+clsi_general <- readr::read_tsv("data-raw/DRGLST.txt") %>%
   filter(CLSI == "X") %>%
   select(WHON5_CODE, 
          disk_dose = POTENCY, 
@@ -76,13 +78,13 @@ clsi_general <- read_tsv("data-raw/DRGLST.txt") %>%
 
 
 # add new EUCAST with read_EUCAST.R
-# 2020-04-14 did that now for 2019 and 2020
 
+# 2020-04-14 did that now for 2019 and 2020
 rsi_trans <- rsi_trans %>%
   filter(guideline != "EUCAST 2019") %>% 
   bind_rows(new_EUCAST) %>% 
   bind_rows(clsi_general) %>% 
-  mutate(uti = site %like% "(UTI|urinary)") %>% 
+  mutate(uti = site %like% "(UTI|urinary|urine)") %>% 
   as.data.frame(stringsAsFactors = FALSE) %>%
   # force classes again
   mutate(mo = as.mo(mo),

data-raw/rsi.md5

@@ -1 +1 @@
-aa80f169fc2cba97f5eedc1d24ca8c03
+1a7fe52f8185c9bb2c470712863d1887

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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9008</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9008</span>
       </span>
     </div>
 

docs/articles/AMR.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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
       </span>
     </div>
 
@@ -193,7 +193,7 @@
       <h1 data-toc-skip>How to conduct AMR data analysis</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">26 May 2021</h4>
+            <h4 class="date">03 June 2021</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd"><code>vignettes/AMR.Rmd</code></a></small>
       <div class="hidden name"><code>AMR.Rmd</code></div>
@@ -202,7 +202,7 @@
 
     
     
-<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 26 May 2021.</p>
+<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 03 June 2021.</p>
 <div id="introduction" class="section level1">
 <h1 class="hasAnchor">
 <a href="#introduction" class="anchor"></a>Introduction</h1>
@@ -233,21 +233,21 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2021-05-26</td>
+<td align="center">2021-06-03</td>
 <td align="center">abcd</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">S</td>
 </tr>
 <tr class="even">
-<td align="center">2021-05-26</td>
+<td align="center">2021-06-03</td>
 <td align="center">abcd</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">R</td>
 </tr>
 <tr class="odd">
-<td align="center">2021-05-26</td>
+<td align="center">2021-06-03</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@@ -344,52 +344,52 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2013-04-02</td>
-<td align="center">X1</td>
-<td align="center">Hospital D</td>
+<td align="center">2014-11-23</td>
+<td align="center">A2</td>
+<td align="center">Hospital B</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
-<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">F</td>
+<td align="center">S</td>
+<td align="center">M</td>
 </tr>
 <tr class="even">
-<td align="center">2015-07-17</td>
-<td align="center">X6</td>
-<td align="center">Hospital A</td>
+<td align="center">2013-08-17</td>
+<td align="center">V3</td>
+<td align="center">Hospital D</td>
 <td align="center">Staphylococcus aureus</td>
 <td align="center">R</td>
-<td align="center">R</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
 <tr class="odd">
-<td align="center">2012-09-03</td>
-<td align="center">C4</td>
+<td align="center">2011-02-20</td>
+<td align="center">B1</td>
 <td align="center">Hospital C</td>
-<td align="center">Staphylococcus aureus</td>
-<td align="center">I</td>
-<td align="center">I</td>
+<td align="center">Streptococcus pneumoniae</td>
+<td align="center">S</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
 <tr class="even">
-<td align="center">2010-02-11</td>
-<td align="center">D2</td>
-<td align="center">Hospital B</td>
+<td align="center">2016-10-04</td>
+<td align="center">U3</td>
+<td align="center">Hospital A</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">M</td>
+<td align="center">F</td>
 </tr>
 <tr class="odd">
-<td align="center">2012-12-14</td>
-<td align="center">L5</td>
+<td align="center">2010-04-22</td>
+<td align="center">F1</td>
 <td align="center">Hospital B</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
@@ -399,12 +399,12 @@
 <td align="center">M</td>
 </tr>
 <tr class="even">
-<td align="center">2016-01-30</td>
-<td align="center">S3</td>
-<td align="center">Hospital D</td>
-<td align="center">Klebsiella pneumoniae</td>
+<td align="center">2013-01-15</td>
+<td align="center">W4</td>
+<td align="center">Hospital B</td>
+<td align="center">Escherichia coli</td>
+<td align="center">S</td>
 <td align="center">S</td>
-<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
@@ -441,16 +441,16 @@ Longest: 1</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">M</td>
-<td align="right">10,375</td>
-<td align="right">51.88%</td>
-<td align="right">10,375</td>
-<td align="right">51.88%</td>
+<td align="right">10,416</td>
+<td align="right">52.08%</td>
+<td align="right">10,416</td>
+<td align="right">52.08%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">F</td>
-<td align="right">9,625</td>
-<td align="right">48.13%</td>
+<td align="right">9,584</td>
+<td align="right">47.92%</td>
 <td align="right">20,000</td>
 <td align="right">100.00%</td>
 </tr>
@@ -505,9 +505,9 @@ Longest: 1</p>
 <span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span>
 <span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span>
 <span class="co"># 2</span>
-<span class="co"># =&gt; Found 10,550 first weighted isolates (phenotype-based, 52.8% of total</span>
+<span class="co"># =&gt; Found 10,645 first weighted isolates (phenotype-based, 53.2% of total</span>
 <span class="co">#    where a microbial ID was available)</span></code></pre></div>
-<p>So only 52.8% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
+<p>So only 53.2% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</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">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
@@ -515,7 +515,7 @@ Longest: 1</p>
 <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span> 
   <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
-<p>So we end up with 10,550 isolates for analysis. Now our data looks like:</p>
+<p>So we end up with 10,645 isolates for analysis. Now our data looks like:</p>
 <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></code></pre></div>
 <table class="table">
@@ -553,89 +553,25 @@ Longest: 1</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="left">1</td>
-<td align="center">2013-04-02</td>
-<td align="center">X1</td>
-<td align="center">Hospital D</td>
-<td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
-<td align="center">R</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">F</td>
-<td align="center">Gram-negative</td>
-<td align="center">Escherichia</td>
-<td align="center">coli</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="even">
 <td align="left">2</td>
-<td align="center">2015-07-17</td>
-<td align="center">X6</td>
-<td align="center">Hospital A</td>
-<td align="center">B_STPHY_AURS</td>
-<td align="center">R</td>
-<td align="center">R</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">F</td>
-<td align="center">Gram-positive</td>
-<td align="center">Staphylococcus</td>
-<td align="center">aureus</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="odd">
-<td align="left">4</td>
-<td align="center">2010-02-11</td>
-<td align="center">D2</td>
-<td align="center">Hospital B</td>
-<td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">M</td>
-<td align="center">Gram-negative</td>
-<td align="center">Escherichia</td>
-<td align="center">coli</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="even">
-<td align="left">6</td>
-<td align="center">2016-01-30</td>
-<td align="center">S3</td>
+<td align="center">2013-08-17</td>
+<td align="center">V3</td>
 <td align="center">Hospital D</td>
-<td align="center">B_KLBSL_PNMN</td>
-<td align="center">R</td>
+<td align="center">B_STPHY_AURS</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
+<td align="center">S</td>
 <td align="center">F</td>
-<td align="center">Gram-negative</td>
-<td align="center">Klebsiella</td>
-<td align="center">pneumoniae</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="odd">
-<td align="left">7</td>
-<td align="center">2012-10-20</td>
-<td align="center">D10</td>
-<td align="center">Hospital B</td>
-<td align="center">B_STPHY_AURS</td>
-<td align="center">R</td>
-<td align="center">R</td>
-<td align="center">R</td>
-<td align="center">S</td>
-<td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Staphylococcus</td>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="left">8</td>
-<td align="center">2016-03-28</td>
-<td align="center">K7</td>
+<td align="left">3</td>
+<td align="center">2011-02-20</td>
+<td align="center">B1</td>
 <td align="center">Hospital C</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">S</td>
@@ -648,6 +584,70 @@ Longest: 1</p>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
+<tr class="odd">
+<td align="left">5</td>
+<td align="center">2010-04-22</td>
+<td align="center">F1</td>
+<td align="center">Hospital B</td>
+<td align="center">B_ESCHR_COLI</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">M</td>
+<td align="center">Gram-negative</td>
+<td align="center">Escherichia</td>
+<td align="center">coli</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="even">
+<td align="left">7</td>
+<td align="center">2014-07-28</td>
+<td align="center">W5</td>
+<td align="center">Hospital B</td>
+<td align="center">B_STPHY_AURS</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">F</td>
+<td align="center">Gram-positive</td>
+<td align="center">Staphylococcus</td>
+<td align="center">aureus</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="odd">
+<td align="left">8</td>
+<td align="center">2015-01-06</td>
+<td align="center">V3</td>
+<td align="center">Hospital A</td>
+<td align="center">B_ESCHR_COLI</td>
+<td align="center">R</td>
+<td align="center">I</td>
+<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">F</td>
+<td align="center">Gram-negative</td>
+<td align="center">Escherichia</td>
+<td align="center">coli</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="even">
+<td align="left">9</td>
+<td align="center">2014-03-16</td>
+<td align="center">H4</td>
+<td align="center">Hospital A</td>
+<td align="center">B_STPHY_AURS</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">M</td>
+<td align="center">Gram-positive</td>
+<td align="center">Staphylococcus</td>
+<td align="center">aureus</td>
+<td align="center">TRUE</td>
+</tr>
 </tbody>
 </table>
 <p>Time for the analysis!</p>
@@ -669,8 +669,8 @@ Longest: 1</p>
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></code></pre></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: character<br>
-Length: 10,550<br>
-Available: 10,550 (100.0%, NA: 0 = 0.0%)<br>
+Length: 10,645<br>
+Available: 10,645 (100.0%, NA: 0 = 0.0%)<br>
 Unique: 4</p>
 <p>Shortest: 16<br>
 Longest: 24</p>
@@ -687,33 +687,33 @@ Longest: 24</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Escherichia coli</td>
-<td align="right">4,566</td>
-<td align="right">43.28%</td>
-<td align="right">4,566</td>
-<td align="right">43.28%</td>
+<td align="right">4,652</td>
+<td align="right">43.70%</td>
+<td align="right">4,652</td>
+<td align="right">43.70%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Staphylococcus aureus</td>
-<td align="right">2,786</td>
-<td align="right">26.41%</td>
-<td align="right">7,352</td>
-<td align="right">69.69%</td>
+<td align="right">2,744</td>
+<td align="right">25.78%</td>
+<td align="right">7,396</td>
+<td align="right">69.48%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Streptococcus pneumoniae</td>
-<td align="right">2,025</td>
-<td align="right">19.19%</td>
-<td align="right">9,377</td>
-<td align="right">88.88%</td>
+<td align="right">2,052</td>
+<td align="right">19.28%</td>
+<td align="right">9,448</td>
+<td align="right">88.76%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Klebsiella pneumoniae</td>
-<td align="right">1,173</td>
-<td align="right">11.12%</td>
-<td align="right">10,550</td>
+<td align="right">1,197</td>
+<td align="right">11.24%</td>
+<td align="right">10,645</td>
 <td align="right">100.00%</td>
 </tr>
 </tbody>
@@ -760,8 +760,8 @@ Longest: 24</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2016-03-28</td>
-<td align="center">K7</td>
+<td align="center">2011-02-20</td>
+<td align="center">B1</td>
 <td align="center">Hospital C</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">S</td>
@@ -775,44 +775,14 @@ Longest: 24</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="center">2010-01-30</td>
-<td align="center">A1</td>
-<td align="center">Hospital A</td>
-<td align="center">B_STRPT_PNMN</td>
-<td align="center">R</td>
-<td align="center">R</td>
-<td align="center">S</td>
-<td align="center">R</td>
-<td align="center">M</td>
-<td align="center">Gram-positive</td>
-<td align="center">Streptococcus</td>
-<td align="center">pneumoniae</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="odd">
-<td align="center">2012-12-10</td>
-<td align="center">M7</td>
+<td align="center">2015-01-06</td>
+<td align="center">V3</td>
 <td align="center">Hospital A</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
 <td align="center">I</td>
 <td align="center">S</td>
 <td align="center">R</td>
-<td align="center">M</td>
-<td align="center">Gram-negative</td>
-<td align="center">Escherichia</td>
-<td align="center">coli</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="even">
-<td align="center">2012-08-04</td>
-<td align="center">Y7</td>
-<td align="center">Hospital B</td>
-<td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">R</td>
 <td align="center">F</td>
 <td align="center">Gram-negative</td>
 <td align="center">Escherichia</td>
@@ -820,13 +790,28 @@ Longest: 24</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
-<td align="center">2016-08-05</td>
-<td align="center">I4</td>
-<td align="center">Hospital A</td>
+<td align="center">2012-05-03</td>
+<td align="center">B2</td>
+<td align="center">Hospital B</td>
+<td align="center">B_STRPT_PNMN</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">M</td>
+<td align="center">Gram-positive</td>
+<td align="center">Streptococcus</td>
+<td align="center">pneumoniae</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="even">
+<td align="center">2017-03-18</td>
+<td align="center">K10</td>
+<td align="center">Hospital D</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
-<td align="center">R</td>
-<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-negative</td>
@@ -834,14 +819,14 @@ Longest: 24</p>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="even">
-<td align="center">2011-05-15</td>
-<td align="center">H2</td>
-<td align="center">Hospital A</td>
+<tr class="odd">
+<td align="center">2010-12-15</td>
+<td align="center">H3</td>
+<td align="center">Hospital B</td>
 <td align="center">B_STRPT_PNMN</td>
-<td align="center">R</td>
-<td align="center">R</td>
-<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-positive</td>
@@ -849,6 +834,21 @@ Longest: 24</p>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
+<tr class="even">
+<td align="center">2017-08-10</td>
+<td align="center">N2</td>
+<td align="center">Hospital C</td>
+<td align="center">B_ESCHR_COLI</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">M</td>
+<td align="center">Gram-negative</td>
+<td align="center">Escherichia</td>
+<td align="center">coli</td>
+<td align="center">TRUE</td>
+</tr>
 </tbody>
 </table>
 <p>If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> function:</p>
@@ -870,50 +870,50 @@ Longest: 24</p>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">AMX</td>
-<td align="center">2148</td>
-<td align="center">153</td>
-<td align="center">2265</td>
-<td align="center">4566</td>
+<td align="center">2232</td>
+<td align="center">119</td>
+<td align="center">2301</td>
+<td align="center">4652</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">AMC</td>
-<td align="center">3344</td>
-<td align="center">157</td>
-<td align="center">1065</td>
-<td align="center">4566</td>
+<td align="center">3424</td>
+<td align="center">165</td>
+<td align="center">1063</td>
+<td align="center">4652</td>
 </tr>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">CIP</td>
-<td align="center">3356</td>
+<td align="center">3386</td>
 <td align="center">0</td>
-<td align="center">1210</td>
-<td align="center">4566</td>
+<td align="center">1266</td>
+<td align="center">4652</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">3983</td>
+<td align="center">4062</td>
 <td align="center">0</td>
-<td align="center">583</td>
-<td align="center">4566</td>
+<td align="center">590</td>
+<td align="center">4652</td>
 </tr>
 <tr class="odd">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMX</td>
 <td align="center">0</td>
 <td align="center">0</td>
-<td align="center">1173</td>
-<td align="center">1173</td>
+<td align="center">1197</td>
+<td align="center">1197</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMC</td>
-<td align="center">930</td>
-<td align="center">43</td>
-<td align="center">200</td>
-<td align="center">1173</td>
+<td align="center">932</td>
+<td align="center">60</td>
+<td align="center">205</td>
+<td align="center">1197</td>
 </tr>
 </tbody>
 </table>
@@ -936,34 +936,34 @@ Longest: 24</p>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">3983</td>
+<td align="center">4062</td>
 <td align="center">0</td>
-<td align="center">583</td>
-<td align="center">4566</td>
+<td align="center">590</td>
+<td align="center">4652</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">GEN</td>
-<td align="center">1063</td>
+<td align="center">1069</td>
 <td align="center">0</td>
-<td align="center">110</td>
-<td align="center">1173</td>
+<td align="center">128</td>
+<td align="center">1197</td>
 </tr>
 <tr class="odd">
 <td align="center">S. aureus</td>
 <td align="center">GEN</td>
-<td align="center">2490</td>
+<td align="center">2444</td>
 <td align="center">0</td>
-<td align="center">296</td>
-<td align="center">2786</td>
+<td align="center">300</td>
+<td align="center">2744</td>
 </tr>
 <tr class="even">
 <td align="center">S. pneumoniae</td>
 <td align="center">GEN</td>
 <td align="center">0</td>
 <td align="center">0</td>
-<td align="center">2025</td>
-<td align="center">2025</td>
+<td align="center">2052</td>
+<td align="center">2052</td>
 </tr>
 </tbody>
 </table>
@@ -977,7 +977,7 @@ Longest: 24</p>
 <p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
 <div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>
-<span class="co"># [1] 0.5443602</span></code></pre></div>
+<span class="co"># [1] 0.5431658</span></code></pre></div>
 <p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> 
@@ -991,19 +991,19 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5542598</td>
+<td align="center">0.5461634</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5400160</td>
+<td align="center">0.5394702</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5508217</td>
+<td align="center">0.5609756</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5322972</td>
+<td align="center">0.5316215</td>
 </tr>
 </tbody>
 </table>
@@ -1022,23 +1022,23 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5542598</td>
-<td align="center">3087</td>
+<td align="center">0.5461634</td>
+<td align="center">3206</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5400160</td>
-<td align="center">3761</td>
+<td align="center">0.5394702</td>
+<td align="center">3737</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5508217</td>
-<td align="center">1643</td>
+<td align="center">0.5609756</td>
+<td align="center">1599</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5322972</td>
-<td align="center">2059</td>
+<td align="center">0.5316215</td>
+<td align="center">2103</td>
 </tr>
 </tbody>
 </table>
@@ -1059,27 +1059,27 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Escherichia</td>
-<td align="center">0.7667543</td>
-<td align="center">0.8723171</td>
-<td align="center">0.9770039</td>
+<td align="center">0.7714961</td>
+<td align="center">0.8731728</td>
+<td align="center">0.9776440</td>
 </tr>
 <tr class="even">
 <td align="center">Klebsiella</td>
-<td align="center">0.8294970</td>
-<td align="center">0.9062234</td>
-<td align="center">0.9795396</td>
+<td align="center">0.8287385</td>
+<td align="center">0.8930660</td>
+<td align="center">0.9824561</td>
 </tr>
 <tr class="odd">
 <td align="center">Staphylococcus</td>
-<td align="center">0.7910983</td>
-<td align="center">0.8937545</td>
-<td align="center">0.9852836</td>
+<td align="center">0.7882653</td>
+<td align="center">0.8906706</td>
+<td align="center">0.9839650</td>
 </tr>
 <tr class="even">
 <td align="center">Streptococcus</td>
-<td align="center">0.5387654</td>
+<td align="center">0.5414230</td>
 <td align="center">0.0000000</td>
-<td align="center">0.5387654</td>
+<td align="center">0.5414230</td>
 </tr>
 </tbody>
 </table>
@@ -1163,16 +1163,16 @@ Longest: 24</p>
 <code class="sourceCode R"><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
 <span class="va">mic_values</span>
 <span class="co"># Class &lt;mic&gt;</span>
-<span class="co">#   [1] 2      2      16     4      0.125  0.5    64     16     128    32    </span>
-<span class="co">#  [11] 4      32     1      0.125  128    2      8      64     64     2     </span>
-<span class="co">#  [21] 8      0.125  0.25   1      16     64     0.25   0.5    0.25   4     </span>
-<span class="co">#  [31] 16     32     0.25   1      0.5    8      64     2      0.25   0.0625</span>
-<span class="co">#  [41] 128    1      2      2      0.0625 0.125  64     8      8      8     </span>
-<span class="co">#  [51] 4      8      0.125  1      128    1      128    2      2      0.5   </span>
-<span class="co">#  [61] 32     64     16     32     32     16     4      1      16     2     </span>
-<span class="co">#  [71] 1      0.125  2      4      0.125  32     2      0.125  8      0.25  </span>
-<span class="co">#  [81] 0.0625 4      0.5    16     128    8      128    0.125  0.0625 1     </span>
-<span class="co">#  [91] 1      0.25   0.0625 128    128    8      0.0625 32     128    0.25</span></code></pre></div>
+<span class="co">#   [1] 4      4      0.25   &gt;=512  0.0625 2      128    2      64     1     </span>
+<span class="co">#  [11] 64     256    32     2      2      256    0.125  128    16     32    </span>
+<span class="co">#  [21] 1      2      0.0625 32     16     16     0.0625 0.125  0.0625 2     </span>
+<span class="co">#  [31] 128    8      0.0625 0.25   4      16     1      0.0625 1      16    </span>
+<span class="co">#  [41] 4      0.0625 2      4      0.0625 256    16     0.5    1      1     </span>
+<span class="co">#  [51] 16     64     &gt;=512  64     64     1      4      0.5    16     1     </span>
+<span class="co">#  [61] 16     256    8      256    256    &gt;=512  8      0.5    2      2     </span>
+<span class="co">#  [71] &gt;=512  8      64     4      8      0.25   2      4      16     0.125 </span>
+<span class="co">#  [81] 0.25   4      0.125  8      0.125  0.0625 &gt;=512  0.125  64     1     </span>
+<span class="co">#  [91] 16     2      0.5    16     0.0625 128    2      0.0625 128    2</span></code></pre></div>
 <div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="co"># base R:</span>
 <span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></code></pre></div>
@@ -1201,10 +1201,10 @@ Longest: 24</p>
 <span class="co">#   to review it.</span>
 <span class="va">disk_values</span>
 <span class="co"># Class &lt;disk&gt;</span>
-<span class="co">#   [1] 31 27 25 19 19 17 23 24 30 28 22 26 18 29 25 24 22 30 17 20 23 24 26 24 27</span>
-<span class="co">#  [26] 22 27 22 17 26 22 31 27 31 31 25 21 18 26 22 21 25 21 26 22 21 20 20 24 19</span>
-<span class="co">#  [51] 25 17 29 26 28 30 30 29 30 28 19 28 22 21 26 25 24 23 21 18 27 20 17 29 30</span>
-<span class="co">#  [76] 17 25 19 30 22 26 22 31 18 19 26 20 18 23 17 30 30 22 21 25 21 17 30 30 24</span></code></pre></div>
+<span class="co">#   [1] 27 28 23 21 23 21 28 31 26 17 23 23 24 29 20 18 27 24 26 24 27 23 30 18 26</span>
+<span class="co">#  [26] 31 19 26 21 27 29 29 19 19 31 25 23 19 26 21 21 20 23 29 22 18 27 28 21 27</span>
+<span class="co">#  [51] 21 18 19 28 26 26 29 20 31 28 30 30 21 21 25 29 28 29 30 25 27 19 23 26 24</span>
+<span class="co">#  [76] 20 21 25 19 26 22 19 30 28 27 18 19 18 25 31 20 19 29 31 31 29 22 20 17 31</span></code></pre></div>
 <div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="co"># base R:</span>
 <span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></code></pre></div>

docs/articles/EUCAST.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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
       </span>
     </div>
 

docs/articles/MDR.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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
       </span>
     </div>
 
@@ -339,19 +339,19 @@ Unique: 2</p>
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
 <span class="co">#   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
-<span class="co"># 1          I         I            I          I            S            S</span>
-<span class="co"># 2          R         I            S          I            I            I</span>
-<span class="co"># 3          S         R            R          R            R            I</span>
-<span class="co"># 4          S         R            S          S            R            S</span>
-<span class="co"># 5          R         S            I          R            S            R</span>
-<span class="co"># 6          R         R            R          R            I            I</span>
+<span class="co"># 1          S         I            R          R            R            S</span>
+<span class="co"># 2          I         R            R          R            R            R</span>
+<span class="co"># 3          S         S            S          R            I            R</span>
+<span class="co"># 4          R         I            R          R            S            S</span>
+<span class="co"># 5          I         R            S          S            R            I</span>
+<span class="co"># 6          I         S            S          R            R            R</span>
 <span class="co">#   kanamycin</span>
 <span class="co"># 1         I</span>
-<span class="co"># 2         I</span>
-<span class="co"># 3         S</span>
+<span class="co"># 2         R</span>
+<span class="co"># 3         R</span>
 <span class="co"># 4         R</span>
-<span class="co"># 5         I</span>
-<span class="co"># 6         I</span></code></pre></div>
+<span class="co"># 5         S</span>
+<span class="co"># 6         S</span></code></pre></div>
 <p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></code></pre></div>
@@ -382,40 +382,40 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistant</td>
-<td align="right">3271</td>
-<td align="right">65.42%</td>
-<td align="right">3271</td>
-<td align="right">65.42%</td>
+<td align="right">3187</td>
+<td align="right">63.74%</td>
+<td align="right">3187</td>
+<td align="right">63.74%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">949</td>
-<td align="right">18.98%</td>
-<td align="right">4220</td>
-<td align="right">84.40%</td>
+<td align="right">1027</td>
+<td align="right">20.54%</td>
+<td align="right">4214</td>
+<td align="right">84.28%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Multi-drug-resistant</td>
-<td align="right">449</td>
-<td align="right">8.98%</td>
-<td align="right">4669</td>
-<td align="right">93.38%</td>
+<td align="right">430</td>
+<td align="right">8.60%</td>
+<td align="right">4644</td>
+<td align="right">92.88%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistant</td>
-<td align="right">240</td>
-<td align="right">4.80%</td>
-<td align="right">4909</td>
-<td align="right">98.18%</td>
+<td align="right">245</td>
+<td align="right">4.90%</td>
+<td align="right">4889</td>
+<td align="right">97.78%</td>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
 <td align="left">Extensively drug-resistant</td>
-<td align="right">91</td>
-<td align="right">1.82%</td>
+<td align="right">111</td>
+<td align="right">2.22%</td>
 <td align="right">5000</td>
 <td align="right">100.00%</td>
 </tr>

docs/articles/PCA.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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
       </span>
     </div>
 

docs/articles/SPSS.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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
       </span>
     </div>
 
@@ -193,7 +193,7 @@
       <h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">26 May 2021</h4>
+            <h4 class="date">03 June 2021</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd"><code>vignettes/SPSS.Rmd</code></a></small>
       <div class="hidden name"><code>SPSS.Rmd</code></div>
@@ -228,7 +228,7 @@
 </li>
 <li>
 <p><strong>R has a huge community.</strong></p>
-<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes">403,383 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
+<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes">404,559 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
 </li>
 <li>
 <p><strong>R understands any data type, including SPSS/SAS/Stata.</strong></p>

docs/articles/WHONET.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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
       </span>
     </div>
 
@@ -221,7 +221,7 @@
 <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/cleaner">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></code></pre></div>
 <p>We will have to transform some variables to simplify and automate the analysis:</p>
 <ul>
-<li>Microorganisms should be transformed to our own microorganism IDs (called an <code>mo</code>) using <a href="https://msberends.github.io/AMR/reference/catalogue_of_life">our Catalogue of Life reference data set</a>, which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with <code><a href="../reference/as.mo.html">as.mo()</a></code>. This function also recognises almost all WHONET abbreviations of microorganisms.</li>
+<li>Microorganisms should be transformed to our own microorganism codes (called an <code>mo</code>) using <a href="https://msberends.github.io/AMR/reference/catalogue_of_life">our Catalogue of Life reference data set</a>, which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with <code><a href="../reference/as.mo.html">as.mo()</a></code>. This function also recognises almost all WHONET abbreviations of microorganisms.</li>
 <li>Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values <code>"S"</code>, <code>"I"</code> or <code>"R"</code>. That is exactly where the <code><a href="../reference/as.rsi.html">as.rsi()</a></code> function is for.</li>
 </ul>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">

docs/articles/benchmarks.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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
       </span>
     </div>
 
@@ -227,18 +227,18 @@
 <span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
 <span class="co">#                                   expr   min    lq  mean median    uq max neval</span>
-<span class="co">#                           as.mo("sau")  10.0  11.0  16.0   11.0  13.0  50    25</span>
-<span class="co">#                          as.mo("stau")  54.0  58.0  72.0   61.0  89.0  99    25</span>
-<span class="co">#                          as.mo("STAU")  53.0  55.0  67.0   56.0  91.0  95    25</span>
-<span class="co">#                        as.mo("staaur")  10.0  11.0  16.0   11.0  13.0  47    25</span>
-<span class="co">#                        as.mo("STAAUR")  10.0  11.0  17.0   12.0  13.0  58    25</span>
-<span class="co">#                     as.mo("S. aureus")  26.0  27.0  36.0   31.0  33.0  70    25</span>
-<span class="co">#                      as.mo("S aureus")  26.0  27.0  40.0   29.0  61.0  68    25</span>
-<span class="co">#         as.mo("Staphylococcus aureus")   2.6   3.2   6.5    3.5   3.8  42    25</span>
-<span class="co">#  as.mo("Staphylococcus aureus (MRSA)") 240.0 250.0 260.0  260.0 270.0 290    25</span>
-<span class="co">#       as.mo("Sthafilokkockus aaureuz") 190.0 190.0 200.0  200.0 210.0 300    25</span>
-<span class="co">#                          as.mo("MRSA")  10.0  11.0  13.0   12.0  13.0  40    25</span>
-<span class="co">#                          as.mo("VISA")  18.0  19.0  32.0   20.0  24.0 130    25</span></code></pre></div>
+<span class="co">#                           as.mo("sau")  13.0  13.0  16.0   15.0  16.0  44    25</span>
+<span class="co">#                          as.mo("stau")  55.0  58.0  75.0   62.0  94.0 110    25</span>
+<span class="co">#                          as.mo("STAU")  55.0  59.0  77.0   89.0  94.0 100    25</span>
+<span class="co">#                        as.mo("staaur")  11.0  13.0  20.0   14.0  16.0  48    25</span>
+<span class="co">#                        as.mo("STAAUR")  11.0  13.0  17.0   15.0  16.0  49    25</span>
+<span class="co">#                     as.mo("S. aureus")  26.0  30.0  41.0   32.0  60.0  68    25</span>
+<span class="co">#                      as.mo("S aureus")  27.0  29.0  44.0   32.0  58.0 160    25</span>
+<span class="co">#         as.mo("Staphylococcus aureus")   3.3   3.9   5.5    4.2   4.7  37    25</span>
+<span class="co">#  as.mo("Staphylococcus aureus (MRSA)") 250.0 260.0 280.0  280.0 290.0 320    25</span>
+<span class="co">#       as.mo("Sthafilokkockus aaureuz") 170.0 200.0 210.0  200.0 220.0 250    25</span>
+<span class="co">#                          as.mo("MRSA")  12.0  14.0  21.0   15.0  17.0  56    25</span>
+<span class="co">#                          as.mo("VISA")  20.0  23.0  33.0   25.0  51.0  59    25</span></code></pre></div>
 <p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="750"></p>
 <p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 200 times slower to determine.</p>
 <p>To improve performance, we implemented two important algorithms to save unnecessary calculations: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
@@ -260,8 +260,8 @@
 <span class="co"># what do these values look like? They are of class &lt;mo&gt;:</span>
 <span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
 <span class="co"># Class &lt;mo&gt;</span>
-<span class="co"># [1] B_STPHY_EPDR B_STRPT_GRPA B_STPHY_AURS B_BCTRD_FRGL B_STPHY_HMNS</span>
-<span class="co"># [6] B_STPHY_CONS</span>
+<span class="co"># [1] B_STPHY_CONS B_ESCHR_COLI B_STPHY_AURS B_STRPT_PYGN B_ESCHR_COLI</span>
+<span class="co"># [6] B_HMPHL_INFL</span>
   
 <span class="co"># as the example_isolates data set has 2,000 rows, we should have 2 million items</span>
 <span class="fu"><a href="https://rdrr.io/r/base/length.html">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
@@ -277,8 +277,8 @@
 <span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
 <span class="co">#        expr min  lq mean median  uq max neval</span>
-<span class="co">#  mo_name(x) 187 223  233    226 229 318    10</span></code></pre></div>
-<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.226 seconds. That is 113 nanoseconds on average. You only lose time on your unique input values.</p>
+<span class="co">#  mo_name(x) 165 238  258    246 253 369    10</span></code></pre></div>
+<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.246 seconds. That is 123 nanoseconds on average. You only lose time on your unique input values.</p>
 </div>
 <div id="precalculated-results" class="section level3">
 <h3 class="hasAnchor">
@@ -291,11 +291,11 @@
                          times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
 <span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
-<span class="co">#  expr   min    lq  mean median    uq   max neval</span>
-<span class="co">#     A  7.28  7.59  8.01   8.03  8.45  8.66    10</span>
-<span class="co">#     B 23.00 24.10 30.30  25.50 27.30 75.30    10</span>
-<span class="co">#     C  1.55  1.74  7.31   1.95  2.01 56.10    10</span></code></pre></div>
-<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0019 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
+<span class="co">#  expr   min    lq  mean median    uq  max neval</span>
+<span class="co">#     A  8.20  8.33 13.30   8.53  9.71 53.2    10</span>
+<span class="co">#     B 22.80 23.50 29.20  24.60 26.80 69.3    10</span>
+<span class="co">#     C  1.82  2.04  2.25   2.16  2.38  2.9    10</span></code></pre></div>
+<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0022 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
                          B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"Staphylococcus"</span><span class="op">)</span>,
@@ -308,15 +308,15 @@
                          times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
 <span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
-<span class="co">#  expr  min   lq mean median   uq  max neval</span>
-<span class="co">#     A 1.42 1.45 1.56   1.50 1.57 2.00    10</span>
-<span class="co">#     B 1.43 1.46 1.49   1.47 1.55 1.59    10</span>
-<span class="co">#     C 1.41 1.43 1.58   1.49 1.57 2.19    10</span>
-<span class="co">#     D 1.41 1.48 1.61   1.54 1.63 2.33    10</span>
-<span class="co">#     E 1.41 1.45 1.64   1.51 1.56 2.68    10</span>
-<span class="co">#     F 1.42 1.52 1.63   1.57 1.71 1.99    10</span>
-<span class="co">#     G 1.41 1.46 1.65   1.56 1.90 1.98    10</span>
-<span class="co">#     H 1.42 1.46 1.59   1.55 1.70 1.88    10</span></code></pre></div>
+<span class="co">#  expr  min   lq mean median   uq   max neval</span>
+<span class="co">#     A 1.66 1.70 1.86   1.77 1.90  2.41    10</span>
+<span class="co">#     B 1.61 1.71 1.99   1.84 2.37  2.56    10</span>
+<span class="co">#     C 1.64 1.72 1.79   1.74 1.77  2.14    10</span>
+<span class="co">#     D 1.68 1.71 2.06   2.06 2.23  2.77    10</span>
+<span class="co">#     E 1.63 1.71 1.85   1.75 1.92  2.43    10</span>
+<span class="co">#     F 1.61 1.67 1.80   1.75 1.86  2.22    10</span>
+<span class="co">#     G 1.63 1.67 4.37   1.96 2.58 25.70    10</span>
+<span class="co">#     H 1.67 1.73 1.88   1.83 2.01  2.28    10</span></code></pre></div>
 <p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package contains all phyla of all known bacteria, it can just return the initial value immediately.</p>
 </div>
 <div id="results-in-other-languages" class="section level3">
@@ -343,14 +343,14 @@
                          times <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
 <span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
-<span class="co">#  expr   min    lq  mean median    uq    max neval</span>
-<span class="co">#    en 17.81 18.24 21.93  18.78 19.44  60.56   100</span>
-<span class="co">#    de 28.82 29.53 37.92  30.33 32.62  81.75   100</span>
-<span class="co">#    nl 32.65 33.61 44.22  34.43 37.44 193.90   100</span>
-<span class="co">#    es 32.51 32.95 41.88  33.70 36.39  80.63   100</span>
-<span class="co">#    it 22.00 22.57 27.98  23.15 25.14  67.04   100</span>
-<span class="co">#    fr 21.71 22.22 27.20  22.83 24.41  66.08   100</span>
-<span class="co">#    pt 21.71 22.54 26.97  23.06 23.94  67.41   100</span></code></pre></div>
+<span class="co">#  expr   min    lq  mean median    uq   max neval</span>
+<span class="co">#    en 19.99 20.43 25.64  21.15 22.38 82.52   100</span>
+<span class="co">#    de 31.03 31.96 38.34  32.88 35.27 82.31   100</span>
+<span class="co">#    nl 35.25 36.19 43.25  37.63 39.66 85.19   100</span>
+<span class="co">#    es 35.01 35.85 40.89  36.91 38.58 83.68   100</span>
+<span class="co">#    it 24.35 24.90 30.43  25.81 28.03 78.90   100</span>
+<span class="co">#    fr 23.87 25.02 31.72  26.03 27.46 83.88   100</span>
+<span class="co">#    pt 24.00 24.99 31.16  26.05 28.06 80.74   100</span></code></pre></div>
 <p>Currently supported non-English languages are German, Dutch, Spanish, Italian, French and Portuguese.</p>
 </div>
   </div>

docs/articles/datasets.html

@@ -39,7 +39,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9008</span>
       </span>
     </div>
 
@@ -187,12 +187,12 @@
 
       
 
-      </header><script src="datasets_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
+      </header><script src="datasets_files/header-attrs-2.7/header-attrs.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Data sets for download / own use</h1>
             
-            <h4 class="date">26 May 2021</h4>
+            <h4 class="date">23 June 2021</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
       <div class="hidden name"><code>datasets.Rmd</code></div>
@@ -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 07:50:24 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>
@@ -1005,27 +1005,27 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <div id="interpretation-from-mic-values-disk-diameters-to-rsi" class="section level2">
 <h2 class="hasAnchor">
 <a href="#interpretation-from-mic-values-disk-diameters-to-rsi" class="anchor"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
-<p>A data set with 20,486 rows and 10 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
+<p>A data set with 21,996 rows and 10 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
 <p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 5 March 2021 09:46:55 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
+<p>It was last updated on 1 June 2021 14:47:11 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.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/rsi_translation.rds">R file</a> (34 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds">R file</a> (37 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.xlsx">Excel file</a> (0.7 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.txt">plain text file</a> (1.7 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.txt">plain text file</a> (1.8 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sas">SAS file</a> (3.5 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sas">SAS file</a> (3.8 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sav">SPSS file</a> (3.8 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sav">SPSS file</a> (2.4 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.dta">Stata file</a> (3.3 MB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.dta">Stata file</a> (3.5 MB)</li>
 </ul>
 <div id="source-5" class="section level3">
 <h3 class="hasAnchor">
 <a href="#source-5" class="anchor"></a>Source</h3>
-<p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2019) and EUCAST (2011-2021).</p>
+<p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2020) and EUCAST (2011-2021).</p>
 </div>
 <div id="example-content-5" class="section level3">
 <h3 class="hasAnchor">

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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9008</span>
       </span>
     </div>
 

docs/articles/resistance_predict.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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
       </span>
     </div>
 

docs/articles/welcome_to_AMR.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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
       </span>
     </div>
 

docs/authors.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9008</span>
       </span>
     </div>
 

docs/index.html

@@ -42,7 +42,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9008</span>
       </span>
     </div>
 
@@ -213,20 +213,16 @@
 <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">
@@ -376,21 +372,33 @@
 <div id="latest-released-version" class="section level4">
 <h4 class="hasAnchor">
 <a href="#latest-released-version" class="anchor"></a>Latest released version</h4>
-<p>This package is <a href="https://msberends.r-universe.dev">available here</a> on the <a href="https://ropensci.org/r-universe/">rOpenSci R-universe platform</a>, as CRAN does not allow frequent updates of large packages (though the <code>AMR</code> package is only 7-9 MB). With CRAN, we apparently cannot update this package frequently enough to implement the latest EUCAST/CLSI guidelines or the latest microbial taxonomy.</p>
-<p>Install this package in R by using the command:</p>
+<p><a href="https://cran.r-project.org/package=AMR"><img src="https://www.r-pkg.org/badges/version-ago/AMR" alt="CRAN"></a> <a href="https://cran.r-project.org/package=AMR"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt="CRANlogs"></a></p>
+<p>This package is available <a href="https://cran.r-project.org/package=AMR">here on the official R network (CRAN)</a>. Install this package in R from CRAN by using the command:</p>
 <div class="sourceCode" id="cb3"><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">"AMR"</span>, repos <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span></code></pre></div>
-<p>It will be downloaded and installed automatically.</p>
+<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">"AMR"</span><span class="op">)</span></code></pre></div>
+<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
 <p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
 </div>
 <div id="latest-development-version" class="section level4">
 <h4 class="hasAnchor">
 <a href="#latest-development-version" class="anchor"></a>Latest development version</h4>
-<p>The latest and unpublished development version can be installed from GitHub using:</p>
+<p>[R-code-check][<a href="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master" class="uri">https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master</a>](<a href="https://github.com/msberends/AMR/actions" class="uri">https://github.com/msberends/AMR/actions</a>) [CodeFactor][<a href="https://www.codefactor.io/repository/github/msberends/amr/badge" class="uri">https://www.codefactor.io/repository/github/msberends/amr/badge</a>](<a href="https://www.codefactor.io/repository/github/msberends/amr" class="uri">https://www.codefactor.io/repository/github/msberends/amr</a>) [Codecov][<a href="https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg" class="uri">https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg</a>](<a href="https://codecov.io/gh/msberends/AMR?branch=master" class="uri">https://codecov.io/gh/msberends/AMR?branch=master</a>)</p>
+<p>The latest and unpublished development version can be installed from GitHub in two ways:</p>
+<ol>
+<li>
+<p>Directly, 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>
-<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>
+</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>
+<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 (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>
 </div>
 </div>

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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9008</span>
       </span>
     </div>
 
@@ -236,15 +236,48 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-170" class="section level1">
-<h1 class="page-header" data-toc-text="1.7.0">
-<a href="#amr-170" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.0</h1>
+    <div id="amr-1719008" class="section level1">
+<h1 class="page-header" data-toc-text="1.7.1.9008">
+<a href="#amr-1719008" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9008</h1>
+<div id="last-updated-23-june-2021" class="section level2">
+<h2 class="hasAnchor">
+<a href="#last-updated-23-june-2021" class="anchor"></a><small>Last updated: 23 June 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 finally 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>
+</ul>
+</li>
+<li>Fixed 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>
+</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> 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>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.</p>
+<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">
 <code class="sourceCode R">
 <span class="co"># select columns with results for carbapenems</span>
@@ -268,6 +301,7 @@
 <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>
@@ -284,14 +318,16 @@
 </ul>
 </li>
 <li>Function <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code> as additional antbiotic column selector and function <code><a href="../reference/AMR-deprecated.html">filter_betalactams()</a></code> as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.</li>
-<li>A <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
+<li>A <code>ggplot()</code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
 </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>
 <li>Custom MDRO guidelines (<code><a href="../reference/mdro.html">mdro()</a></code>, <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code>):
 <ul>
 <li>Custom MDRO guidelines can now be combined with other custom MDRO guidelines using <code><a href="https://rdrr.io/r/base/c.html">c()</a></code>
@@ -340,6 +376,7 @@
 <h3 class="hasAnchor">
 <a href="#other" class="anchor"></a>Other</h3>
 <ul>
+<li>As requested by CRAN administrators: decreased package size by 3 MB in costs of a slower loading time of the package</li>
 <li>All unit tests are now processed by the <code>tinytest</code> package, instead of the <code>testthat</code> package. The <code>testthat</code> package unfortunately requires tons of dependencies that are also heavy and only usable for recent R versions, disallowing developers to test a package under any R 3.* version. On the contrary, the <code>tinytest</code> package is very lightweight and dependency-free.</li>
 </ul>
 </div>
@@ -382,7 +419,7 @@
 <span class="co">#&gt; Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
 </li>
 <li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
-<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
+<li><p><code>ggplot()</code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
 <li>
 <p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
@@ -423,9 +460,9 @@
 </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>
@@ -439,7 +476,7 @@
 <li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
 <li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
 <li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
-<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
+<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
 </ul>
 </li>
 <li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>
@@ -456,7 +493,7 @@
 <code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> now detects if the column name resembles an antibiotic name or code and now returns <code>TRUE</code> immediately if the input contains any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.</li>
 <li>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> now support less than a day as value for argument <code>episode_days</code> (e.g., to include one patient/test per hour)</li>
 <li>Argument <code>ampc_cephalosporin_resistance</code> in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> now also applies to value “I” (not only “S”)</li>
-<li>Functions <code><a href="https://docs.ropensci.org/skimr/reference/print.html">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code>
+<li>Functions <code><a href="https://rdrr.io/r/base/print.html">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code>
 </li>
 <li>Improved speed and reliability of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>. As this also internally improves the reliability of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>, this might have a slight impact on the results of those functions.</li>
 <li>Fix for <code><a href="../reference/mo_property.html">mo_name()</a></code> when used in other languages than English</li>
@@ -477,7 +514,7 @@
 <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>
@@ -502,9 +539,9 @@
 <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>
@@ -608,7 +645,7 @@
 <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> 
@@ -619,9 +656,9 @@
 <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>
@@ -724,9 +761,9 @@
 <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>
@@ -791,7 +828,7 @@
 <p>Making this package independent of especially the tidyverse (e.g. packages <code>dplyr</code> and <code>tidyr</code>) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.</p>
 <p>Negative effects of this change are:</p>
 <ul>
-<li>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>.</li>
+<li>Function <code>freq()</code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code>freq()</code>.</li>
 <li><del>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code>&lt;ord&gt;</code>, not <code>&lt;rsi&gt;</code> anymore. This is purely a visual effect.</del></li>
 <li><del>All functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</del></li>
 <li>For developers: classes <code>mo</code> and <code>ab</code> now both also inherit class <code>character</code>, to support any data transformation. This change invalidates code that checks for class length == 1.</li>
@@ -799,9 +836,9 @@
 </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>
@@ -853,9 +890,9 @@ 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>
@@ -886,9 +923,9 @@ 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>
@@ -1123,7 +1160,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <span class="co">#&gt; invalid microorganism code, NA generated</span></code></pre></div>
 <p>This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</p>
 </li>
-<li><p>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
+<li><p>Function <code>freq()</code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code>freq()</code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
 <li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
 </ul>
 </div>
@@ -1194,9 +1231,9 @@ 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>
@@ -1306,9 +1343,9 @@ 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>
@@ -1354,9 +1391,9 @@ 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>
@@ -1390,7 +1427,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>The <code><a href="../reference/age.html">age()</a></code> function gained a new argument <code>exact</code> to determine ages with decimals</li>
 <li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code><a href="../reference/as.rsi.html">rsi()</a></code>
 </li>
-<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>):
+<li>Frequency tables (<code>freq()</code>):
 <ul>
 <li><p>speed improvement for microbial IDs</p></li>
 <li><p>fixed factor level names for R Markdown</p></li>
@@ -1400,12 +1437,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span> 
-  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span> 
+  <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span> 
   <span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span>
 <span class="co"># grouped boxplots:</span>
 <span class="va">septic_patients</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://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span>
+  <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span>
   <span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
 </li>
 </ul>
@@ -1415,7 +1452,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
 </li>
 <li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
-<li>Fix for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> for when all values are <code>NA</code>
+<li>Fix for <code>freq()</code> for when all values are <code>NA</code>
 </li>
 <li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
 <li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
@@ -1440,9 +1477,9 @@ 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>
@@ -1559,9 +1596,9 @@ 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>
@@ -1654,7 +1691,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 </ul>
 </li>
-<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function):
+<li>Frequency tables (<code>freq()</code> function):
 <ul>
 <li>
 <p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
@@ -1664,15 +1701,15 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <span class="co"># OLD WAY</span>
 <span class="va">septic_patients</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>genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</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://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
+  <span class="fu">freq</span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
 <span class="co"># NEW WAY</span>
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span> 
-  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
+  <span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
 
 <span class="co"># Even supports grouping variables:</span>
 <span class="va">septic_patients</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">gender</span><span class="op">)</span> <span class="op">%&gt;%</span> 
-  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+  <span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
 </li>
 <li><p>Header info is now available as a list, with the <code>header</code> function</p></li>
 <li><p>The argument <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</p></li>
@@ -1717,9 +1754,9 @@ 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>
@@ -1754,7 +1791,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Using <code>portion_*</code> functions now throws a warning when total available isolate is below argument <code>minimum</code></p></li>
 <li><p>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</p></li>
 <li>
-<p>Frequency tables - <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>:</p>
+<p>Frequency tables - <code>freq()</code>:</p>
 <ul>
 <li>
 <p>Support for grouping variables, test with:</p>
@@ -1762,14 +1799,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <code class="sourceCode R">
 <span class="va">septic_patients</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://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
+  <span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
 </li>
 <li>
 <p>Support for (un)selecting columns:</p>
 <div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span> 
-  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span> 
+  <span class="fu">freq</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/select.html">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">count</span>, <span class="op">-</span><span class="va">cum_count</span><span class="op">)</span> <span class="co"># only get item, percent, cum_percent</span></code></pre></div>
 </li>
 <li><p>Check for <code><a href="https://hms.tidyverse.org/reference/Deprecated.html">hms::is.hms</a></code></p></li>
@@ -1787,7 +1824,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Removed diacritics from all authors (columns <code>microorganisms$ref</code> and <code>microorganisms.old$ref</code>) to comply with CRAN policy to only allow ASCII characters</p></li>
 <li><p>Fix for <code>mo_property</code> not working properly</p></li>
 <li><p>Fix for <code>eucast_rules</code> where some Streptococci would become ceftazidime R in EUCAST rule 4.5</p></li>
-<li><p>Support for named vectors of class <code>mo</code>, useful for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">top_freq()</a></code></p></li>
+<li><p>Support for named vectors of class <code>mo</code>, useful for <code>top_freq()</code></p></li>
 <li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> argument</p></li>
 <li>
 <p>AI improvements for <code>as.mo</code>:</p>
@@ -1907,9 +1944,9 @@ 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>
@@ -1954,13 +1991,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <div class="sourceCode" id="cb49"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span><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="va">age</span>, <span class="va">gender</span><span class="op">)</span>, ncol <span class="op">=</span> <span class="fl">2</span><span class="op">)</span><span class="op">)</span>
-<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
+<span class="fu">freq</span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
 <p>For lists, subsetting is possible:</p>
 <div class="sourceCode" id="cb50"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span>age <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">age</span>, gender <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">gender</span><span class="op">)</span>
-<span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
-<span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
+<span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
+<span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
 </li>
 </ul>
 </div>
@@ -2033,13 +2070,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>A vignette to explain its usage</li>
 <li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li>
-<li>Support for <code>table</code> to use as input: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(table(x, y))</a></code>
+<li>Support for <code>table</code> to use as input: <code>freq(table(x, y))</code>
 </li>
 <li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><a href="https://rdrr.io/r/graphics/hist.html">hist(freq(df$age))</a></code>
 </li>
 <li>Support for <code>as.vector</code>, <code>as.data.frame</code>, <code>as_tibble</code> and <code>format</code>
 </li>
-<li>Support for quasiquotation: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
+<li>Support for quasiquotation: <code>freq(mydata, mycolumn)</code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
 </li>
 <li>Function <code>top_freq</code> function to return the top/below <em>n</em> items as vector</li>
 <li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li>
@@ -2048,9 +2085,9 @@ 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>
@@ -2133,9 +2170,9 @@ 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: 2021-05-26T12:00Z
+last_built: 2021-06-23T08:16Z
 urls:
   reference: https://msberends.github.io/AMR//reference
   article: https://msberends.github.io/AMR//articles

docs/reference/AMR-deprecated.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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
       </span>
     </div>
 
@@ -431,7 +431,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
 
     
 
-<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>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<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>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
       </span>
     </div>
 
@@ -277,7 +277,7 @@
 
     
 
-<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>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<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="contact-us"><a class="anchor" href="#contact-us"></a>Contact Us</h2>
 
     
@@ -286,7 +286,7 @@
 <p>Matthijs S. Berends <br />
 m.s.berends [at] umcg [dot] nl <br />
 University of Groningen
-Department of Medical Microbiology
+Department of Medical Microbiology and Infection Prevention <br />
 University Medical Center Groningen <br />
 Post Office Box 30001 <br />
 9700 RB Groningen <br />

docs/reference/WHOCC.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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
       </span>
     </div>
 
@@ -257,7 +257,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
 
     
 
-<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>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<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="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='fu'><a href='as.ab.html'>as.ab</a></span><span class='op'>(</span><span class='st'>"meropenem"</span><span class='op'>)</span>

docs/reference/WHONET.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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
       </span>
     </div>
 
@@ -285,7 +285,7 @@
 
     
 
-<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>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<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>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

docs/reference/ab_from_text.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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
       </span>
     </div>
 
@@ -317,7 +317,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<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>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<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="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># mind the bad spelling of amoxicillin in this line, </span>

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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
       </span>
     </div>
 
@@ -342,7 +342,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<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>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<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='antibiotics.html'>antibiotics</a></p></div>

docs/reference/age.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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
       </span>
     </div>
 
@@ -287,7 +287,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<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>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<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>To split ages into groups, use the <code><a href='age_groups.html'>age_groups()</a></code> function.</p></div>

docs/reference/age_groups.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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
       </span>
     </div>
 
@@ -288,7 +288,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<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>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<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>To determine ages, based on one or more reference dates, use the <code><a href='age.html'>age()</a></code> function.</p></div>

docs/reference/antibiotic_class_selectors.html

@@ -49,8 +49,7 @@
   <script src="../extra.js"></script>
 
 <meta property="og:title" content="Antibiotic Class Selectors — antibiotic_class_selectors" />
-<meta property="og:description" content="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. 
-" />
+<meta property="og:description" content="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." />
 <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
 
 
@@ -83,7 +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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9007</span>
       </span>
     </div>
 
@@ -240,14 +239,15 @@
     </div>
 
     <div class="ref-description">
-    <p>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>
-</strong></p>
+    <p>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.</p>
     </div>
 
     <pre class="usage"><span class='fu'>ab_class</span><span class='op'>(</span><span class='va'>ab_class</span>, only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
 
 <span class='fu'>aminoglycosides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
 
+<span class='fu'>aminopenicillins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
+
 <span class='fu'>betalactams</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
 
 <span class='fu'>carbapenems</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
@@ -268,13 +268,25 @@
 
 <span class='fu'>glycopeptides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
 
+<span class='fu'>lincosamides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
+
+<span class='fu'>lipoglycopeptides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
+
 <span class='fu'>macrolides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
 
 <span class='fu'>oxazolidinones</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
 
 <span class='fu'>penicillins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
 
-<span class='fu'>tetracyclines</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre>
+<span class='fu'>polymyxins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
+
+<span class='fu'>streptogramins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
+
+<span class='fu'>quinolones</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
+
+<span class='fu'>tetracyclines</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
+
+<span class='fu'>ureidopenicillins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -291,11 +303,37 @@
 
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
-    <p><strong>
-</strong></p>
-<p>These functions can be used in data set calls for selecting columns and filtering rows, see <em>Examples</em>. They support base R, but work more convenient in dplyr functions such as <code><a href='https://dplyr.tidyverse.org/reference/select.html'>select()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>.</p>
-<p>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 <a href='antibiotics.html'>antibiotics</a> data set. This means that a selector like e.g. <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.</p>
-<p>The group of betalactams consists of all carbapenems, cephalosporins and penicillins.</p>
+    <p>These functions can be used in data set calls for selecting columns and filtering rows. They are heavily inspired by the <a href='https://tidyselect.r-lib.org/reference/language.html'>Tidyverse selection helpers</a>, but also work in base <span style="R">R</span> and not only in <code>dplyr</code> verbs. Nonetheless, they are very convenient to use with <code>dplyr</code> functions such as <code><a href='https://dplyr.tidyverse.org/reference/select.html'>select()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>, see <em>Examples</em>.</p>
+<p>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 <a href='antibiotics.html'>antibiotics</a> data set. This means that a selector such as <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. Use the <code>ab_class()</code> function to filter/select on a manually defined antibiotic class.</p>
+    <h2 class="hasAnchor" id="full-list-of-supported-agents"><a class="anchor" href="#full-list-of-supported-agents"></a>Full list of supported agents</h2>
+
+    
+
+<ul>
+<li><p><code>aminoglycosides()</code> can select amikacin (AMK), amikacin/fosfomycin (AKF), amphotericin B-high (AMH), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB) and tobramycin-high (TOH)</p></li>
+<li><p><code>aminopenicillins()</code> can select amoxicillin (AMX) and ampicillin (AMP)</p></li>
+<li><p><code>betalactams()</code> can select amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefaloridine (RID), cefamandole (MAN), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (Cefcatacol) (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), cefuroxime (CXM), cefuroxime axetil (CXA), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (Amdinocillin) (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), methicillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), phenethicillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC)</p></li>
+<li><p><code>carbapenems()</code> can select biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA) and tebipenem (TBP)</p></li>
+<li><p><code>cephalosporins()</code> can select cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefaloridine (RID), cefamandole (MAN), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (Cefcatacol) (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), cefuroxime (CXM), cefuroxime axetil (CXA), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP), cephradine (CED), latamoxef (LTM) and loracarbef (LOR)</p></li>
+<li><p><code>cephalosporins_1st()</code> can select cefacetrile (CAC), cefadroxil (CFR), cefaloridine (RID), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP) and cephradine (CED)</p></li>
+<li><p><code>cephalosporins_2nd()</code> can select cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening (FOX1), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA) and loracarbef (LOR)</p></li>
+<li><p><code>cephalosporins_3rd()</code> can select cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO) and latamoxef (LTM)</p></li>
+<li><p><code>cephalosporins_4th()</code> can select cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetecol (Cefcatacol) (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO) and cefquinome (CEQ)</p></li>
+<li><p><code>cephalosporins_5th()</code> can select ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI) and ceftolozane/tazobactam (CZT)</p></li>
+<li><p><code>fluoroquinolones()</code> can select besifloxacin (BES), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nifuroquine (NIF), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA)</p></li>
+<li><p><code>glycopeptides()</code> can select avoparcin (AVO), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN) and vancomycin-macromethod (VAM)</p></li>
+<li><p><code>lincosamides()</code> can select acetylmidecamycin (ACM), acetylspiramycin (ASP), clindamycin (CLI), gamithromycin (GAM), kitasamycin (Leucomycin) (KIT), lincomycin (LIN), meleumycin (MEL), nafithromycin (ZWK), pirlimycin (PRL), primycin (PRM), solithromycin (SOL), tildipirosin (TIP), tilmicosin (TIL), tulathromycin (TUL), tylosin (TYL) and tylvalosin (TYL1)</p></li>
+<li><p><code>lipoglycopeptides()</code> can select dalbavancin (DAL), oritavancin (ORI) and telavancin (TLV)</p></li>
+<li><p><code>macrolides()</code> can select acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (Leucomycin) (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), pirlimycin (PRL), primycin (PRM), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL) and tylvalosin (TYL1)</p></li>
+<li><p><code>oxazolidinones()</code> can select cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD) and thiacetazone (THA)</p></li>
+<li><p><code>penicillins()</code> can select amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), carbenicillin (CRB), carindacillin (CRN), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (Amdinocillin) (MEC), metampicillin (MTM), methicillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), phenethicillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC)</p></li>
+<li><p><code>polymyxins()</code> can select colistin (COL), polymyxin B (PLB) and polymyxin B/polysorbate 80 (POP)</p></li>
+<li><p><code>streptogramins()</code> can select pristinamycin (PRI) and quinupristin/dalfopristin (QDA)</p></li>
+<li><p><code>quinolones()</code> can select besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA)</p></li>
+<li><p><code>tetracyclines()</code> can select cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), tetracycline (TCY) and tigecycline (TGC)</p></li>
+<li><p><code>ureidopenicillins()</code> can select azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP) and piperacillin/tazobactam (TZP)</p></li>
+</ul>
+
     <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
 
     
@@ -312,13 +350,13 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<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>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<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="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <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='co'># Base R ------------------------------------------------------------------</span>
+<span class='co'># base R ------------------------------------------------------------------</span>
 
 <span class='co'># select columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
 <span class='va'>example_isolates</span><span class='op'>[</span>, <span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span><span class='op'>]</span>
@@ -345,6 +383,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 <span class='co'># \donttest{</span>
 <span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
 
+  <span class='co'># get AMR for all aminoglycosides e.g., per hospital:</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'>aminoglycosides</span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>resistance</span><span class='op'>)</span><span class='op'>)</span>
+
   <span class='co'># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</span>
   <span class='va'>example_isolates</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='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>
@@ -371,7 +414,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
   <span class='va'>example_isolates</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'>mo</span>, <span class='fu'>ab_class</span><span class='op'>(</span><span class='st'>"mycobact"</span><span class='op'>)</span><span class='op'>)</span>
     
-    
   <span class='co'># get bug/drug combinations for only macrolides in Gram-positives:</span>
   <span class='va'>example_isolates</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='mo_property.html'>mo_is_gram_positive</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
@@ -379,14 +421,12 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
     <span class='fu'><a href='bug_drug_combinations.html'>bug_drug_combinations</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
     <span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span><span class='op'>(</span><span class='op'>)</span>
     
-    
   <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>some_column <span class='op'>=</span> <span class='st'>"some_value"</span>,
              J01CA01 <span class='op'>=</span> <span class='st'>"S"</span><span class='op'>)</span> <span class='op'>%&gt;%</span>   <span class='co'># ATC code of ampicillin</span>
     <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='fu'>penicillins</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>         <span class='co'># only the 'J01CA01' column will be selected</span>
     
     
   <span class='co'># with dplyr 1.0.0 and higher (that adds 'across()'), this is all equal:</span>
-  <span class='co'># (though the row names on the first are more correct)</span>
   <span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>==</span> <span class='st'>"R"</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/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>==</span> <span class='st'>"R"</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/filter.html'>filter</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'>carbapenems</span><span class='op'>(</span><span class='op'>)</span>, <span class='op'>~</span><span class='va'>.x</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span><span class='op'>)</span>

docs/reference/antibiotics.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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
       </span>
     </div>
 
@@ -326,7 +326,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
 
     
 
-<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>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<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>, <a href='intrinsic_resistant.html'>intrinsic_resistant</a></p></div>

docs/reference/as.ab.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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
       </span>
     </div>
 
@@ -314,7 +314,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
 
     
 
-<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>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<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'>

docs/reference/as.disk.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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
       </span>
     </div>
 
@@ -276,7 +276,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<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>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<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><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>

docs/reference/as.mic.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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
       </span>
     </div>
 
@@ -307,7 +307,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<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>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<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><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>

docs/reference/as.mo.html

@@ -6,7 +6,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-<title>Transform Input to a Microorganism ID — as.mo • AMR (for R)</title>
+<title>Transform Input to a Microorganism Code — as.mo • AMR (for R)</title>
 
 <!-- favicons -->
 <link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@@ -48,8 +48,8 @@
   <link href="../extra.css" rel="stylesheet">
   <script src="../extra.js"></script>
 
-<meta property="og:title" content="Transform Input to a Microorganism ID — as.mo" />
-<meta property="og:description" content="Use this function to determine a valid microorganism ID (mo). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like &quot;Staphylococcus aureus&quot;), an abbreviated name (such as &quot;S. aureus&quot;), an abbreviation known in the field (such as &quot;MRSA&quot;), or just a genus. See Examples." />
+<meta property="og:title" content="Transform Input to a Microorganism Code — as.mo" />
+<meta property="og:description" content="Use this function to determine a valid microorganism code (mo). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like &quot;Staphylococcus aureus&quot;), an abbreviated name (such as &quot;S. aureus&quot;), an abbreviation known in the field (such as &quot;MRSA&quot;), or just a genus. 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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
       </span>
     </div>
 
@@ -233,13 +233,13 @@
 <div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
-    <h1>Transform Input to a Microorganism ID</h1>
+    <h1>Transform Input to a Microorganism Code</h1>
     <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mo.R'><code>R/mo.R</code></a></small>
     <div class="hidden name"><code>as.mo.Rd</code></div>
     </div>
 
     <div class="ref-description">
-    <p>Use this function to determine a valid microorganism ID (<code>mo</code>). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see <em>Source</em>). The input can be almost anything: a full name (like <code>"Staphylococcus aureus"</code>), an abbreviated name (such as <code>"S. aureus"</code>), an abbreviation known in the field (such as <code>"MRSA"</code>), or just a genus. See <em>Examples</em>.</p>
+    <p>Use this function to determine a valid microorganism code (<code>mo</code>). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see <em>Source</em>). The input can be almost anything: a full name (like <code>"Staphylococcus aureus"</code>), an abbreviated name (such as <code>"S. aureus"</code>), an abbreviation known in the field (such as <code>"MRSA"</code>), or just a genus. See <em>Examples</em>.</p>
     </div>
 
     <pre class="usage"><span class='fu'>as.mo</span><span class='op'>(</span>
@@ -314,7 +314,7 @@
 <h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>General Info</h3>
 
 
-<p>A microorganism ID from this package (class: <code>mo</code>) is human readable and typically looks like these examples:</p><pre>  Code               Full name
+<p>A microorganism (MO) code from this package (class: <code>mo</code>) is human readable and typically looks like these examples:</p><pre>  Code               Full name
   ---------------    --------------------------------------
   B_KLBSL            Klebsiella
   B_KLBSL_PNMN       Klebsiella pneumoniae
@@ -422,7 +422,7 @@ 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>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<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> for the <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> that is being used to determine ID's.</p>