v1.5.0

.github/workflows/check.yaml

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -56,16 +56,24 @@ jobs:
           - {os: windows-latest, r: 'devel',   allowfail: false}
           - {os: windows-latest, r: 'release', allowfail: false}
           - {os: windows-latest, r: 'oldrel',  allowfail: false}
-          - {os: ubuntu-16.04,   r: 'devel',   allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-20.04,   r: 'devel',   allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: 'release', allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: 'oldrel',  allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: '3.2',     allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: '3.1',     allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: '3.0',     allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-16.04,   r: 'devel',   allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
           - {os: ubuntu-16.04,   r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: 'oldrel',  allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: 'oldrel',  allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
           - {os: ubuntu-16.04,   r: '4.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
           - {os: ubuntu-16.04,   r: '3.6',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
           - {os: ubuntu-16.04,   r: '3.5',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: '3.4',     allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: '3.3',     allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          # - {os: ubuntu-16.04,   r: '3.2',     allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          # older R versions cannot be tested, since tidyverse only supports last 4 R x.x versions
+          - {os: ubuntu-16.04,   r: '3.4',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: '3.3',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: '3.2',     allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: '3.1',     allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: '3.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -80,34 +88,45 @@ jobs:
       - uses: r-lib/actions/setup-pandoc@master
 
       - name: Query dependencies
+        if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
         run: |
           install.packages('remotes')
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
         shell: Rscript {0}
 
       - name: Cache R packages
-        if: runner.os != 'Windows'
+        if: runner.os != 'Windows' && matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
         uses: actions/cache@v1
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-r-${{ matrix.config.r }}-3-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-3-
+          key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-3-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-3-
 
       - name: Install Linux dependencies
-        if: runner.os == 'Linux'
+        if: runner.os == 'Linux' && matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
         env:
           RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
         run: |
           Rscript -e "remotes::install_github('r-hub/sysreqs')"
           sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
           sudo -s eval "$sysreqs"
+          
+      - name: Install Linux dependencies on old R versions
+        if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        # update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
+        # we don't want to depend on the sysreqs pkg here, as it requires a quite new R version
+        run: |
+          sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev
 
       - name: Install macOS dependencies
         if: matrix.config.os == 'macOS-latest' && matrix.config.r == 'devel'
         run: |
           brew install mariadb-connector-c
 
-      - name: Install dependencies
+      - name: Install package dependencies
+        if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
         run: |
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
@@ -116,15 +135,26 @@ jobs:
       - name: Session info
         run: |
           options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
+          utils::sessionInfo()
+          as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
         shell: Rscript {0}
 
-      - name: Run Check
+      - name: Run R CMD check
+        if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
         env:
           _R_CHECK_CRAN_INCOMING_: false
         run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
+        
+      - name: Run R CMD check on older R versions
+        if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2'
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+          _R_CHECK_FORCE_SUGGESTS_: false
+          _R_CHECK_LENGTH_1_CONDITION_: verbose
+          _R_CHECK_LENGTH_1_LOGIC2_: verbose
+        run: |
+          R CMD check data-raw/AMR_*.tar.gz --no-manual --no-build-vignettes
 
       - name: Show testthat output
         if: always()
@@ -135,5 +165,5 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
           path: check

.github/workflows/codecovr.yaml

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

.github/workflows/lintr.yaml

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -66,5 +66,5 @@ jobs:
         shell: Rscript {0}
 
       - name: Lint
-        run: lintr::lint_package(linters = lintr::with_defaults(line_length_linter = NULL, trailing_whitespace_linter = NULL, object_name_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL, object_length_linter = lintr::object_length_linter(length = 50L)), exclusions = list("R/aa_helper_pm_functions.R"))
+        run: lintr::lint_package(linters = lintr::with_defaults(line_length_linter = NULL, trailing_whitespace_linter = NULL, object_name_linter = NULL, cyclocomp_linter = NULL, object_length_linter = lintr::object_length_linter(length = 50L)), exclusions = list("R/aa_helper_pm_functions.R"))
         shell: Rscript {0}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.4.0.9045
-Date: 2020-12-25
+Version: 1.5.0
+Date: 2021-01-05
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 
@@ -29,6 +29,8 @@ Authors@R: c(
            family = "Meijer", given = c("Bart", "C."), email = "b.meijerg@certe.nl"),
     person(role = "ctb",
            family = "Ny", given = "Sofia", email = "sofia.ny@folkhalsomyndigheten.se"),
+    person(role = "ctb",
+           family = "Schade", given = c("Rogier", "P."), email = "r.schade@amsterdamumc.nl"),
     person(role = "ctb",
            family = "Souverein", given = "Dennis", email = "d.souvereing@streeklabhaarlem.nl"),
     person(role = "ctb",
@@ -55,7 +57,6 @@ Suggests:
     skimr,
     testthat,
     tidyr,
-    tidyselect,
     xml2
 VignetteBuilder: knitr,rmarkdown
 URL: https://msberends.github.io/AMR/, https://github.com/msberends/AMR

NAMESPACE

@@ -137,6 +137,7 @@ export(fluoroquinolones)
 export(full_join_microorganisms)
 export(g.test)
 export(geom_rsi)
+export(get_episode)
 export(get_locale)
 export(get_mo_source)
 export(ggplot_pca)

NEWS.md

@@ -1,9 +1,9 @@
-# AMR 1.4.0.9045
-## <small>Last updated: 25 December 2020</small>
+# AMR 1.5.0
+
+*Note: the rules of 'EUCAST Clinical Breakpoints v11.0 (2021)' will be added in the next release, to be expected in February/March 2021.*
 
 ### New
-* Function `is_new_episode()` to determine patient episodes which are not necessarily based on microorganisms. It also supports grouped variables with e.g. `mutate()`, `filter()` and `summarise()` of the `dplyr` package:
-  
+* Functions `get_episode()` and `is_new_episode()` to determine (patient) episodes which are not necessarily based on microorganisms. The `get_episode()` function returns the index number of the episode per group, while the `is_new_episode()` function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode. They also support `dplyr`s grouping (i.e. using `group_by()`):
   ```r
   library(dplyr)
   example_isolates %>%
@@ -12,9 +12,10 @@
   ```
 * Functions `mo_is_gram_negative()` and `mo_is_gram_positive()` as wrappers around `mo_gramstain()`. They always return `TRUE` or `FALSE` (except when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.
 * Function `mo_is_intrinsic_resistant()` to test for intrinsic resistance, based on [EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2](https://www.eucast.org/expert_rules_and_intrinsic_resistance/) from 2020.
-* Functions `random_mic()`, `random_disk()` and `random_rsi()` for random number generation. They take microorganism names and antibiotic names as input to make generation more realistic.
+* Functions `random_mic()`, `random_disk()` and `random_rsi()` for random value generation. The functions `random_mic()` and `random_disk()` take microorganism names and antibiotic names as input to make generation more realistic.
 
 ### Changed
+* New argument `ampc_cephalosporin_resistance` in `eucast_rules()` to correct for AmpC de-repressed cephalosporin-resistant mutants
 * Interpretation of antimicrobial resistance - `as.rsi()`:
   * Reference data used for `as.rsi()` can now be set by the user, using the `reference_data` argument. This allows for using own interpretation guidelines. The user-set data must have the same structure as `rsi_translation`.
   * Better determination of disk zones and MIC values when running `as.rsi()` on a data.frame
@@ -22,7 +23,20 @@
   * `as.rsi()` on a data.frame will not print a message anymore if the values are already clean R/SI values
   * If using `as.rsi()` on MICs or disk diffusion while there is intrinsic antimicrobial resistance, a warning will be thrown to remind about this
   * Fix for using `as.rsi()` on a `data.frame` that only contains one column for antibiotic interpretations
-* Some functions are now context-aware when used inside `dplyr` verbs, such as `filter()`, `mutate()` and `summarise()`. This means that then the data argument does not need to be set anymore. This is the case for the new functions `mo_is_gram_negative()`, `mo_is_gram_positive()`, `mo_is_intrinsic_resistant()` and for the existing functions `first_isolate()`, `key_antibiotics()`, `mdro()`, `brmo()`, `mrgn()`, `mdr_tb()`, `mdr_cmi2012()`, `eucast_exceptional_phenotypes()`. This was already the case for antibiotic selection functions (such as using `penicillins()` in `dplyr::select()`).
+* Some functions are now context-aware when used inside `dplyr` verbs, such as `filter()`, `mutate()` and `summarise()`. This means that then the data argument does not need to be set anymore. This is the case for the new functions:
+  * `mo_is_gram_negative()`
+  * `mo_is_gram_positive()`
+  * `mo_is_intrinsic_resistant()`
+  
+  ... and for the existing functions:
+  * `first_isolate()`,
+  * `key_antibiotics()`,
+  * `mdro()`,
+  * `brmo()`,
+  * `mrgn()`,
+  * `mdr_tb()`,
+  * `mdr_cmi2012()`,
+  * `eucast_exceptional_phenotypes()`
   
   ```r
   # to select first isolates that are Gram-negative 
@@ -33,6 +47,12 @@
     select(mo, cephalosporins(), aminoglycosides()) %>% 
     as_tibble()
   ```
+* For antibiotic selection functions (such as `cephalosporins()`, `aminoglycosides()`) to select columns based on a certain antibiotic group, the dependency on the `tidyselect` package was removed, meaning that they can now also be used without the need to have this package installed and now also work in base R function calls (they rely on R 3.2 or later):
+  ```r
+  # above example in base R:
+  example_isolates[which(first_isolate() & mo_is_gram_negative()),
+                   c("mo", cephalosporins(), aminoglycosides())]
+  ```
 * For all function arguments in the code, it is now defined what the exact type of user input should be (inspired by the [`typed`](https://github.com/moodymudskipper/typed) package). If the user input for a certain function does not meet the requirements for a specific argument (such as the class or length), an informative error will be thrown. This makes the package more robust and the use of it more reproducible and reliable. In total, more than 420 arguments were defined.
 * Fix for `set_mo_source()`, that previously would not remember the file location of the original file
 * Deprecated function `p_symbol()` that not really fits the scope of this package. It will be removed in a future version. See [here](https://github.com/msberends/AMR/blob/v1.4.0/R/p_symbol.R) for the source code to preserve it.
@@ -52,7 +72,10 @@
 ### Other
 * All messages and warnings thrown by this package now break sentences on whole words
 * More extensive unit tests
-* Internal calls to `options()` were all removed in favour of a new internal environment `mo_env`
+* Internal calls to `options()` were all removed in favour of a new internal environment `pkg_env`
+* Improved internal type setting (among other things: replaced all `sapply()` calls with `vapply()`)
+* Added CodeFactor as a continuous code review to this package: <https://www.codefactor.io/repository/github/msberends/amr/>
+* Added Dr. Rogier Schade as contributor
 
 # AMR 1.4.0
 

R/aa_helper_functions.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       #
@@ -119,8 +119,8 @@ search_type_in_df <- function(x, type, info = TRUE) {
 
   # -- mo
   if (type == "mo") {
-    if (any(sapply(x, is.mo))) {
-      found <- sort(colnames(x)[sapply(x, is.mo)])[1]
+    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,
@@ -152,8 +152,8 @@ search_type_in_df <- function(x, type, info = TRUE) {
                              "`, but this column contains no valid dates. Transform its values to valid dates first.")),
              call. = FALSE)
       }
-    } else if (any(sapply(x, function(x) inherits(x, c("Date", "POSIXct"))))) {
-      found <- sort(colnames(x)[sapply(x, function(x) inherits(x, c("Date", "POSIXct")))])[1]
+    } 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]
     }
   }
   # -- patient id
@@ -202,7 +202,7 @@ search_type_in_df <- function(x, type, info = TRUE) {
 }
 
 is_possibly_regex <- function(x) {
-  tryCatch(sapply(strsplit(x, ""),
+  tryCatch(vapply(FUN.VALUE = character(1), strsplit(x, ""),
                   function(y) any(y %in% c("$", "(", ")", "*", "+", "-", ".", "?", "[", "]", "^", "{", "|", "}", "\\"), na.rm = TRUE)),
            error = function(e) rep(TRUE, length(x)))
 }
@@ -210,7 +210,7 @@ is_possibly_regex <- function(x) {
 stop_ifnot_installed <- function(package) {
   # no "utils::installed.packages()" since it requires non-staged install since R 3.6.0
   # https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html
-  sapply(package, function(pkg)
+  vapply(FUN.VALUE = character(1), package, function(pkg)
     tryCatch(get(".packageName", envir = asNamespace(pkg)),
              error = function(e) {
                if (package == "rstudioapi") {
@@ -260,7 +260,8 @@ word_wrap <- function(...,
   
   if (msg %like% "\n") {
     # run word_wraps() over every line here, bind them and return again
-    return(paste0(sapply(trimws(unlist(strsplit(msg, "\n")), which = "right"),
+    return(paste0(vapply(FUN.VALUE = character(1),
+                         trimws(unlist(strsplit(msg, "\n")), which = "right"),
                          word_wrap, 
                          add_fn = add_fn,
                          as_note = FALSE,
@@ -457,7 +458,7 @@ meet_criteria <- function(object,
     stop_if(allow_NULL == FALSE, "argument `", obj_name, "` must not be NULL", call = call_depth)
     return(invisible())
   }
-  if (is.null(dim(object)) && length(object) == 1 && is.na(object)) {
+  if (is.null(dim(object)) && length(object) == 1 && suppressWarnings(is.na(object))) { # suppressWarnings for functions
     stop_if(allow_NA == FALSE, "argument `", obj_name, "` must not be NA", call = call_depth)
     return(invisible())
   }
@@ -512,7 +513,11 @@ meet_criteria <- function(object,
                call = call_depth)
   }
   if (!is.null(contains_column_class)) {
-    stop_ifnot(any(sapply(object, function(col, columns_class = contains_column_class) inherits(col, columns_class)), na.rm = TRUE),
+    stop_ifnot(any(vapply(FUN.VALUE = logical(1), 
+                          object,
+                          function(col, columns_class = contains_column_class) {
+                            inherits(col, columns_class)
+                          }), na.rm = TRUE),
                "the data provided in argument `", obj_name,
                "` must contain at least one column of class <", contains_column_class, ">. ",
                "See ?as.", contains_column_class, ".",
@@ -522,36 +527,97 @@ meet_criteria <- function(object,
 }
 
 get_current_data <- function(arg_name, call) {
-  # this mimics dplyr::cur_data_all for users that use our context-aware functions in dplyr verbs
-  cur_data_all_dplyr <- import_fn("cur_data_all", "dplyr", error_on_fail = FALSE)
-  if (is.null(cur_data_all_dplyr)) {
-    # dplyr not installed
-    stop_("argument `", arg_name, "` is missing, with no default", call = call)
+  if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2) {
+    if (is.na(arg_name)) {
+      warning_("this function can only be used in R >= 3.2", call = call)
+      return(data.frame())
+    } else {
+      stop_("argument `", arg_name, "` is missing with no default", call = call)
+    }
+  }
+  
+  # try a (base R) method, by going over the complete system call stack with sys.frames()
+  not_set <- TRUE
+  frms <- lapply(sys.frames(), function(el) {
+    if (".Generic" %in% names(el)) {
+      if (tryCatch(not_set == TRUE && ".data" %in% names(el) && is.data.frame(el$`.data`), error = function(e) FALSE)) {
+        # dplyr? - an element `.data` will be in the system call stack
+        not_set <<- FALSE
+        el$`.data`
+      } else if (tryCatch(not_set == TRUE && any(c("x", "xx") %in% names(el)), error = function(e) FALSE)) {
+        # otherwise try 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
+      }
+    } else {
+      NULL
+    }
+  })
+  vars_df <- tryCatch(frms[[which(!vapply(FUN.VALUE = logical(1), frms, is.null))]], error = function(e) NULL)
+  if (is.data.frame(vars_df)) {
+    return(vars_df)
+  }
+  
+  # nothing worked, so:
+  if (is.na(arg_name)) {
+    stop_("this function must be used inside valid dplyr selection verbs or inside a data.frame call", 
+          call = call)
+  } else {
+    stop_("argument `", arg_name, "` is missing with no default ",
+          "or function not used inside a valid dplyr verb", 
+          call = call)
   }
-  tryCatch(cur_data_all_dplyr(),
-           # dplyr installed, but not used inside dplyr verb
-           error = function(e) stop_("argument `", arg_name, "` is missing with no default ",
-                                     "or function not used inside a valid dplyr verb", 
-                                     # tryCatch adds 4 system calls, subtract them
-                                     call = call - 4))
 }
 
-get_root_env_address <- function() {
-  sub("<environment: (.*)>", "\\1", utils::capture.output(sys.frames()[[1]]))
+unique_call_id <- function(entire_session = FALSE) {
+  if (entire_session == TRUE) {
+    c(envir = "session",
+      call = "session")
+  } else {
+    # combination of environment ID (like "0x7fed4ee8c848")
+    # and highest system call
+    c(envir = gsub("<environment: (.*)>", "\\1", utils::capture.output(sys.frames()[[1]])),
+      call = paste0(deparse(sys.calls()[[1]]), collapse = ""))
+  }
 }
 
-remember_thrown_message <- function(fn) {
-  assign(x = paste0("address_", fn),
-         value = get_root_env_address(),
-         envir = mo_env)
+remember_thrown_message <- function(fn, entire_session = FALSE) {
+  # this is to prevent that messages/notes will be printed for every dplyr group
+  # e.g. this would show a msg 4 times: example_isolates %>% group_by(hospital_id) %>% filter(mo_is_gram_negative())
+  assign(x = paste0("thrown_msg_", fn),
+         value = unique_call_id(entire_session = entire_session),
+         envir = pkg_env)
 }
 
-message_not_thrown_before <- function(fn) {
-  is.null(mo_env[[paste0("address_", fn)]]) || !identical(mo_env[[paste0("address_", fn)]], get_root_env_address())
+message_not_thrown_before <- function(fn, entire_session = FALSE) {
+  is.null(pkg_env[[paste0("thrown_msg_", fn)]]) || !identical(pkg_env[[paste0("thrown_msg_", fn)]], unique_call_id(entire_session))
+}
+
+reset_all_thrown_messages <- function() {
+  # for unit tests, where the environment and highest system call do not change
+  pkg_env_contents <- ls(envir = pkg_env)
+  rm(list = pkg_env_contents[pkg_env_contents %like% "^thrown_msg_"],
+     envir = pkg_env)
 }
 
 has_colour <- function() {
-  # this is a base R version of crayon::has_color
+  # this is a base R version of crayon::has_color, but disables colours on emacs
+  
+  if (Sys.getenv("EMACS") != "" || Sys.getenv("INSIDE_EMACS") != "") {
+    # disable on emacs, which only supports 8 colours
+    return(FALSE)
+  }
   enabled <- getOption("crayon.enabled")
   if (!is.null(enabled)) {
     return(isTRUE(enabled))
@@ -581,20 +647,6 @@ has_colour <- function() {
     }
     return(FALSE)
   }
-  emacs_version <- function() {
-    ver <- Sys.getenv("INSIDE_EMACS")
-    if (ver == "") {
-      return(NA_integer_)
-    }
-    ver <- gsub("'", "", ver)
-    ver <- strsplit(ver, ",", fixed = TRUE)[[1]]
-    ver <- strsplit(ver, ".", fixed = TRUE)[[1]]
-    as.numeric(ver)
-  }
-  if ((Sys.getenv("EMACS") != "" || Sys.getenv("INSIDE_EMACS") != "") &&
-      !is.na(emacs_version()[1]) && emacs_version()[1] >= 23) {
-    return(TRUE)
-  }
   if ("COLORTERM" %in% names(Sys.getenv())) {
     return(TRUE)
   }
@@ -656,6 +708,15 @@ font_grey_bg <- function(..., collapse = " ") {
 font_green_bg <- function(..., collapse = " ") {
   try_colour(..., before = "\033[42m", after = "\033[49m", collapse = collapse)
 }
+font_rsi_R_bg <- function(..., collapse = " ") {
+  try_colour(..., before = "\033[48;5;202m", after = "\033[49m", collapse = collapse)
+}
+font_rsi_S_bg <- function(..., collapse = " ") {
+  try_colour(..., before = "\033[48;5;76m", after = "\033[49m", collapse = collapse)
+}
+font_rsi_I_bg <- function(..., collapse = " ") {
+  try_colour(..., before = "\033[48;5;148m", after = "\033[49m", collapse = collapse)
+}
 font_red_bg <- function(..., collapse = " ") {
   try_colour(..., before = "\033[41m", after = "\033[49m", collapse = collapse)
 }

R/aa_helper_pm_functions.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/ab.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/ab_class_selectors.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -25,11 +25,11 @@
 
 #' Antibiotic class selectors
 #' 
-#' Use these selection helpers inside any function that allows [Tidyverse selection helpers](https://tidyselect.r-lib.org/reference/language.html), such as [`select()`][dplyr::select()] and [`pivot_longer()`][tidyr::pivot_longer()]. They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.
+#' These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.
 #' @inheritParams filter_ab_class 
-#' @details All columns 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.
+#' @details \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 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, "."), "")}}
 #' 
-#' **N.B. These functions require the `tidyselect` package to be installed**, that comes with the `dplyr` package. An error will be thrown if the `tidyselect` package is not installed, or if the functions are used outside a function that allows [Tidyverse selection helpers](https://tidyselect.r-lib.org/reference/language.html) such as [`select()`][dplyr::select()] and [`pivot_longer()`][tidyr::pivot_longer()]`.
+#' All columns 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.
 #' @rdname antibiotic_class_selectors
 #' @seealso [filter_ab_class()] for the `filter()` equivalent.
 #' @name antibiotic_class_selectors
@@ -37,6 +37,14 @@
 #' @inheritSection AMR Reference data publicly available
 #' @inheritSection AMR Read more on our website!
 #' @examples 
+#' # `example_isolates` is a dataset available in the AMR package.
+#' # See ?example_isolates.
+#' 
+#' # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
+#' example_isolates[, c(carbapenems())]
+#' # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
+#' example_isolates[, c("mo", aminoglycosides())]
+#' 
 #' if (require("dplyr")) {
 #' 
 #'   # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
@@ -63,7 +71,12 @@
 #'   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 equal:
+#'   # (though the row names on the first are more correct)
+#'   example_isolates %>% filter_carbapenems("R", "all")
+#'   example_isolates %>% filter(across(carbapenems(), ~. == "R"))
 #' }
 ab_class <- function(ab_class) {
   ab_selector(ab_class, function_name = "ab_class")
@@ -150,11 +163,15 @@ tetracyclines <- function() {
 ab_selector <- function(ab_class, function_name) {
   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)
-
-  peek_vars_tidyselect <- import_fn("peek_vars", "tidyselect")
-  vars_vct <- peek_vars_tidyselect(fn = function_name)
-  vars_df <- data.frame(as.list(vars_vct), stringsAsFactors = FALSE)[1, , drop = FALSE]
-  colnames(vars_df) <- vars_vct
+  
+  if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 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)
+  }
+  
+  vars_df <- get_current_data(arg_name = NA, call = -3)
   ab_in_data <- get_column_abx(vars_df, info = FALSE)
   
   if (length(ab_in_data) == 0) {
@@ -175,15 +192,19 @@ ab_selector <- function(ab_class, function_name) {
   }
   # get the columns with a group names in the chosen ab class
   agents <- ab_in_data[names(ab_in_data) %in% ab_reference$ab]
-  if (length(agents) == 0) {
-    message_("No antimicrobial agents of class ", ab_group, " found", examples, ".")
-  } else {
-    message_("Selecting ", ab_group, ": ",
-             paste(paste0("'", font_bold(agents, collapse = NULL),
-                          "' (", ab_name(names(agents), tolower = TRUE, language = NULL), ")"),
-                   collapse = ", "),
-             as_note = FALSE,
-             extra_indent = nchar(paste0("Selecting ", ab_group, ": ")))
-  }
+  if (message_not_thrown_before(function_name)) {
+    if (length(agents) == 0) {
+      message_("No antimicrobial agents of class ", ab_group, " found", examples, ".")
+    } else {
+      agents_formatted <- paste0("column '", font_bold(agents, collapse = NULL), "'")
+      agents_names <- ab_name(names(agents), tolower = TRUE, language = NULL)
+      agents_formatted[agents != agents_names] <- paste0(agents_formatted[agents != agents_names],
+                                                         " (", agents_names[agents != agents_names], ")")
+      message_("Selecting ", ab_group, ": ", paste(agents_formatted, collapse = ", "),
+               as_note = FALSE,
+               extra_indent = nchar(paste0("Selecting ", ab_group, ": ")))
+    }
+   remember_thrown_message(function_name)
+ }
   unname(agents)
 }

R/ab_from_text.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -33,7 +33,7 @@
 #' @param translate_ab if `type = "drug"`: a column name of the [antibiotics] data set to translate the antibiotic abbreviations to, using [ab_property()]. Defaults to `FALSE`. Using `TRUE` is equal to using "name".
 #' @param thorough_search logical to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to `TRUE` will take considerably more time than when using `FALSE`. At default, it will turn `TRUE` when all input elements contain a maximum of three words.
 #' @param ... arguments passed on to [as.ab()]
-#' @details This function is also internally used by [as.ab()], although it then only searches for the first drug name and will throw a note if more drug names could have been returned.
+#' @details This function is also internally used by [as.ab()], although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the [as.ab()] function may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems.
 #' 
 #' ## Argument `type`
 #' At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses [as.ab()] internally, it will correct for misspelling.
@@ -115,7 +115,7 @@ ab_from_text <- function(text,
     translate_ab <- get_translate_ab(translate_ab)
     
     if (isTRUE(thorough_search) | 
-        (isTRUE(is.null(thorough_search)) & max(sapply(text_split_all, length), na.rm = TRUE) <= 3)) {
+        (isTRUE(is.null(thorough_search)) & max(vapply(FUN.VALUE = double(1), text_split_all, length), na.rm = TRUE) <= 3)) {
       text_split_all <- text_split_all[nchar(text_split_all) >= 4 & grepl("[a-z]+", text_split_all)]
       result <- lapply(text_split_all, function(text_split) {
         progress$tick()
@@ -203,7 +203,7 @@ ab_from_text <- function(text,
   
   # collapse text if needed
   if (!is.null(collapse)) {
-    result <- sapply(result, function(x) {
+    result <- vapply(FUN.VALUE = character(1), result, function(x) {
       if (length(x) == 1 & all(is.na(x))) {
         NA_character_
       } else {

R/ab_property.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/age.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/amr.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/atc_online.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/availability.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -46,11 +46,11 @@ availability <- function(tbl, width = NULL) {
   meet_criteria(tbl, allow_class = "data.frame")
   meet_criteria(width, allow_class = "numeric", allow_NULL = TRUE)
   
-  x <- sapply(tbl, function(x) {
+  x <- vapply(FUN.VALUE = double(1), tbl, function(x) {
     1 - sum(is.na(x)) / length(x) 
   })
-  n <- sapply(tbl, function(x) length(x[!is.na(x)]))
-  R <- sapply(tbl, function(x) ifelse(is.rsi(x), resistance(x, minimum = 0), NA))
+  n <- vapply(FUN.VALUE = double(1), tbl, function(x) length(x[!is.na(x)]))
+  R <- vapply(FUN.VALUE = double(1), tbl, function(x) ifelse(is.rsi(x), resistance(x, minimum = 0), NA_real_))
   R_print <- character(length(R))
   R_print[!is.na(R)] <- percentage(R[!is.na(R)])
   R_print[is.na(R)] <- ""

R/bug_drug_combinations.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -75,7 +75,7 @@ bug_drug_combinations <- function(x,
   x_class <- class(x)
   x <- as.data.frame(x, stringsAsFactors = FALSE)
   x[, col_mo] <- FUN(x[, col_mo, drop = TRUE], ...)
-  x <- x[, c(col_mo, names(which(sapply(x, is.rsi)))), drop = FALSE]
+  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]))
   
@@ -89,7 +89,7 @@ bug_drug_combinations <- function(x,
   
   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(sapply(x, is.rsi))), drop = FALSE]
+    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))
@@ -165,7 +165,7 @@ format.bug_drug_combinations <- function(x,
   
   remove_NAs <- function(.data) {
     cols <- colnames(.data)
-    .data <- as.data.frame(sapply(.data, function(x) ifelse(is.na(x), "", x), simplify = FALSE),
+    .data <- as.data.frame(lapply(.data, function(x) ifelse(is.na(x), "", x)),
                            stringsAsFactors = FALSE)
     colnames(.data) <- cols
     .data
@@ -235,7 +235,7 @@ format.bug_drug_combinations <- function(x,
   }
   
   if (remove_intrinsic_resistant == TRUE) {
-    y <- y[, !sapply(y, function(col) all(col %like% "100", na.rm = TRUE) & !any(is.na(col))), drop = FALSE]
+    y <- y[, !vapply(FUN.VALUE = logical(1), y, function(col) all(col %like% "100", na.rm = TRUE) & !any(is.na(col))), drop = FALSE]
   }
   
   rownames(y) <- NULL

R/catalogue_of_life.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -44,7 +44,7 @@ format_included_data_number <- function(data) {
 #' This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life.
 #' @section Catalogue of Life:
 #' \if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
-#' This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <http://www.catalogueoflife.org>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, [lpsn.dsmz.de](https://lpsn.dsmz.de)). This supplementation is needed until the [CoL+ project](https://github.com/Sp2000/colplus) is finished, which we await.
+#' This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <http://www.catalogueoflife.org>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, [lpsn.dsmz.de](https://lpsn.dsmz.de)). This supplementation is needed until the [CoL+ project](https://github.com/CatalogueOfLife/general) is finished, which we await.
 #'
 #' [Click here][catalogue_of_life] for more information about the included taxa. Check which versions of the CoL and LSPN were included in this package with [catalogue_of_life_version()].
 #' @section Included taxa:

R/count.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/data.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -120,7 +120,7 @@
 #' In February 2020, the DSMZ records were merged with the List of Prokaryotic names with Standing in Nomenclature (LPSN).
 #' @source Catalogue of Life: Annual Checklist (public online taxonomic database), <http://www.catalogueoflife.org> (check included annual version with [catalogue_of_life_version()]).
 #' 
-#' Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: 10.1099/ijsem.0.002786
+#' Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; \doi{10.1099/ijsem.0.002786}
 #'
 #' Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, <https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date> and <https://lpsn.dsmz.de> (check included version with [catalogue_of_life_version()]).
 #' @inheritSection AMR Reference data publicly available
@@ -147,7 +147,7 @@ catalogue_of_life <- list(
 #' - `prevalence`\cr Prevalence of the microorganism, see [as.mo()]
 #' @source Catalogue of Life: Annual Checklist (public online taxonomic database), <http://www.catalogueoflife.org> (check included annual version with [catalogue_of_life_version()]).
 #' 
-#' Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: 10.1099/ijsem.0.002786
+#' Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; \doi{10.1099/ijsem.0.002786}
 #' @inheritSection AMR Reference data publicly available
 #' @inheritSection AMR Read more on our website!
 #' @seealso [as.mo()] [mo_property()] [microorganisms]
@@ -178,7 +178,7 @@ catalogue_of_life <- list(
 #' - `gender`\cr gender of the patient
 #' - `patient_id`\cr ID of the patient
 #' - `mo`\cr ID of microorganism created with [as.mo()], see also [microorganisms]
-#' - `PEN:RIF`\cr `r sum(sapply(example_isolates, is.rsi))` different antibiotics with class [`rsi`] (see [as.rsi()]); these column names occur in the [antibiotics] data set and can be translated with [ab_name()]
+#' - `PEN:RIF`\cr `r sum(vapply(FUN.VALUE = logical(1), example_isolates, is.rsi))` different antibiotics with class [`rsi`] (see [as.rsi()]); these column names occur in the [antibiotics] data set and can be translated with [ab_name()]
 #' @inheritSection AMR Reference data publicly available
 #' @inheritSection AMR Read more on our website!
 "example_isolates"
@@ -225,7 +225,7 @@ catalogue_of_life <- list(
 #' - `Inducible clindamycin resistance`\cr Clindamycin can be induced?
 #' - `Comment`\cr Other comments
 #' - `Date of data entry`\cr Date this data was entered in WHONET
-#' - `AMP_ND10:CIP_EE`\cr `r sum(sapply(WHONET, is.rsi))` different antibiotics. You can lookup the abbreviations in the [antibiotics] data set, or use e.g. [`ab_name("AMP")`][ab_name()] to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using [as.rsi()].
+#' - `AMP_ND10:CIP_EE`\cr `r sum(vapply(FUN.VALUE = logical(1), WHONET, is.rsi))` different antibiotics. You can lookup the abbreviations in the [antibiotics] data set, or use e.g. [`ab_name("AMP")`][ab_name()] to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using [as.rsi()].
 #' @inheritSection AMR Reference data publicly available
 #' @inheritSection AMR Read more on our website!
 "WHONET"

R/deprecated.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/disk.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -69,13 +69,13 @@ as.disk <- function(x, na.rm = FALSE) {
     
     na_before <- length(x[is.na(x)])
     
-    # heavily based on the function from our cleaner package:
+    # heavily based on cleaner::clean_double():
     clean_double2 <- function(x, remove = "[^0-9.,-]", fixed = FALSE) {
       x <- gsub(",", ".", x)
       # remove ending dot/comma
       x <- gsub("[,.]$", "", x)
       # only keep last dot/comma
-      reverse <- function(x) sapply(lapply(strsplit(x, NULL), rev), paste, collapse = "")
+      reverse <- function(x) vapply(FUN.VALUE = character(1), lapply(strsplit(x, NULL), rev), paste, collapse = "")
       x <- sub("{{dot}}", ".", 
                gsub(".", "",
                     reverse(sub(".", "}}tod{{",

R/episode.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -25,26 +25,34 @@
 
 #' Determine (new) episodes for patients
 #' 
-#' This function determines which items in a vector can be considered (the start of) a new episode, based on the argument `episode_days`. This can be used to determine clinical episodes for any epidemiological analysis.
+#' These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument `episode_days`. This can be used to determine clinical episodes for any epidemiological analysis. The [get_episode()] function returns the index number of the episode per group, while the [is_new_episode()] function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode.
 #' @inheritSection lifecycle Stable lifecycle
 #' @param x vector of dates (class `Date` or `POSIXt`)
-#' @param episode_days length of the required episode in days, defaults to 365. Every element in the input will return `TRUE` after this number of days has passed since the last included date, independent of calendar years. Please see *Details*.
+#' @param episode_days length of the required episode in days, please see *Details*
 #' @param ... arguments passed on to [as.Date()]
 #' @details 
 #' Dates are first sorted from old to new. The oldest date will mark the start of the first episode. After this date, the next date will be marked that is at least `episode_days` days later than the start of the first episode. From that second marked date on, the next date will be marked that is at least `episode_days` days later than the start of the second episode which will be the start of the third episode, and so on. Before the vector is being returned, the original order will be restored.
 #' 
-#' The [first_isolate()] function is a wrapper around the [is_new_episode()] function, but more efficient for data sets containing microorganism codes or names.
+#' The [first_isolate()] function is a wrapper around the [is_new_episode()] function, but is more efficient for data sets containing microorganism codes or names.
 #' 
-#' The `dplyr` package is not required for this function to work, but this function works conveniently inside `dplyr` verbs such as [`filter()`][dplyr::filter()], [`mutate()`][dplyr::mutate()] and [`summarise()`][dplyr::summarise()].
-#' @return a [logical] vector
+#' The `dplyr` package is not required for these functions to work, but these functions support [variable grouping][dplyr::group_by()] and work conveniently inside `dplyr` verbs such as [`filter()`][dplyr::filter()], [`mutate()`][dplyr::mutate()] and [`summarise()`][dplyr::summarise()].
+#' @return 
+#' * [get_episode()]: a [double] vector
+#' * [is_new_episode()]: a [logical] vector
+#' @seealso [first_isolate()]
+#' @rdname get_episode
 #' @export
 #' @inheritSection AMR Read more on our website!
 #' @examples
 #' # `example_isolates` is a dataset available in the AMR package.
 #' # See ?example_isolates.
 #' 
-#' is_new_episode(example_isolates$date)
+#' get_episode(example_isolates$date, episode_days = 60)
 #' is_new_episode(example_isolates$date, episode_days = 60)
+#' 
+#' # filter on results from the third 60-day episode only, using base R
+#' example_isolates[which(get_episode(example_isolates$date, 60) == 3), ]
+#' 
 #' \donttest{
 #' if (require("dplyr")) {
 #'   # is_new_episode() can also be used in dplyr verbs to determine patient
@@ -54,7 +62,15 @@
 #'                               size = 2000,
 #'                               replace = TRUE)) %>% 
 #'     group_by(condition) %>%
-#'     mutate(new_episode = is_new_episode(date))
+#'     mutate(new_episode = is_new_episode(date, 365))
+#'     
+#'   example_isolates %>%
+#'     group_by(hospital_id, patient_id) %>%
+#'     transmute(date, 
+#'               patient_id,
+#'               new_index = get_episode(date, 60),
+#'               new_logical = is_new_episode(date, 60))
+#'   
 #'   
 #'   example_isolates %>%
 #'     group_by(hospital_id) %>% 
@@ -71,7 +87,7 @@
 #'     
 #'   y <- example_isolates %>%
 #'     group_by(patient_id, mo) %>%
-#'     filter(is_new_episode(date))
+#'     filter(is_new_episode(date, 365))
 #'
 #'   identical(x$patient_id, y$patient_id)
 #'   
@@ -79,21 +95,52 @@
 #'   # since you can now group on anything that seems relevant:
 #'   example_isolates %>%
 #'     group_by(patient_id, mo, hospital_id, ward_icu) %>%
-#'     mutate(flag_episode = is_new_episode(date))
+#'     mutate(flag_episode = is_new_episode(date, 365))
 #' }
 #' }
-is_new_episode <- function(x, episode_days = 365, ...) {
+get_episode <- function(x, episode_days, ...) {
   meet_criteria(x, allow_class = c("Date", "POSIXt"))
   meet_criteria(episode_days, allow_class = c("numeric", "double", "integer"), has_length = 1)
   
+  exec_episode(type = "sequential",
+               x = x, 
+               episode_days = episode_days,
+               ... = ...)
+}
+
+#' @rdname get_episode
+#' @export
+is_new_episode <- function(x, episode_days, ...) {
+  meet_criteria(x, allow_class = c("Date", "POSIXt"))
+  meet_criteria(episode_days, allow_class = c("numeric", "double", "integer"), has_length = 1)
+  
+  exec_episode(type = "logical",
+               x = x, 
+               episode_days = episode_days,
+               ... = ...)
+}
+
+exec_episode <- function(type, x, episode_days, ...) {
   x <- as.double(as.Date(x, ...)) # as.Date() for POSIX classes
   if (length(x) == 1) {
-    return(TRUE)
+    if (type == "logical") {
+      return(TRUE)
+    } else if (type == "sequential") {
+      return(1)
+    }
   } else if (length(x) == 2) {
     if (max(x) - min(x) >= episode_days) {
-      return(c(TRUE, TRUE))
+      if (type == "logical") {
+        return(c(TRUE, TRUE))
+      } else if (type == "sequential") {
+        return(c(1, 2))
+      }
     } else {
-      return(c(TRUE, FALSE))
+      if (type == "logical") {
+        return(c(TRUE, FALSE))
+      } else if (type == "sequential") {
+        return(c(1, 1))
+      }
     }
   }
   
@@ -107,13 +154,22 @@ is_new_episode <- function(x, episode_days = 365, ...) {
     for (i in 2:length(x)) {
       if (isTRUE((x[i] - start) >= episode_days)) {
         ind <- ind + 1
-        indices[ind] <- i
+        if (type == "logical") {
+          indices[ind] <- i
+        }
         start <- x[i]
       }
+      if (type == "sequential") {
+        indices[i] <- ind
+      }
+    }
+    if (type == "logical") {
+      result <- rep(FALSE, length(x))
+      result[indices] <- TRUE
+      result
+    } else if (type == "sequential") {
+      indices
     }
-    result <- rep(FALSE, length(x))
-    result[indices] <- TRUE
-    result
   }
   
   df <- data.frame(x = x,

R/eucast_rules.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -64,6 +64,8 @@ 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. Currently supported: `r paste0(names(EUCAST_VERSION_BREAKPOINTS), collapse = ", ")`.
 #' @param version_expertrules the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Currently supported: `r paste0(names(EUCAST_VERSION_EXPERT_RULES), collapse = ", ")`.
+#' @param ampc_cephalosporin_resistance a character value that should be applied 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 susceptible (S) results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these agents. A value of `NA` for this argument will remove results for these agents, while e.g. a value of `"R"` will make the results for these agents resistant. Use `NULL` to not alter the results for AmpC de-repressed cephalosporin-resistant mutants. \cr For *EUCAST Expert Rules* v3.2, this rule applies to: *`r gsub("[)(^]", "", gsub("|", ", ", eucast_rules_file[which(eucast_rules_file$reference.version == 3.2 & eucast_rules_file$reference.rule %like% "ampc"), "this_value"][1], fixed = TRUE))`*.
+#' 
 #' @param ... column name of an antibiotic, please see section *Antibiotics* below
 #' @inheritParams first_isolate
 #' @details
@@ -81,7 +83,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
 #' 
 #' Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.
 #' 
-#' Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include `"other"` to the `rules` argument, or use `eucast_rules(..., rules = "all")`.
+#' Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include `"other"` to the `rules` argument, or use `eucast_rules(..., rules = "all")`. You can also set the option `AMR_eucastrules`, i.e. run `options(AMR_eucastrules = "all")`.
 #' @section Antibiotics:
 #' To define antibiotics column names, leave as it is to determine it automatically with [guess_ab_col()] or input a text (case-insensitive), or use `NULL` to skip a column (e.g. `TIC = NULL` to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
 #'
@@ -94,7 +96,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
 #' @return The input of `x`, possibly with edited values of antibiotics. Or, if `verbose = TRUE`, a [data.frame] with all original and new values of the affected bug-drug combinations.
 #' @source
 #' - EUCAST Expert Rules. Version 2.0, 2012.\cr
-#'   Leclercq et al. **EUCAST expert rules in antimicrobial susceptibility testing.** *Clin Microbiol Infect.* 2013;19(2):141-60.  [(link)](https://doi.org/10.1111/j.1469-0691.2011.03703.x)
+#'   Leclercq et al. **EUCAST expert rules in antimicrobial susceptibility testing.** *Clin Microbiol Infect.* 2013;19(2):141-60; \doi{https://doi.org/10.1111/j.1469-0691.2011.03703.x}
 #' - EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf)
 #' - EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf)
 #' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx)
@@ -149,6 +151,7 @@ eucast_rules <- function(x,
                          verbose = FALSE,
                          version_breakpoints = 10.0,
                          version_expertrules = 3.2,
+                         ampc_cephalosporin_resistance = NA,
                          ...) {
   meet_criteria(x, allow_class = "data.frame")
   meet_criteria(col_mo, allow_class = "character", has_length = 1, is_in = colnames(x), allow_NULL = TRUE)
@@ -157,6 +160,7 @@ eucast_rules <- function(x,
   meet_criteria(verbose, allow_class = "logical", has_length = 1)
   meet_criteria(version_breakpoints, allow_class = "numeric", has_length = 1)
   meet_criteria(version_expertrules, allow_class = "numeric", has_length = 1)
+  meet_criteria(ampc_cephalosporin_resistance, allow_class = c("rsi", "character"), has_length = 1, allow_NA = TRUE, allow_NULL = TRUE, is_in = c("R", "S", "I"))
   
   x_deparsed <- deparse(substitute(x))
   if (length(x_deparsed) > 1 || !all(x_deparsed %like% "[a-z]+")) {
@@ -534,7 +538,7 @@ eucast_rules <- function(x,
       strsplit(",") %pm>%
       unlist() %pm>%
       trimws() %pm>%
-      sapply(function(x) if (x %in% antibiotics$ab) ab_name(x, language = NULL, tolower = TRUE) else x) %pm>%
+      vapply(FUN.VALUE = character(1), function(x) if (x %in% antibiotics$ab) ab_name(x, language = NULL, tolower = TRUE) else x) %pm>%
       sort() %pm>%
       paste(collapse = ", ")
     x <- gsub("_", " ", x, fixed = TRUE)
@@ -597,13 +601,14 @@ eucast_rules <- function(x,
   x <- as.data.frame(x, stringsAsFactors = FALSE) # no tibbles, data.tables, etc.
   rownames(x) <- NULL # will later be restored with old_attributes
   # create unique row IDs - combination of the MO and all ABx columns (so they will only run once per unique combination)
-  x$`.rowid` <- sapply(as.list(as.data.frame(t(x[, c(col_mo, cols_ab), drop = FALSE]),
+  x$`.rowid` <- vapply(FUN.VALUE = character(1),
+                       as.list(as.data.frame(t(x[, c(col_mo, cols_ab), drop = FALSE]),
                                              stringsAsFactors = FALSE)),
                        function(x) {
                          x[is.na(x)] <- "."
                          paste0(x, collapse = "")
                        })
-
+  
   # save original table, with the new .rowid column
   x.bak <- x
   # keep only unique rows for MO and ABx
@@ -731,7 +736,7 @@ eucast_rules <- function(x,
   # Official EUCAST rules ---------------------------------------------------
   eucast_notification_shown <- FALSE
   if (!is.null(list(...)$eucast_rules_df)) {
-    # this allows: eucast_rules(x, eucast_rules_df = AMR:::eucast_rules_file %pm>% filter(is.na(have_these_values)))
+    # this allows: eucast_rules(x, eucast_rules_df = AMR:::eucast_rules_file %>% filter(is.na(have_these_values)))
     eucast_rules_df <- list(...)$eucast_rules_df
   } else {
     # otherwise internal data file, created in data-raw/internals.R
@@ -749,6 +754,13 @@ eucast_rules <- function(x,
                               !reference.rule_group %like% "expert" |
                                 (reference.rule_group %like% "expert" & reference.version == version_expertrules))
   }
+  # filter out AmpC de-repressed cephalosporin-resistant mutants ----
+  if (is.null(ampc_cephalosporin_resistance)) {
+    eucast_rules_df <- subset(eucast_rules_df,
+                              !reference.rule %like% "ampc")
+  } else {
+    eucast_rules_df[which(eucast_rules_df$reference.rule %like% "ampc"), "to_value"] <- as.character(ampc_cephalosporin_resistance)
+  }
   
   for (i in seq_len(nrow(eucast_rules_df))) {
     
@@ -946,7 +958,7 @@ eucast_rules <- function(x,
                     by = c(".rowid" = "rowid")) %pm>% 
       pm_select(-`.rowid`) %pm>% 
       pm_select(row, pm_everything()) %pm>% 
-      pm_filter(!is.na(new)) %pm>%
+      pm_filter(!is.na(new) | is.na(new) & !is.na(old)) %pm>%
       pm_arrange(row, rule_group, rule_name, col)
     rownames(verbose_info) <- NULL
   }
@@ -1007,6 +1019,7 @@ eucast_rules <- function(x,
     if (total_n_changed > 0) {
       changed_summary <- verbose_info %pm>%
         pm_filter(!is.na(old)) %pm>%
+        pm_mutate(new = ifelse(is.na(new), "NA", new)) %pm>%
         pm_count(old, new, name = "n")
       cat(paste("   -", 
                 paste0(formatnr(changed_summary$n), " test result", ifelse(changed_summary$n > 1, "s", ""), " changed from ", 
@@ -1082,18 +1095,18 @@ edit_rsi <- function(x,
   
   if (length(rows) > 0 & length(cols) > 0) {
     new_edits <- x
-    if (any(!sapply(x[, cols, drop = FALSE], is.rsi), na.rm = TRUE)) {
-      track_changes$rsi_warn <- cols[!sapply(x[, cols, drop = FALSE], is.rsi)]
+    if (any(!vapply(FUN.VALUE = logical(1), x[, cols, drop = FALSE], is.rsi), na.rm = TRUE)) {
+      track_changes$rsi_warn <- cols[!vapply(FUN.VALUE = logical(1), x[, cols, drop = FALSE], is.rsi)]
     }
     tryCatch(
       # insert into original table
       new_edits[rows, cols] <- to,
       warning = function(w) {
         if (w$message %like% "invalid factor level") {
-          xyz <- sapply(cols, function(col) {
+          xyz <- vapply(FUN.VALUE = logical(1), cols, function(col) {
             new_edits[, col] <<- factor(x = as.character(pm_pull(new_edits, col)),
-                                       levels = unique(c(to, levels(pm_pull(new_edits, col)))))
-            invisible()
+                                        levels = unique(c(to, levels(pm_pull(new_edits, col)))))
+            TRUE
           })
           suppressWarnings(new_edits[rows, cols] <<- to)
           warning_('Value "', to, '" added to the factor levels of column(s) `', paste(cols, collapse = "`, `"), "` because this value was not an existing factor level. A better way is to use as.rsi() on beforehand on antimicrobial columns to guarantee the right structure.", call = FALSE)
@@ -1134,7 +1147,7 @@ edit_rsi <- function(x,
                                   stringsAsFactors = FALSE)
         colnames(verbose_new) <- c("rowid", "col", "mo_fullname", "old", "new",
                                    "rule", "rule_group", "rule_name", "rule_source")
-        verbose_new <- verbose_new %pm>% pm_filter(old != new | is.na(old))
+        verbose_new <- verbose_new %pm>% pm_filter(old != new | is.na(old) | is.na(new) & !is.na(old))
         # save changes to data set 'verbose_info'
         track_changes$verbose_info <- rbind(track_changes$verbose_info,
                                             verbose_new,

R/filter_ab_class.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -71,6 +71,7 @@
 #'     filter_fluoroquinolones("R", "all")
 #'   
 #'   # with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:
+#'   # (though the row names on the first are more correct)
 #'   example_isolates %>% filter_carbapenems("R", "all")
 #'   example_isolates %>% filter(across(carbapenems(), ~. == "R"))
 #' }
@@ -164,7 +165,7 @@ filter_ab_class <- function(x,
                  collapse = scope_txt),
            operator, toString(result), as_note = FALSE)
   x_transposed <- as.list(as.data.frame(t(x[, agents, drop = FALSE]), stringsAsFactors = FALSE))
-  filtered <- sapply(x_transposed, function(y) scope_fn(y %in% result, na.rm = TRUE))
+  filtered <- vapply(FUN.VALUE = logical(1), x_transposed, function(y) scope_fn(y %in% result, na.rm = TRUE))
   x <- x[which(filtered), , drop = FALSE]
   class(x) <- x_class
   x

R/first_isolate.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -27,7 +27,7 @@
 #'
 #' Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. To determine patient episodes not necessarily based on microorganisms, use [is_new_episode()] that also supports grouping with the `dplyr` package.
 #' @inheritSection lifecycle Stable lifecycle
-#' @param x a [data.frame] containing isolates. Can be omitted when used inside `dplyr` verbs, such as [`filter()`][dplyr::filter()], [`mutate()`][dplyr::mutate()] and [`summarise()`][dplyr::summarise()].
+#' @param x a [data.frame] containing isolates. Can be left blank when used inside `dplyr` verbs, such as [`filter()`][dplyr::filter()], [`mutate()`][dplyr::mutate()] and [`summarise()`][dplyr::summarise()].
 #' @param col_date column name of the result date (or date that is was received on the lab), defaults to the first column with a date class
 #' @param col_patient_id column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive)
 #' @param col_mo column name of the IDs of the microorganisms (see [as.mo()]), defaults to the first column of class [`mo`]. Values will be coerced using [as.mo()].
@@ -46,7 +46,7 @@
 #' @param include_unknown logical to determine whether 'unknown' microorganisms should be included too, i.e. microbial code `"UNKNOWN"`, which defaults to `FALSE`. For WHONET users, this means that all records with organism code `"con"` (*contamination*) will be excluded at default. Isolates with a microbial ID of `NA` will always be excluded as first isolate.
 #' @param ... arguments passed on to [first_isolate()] when using [filter_first_isolate()], or arguments passed on to [key_antibiotics()] when using [filter_first_weighted_isolate()]
 #' @details 
-#' These functions are context-aware when used inside `dplyr` verbs, such as `filter()`, `mutate()` and `summarise()`. This means that then the `x` argument can be omitted, please see *Examples*.
+#' These functions are context-aware when used inside `dplyr` verbs, such as `filter()`, `mutate()` and `summarise()`. This means that then the `x` argument can be left blank, please see *Examples*.
 #' 
 #' The [first_isolate()] function is a wrapper around the [is_new_episode()] function, but more efficient for data sets containing microorganism codes or names.
 #' 

R/g.test.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/ggplot_pca.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -306,7 +306,6 @@ pca_calculations <- function(pca_model,
     d <- pca_model$svd
     u <- predict(pca_model)$x / nobs.factor
     v <- pca_model$scaling
-    d.total <- sum(d ^ 2)
   } else {
     stop("Expected an object of class prcomp, princomp, PCA, or lda")
   }

R/ggplot_rsi.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/globals.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -60,6 +60,7 @@ globalVariables(c(".rowid",
                   "old_name",
                   "pattern",
                   "R",
+                  "reference.rule",
                   "reference.rule_group",
                   "reference.version",
                   "rsi_translation",

R/guess_ab_col.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -139,13 +139,13 @@ get_column_abx <- function(x,
   }
   x_bak <- x
   # only check columns that are a valid AB code, ATC code, name, abbreviation or synonym,
-  # or already have the rsi class (as.rsi) 
-  # and that have no more than 50% invalid values
+  # or already have the <rsi> class (as.rsi) 
+  # and that they have no more than 50% invalid values
   vectr_antibiotics <- unique(toupper(unlist(antibiotics[, c("ab", "atc", "name", "abbreviations", "synonyms")])))
   vectr_antibiotics <- vectr_antibiotics[!is.na(vectr_antibiotics) & nchar(vectr_antibiotics) >= 3]
-  x_columns <- sapply(colnames(x), function(col, df = x_bak) {
-    if (toupper(col) %in% vectr_antibiotics | 
-        is.rsi(as.data.frame(df, stringsAsFactors = FALSE)[, col, drop = TRUE]) |
+  x_columns <- vapply(FUN.VALUE = character(1), colnames(x), function(col, df = x_bak) {
+    if (toupper(col) %in% vectr_antibiotics || 
+        is.rsi(as.data.frame(df, stringsAsFactors = FALSE)[, col, drop = TRUE]) ||
         is.rsi.eligible(as.data.frame(df, stringsAsFactors = FALSE)[, col, drop = TRUE],
                         threshold = 0.5)) {
       return(col)

R/join_microorganisms.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/key_antibiotics.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -27,7 +27,7 @@
 #'
 #' These function can be used to determine first isolates (see [first_isolate()]). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates can then be called first *weighted* isolates.
 #' @inheritSection lifecycle Stable lifecycle
-#' @param x a [data.frame] with antibiotics columns, like `AMX` or `amox`. Can be omitted when used inside `dplyr` verbs, such as `filter()`, `mutate()` and `summarise()`.
+#' @param x a [data.frame] with antibiotics columns, like `AMX` or `amox`. Can be left blank when used inside `dplyr` verbs, such as `filter()`, `mutate()` and `summarise()`.
 #' @param y,z character vectors to compare
 #' @inheritParams first_isolate
 #' @param universal_1,universal_2,universal_3,universal_4,universal_5,universal_6 column names of **broad-spectrum** antibiotics, case-insensitive. See details for which antibiotics will be used at default (which are guessed with [guess_ab_col()]).
@@ -36,7 +36,7 @@
 #' @param warnings give a warning about missing antibiotic columns (they will be ignored)
 #' @param ... other arguments passed on to functions
 #' @details 
-#' The [key_antibiotics()] function is context-aware when used inside `dplyr` verbs, such as `filter()`, `mutate()` and `summarise()`. This means that then the `x` argument can be omitted, please see *Examples*.
+#' The [key_antibiotics()] function is context-aware when used inside `dplyr` verbs, such as `filter()`, `mutate()` and `summarise()`. This means that then the `x` argument can be left blank, please see *Examples*.
 #' 
 #' The function [key_antibiotics()] returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using [key_antibiotics_equal()], to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (`"."`) by [key_antibiotics()] and ignored by [key_antibiotics_equal()].
 #' 

R/kurtosis.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -71,5 +71,5 @@ kurtosis.matrix <- function(x, na.rm = FALSE, excess = FALSE) {
 kurtosis.data.frame <- function(x, na.rm = FALSE, excess = FALSE) {
   meet_criteria(na.rm, allow_class = "logical", has_length = 1)
   meet_criteria(excess, allow_class = "logical", has_length = 1)
-  sapply(x, kurtosis.default, na.rm = na.rm, excess = excess)
+  vapply(FUN.VALUE = double(1), x, kurtosis.default, na.rm = na.rm, excess = excess)
 }

R/lifecycle.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/like.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -102,7 +102,7 @@ like <- function(x, pattern, ignore.case = TRUE) {
           res[i] <- grepl(pattern[i], x[i], ignore.case = FALSE, fixed = fixed)
         }
       }
-      res <- sapply(pattern, function(pttrn) grepl(pttrn, x, ignore.case = FALSE, fixed = fixed))
+      res <- vapply(FUN.VALUE = logical(1), pattern, function(pttrn) grepl(pttrn, x, ignore.case = FALSE, fixed = fixed))
       res2 <- as.logical(rowSums(res))
       # get only first item of every hit in pattern
       res2[duplicated(res)] <- FALSE

R/mdro.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -27,7 +27,7 @@
 #'
 #' Determine which isolates are multidrug-resistant organisms (MDRO) according to international and national guidelines.
 #' @inheritSection lifecycle Stable lifecycle
-#' @param x a [data.frame] with antibiotics columns, like `AMX` or `amox`. Can be omitted when used inside `dplyr` verbs, such as [`filter()`][dplyr::filter()], [`mutate()`][dplyr::mutate()] and [`summarise()`][dplyr::summarise()].
+#' @param x a [data.frame] with antibiotics columns, like `AMX` or `amox`. Can be left blank when used inside `dplyr` verbs, such as [`filter()`][dplyr::filter()], [`mutate()`][dplyr::mutate()] and [`summarise()`][dplyr::summarise()].
 #' @param guideline a specific guideline to follow. When left empty, the publication by Magiorakos *et al.* (2012, Clinical Microbiology and Infection) will be followed, please see *Details*.
 #' @inheritParams eucast_rules
 #' @param pct_required_classes minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for *S. aureus*. Setting this `pct_required_classes` argument to `0.5` (default) means that for every *S. aureus* isolate at least 8 different classes must be available. Any lower number of available classes will return `NA` for that isolate.
@@ -35,7 +35,7 @@
 #' @param verbose a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.
 #' @inheritSection eucast_rules Antibiotics
 #' @details 
-#' These functions are context-aware when used inside `dplyr` verbs, such as `filter()`, `mutate()` and `summarise()`. This means that then the `x` argument can be omitted, please see *Examples*.
+#' These functions are context-aware when used inside `dplyr` verbs, such as `filter()`, `mutate()` and `summarise()`. This means that then the `x` argument can be left blank, please see *Examples*.
 #' 
 #' For the `pct_required_classes` argument, values above 1 will be divided by 100. This is to support both fractions (`0.75` or `3/4`) and percentages (`75`).
 #' 
@@ -59,7 +59,7 @@
 #' 
 #' * `guideline = "MRGN"`
 #'
-#'   The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6
+#'   The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7; \doi{10.1186/s13756-015-0047-6}
 #' 
 #' * `guideline = "BRMO"`
 #'
@@ -193,28 +193,28 @@ mdro <- function(x,
     guideline$name <- "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance."
     guideline$author <- "Magiorakos AP, Srinivasan A, Carey RB, ..., Vatopoulos A, Weber JT, Monnet DL"
     guideline$version <- NA
-    guideline$source <- "Clinical Microbiology and Infection 18:3, 2012. DOI: 10.1111/j.1469-0691.2011.03570.x"
+    guideline$source_url <- "Clinical Microbiology and Infection 18:3, 2012; doi: 10.1111/j.1469-0691.2011.03570.x"
     guideline$type <- "MDRs/XDRs/PDRs"
     
   } else if (guideline$code == "eucast3.1") {
     guideline$name <- "EUCAST Expert Rules, \"Intrinsic Resistance and Exceptional Phenotypes Tables\""
     guideline$author <- "EUCAST (European Committee on Antimicrobial Susceptibility Testing)"
     guideline$version <- "3.1, 2016"
-    guideline$source <- "https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf"
+    guideline$source_url <- "https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf"
     guideline$type <- "EUCAST Exceptional Phenotypes"
     
   } else if (guideline$code == "eucast3.2") {
     guideline$name <- "EUCAST Expert Rules, \"Intrinsic Resistance and Unusual Phenotypes\""
     guideline$author <- "EUCAST (European Committee on Antimicrobial Susceptibility Testing)"
     guideline$version <- "3.2, 2020"
-    guideline$source <- "https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf"
+    guideline$source_url <- "https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf"
     guideline$type <- "EUCAST Unusual Phenotypes"
     
   } else if (guideline$code == "tb") {
     guideline$name <- "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis"
     guideline$author <- "WHO (World Health Organization)"
     guideline$version <- "WHO/HTM/TB/2014.11, 2014"
-    guideline$source <- "https://www.who.int/tb/publications/pmdt_companionhandbook/en/"
+    guideline$source_url <- "https://www.who.int/tb/publications/pmdt_companionhandbook/en/"
     guideline$type <- "MDR-TB's"
     
     # support per country:
@@ -222,14 +222,14 @@ mdro <- function(x,
     guideline$name <- "Cross-border comparison of the Dutch and German guidelines on multidrug-resistant Gram-negative microorganisms"
     guideline$author <- "M\u00fcller J, Voss A, K\u00f6ck R, ..., Kern WV, Wendt C, Friedrich AW"
     guideline$version <- NA
-    guideline$source <- "Antimicrobial Resistance and Infection Control 4:7, 2015. DOI: 10.1186/s13756-015-0047-6"
+    guideline$source_url <- "Antimicrobial Resistance and Infection Control 4:7, 2015; doi: 10.1186/s13756-015-0047-6"
     guideline$type <- "MRGNs"
     
   } else if (guideline$code == "brmo") {
     guideline$name <- "WIP-Richtlijn Bijzonder Resistente Micro-organismen (BRMO)"
     guideline$author <- "RIVM (Rijksinstituut voor de Volksgezondheid)"
     guideline$version <- "Revision as of December 2017"
-    guideline$source <- "https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH"
+    guideline$source_url <- "https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH"
     guideline$type <- "BRMOs"
   } else {
     stop("This guideline is currently unsupported: ", guideline$code, call. = FALSE)
@@ -413,6 +413,7 @@ mdro <- function(x,
                               ...)
   }
   
+  # nolint start
   AMC <- cols_ab["AMC"]
   AMK <- cols_ab["AMK"]
   AMP <- cols_ab["AMP"]
@@ -555,6 +556,7 @@ mdro <- function(x,
   abx_tb <- c(CAP, ETH, GAT, INH, PZA, RIF, RIB, RFP)
   abx_tb <- abx_tb[!is.na(abx_tb)]
   stop_if(guideline$code == "tb" & length(abx_tb) == 0, "no antimycobacterials found in data set")
+  # nolint end
   
   if (combine_SI == TRUE) {
     search_result <- "R"
@@ -574,8 +576,8 @@ mdro <- function(x,
         ifelse(!is.na(guideline$version),
                paste0(word_wrap(paste0(font_bold("Version:   "), guideline$version), extra_indent = 11, as_note = FALSE), "\n"),
                ""),
-        word_wrap(paste0(font_bold("Source:    "), guideline$source), extra_indent = 11, as_note = FALSE), "\n",
-        "\n", sep = "")
+        paste0(font_bold("Source:    "), guideline$source_url),
+        "\n\n", sep = "")
   }
   
   ab_missing <- function(ab) {
@@ -585,9 +587,8 @@ mdro <- function(x,
     x[!is.na(x)]
   }
   
-  verbose_df <- NULL
-  
   # antibiotic classes
+  # nolint start
   aminoglycosides <- c(TOB, GEN)
   cephalosporins <- c(CDZ, CAC, CEC, CFR, RID, MAN, CTZ, CZD, CZO, CDR, DIT, FEP, CAT, CFM, CMX, CMZ, DIZ, CID, CFP, CSL, CND, CTX, CTT, CTF, FOX, CPM, CPO, CPD, CPR, CRD, CFS, CPT, CAZ, CCV, CTL, CTB, CZX, BPR, CFM1, CEI, CRO, CXM, LEX, CEP, HAP, CED, LTM, LOR)
   cephalosporins_1st <- c(CAC, CFR, RID, CTZ, CZD, CZO, CRD, CTL, LEX, CEP, HAP, CED)
@@ -595,6 +596,7 @@ mdro <- function(x,
   cephalosporins_3rd <- c(CDZ, CDR, DIT, CAT, CFM, CMX, DIZ, CFP, CSL, CTX, CPM, CPD, CFS, CAZ, CCV, CTB, CZX, CRO, LTM)
   carbapenems <- c(DOR, ETP, IPM, MEM, MEV)
   fluoroquinolones <- c(CIP, ENX, FLE, GAT, GEM, GRX, LVX, LOM, MFX, NOR, OFX, PAZ, PEF, PRU, RFL, SPX, TMX, TVA)
+  # nolint end
   
   # helper function for editing the table
   trans_tbl <- function(to, rows, cols, any_all) {
@@ -604,9 +606,10 @@ mdro <- function(x,
       x[, cols] <- as.data.frame(lapply(x[, cols, drop = FALSE],
                                         function(col) as.rsi(col)), 
                                  stringsAsFactors = FALSE)
-      x[rows, "columns_nonsusceptible"] <<- sapply(rows, 
+      x[rows, "columns_nonsusceptible"] <<- vapply(FUN.VALUE = character(1),
+                                                   rows, 
                                                    function(row, group_vct = cols) {
-                                                     cols_nonsus <- sapply(x[row, group_vct, drop = FALSE], 
+                                                     cols_nonsus <- vapply(FUN.VALUE = logical(1), x[row, group_vct, drop = FALSE], 
                                                                            function(y) y %in% search_result)
                                                      paste(sort(c(unlist(strsplit(x[row, "columns_nonsusceptible", drop = TRUE], ", ")),
                                                                   names(cols_nonsus)[cols_nonsus])), 
@@ -620,7 +623,7 @@ mdro <- function(x,
       }
       x_transposed <- as.list(as.data.frame(t(x[, cols, drop = FALSE]),
                                             stringsAsFactors = FALSE))
-      row_filter <- sapply(x_transposed, function(y) search_function(y %in% search_result, na.rm = TRUE))
+      row_filter <- vapply(FUN.VALUE = logical(1), x_transposed, function(y) search_function(y %in% search_result, na.rm = TRUE))
       row_filter <- x[which(row_filter), "row_number", drop = TRUE]
       rows <- rows[rows %in% row_filter]
       x[rows, "MDRO"] <<- to
@@ -638,21 +641,27 @@ mdro <- function(x,
                                               function(col) as.rsi(col)),
                                        stringsAsFactors = FALSE)
       x[rows, "classes_in_guideline"] <<- length(lst)
-      x[rows, "classes_available"] <<- sapply(rows, 
+      x[rows, "classes_available"] <<- vapply(FUN.VALUE = double(1),
+                                              rows, 
                                               function(row, group_tbl = lst) {
-                                                sum(sapply(group_tbl, function(group) any(unlist(x[row, group[!is.na(group)], drop = TRUE]) %in% c("S", "I", "R"))))
+                                                sum(vapply(FUN.VALUE = logical(1),
+                                                           group_tbl, 
+                                                           function(group) any(unlist(x[row, group[!is.na(group)], drop = TRUE]) %in% c("S", "I", "R"))))
                                               })
       
       if (verbose == TRUE) {
-        x[rows, "columns_nonsusceptible"] <<- sapply(rows, 
+        x[rows, "columns_nonsusceptible"] <<- vapply(FUN.VALUE = character(1),
+                                                     rows, 
                                                      function(row, group_vct = lst_vector) {
-                                                       cols_nonsus <- sapply(x[row, group_vct, drop = FALSE], function(y) y %in% search_result)
+                                                       cols_nonsus <- vapply(FUN.VALUE = logical(1), x[row, group_vct, drop = FALSE], function(y) y %in% search_result)
                                                        paste(sort(names(cols_nonsus)[cols_nonsus]), collapse = ", ")
                                                      })
       }
-      x[rows, "classes_affected"] <<- sapply(rows, 
+      x[rows, "classes_affected"] <<- vapply(FUN.VALUE = double(1),
+                                             rows, 
                                              function(row, group_tbl = lst) {
-                                               sum(sapply(group_tbl, 
+                                               sum(vapply(FUN.VALUE = logical(1),
+                                                          group_tbl, 
                                                           function(group) {
                                                             any(unlist(x[row, group[!is.na(group)], drop = TRUE]) %in% search_result, na.rm = TRUE)
                                                           }),
@@ -661,7 +670,7 @@ mdro <- function(x,
       # for PDR; all agents are R (or I if combine_SI = FALSE)
       x_transposed <- as.list(as.data.frame(t(x[rows, lst_vector, drop = FALSE]),
                                             stringsAsFactors = FALSE))
-      row_filter <- sapply(x_transposed, function(y) all(y %in% search_result, na.rm = TRUE))
+      row_filter <- vapply(FUN.VALUE = logical(1), x_transposed, function(y) all(y %in% search_result, na.rm = TRUE))
       x[which(row_filter), "classes_affected"] <<- 999
     }
     

R/mic.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -107,14 +107,14 @@ as.mic <- function(x, na.rm = FALSE) {
     
     # these are allowed MIC values and will become factor levels
     ops <- c("<", "<=", "", ">=", ">")
-    lvls <- c(c(t(sapply(ops, function(x) paste0(x, "0.00", 1:9)))),
-              unique(c(t(sapply(ops, function(x) paste0(x, sort(as.double(paste0("0.0", 
+    lvls <- c(c(t(vapply(FUN.VALUE = character(9), ops, function(x) paste0(x, "0.00", 1:9)))),
+              unique(c(t(vapply(FUN.VALUE = character(104), ops, function(x) paste0(x, sort(as.double(paste0("0.0", 
                                                                                  sort(c(1:99, 125, 128, 256, 512, 625)))))))))),
-              unique(c(t(sapply(ops, function(x) paste0(x, sort(as.double(paste0("0.", 
+              unique(c(t(vapply(FUN.VALUE = character(103), ops, function(x) paste0(x, sort(as.double(paste0("0.", 
                                                                                  c(1:99, 125, 128, 256, 512))))))))),
-              c(t(sapply(ops, function(x) paste0(x, sort(c(1:9, 1.5)))))),
-              c(t(sapply(ops, function(x) paste0(x, c(10:98)[9:98 %% 2 == TRUE])))),
-              c(t(sapply(ops, function(x) paste0(x, sort(c(2 ^ c(7:10), 80 * c(2:12))))))))
+              c(t(vapply(FUN.VALUE = character(10), ops, function(x) paste0(x, sort(c(1:9, 1.5)))))),
+              c(t(vapply(FUN.VALUE = character(45), ops, function(x) paste0(x, c(10:98)[9:98 %% 2 == TRUE])))),
+              c(t(vapply(FUN.VALUE = character(15), ops, function(x) paste0(x, sort(c(2 ^ c(7:10), 80 * c(2:12))))))))
     
     na_before <- x[is.na(x) | x == ""] %pm>% length()
     x[!x %in% lvls] <- NA

R/mo.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       #
@@ -102,10 +102,10 @@
 #' @inheritSection catalogue_of_life Catalogue of Life
 #  (source as a section here, so it can be inherited by other man pages:)
 #' @section Source:
-#' 1. Becker K *et al.* **Coagulase-Negative Staphylococci**. 2014. Clin Microbiol Rev. 27(4): 870–926. <https://dx.doi.org/10.1128/CMR.00109-13>
-#' 2. Becker K *et al.* **Implications of identifying the recently defined members of the *S. aureus* complex, *S. argenteus* and *S. schweitzeri*: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).** 2019. Clin Microbiol Infect. <https://doi.org/10.1016/j.cmi.2019.02.028>
-#' 3. Becker K *et al.* **Emergence of coagulase-negative staphylococci** 2020. Expert Rev Anti Infect Ther. 18(4):349-366. <https://dx.doi.org/10.1080/14787210.2020.1730813>
-#' 4. Lancefield RC **A serological differentiation of human and other groups of hemolytic streptococci**. 1933. J Exp Med. 57(4): 571–95. <https://dx.doi.org/10.1084/jem.57.4.571>
+#' 1. Becker K *et al.* **Coagulase-Negative Staphylococci**. 2014. Clin Microbiol Rev. 27(4): 870–926; \doi{10.1128/CMR.00109-13}
+#' 2. Becker K *et al.* **Implications of identifying the recently defined members of the *S. aureus* complex, *S. argenteus* and *S. schweitzeri*: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).** 2019. Clin Microbiol Infect; \doi{10.1016/j.cmi.2019.02.028}
+#' 3. Becker K *et al.* **Emergence of coagulase-negative staphylococci** 2020. Expert Rev Anti Infect Ther. 18(4):349-366; \doi{10.1080/14787210.2020.1730813}
+#' 4. Lancefield RC **A serological differentiation of human and other groups of hemolytic streptococci**. 1933. J Exp Med. 57(4): 571–95; \doi{10.1084/jem.57.4.571}
 #' 5. Catalogue of Life: Annual Checklist (public online taxonomic database), <http://www.catalogueoflife.org> (check included annual version with [catalogue_of_life_version()]).
 #' @export
 #' @return A [character] [vector] with additional class [`mo`]
@@ -361,11 +361,11 @@ exec_as.mo <- function(x,
     # keep track of time - give some hints to improve speed if it takes a long time
     start_time <- Sys.time()
     
-    mo_env$mo_failures <- NULL
-    mo_env$mo_uncertainties <- NULL
-    mo_env$mo_renamed <- NULL
+    pkg_env$mo_failures <- NULL
+    pkg_env$mo_uncertainties <- NULL
+    pkg_env$mo_renamed <- NULL
   }
-  mo_env$mo_renamed_last_run <- NULL
+  pkg_env$mo_renamed_last_run <- NULL
 
   failures <- character(0)
   uncertainty_level <- translate_allow_uncertain(allow_uncertain)
@@ -438,7 +438,7 @@ exec_as.mo <- function(x,
 
     strip_whitespace <- function(x, dyslexia_mode) {
       # all whitespaces (tab, new lines, etc.) should be one space
-      # and spaces before and after should be omitted
+      # and spaces before and after should be left blank
       trimmed <- trimws2(x)
       # also, make sure the trailing and leading characters are a-z or 0-9
       # in case of non-regex
@@ -598,7 +598,7 @@ exec_as.mo <- function(x,
         } else {
           x[i] <- lookup(fullname == found["fullname_new"], haystack = MO_lookup)
         }
-        mo_env$mo_renamed_last_run <- found["fullname"]
+        pkg_env$mo_renamed_last_run <- found["fullname"]
         was_renamed(name_old = found["fullname"],
                     name_new = lookup(fullname == found["fullname_new"], "fullname", haystack = MO_lookup),
                     ref_old = found["ref"],
@@ -973,7 +973,7 @@ exec_as.mo <- function(x,
           } else {
             x[i] <- lookup(fullname == found["fullname_new"], haystack = MO_lookup)
           }
-          mo_env$mo_renamed_last_run <- found["fullname"]
+          pkg_env$mo_renamed_last_run <- found["fullname"]
           was_renamed(name_old = found["fullname"],
                       name_new = lookup(fullname == found["fullname_new"], "fullname", haystack = MO_lookup),
                       ref_old = found["ref"],
@@ -1025,7 +1025,7 @@ exec_as.mo <- function(x,
                           ref_old = found["ref"],
                           ref_new = lookup(fullname == found["fullname_new"], "ref", haystack = MO_lookup),
                           mo = lookup(fullname == found["fullname_new"], "mo", haystack = MO_lookup))
-              mo_env$mo_renamed_last_run <- found["fullname"]
+              pkg_env$mo_renamed_last_run <- found["fullname"]
               uncertainties <<- rbind(uncertainties,
                                       format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
                                                                input = a.x_backup,
@@ -1396,7 +1396,7 @@ exec_as.mo <- function(x,
   # handling failures ----
   failures <- failures[!failures %in% c(NA, NULL, NaN)]
   if (length(failures) > 0 & initial_search == TRUE) {
-    mo_env$mo_failures <- sort(unique(failures))
+    pkg_env$mo_failures <- sort(unique(failures))
     plural <- c("value", "it", "was")
     if (pm_n_distinct(failures) > 1) {
       plural <- c("values", "them", "were")
@@ -1423,7 +1423,7 @@ exec_as.mo <- function(x,
   # handling uncertainties ----
   if (NROW(uncertainties) > 0 & initial_search == TRUE) {
     uncertainties <- as.list(pm_distinct(uncertainties, input, .keep_all = TRUE))
-    mo_env$mo_uncertainties <- uncertainties
+    pkg_env$mo_uncertainties <- uncertainties
 
     plural <- c("", "it", "was")
     if (length(uncertainties$input) > 1) {
@@ -1559,13 +1559,13 @@ was_renamed <- function(name_old, name_new, ref_old = "", ref_new = "", mo = "")
                           new_ref = ref_new,
                           mo = mo,
                           stringsAsFactors = FALSE)
-  already_set <- mo_env$mo_renamed
+  already_set <- pkg_env$mo_renamed
   if (!is.null(already_set)) {
-    mo_env$mo_renamed = rbind(already_set,
+    pkg_env$mo_renamed = rbind(already_set,
                                newly_set,
                                stringsAsFactors = FALSE)
   } else {
-    mo_env$mo_renamed <- newly_set
+    pkg_env$mo_renamed <- newly_set
   }
 }
 
@@ -1573,9 +1573,9 @@ format_uncertainty_as_df <- function(uncertainty_level,
                                      input,
                                      result_mo,
                                      candidates = NULL) {
-  if (!is.null(mo_env$mo_renamed_last_run)) {
-    fullname <- mo_env$mo_renamed_last_run
-    mo_env$mo_renamed_last_run <- NULL
+  if (!is.null(pkg_env$mo_renamed_last_run)) {
+    fullname <- pkg_env$mo_renamed_last_run
+    pkg_env$mo_renamed_last_run <- NULL
     renamed_to <- MO_lookup[match(result_mo, MO_lookup$mo), "fullname", drop = TRUE][1]
   } else {
     fullname <- MO_lookup[match(result_mo, MO_lookup$mo), "fullname", drop = TRUE][1]
@@ -1764,16 +1764,16 @@ unique.mo <- function(x, incomparables = FALSE, ...) {
 #' @rdname as.mo
 #' @export
 mo_failures <- function() {
-  mo_env$mo_failures
+  pkg_env$mo_failures
 }
 
 #' @rdname as.mo
 #' @export
 mo_uncertainties <- function() {
-  if (is.null(mo_env$mo_uncertainties)) {
+  if (is.null(pkg_env$mo_uncertainties)) {
     return(NULL)
   }
-  set_clean_class(as.data.frame(mo_env$mo_uncertainties, 
+  set_clean_class(as.data.frame(pkg_env$mo_uncertainties, 
                                 stringsAsFactors = FALSE),
                   new_class = c("mo_uncertainties", "data.frame"))
 }
@@ -1842,7 +1842,7 @@ print.mo_uncertainties <- function(x, ...) {
 #' @rdname as.mo
 #' @export
 mo_renamed <- function() {
-  items <- mo_env$mo_renamed
+  items <- pkg_env$mo_renamed
   if (is.null(items)) {
     items <- data.frame(stringsAsFactors = FALSE)
   } else {
@@ -1906,20 +1906,20 @@ translate_allow_uncertain <- function(allow_uncertain) {
 }
 
 get_mo_failures_uncertainties_renamed <- function() {
-  remember <- list(failures = mo_env$mo_failures,
-                   uncertainties = mo_env$mo_uncertainties,
-                   renamed = mo_env$mo_renamed)
+  remember <- list(failures = pkg_env$mo_failures,
+                   uncertainties = pkg_env$mo_uncertainties,
+                   renamed = pkg_env$mo_renamed)
   # empty them, otherwise mo_shortname("Chlamydophila psittaci") will give 3 notes
-  mo_env$mo_failures <- NULL
-  mo_env$mo_uncertainties <- NULL
-  mo_env$mo_renamed <- NULL
+  pkg_env$mo_failures <- NULL
+  pkg_env$mo_uncertainties <- NULL
+  pkg_env$mo_renamed <- NULL
   remember
 }
 
 load_mo_failures_uncertainties_renamed <- function(metadata) {
-  mo_env$mo_failures <- metadata$failures
-  mo_env$mo_uncertainties <- metadata$uncertainties
-  mo_env$mo_renamed <- metadata$renamed
+  pkg_env$mo_failures <- metadata$failures
+  pkg_env$mo_uncertainties <- metadata$uncertainties
+  pkg_env$mo_renamed <- metadata$renamed
 }
 
 trimws2 <- function(x) {
@@ -2006,5 +2006,3 @@ repair_reference_df <- function(reference_df) {
   reference_df[, "mo"] <- as.mo(reference_df[, "mo", drop = TRUE])
   reference_df
 }
-
-mo_env <- new.env(hash = FALSE)

R/mo_matching_score.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/mo_property.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       #
@@ -27,7 +27,7 @@
 #'
 #' Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with [as.mo()], which makes it possible to use microbial abbreviations, codes and names as input. Please see *Examples*.
 #' @inheritSection lifecycle Stable lifecycle
-#' @param x any character (vector) that can be coerced to a valid microorganism code with [as.mo()]. Can be omitted for auto-guessing the column containing microorganism codes when used inside `dplyr` verbs, such as [`filter()`][dplyr::filter()], [`mutate()`][dplyr::mutate()] and [`summarise()`][dplyr::summarise()], please see *Examples*.
+#' @param x any character (vector) that can be coerced to a valid microorganism code with [as.mo()]. Can be left blank for auto-guessing the column containing microorganism codes when used inside `dplyr` verbs, such as [`filter()`][dplyr::filter()], [`mutate()`][dplyr::mutate()] and [`summarise()`][dplyr::summarise()], please see *Examples*.
 #' @param property one of the column names of the [microorganisms] data set: `r paste0('"``', colnames(microorganisms), '\``"', collapse = ", ")`, or must be `"shortname"`
 #' @param language language of the returned text, defaults to system language (see [get_locale()]) and can be overwritten by setting the option `AMR_locale`, e.g. `options(AMR_locale = "de")`, see [translate]. Also used to translate text like "no growth". Use `language = NULL` or `language = ""` to prevent translation.
 #' @param ... other arguments passed on to [as.mo()], such as 'allow_uncertain' and 'ignore_pattern'
@@ -162,8 +162,8 @@
 #' }
 mo_name <- function(x, language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_name")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -179,8 +179,8 @@ mo_fullname <- mo_name
 #' @export
 mo_shortname <- function(x, language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_shortname")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -217,8 +217,8 @@ mo_shortname <- function(x, language = get_locale(), ...) {
 #' @export
 mo_subspecies <- function(x, language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_subspecies")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -230,8 +230,8 @@ mo_subspecies <- function(x, language = get_locale(), ...) {
 #' @export
 mo_species <- function(x, language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_species")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -243,8 +243,8 @@ mo_species <- function(x, language = get_locale(), ...) {
 #' @export
 mo_genus <- function(x, language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_genus")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -256,8 +256,8 @@ mo_genus <- function(x, language = get_locale(), ...) {
 #' @export
 mo_family <- function(x, language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_family")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -269,8 +269,8 @@ mo_family <- function(x, language = get_locale(), ...) {
 #' @export
 mo_order <- function(x, language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_order")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -282,8 +282,8 @@ mo_order <- function(x, language = get_locale(), ...) {
 #' @export
 mo_class <- function(x, language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_class")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -295,8 +295,8 @@ mo_class <- function(x, language = get_locale(), ...) {
 #' @export
 mo_phylum <- function(x, language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_phylum")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -308,8 +308,8 @@ mo_phylum <- function(x, language = get_locale(), ...) {
 #' @export
 mo_kingdom <- function(x, language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_kingdom")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -325,8 +325,8 @@ mo_domain <- mo_kingdom
 #' @export
 mo_type <- function(x, language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_type")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -338,8 +338,8 @@ mo_type <- function(x, language = get_locale(), ...) {
 #' @export
 mo_gramstain <- function(x, language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_gramstain")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -376,8 +376,8 @@ mo_gramstain <- function(x, language = get_locale(), ...) {
 #' @export
 mo_is_gram_negative <- function(x, language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_is_gram_negative")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -395,8 +395,8 @@ mo_is_gram_negative <- function(x, language = get_locale(), ...) {
 #' @export
 mo_is_gram_positive <- function(x, language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_is_gram_positive")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -414,8 +414,8 @@ mo_is_gram_positive <- function(x, language = get_locale(), ...) {
 #' @export
 mo_is_intrinsic_resistant <- function(x, ab, language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_is_intrinsic_resistant")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(ab, allow_NA = FALSE)
@@ -433,12 +433,12 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_locale(), ...) {
     stop_("length of `x` and `ab` must be equal, or one of them must be of length 1.")
   }
   
-  # show used version number once per session
-  if (is.null(getOption("AMR_intrinsic_resistance_note", NULL))) {
+  # show used version number once per session (pkg_env will reload every session)
+  if (message_not_thrown_before("intrinsic_resistant_version", entire_session = TRUE)) {
     message_("Determining intrinsic resistance based on ",
-             format_eucast_version_nr(3.2, FALSE), ". ",
-             font_bold("This note is shown only once per session."))
-    options(AMR_intrinsic_resistance_note = "shown")
+             format_eucast_version_nr(3.2, markdown = FALSE), ". ",
+             font_red("This note will be shown once per session."))
+    remember_thrown_message("intrinsic_resistant_version", entire_session = TRUE)
   }
   
   # runs against internal vector: INTRINSIC_R (see zzz.R)
@@ -449,8 +449,8 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_locale(), ...) {
 #' @export
 mo_snomed <- function(x, language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_snomed")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -462,8 +462,8 @@ mo_snomed <- function(x, language = get_locale(), ...) {
 #' @export
 mo_ref <- function(x, language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_ref")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -475,8 +475,8 @@ mo_ref <- function(x, language = get_locale(), ...) {
 #' @export
 mo_authors <- function(x, language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_authors")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -491,8 +491,8 @@ mo_authors <- function(x, language = get_locale(), ...) {
 #' @export
 mo_year <- function(x, language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_year")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -507,8 +507,8 @@ mo_year <- function(x, language = get_locale(), ...) {
 #' @export
 mo_rank <- function(x, language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_rank")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -520,8 +520,8 @@ mo_rank <- function(x, language = get_locale(), ...) {
 #' @export
 mo_taxonomy <- function(x, language = get_locale(),  ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_taxonomy")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -546,8 +546,8 @@ mo_taxonomy <- function(x, language = get_locale(),  ...) {
 #' @export
 mo_synonyms <- function(x, language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_synonyms")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -579,8 +579,8 @@ mo_synonyms <- function(x, language = get_locale(), ...) {
 #' @export
 mo_info <- function(x, language = get_locale(),  ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_info")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -609,8 +609,8 @@ mo_info <- function(x, language = get_locale(),  ...) {
 #' @export
 mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_url")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(open, allow_class = "logical", has_length = 1)
@@ -646,8 +646,8 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
 #' @export
 mo_property <- function(x, property = "fullname", language = get_locale(), ...) {
   if (missing(x)) {
-    # this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_property")
   }
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(microorganisms))
@@ -701,7 +701,7 @@ mo_validate <- function(x, property, language, ...) {
 }
 
 find_mo_col <- function(fn) {
-  # this function tries to find an mo column using dplyr::cur_data_all() for mo_is_*() functions,
+  # this function tries to find an mo column in the data the function was called in,
   # which is useful when functions are used within dplyr verbs
   df <- get_current_data(arg_name = "x", call = -3) # will return an error if not found
   mo <- NULL

R/mo_source.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -132,7 +132,7 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s
   stop_ifnot(interactive(), "this function can only be used in interactive mode, since it must ask for the user's permission to write a file to their home folder.")
 
   if (is.null(path) || path %in% c(FALSE, "")) {
-    mo_env$mo_source <- NULL
+    pkg_env$mo_source <- NULL
     if (file.exists(mo_source_destination)) {
       unlink(mo_source_destination)
       message_("Removed mo_source file '", font_bold(mo_source_destination), "'",
@@ -149,8 +149,8 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s
     
   } else if (path %like% "[.]xlsx?$") {
     # is Excel file (old or new)
-    read_excel <- import_fn("read_excel", "readxl")
-    df <- read_excel(path)
+    stop_ifnot_installed("readxl")
+    df <- readxl::read_excel(path)
     
   } else if (path %like% "[.]tsv$") {
     df <- utils::read.table(header = TRUE, sep = "\t", stringsAsFactors = FALSE)
@@ -214,7 +214,7 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s
   attr(df, "mo_source_destination") <- mo_source_destination
   attr(df, "mo_source_timestamp") <- file.mtime(path)
   saveRDS(df, mo_source_destination)
-  mo_env$mo_source <- df
+  pkg_env$mo_source <- df
   message_(action, " mo_source file '", font_bold(mo_source_destination),
            "' (", formatted_filesize(mo_source_destination),
            ") from '", font_bold(path),
@@ -232,17 +232,17 @@ get_mo_source <- function(destination = getOption("AMR_mo_source", "~/mo_source.
     }
     return(NULL)
   }
-  if (is.null(mo_env$mo_source)) {
-    mo_env$mo_source <- readRDS(path.expand(destination))
+  if (is.null(pkg_env$mo_source)) {
+    pkg_env$mo_source <- readRDS(path.expand(destination))
   }
   
-  old_time <- attributes(mo_env$mo_source)$mo_source_timestamp
-  new_time <- file.mtime(attributes(mo_env$mo_source)$mo_source_location)
+  old_time <- attributes(pkg_env$mo_source)$mo_source_timestamp
+  new_time <- file.mtime(attributes(pkg_env$mo_source)$mo_source_location)
   if (interactive() && !identical(old_time, new_time)) {
     # source file was updated, also update reference
-    set_mo_source(attributes(mo_env$mo_source)$mo_source_location)
+    set_mo_source(attributes(pkg_env$mo_source)$mo_source_location)
   }
-  mo_env$mo_source
+  pkg_env$mo_source
 }
 
 check_validity_mo_source <- function(x, refer_to_name = "`reference_df`", stop_on_error = TRUE) {
@@ -251,7 +251,7 @@ check_validity_mo_source <- function(x, refer_to_name = "`reference_df`", stop_o
   if (paste(deparse(substitute(x)), collapse = "") == "get_mo_source()") {
     return(TRUE)
   }
-  if (is.null(mo_env$mo_source) && (identical(x, get_mo_source()))) {
+  if (is.null(pkg_env$mo_source) && (identical(x, get_mo_source()))) {
     return(TRUE)
   }
   if (is.null(x)) {

R/pca.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -97,7 +97,7 @@ pca <- function(x,
     }
     
     x <- as.data.frame(new_list, stringsAsFactors = FALSE)
-    if (any(sapply(x, function(y) !is.numeric(y)))) {
+    if (any(vapply(FUN.VALUE = logical(1), x, function(y) !is.numeric(y)))) {
       warning_("Be sure to first calculate the resistance (or susceptibility) of variables with antimicrobial test results, since PCA works with numeric variables only. Please see Examples in ?pca.")
     }
     
@@ -106,21 +106,21 @@ pca <- function(x,
              error = function(e) warning("column names could not be set"))
     
     # keep only numeric columns
-    x <- x[, sapply(x, function(y) is.numeric(y))]
+    x <- x[, vapply(FUN.VALUE = logical(1), x, function(y) is.numeric(y))]
     # bind the data set with the non-numeric columns
-    x <- cbind(x.bak[, sapply(x.bak, function(y) !is.numeric(y) & !all(is.na(y))), drop = FALSE], x)
+    x <- cbind(x.bak[, vapply(FUN.VALUE = logical(1), x.bak, function(y) !is.numeric(y) & !all(is.na(y))), drop = FALSE], x)
   }
   
   x <- pm_ungroup(x)  # would otherwise select the grouping vars
   x <- x[rowSums(is.na(x)) == 0, ] # remove columns containing NAs
   
-  pca_data <- x[, which(sapply(x, function(x) is.numeric(x)))]
+  pca_data <- x[, which(vapply(FUN.VALUE = logical(1), x, function(x) is.numeric(x)))]
   
   message_("Columns selected for PCA: ", paste0(font_bold(colnames(pca_data)), collapse = "/"),
            ". Total observations available: ", nrow(pca_data), ".")
   
   pca_model <- prcomp(pca_data, retx = retx, center = center, scale. = scale., tol = tol, rank. = rank.)
-  attr(pca_model, "non_numeric_cols") <- x[, sapply(x, function(y) !is.numeric(y) & !all(is.na(y))), drop = FALSE]
+  attr(pca_model, "non_numeric_cols") <- x[, vapply(FUN.VALUE = logical(1), x, function(y) !is.numeric(y) & !all(is.na(y))), drop = FALSE]
   class(pca_model) <- c("pca", class(pca_model))
   pca_model
 }

R/proportion.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/random.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/resistance_predict.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -192,7 +192,9 @@ resistance_predict <- function(x,
   rownames(df) <- NULL
   
   df <- subset(df, sum(df$R + df$S, na.rm = TRUE) >= minimum)
+  # nolint start
   df_matrix <- as.matrix(df[, c("R", "S"), drop = FALSE])
+  # nolint end
   
   stop_if(NROW(df) == 0, "there are no observations")
   

R/rsi.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -544,7 +544,7 @@ as.rsi.data.frame <- function(x,
     sel <- sel[sel != col_mo]
   }
 
-  ab_cols <- colnames(x)[sapply(x, function(y) {
+  ab_cols <- colnames(x)[vapply(FUN.VALUE = logical(1), x, function(y) {
     i <<- i + 1
     check <- is.mic(y) | is.disk(y)
     ab <- colnames(x)[i]
@@ -571,11 +571,11 @@ as.rsi.data.frame <- function(x,
           "no columns with MIC values, disk zones or antibiotic column names found in this data set. Use as.mic() or as.disk() to transform antimicrobial columns.")
   # set type per column
   types <- character(length(ab_cols))
-  types[sapply(x.bak[, ab_cols, drop = FALSE], is.disk)] <- "disk"
-  types[sapply(x.bak[, ab_cols, drop = FALSE], is.mic)] <- "mic"
-  types[types == "" & sapply(x[, ab_cols, drop = FALSE], all_valid_disks)] <- "disk"
-  types[types == "" & sapply(x[, ab_cols, drop = FALSE], all_valid_mics)] <- "mic"
-  types[types == "" & !sapply(x.bak[, ab_cols, drop = FALSE], is.rsi)] <- "rsi"
+  types[vapply(FUN.VALUE = logical(1), x.bak[, ab_cols, drop = FALSE], is.disk)] <- "disk"
+  types[vapply(FUN.VALUE = logical(1), x.bak[, ab_cols, drop = FALSE], is.mic)] <- "mic"
+  types[types == "" & vapply(FUN.VALUE = logical(1), x[, ab_cols, drop = FALSE], all_valid_disks)] <- "disk"
+  types[types == "" & vapply(FUN.VALUE = logical(1), x[, ab_cols, drop = FALSE], all_valid_mics)] <- "mic"
+  types[types == "" & !vapply(FUN.VALUE = logical(1), x.bak[, ab_cols, drop = FALSE], is.rsi)] <- "rsi"
   if (any(types %in% c("mic", "disk"), na.rm = TRUE)) {
     # now we need an mo column
     stop_if(is.null(col_mo), "`col_mo` must be set")
@@ -844,9 +844,9 @@ exec_as.rsi <- function(method,
 pillar_shaft.rsi <- function(x, ...) {
   out <- trimws(format(x))
   out[is.na(x)] <- font_grey(" NA")
-  out[x == "S"] <- font_green_bg(font_white("  S  "))
-  out[x == "I"] <- font_yellow_bg(font_black("  I  "))
-  out[x == "R"] <- font_red_bg(font_white("  R  "))
+  out[x == "R"] <- font_rsi_R_bg(font_black("  R  "))
+  out[x == "S"] <- font_rsi_S_bg(font_black("  S  "))
+  out[x == "I"] <- font_rsi_I_bg(font_black("  I  "))
   create_pillar_column(out, align = "left", width = 5)
 }
 
@@ -861,7 +861,8 @@ freq.rsi <- function(x, ...) {
   x_name <- gsub(".*[$]", "", x_name)
   if (x_name %in% c("x", ".")) {
     # try again going through system calls
-    x_name <- stats::na.omit(sapply(sys.calls(), 
+    x_name <- stats::na.omit(vapply(FUN.VALUE = character(1),
+                                    sys.calls(), 
                                     function(call) {
                                       call_txt <- as.character(call)
                                       ifelse(call_txt[1] %like% "freq$", call_txt[length(call_txt)], character(0))
@@ -906,8 +907,8 @@ get_skimmers.rsi <- function(column) {
     if (is.null(vars) | is.null(i)) {
       NA_character_
     } else {
-      lengths <- sapply(vars, length)
-      when_starts_rsi <- which(names(sapply(vars, length)) == "rsi")
+      lengths <- vapply(FUN.VALUE = double(1), vars, length)
+      when_starts_rsi <- which(names(vapply(FUN.VALUE = double(1), vars, length)) == "rsi")
       offset <- sum(lengths[c(1:when_starts_rsi - 1)])
       var <- vars$rsi[i - offset]
       if (!isFALSE(var == "data")) {
@@ -1115,8 +1116,8 @@ unique.rsi <- function(x, incomparables = FALSE, ...) {
 
 check_reference_data <- function(reference_data) {
   if (!identical(reference_data, AMR::rsi_translation)) {
-    class_rsi <- sapply(rsi_translation, function(x) paste0("<", class(x), ">", collapse = " and "))
-    class_ref <- sapply(reference_data, function(x) paste0("<", class(x), ">", collapse = " and "))
+    class_rsi <- vapply(FUN.VALUE = character(1), rsi_translation, function(x) paste0("<", class(x), ">", collapse = " and "))
+    class_ref <- vapply(FUN.VALUE = character(1), reference_data, function(x) paste0("<", class(x), ">", collapse = " and "))
     if (!all(names(class_rsi) == names(class_ref))) {
       stop_("`reference_data` must have the same column names as the 'rsi_translation' data set.", call = -2)
     }

R/rsi_calc.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -129,12 +129,12 @@ rsi_calc <- function(...,
                  MARGIN = 1,
                  FUN = min)
       numerator <- sum(as.integer(y) %in% as.integer(ab_result), na.rm = TRUE)
-      denominator <- sum(sapply(x_transposed, function(y) !(any(is.na(y)))))
+      denominator <- sum(vapply(FUN.VALUE = logical(1), x_transposed, function(y) !(any(is.na(y)))))
     } else {
       # may contain NAs in any column
       other_values <- setdiff(c(NA, levels(ab_result)), ab_result)
-      numerator <- sum(sapply(x_transposed, function(y) any(y %in% ab_result, na.rm = TRUE)))
-      denominator <- sum(sapply(x_transposed, function(y) !(all(y %in% other_values) & any(is.na(y)))))
+      numerator <- sum(vapply(FUN.VALUE = logical(1), x_transposed, function(y) any(y %in% ab_result, na.rm = TRUE)))
+      denominator <- sum(vapply(FUN.VALUE = logical(1), x_transposed, function(y) !(all(y %in% other_values) & any(is.na(y)))))
     }
   } else {
     # x is not a data.frame
@@ -147,12 +147,10 @@ rsi_calc <- function(...,
   }
   
   if (print_warning == TRUE) {
-    # since rsi_calc() is always called from a count() or proportion() function, we use -1:
-    cll <- gsub("[^a-zA-Z0-9_]+", "_", paste(deparse(sys.calls()[[length(sys.calls()) - 1]]), collapse = ""))
-    if (message_not_thrown_before(cll)) {
+    if (message_not_thrown_before("rsi_calc")) {
       warning_("Increase speed by transforming to class <rsi> on beforehand: your_data %>% mutate_if(is.rsi.eligible, as.rsi)",
                call = FALSE)
-      remember_thrown_message(cll)
+      remember_thrown_message("rsi_calc")
     }
   }
   
@@ -209,10 +207,10 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
   if (inherits(data, "grouped_df")) {
     data_has_groups <- TRUE
     groups <- setdiff(names(attributes(data)$groups), ".rows")
-    data <- data[, c(groups, colnames(data)[sapply(data, is.rsi)]), drop = FALSE]
+    data <- data[, c(groups, colnames(data)[vapply(FUN.VALUE = logical(1), data, is.rsi)]), drop = FALSE]
   } else {
     data_has_groups <- FALSE
-    data <- data[, colnames(data)[sapply(data, is.rsi)], drop = FALSE]
+    data <- data[, colnames(data)[vapply(FUN.VALUE = logical(1), data, is.rsi)], drop = FALSE]
   }
   
   data <- as.data.frame(data, stringsAsFactors = FALSE)

R/rsi_df.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/skewness.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -66,5 +66,5 @@ skewness.matrix <- function(x, na.rm = FALSE) {
 #' @export
 skewness.data.frame <- function(x, na.rm = FALSE) {
   meet_criteria(na.rm, allow_class = "logical", has_length = 1)
-  sapply(x, skewness.default, na.rm = na.rm)
+  vapply(FUN.VALUE = double(1), x, skewness.default, na.rm = na.rm)
 }

R/translate.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/whocc.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/zzz.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -23,6 +23,9 @@
 # how to conduct AMR analysis: https://msberends.github.io/AMR/        #
 # ==================================================================== #
 
+# set up package environment, used by numerous AMR functions
+pkg_env <- new.env(hash = FALSE)
+
 .onLoad <- function(libname, pkgname) {
   
   assign(x = "AB_lookup",

README.md

@@ -2,8 +2,11 @@
 
 # `AMR` (for R)
 
-[![CRAN_Badge](https://www.r-pkg.org/badges/version-ago/AMR)](https://cran.R-project.org/package=AMR) [![CRAN_Downloads](https://cranlogs.r-pkg.org/badges/grand-total/AMR)](https://cran.R-project.org/package=AMR)
-[![CodeCov](https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg)](https://codecov.io/gh/msberends/AMR/branch/master)
+[![CRAN](https://www.r-pkg.org/badges/version-ago/AMR)](https://cran.r-project.org/package=AMR)
+[![CRANlogs](https://cranlogs.r-pkg.org/badges/grand-total/AMR)](https://cran.r-project.org/package=AMR)
+![R-code-check](https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master)
+[![CodeFactor](https://www.codefactor.io/repository/github/msberends/amr/badge)](https://www.codefactor.io/repository/github/msberends/amr)
+[![Codecov](https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg)](https://codecov.io/gh/msberends/AMR?branch=master)
 
 <img src="https://msberends.github.io/AMR/works_great_on.png" align="center" height="150px" />
 

_pkgdown.yml

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -217,4 +217,4 @@ template:
   assets: "pkgdown/logos" # use logos in this folder
   params:
     noindex: false
-    template: "flatly"
+    bootswatch: "flatly"

codecov.yml

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

cran-comments.md

@@ -1,3 +1 @@
-* Edited the unit tests, so they will run under 10 minutes on CRAN (using testthat::skip_on_cran() on some tests).
-
 * Since version 0.3.0 (2018-08-14), CHECK returns a NOTE for having a data directory over 3 MB. This is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package.

data-raw/eucast_rules.tsv

@@ -300,3 +300,6 @@ genus_species	is	Moraxella catarrhalis	NAL	S	fluoroquinolones	S	Expert Rules on
 genus_species	is	Moraxella catarrhalis	NAL	R	fluoroquinolones	R	Expert Rules on Moraxella catarrhalis	Expert Rules	3.2	
 genus	is	Campylobacter	ERY	S	CLR, AZM	S	Expert Rules on Campylobacter	Expert Rules	3.2	
 genus_species	is	Campylobacter	ERY	R	CLR, AZM	R	Expert Rules on Campylobacter	Expert Rules	3.2	
+fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter (braakii|freundii|gillenii|murliniae|rodenticum|sedlakii|werkmanii|youngae)|Hafnia alvei|Serratia|Morganella morganii|Providencia)	CTX	S	CTX, CRO, CAZ		Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins)	Expert Rules	3.2	This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
+fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter (braakii|freundii|gillenii|murliniae|rodenticum|sedlakii|werkmanii|youngae)|Hafnia alvei|Serratia|Morganella morganii|Providencia)	CRO	S	CTX, CRO, CAZ		Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins)	Expert Rules	3.2	This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
+fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter (braakii|freundii|gillenii|murliniae|rodenticum|sedlakii|werkmanii|youngae)|Hafnia alvei|Serratia|Morganella morganii|Providencia)	CAZ	S	CTX, CRO, CAZ		Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins)	Expert Rules	3.2	This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument

data-raw/internals.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

data-raw/loinc.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

data-raw/poorman_prepend.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

data-raw/read_EUCAST.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

data-raw/reproduction_of_antibiotics.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

data-raw/reproduction_of_antivirals.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

data-raw/reproduction_of_example_isolates_unclean.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

data-raw/reproduction_of_intrinsic_resistant.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -24,6 +24,7 @@
 # ==================================================================== #
 
 library(AMR)
+library(dplyr)
 int_resis <- data.frame(microorganism = microorganisms$mo, stringsAsFactors = FALSE)
 for (i in seq_len(nrow(antibiotics))) {
   int_resis$new <- as.rsi("S")
@@ -45,3 +46,6 @@ int_resis2$microorganism <- mo_name(int_resis2$microorganism, language = NULL)
 intrinsic_resistant <- as.data.frame(int_resis2, stringsAsFactors = FALSE)
 usethis::use_data(intrinsic_resistant, internal = FALSE, overwrite = TRUE, version = 2, compress = "xz")
 rm(intrinsic_resistant)
+
+# AFTER THIS:
+# DO NOT FORGET TO UPDATE THE VERSION NUMBER IN mo_is_intrinsic_resistant()

data-raw/reproduction_of_microorganisms.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

data-raw/snomed.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

docs/404.html

@@ -19,8 +19,8 @@
 <!-- jquery -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
 <!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
 
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
 
@@ -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">1.4.0.9045</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -19,8 +19,8 @@
 <!-- jquery -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
 <!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
 
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
 
@@ -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">1.4.0.9045</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 

docs/articles/AMR.html

@@ -12,7 +12,7 @@
 <link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
 <link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
 <link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
-<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
 <script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
@@ -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">1.4.0.9044</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 
@@ -193,7 +193,7 @@
       <h1 data-toc-skip>How to conduct AMR analysis</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">24 December 2020</h4>
+            <h4 class="date">29 December 2020</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 24 December 2020.</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 29 December 2020.</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">2020-12-24</td>
+<td align="center">2020-12-29</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">2020-12-24</td>
+<td align="center">2020-12-29</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">2020-12-24</td>
+<td align="center">2020-12-29</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@@ -352,30 +352,8 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2012-10-07</td>
-<td align="center">D7</td>
-<td align="center">Hospital B</td>
-<td align="center">Escherichia coli</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>
-</tr>
-<tr class="even">
-<td align="center">2016-11-19</td>
-<td align="center">V9</td>
-<td align="center">Hospital A</td>
-<td align="center">Klebsiella pneumoniae</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">2015-03-30</td>
-<td align="center">D9</td>
+<td align="center">2014-02-24</td>
+<td align="center">H4</td>
 <td align="center">Hospital D</td>
 <td align="center">Staphylococcus aureus</td>
 <td align="center">R</td>
@@ -385,34 +363,56 @@
 <td align="center">M</td>
 </tr>
 <tr class="even">
-<td align="center">2012-06-28</td>
-<td align="center">Z4</td>
+<td align="center">2017-04-27</td>
+<td align="center">Q3</td>
 <td align="center">Hospital B</td>
 <td align="center">Staphylococcus aureus</td>
 <td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
 <tr class="odd">
-<td align="center">2014-03-04</td>
-<td align="center">M4</td>
-<td align="center">Hospital C</td>
-<td align="center">Staphylococcus aureus</td>
+<td align="center">2013-03-12</td>
+<td align="center">Q4</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">F</td>
+</tr>
+<tr class="even">
+<td align="center">2013-03-24</td>
+<td align="center">H9</td>
+<td align="center">Hospital A</td>
+<td align="center">Escherichia coli</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">M</td>
+</tr>
+<tr class="odd">
+<td align="center">2017-03-11</td>
+<td align="center">M1</td>
+<td align="center">Hospital A</td>
+<td align="center">Streptococcus pneumoniae</td>
+<td align="center">R</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">2014-08-18</td>
-<td align="center">D2</td>
-<td align="center">Hospital B</td>
-<td align="center">Escherichia coli</td>
-<td align="center">R</td>
-<td align="center">R</td>
+<td align="center">2011-12-21</td>
+<td align="center">M5</td>
+<td align="center">Hospital A</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>
@@ -449,16 +449,16 @@ Longest: 1</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">M</td>
-<td align="right">10,392</td>
-<td align="right">51.96%</td>
-<td align="right">10,392</td>
-<td align="right">51.96%</td>
+<td align="right">10,444</td>
+<td align="right">52.22%</td>
+<td align="right">10,444</td>
+<td align="right">52.22%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">F</td>
-<td align="right">9,608</td>
-<td align="right">48.04%</td>
+<td align="right">9,556</td>
+<td align="right">47.78%</td>
 <td align="right">20,000</td>
 <td align="right">100.00%</td>
 </tr>
@@ -503,7 +503,7 @@ Longest: 1</p>
 <span class="co"># NOTE: Using column 'bacteria' as input for `col_mo`.</span>
 <span class="co"># NOTE: Using column 'date' as input for `col_date`.</span>
 <span class="co"># NOTE: Using column 'patient_id' as input for `col_patient_id`.</span></code></pre></div>
-<p>So only 28.4% 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 28.3% 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="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="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 id="first-weighted-isolates" class="section level2">
 <h2 class="hasAnchor">
 <a href="#first-weighted-isolates" class="anchor"></a>First <em>weighted</em> isolates</h2>
-<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient M9, sorted on date:</p>
+<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient Z4, sorted on date:</p>
 <table class="table">
 <thead><tr class="header">
 <th align="center">isolate</th>
@@ -531,43 +531,43 @@ Longest: 1</p>
 <tbody>
 <tr class="odd">
 <td align="center">1</td>
-<td align="center">2010-01-25</td>
-<td align="center">M9</td>
+<td align="center">2010-07-01</td>
+<td align="center">Z4</td>
 <td align="center">B_ESCHR_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">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">2</td>
-<td align="center">2010-02-01</td>
-<td align="center">M9</td>
+<td align="center">2010-08-01</td>
+<td align="center">Z4</td>
 <td align="center">B_ESCHR_COLI</td>
+<td align="center">I</td>
 <td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="odd">
 <td align="center">3</td>
-<td align="center">2010-02-22</td>
-<td align="center">M9</td>
+<td align="center">2010-08-18</td>
+<td align="center">Z4</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">I</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="even">
 <td align="center">4</td>
-<td align="center">2010-08-12</td>
-<td align="center">M9</td>
+<td align="center">2010-10-16</td>
+<td align="center">Z4</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">I</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
@@ -575,19 +575,19 @@ Longest: 1</p>
 </tr>
 <tr class="odd">
 <td align="center">5</td>
-<td align="center">2010-08-17</td>
-<td align="center">M9</td>
+<td align="center">2010-12-23</td>
+<td align="center">Z4</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">R</td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="even">
 <td align="center">6</td>
-<td align="center">2010-09-18</td>
-<td align="center">M9</td>
+<td align="center">2010-12-25</td>
+<td align="center">Z4</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@@ -597,51 +597,51 @@ Longest: 1</p>
 </tr>
 <tr class="odd">
 <td align="center">7</td>
-<td align="center">2011-07-05</td>
-<td align="center">M9</td>
+<td align="center">2011-01-07</td>
+<td align="center">Z4</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
-<td align="center">TRUE</td>
+<td align="center">FALSE</td>
 </tr>
 <tr class="even">
 <td align="center">8</td>
-<td align="center">2011-07-19</td>
-<td align="center">M9</td>
+<td align="center">2011-01-30</td>
+<td align="center">Z4</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">S</td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="odd">
 <td align="center">9</td>
-<td align="center">2011-07-20</td>
-<td align="center">M9</td>
+<td align="center">2011-05-19</td>
+<td align="center">Z4</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">S</td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="even">
 <td align="center">10</td>
-<td align="center">2011-09-04</td>
-<td align="center">M9</td>
+<td align="center">2011-06-21</td>
+<td align="center">Z4</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">S</td>
+<td align="center">R</td>
+<td align="center">S</td>
 <td align="center">FALSE</td>
 </tr>
 </tbody>
 </table>
-<p>Only 2 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
+<p>Only 1 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
 <p>If a column exists with a name like ‘key(…)ab’ the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> function will automatically use it and determine the first weighted isolates. Mind the NOTEs in below output:</p>
 <div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span> 
@@ -665,68 +665,68 @@ Longest: 1</p>
 <tbody>
 <tr class="odd">
 <td align="center">1</td>
-<td align="center">2010-01-25</td>
-<td align="center">M9</td>
+<td align="center">2010-07-01</td>
+<td align="center">Z4</td>
 <td align="center">B_ESCHR_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">TRUE</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">2</td>
-<td align="center">2010-02-01</td>
-<td align="center">M9</td>
+<td align="center">2010-08-01</td>
+<td align="center">Z4</td>
 <td align="center">B_ESCHR_COLI</td>
+<td align="center">I</td>
 <td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">3</td>
-<td align="center">2010-02-22</td>
-<td align="center">M9</td>
+<td align="center">2010-08-18</td>
+<td align="center">Z4</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">I</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="even">
 <td align="center">4</td>
-<td align="center">2010-08-12</td>
-<td align="center">M9</td>
+<td align="center">2010-10-16</td>
+<td align="center">Z4</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">I</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
-<td align="center">FALSE</td>
+<td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">5</td>
-<td align="center">2010-08-17</td>
-<td align="center">M9</td>
+<td align="center">2010-12-23</td>
+<td align="center">Z4</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">R</td>
 <td align="center">FALSE</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">6</td>
-<td align="center">2010-09-18</td>
-<td align="center">M9</td>
+<td align="center">2010-12-25</td>
+<td align="center">Z4</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@@ -737,23 +737,23 @@ Longest: 1</p>
 </tr>
 <tr class="odd">
 <td align="center">7</td>
-<td align="center">2011-07-05</td>
-<td align="center">M9</td>
+<td align="center">2011-01-07</td>
+<td align="center">Z4</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
-<td align="center">TRUE</td>
+<td align="center">FALSE</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">8</td>
-<td align="center">2011-07-19</td>
-<td align="center">M9</td>
+<td align="center">2011-01-30</td>
+<td align="center">Z4</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">S</td>
 <td align="center">FALSE</td>
@@ -761,36 +761,36 @@ Longest: 1</p>
 </tr>
 <tr class="odd">
 <td align="center">9</td>
-<td align="center">2011-07-20</td>
-<td align="center">M9</td>
+<td align="center">2011-05-19</td>
+<td align="center">Z4</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">S</td>
 <td align="center">FALSE</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">10</td>
-<td align="center">2011-09-04</td>
-<td align="center">M9</td>
+<td align="center">2011-06-21</td>
+<td align="center">Z4</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">S</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">FALSE</td>
 <td align="center">FALSE</td>
-<td align="center">TRUE</td>
 </tr>
 </tbody>
 </table>
-<p>Instead of 2, now 8 isolates are flagged. In total, 78.4% of all isolates are marked ‘first weighted’ - 50.0% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
+<p>Instead of 1, now 8 isolates are flagged. In total, 79.0% of all isolates are marked ‘first weighted’ - 50.7% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
 <p>As with <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
 <div class="sourceCode" id="cb19"><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_weighted_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
-<p>So we end up with 15,683 isolates for analysis.</p>
+<p>So we end up with 15,805 isolates for analysis.</p>
 <p>We can remove unneeded columns:</p>
 <div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data_1st</span> <span class="op">%&gt;%</span> 
@@ -800,7 +800,6 @@ Longest: 1</p>
 <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">
 <colgroup>
-<col width="2%">
 <col width="8%">
 <col width="8%">
 <col width="8%">
@@ -816,7 +815,6 @@ Longest: 1</p>
 <col width="11%">
 </colgroup>
 <thead><tr class="header">
-<th align="left"></th>
 <th align="center">date</th>
 <th align="center">patient_id</th>
 <th align="center">hospital</th>
@@ -833,14 +831,58 @@ Longest: 1</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="left">1</td>
-<td align="center">2012-10-07</td>
-<td align="center">D7</td>
+<td align="center">2014-02-24</td>
+<td align="center">H4</td>
+<td align="center">Hospital D</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">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="center">2017-04-27</td>
+<td align="center">Q3</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">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="center">2013-03-12</td>
+<td align="center">Q4</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">R</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="center">2013-03-24</td>
+<td align="center">H9</td>
+<td align="center">Hospital A</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
 <td align="center">S</td>
-<td align="center">R</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 <td align="center">Gram-negative</td>
@@ -848,84 +890,34 @@ Longest: 1</p>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="even">
-<td align="left">2</td>
-<td align="center">2016-11-19</td>
-<td align="center">V9</td>
+<tr class="odd">
+<td align="center">2017-03-11</td>
+<td align="center">M1</td>
 <td align="center">Hospital A</td>
-<td align="center">B_KLBSL_PNMN</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">3</td>
-<td align="center">2015-03-30</td>
-<td align="center">D9</td>
-<td align="center">Hospital D</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">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">5</td>
-<td align="center">2014-03-04</td>
-<td align="center">M4</td>
-<td align="center">Hospital C</td>
-<td align="center">B_STPHY_AURS</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-positive</td>
-<td align="center">Staphylococcus</td>
-<td align="center">aureus</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="odd">
-<td align="left">7</td>
-<td align="center">2011-02-08</td>
-<td align="center">S3</td>
-<td align="center">Hospital D</td>
 <td align="center">B_STRPT_PNMN</td>
-<td align="center">S</td>
-<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
-<td align="center">F</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="left">8</td>
-<td align="center">2015-12-31</td>
-<td align="center">I5</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">2011-12-21</td>
+<td align="center">M5</td>
+<td align="center">Hospital A</td>
+<td align="center">B_STRPT_PNMN</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>
-<td align="center">Escherichia</td>
-<td align="center">coli</td>
+<td align="center">Gram-positive</td>
+<td align="center">Streptococcus</td>
+<td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 </tbody>
@@ -949,8 +941,8 @@ 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: 15,683<br>
-Available: 15,683 (100%, NA: 0 = 0%)<br>
+Length: 15,805<br>
+Available: 15,805 (100%, NA: 0 = 0%)<br>
 Unique: 4</p>
 <p>Shortest: 16<br>
 Longest: 24</p>
@@ -967,33 +959,33 @@ Longest: 24</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Escherichia coli</td>
-<td align="right">7,815</td>
-<td align="right">49.83%</td>
-<td align="right">7,815</td>
-<td align="right">49.83%</td>
+<td align="right">7,828</td>
+<td align="right">49.53%</td>
+<td align="right">7,828</td>
+<td align="right">49.53%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Staphylococcus aureus</td>
-<td align="right">4,001</td>
-<td align="right">25.51%</td>
-<td align="right">11,816</td>
-<td align="right">75.34%</td>
+<td align="right">3,963</td>
+<td align="right">25.07%</td>
+<td align="right">11,791</td>
+<td align="right">74.60%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Streptococcus pneumoniae</td>
-<td align="right">2,330</td>
-<td align="right">14.86%</td>
-<td align="right">14,146</td>
-<td align="right">90.20%</td>
+<td align="right">2,392</td>
+<td align="right">15.13%</td>
+<td align="right">14,183</td>
+<td align="right">89.74%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Klebsiella pneumoniae</td>
-<td align="right">1,537</td>
-<td align="right">9.80%</td>
-<td align="right">15,683</td>
+<td align="right">1,622</td>
+<td align="right">10.26%</td>
+<td align="right">15,805</td>
 <td align="right">100.00%</td>
 </tr>
 </tbody>
@@ -1020,50 +1012,50 @@ Longest: 24</p>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">AMX</td>
-<td align="center">3744</td>
-<td align="center">257</td>
-<td align="center">3814</td>
-<td align="center">7815</td>
+<td align="center">3777</td>
+<td align="center">245</td>
+<td align="center">3806</td>
+<td align="center">7828</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">AMC</td>
-<td align="center">6185</td>
-<td align="center">294</td>
-<td align="center">1336</td>
-<td align="center">7815</td>
+<td align="center">6159</td>
+<td align="center">278</td>
+<td align="center">1391</td>
+<td align="center">7828</td>
 </tr>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">CIP</td>
-<td align="center">5934</td>
+<td align="center">5997</td>
 <td align="center">0</td>
-<td align="center">1881</td>
-<td align="center">7815</td>
+<td align="center">1831</td>
+<td align="center">7828</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">7005</td>
+<td align="center">6984</td>
 <td align="center">0</td>
-<td align="center">810</td>
-<td align="center">7815</td>
+<td align="center">844</td>
+<td align="center">7828</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">1537</td>
-<td align="center">1537</td>
+<td align="center">1622</td>
+<td align="center">1622</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMC</td>
-<td align="center">1225</td>
-<td align="center">45</td>
-<td align="center">267</td>
-<td align="center">1537</td>
+<td align="center">1271</td>
+<td align="center">63</td>
+<td align="center">288</td>
+<td align="center">1622</td>
 </tr>
 </tbody>
 </table>
@@ -1072,7 +1064,7 @@ Longest: 24</p>
 <code class="sourceCode R"><span class="va">data_1st</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">fluoroquinolones</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span> 
   <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
-<pre><code># Selecting fluoroquinolones: 'CIP' (ciprofloxacin)</code></pre>
+<pre><code># Selecting fluoroquinolones: column 'CIP' (ciprofloxacin)</code></pre>
 <table class="table">
 <thead><tr class="header">
 <th align="center">mo</th>
@@ -1086,34 +1078,34 @@ Longest: 24</p>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">CIP</td>
-<td align="center">5934</td>
+<td align="center">5997</td>
 <td align="center">0</td>
-<td align="center">1881</td>
-<td align="center">7815</td>
+<td align="center">1831</td>
+<td align="center">7828</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">CIP</td>
-<td align="center">1189</td>
+<td align="center">1266</td>
 <td align="center">0</td>
-<td align="center">348</td>
-<td align="center">1537</td>
+<td align="center">356</td>
+<td align="center">1622</td>
 </tr>
 <tr class="odd">
 <td align="center">S. aureus</td>
 <td align="center">CIP</td>
-<td align="center">3064</td>
+<td align="center">3017</td>
 <td align="center">0</td>
-<td align="center">937</td>
-<td align="center">4001</td>
+<td align="center">946</td>
+<td align="center">3963</td>
 </tr>
 <tr class="even">
 <td align="center">S. pneumoniae</td>
 <td align="center">CIP</td>
-<td align="center">1780</td>
+<td align="center">1844</td>
 <td align="center">0</td>
-<td align="center">550</td>
-<td align="center">2330</td>
+<td align="center">548</td>
+<td align="center">2392</td>
 </tr>
 </tbody>
 </table>
@@ -1126,7 +1118,7 @@ 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="cb27"><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] 0.5342728</span></code></pre></div>
+<span class="co"># [1] 0.5358431</span></code></pre></div>
 <p>Or can be used in conjuction 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="cb28"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> 
@@ -1141,19 +1133,19 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5253802</td>
+<td align="center">0.5273258</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5367779</td>
+<td align="center">0.5421512</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5470814</td>
+<td align="center">0.5394139</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5334627</td>
+<td align="center">0.5350195</td>
 </tr>
 </tbody>
 </table>
@@ -1173,23 +1165,23 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5253802</td>
-<td align="center">4669</td>
+<td align="center">0.5273258</td>
+<td align="center">4794</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5367779</td>
-<td align="center">5574</td>
+<td align="center">0.5421512</td>
+<td align="center">5504</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5470814</td>
-<td align="center">2347</td>
+<td align="center">0.5394139</td>
+<td align="center">2423</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5334627</td>
-<td align="center">3093</td>
+<td align="center">0.5350195</td>
+<td align="center">3084</td>
 </tr>
 </tbody>
 </table>
@@ -1211,27 +1203,27 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Escherichia</td>
-<td align="center">0.8290467</td>
-<td align="center">0.8963532</td>
-<td align="center">0.9843890</td>
+<td align="center">0.8223045</td>
+<td align="center">0.8921819</td>
+<td align="center">0.9842872</td>
 </tr>
 <tr class="even">
 <td align="center">Klebsiella</td>
-<td align="center">0.8262850</td>
-<td align="center">0.9095641</td>
-<td align="center">0.9837345</td>
+<td align="center">0.8224414</td>
+<td align="center">0.8927250</td>
+<td align="center">0.9833539</td>
 </tr>
 <tr class="odd">
 <td align="center">Staphylococcus</td>
-<td align="center">0.8307923</td>
-<td align="center">0.9122719</td>
-<td align="center">0.9872532</td>
+<td align="center">0.8268988</td>
+<td align="center">0.9192531</td>
+<td align="center">0.9861216</td>
 </tr>
 <tr class="even">
 <td align="center">Streptococcus</td>
-<td align="center">0.5351931</td>
+<td align="center">0.5447324</td>
 <td align="center">0.0000000</td>
-<td align="center">0.5351931</td>
+<td align="center">0.5447324</td>
 </tr>
 </tbody>
 </table>

docs/articles/EUCAST.html

@@ -12,7 +12,7 @@
 <link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
 <link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
 <link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
-<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
 <script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
@@ -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">1.4.0.9044</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 

docs/articles/MDR.html

@@ -12,7 +12,7 @@
 <link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
 <link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
 <link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
-<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
 <script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
@@ -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">1.4.0.9044</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 
@@ -311,19 +311,19 @@ Unique: 2</p>
 <div class="sourceCode" id="cb5"><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          S         S            R          I            R            S</span>
-<span class="co"># 2          I         S            R          I            I            R</span>
-<span class="co"># 3          R         R            R          S            I            R</span>
-<span class="co"># 4          I         I            R          R            S            S</span>
-<span class="co"># 5          I         R            I          S            S            R</span>
-<span class="co"># 6          I         R            I          I            S            I</span>
+<span class="co"># 1          S         R            S          S            I            R</span>
+<span class="co"># 2          R         I            S          I            S            I</span>
+<span class="co"># 3          I         I            R          S            I            S</span>
+<span class="co"># 4          R         S            R          I            R            S</span>
+<span class="co"># 5          I         R            I          I            I            R</span>
+<span class="co"># 6          I         R            I          R            S            R</span>
 <span class="co">#   kanamycin</span>
 <span class="co"># 1         R</span>
-<span class="co"># 2         S</span>
+<span class="co"># 2         I</span>
 <span class="co"># 3         I</span>
 <span class="co"># 4         I</span>
-<span class="co"># 5         I</span>
-<span class="co"># 6         R</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="cb6"><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>
@@ -354,40 +354,40 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistant</td>
-<td align="right">3214</td>
-<td align="right">64.28%</td>
-<td align="right">3214</td>
-<td align="right">64.28%</td>
+<td align="right">3286</td>
+<td align="right">65.72%</td>
+<td align="right">3286</td>
+<td align="right">65.72%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">997</td>
-<td align="right">19.94%</td>
-<td align="right">4211</td>
-<td align="right">84.22%</td>
+<td align="right">992</td>
+<td align="right">19.84%</td>
+<td align="right">4278</td>
+<td align="right">85.56%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Multi-drug-resistant</td>
-<td align="right">442</td>
-<td align="right">8.84%</td>
-<td align="right">4653</td>
-<td align="right">93.06%</td>
+<td align="right">424</td>
+<td align="right">8.48%</td>
+<td align="right">4702</td>
+<td align="right">94.04%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistant</td>
-<td align="right">239</td>
-<td align="right">4.78%</td>
-<td align="right">4892</td>
-<td align="right">97.84%</td>
+<td align="right">214</td>
+<td align="right">4.28%</td>
+<td align="right">4916</td>
+<td align="right">98.32%</td>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
 <td align="left">Extensively drug-resistant</td>
-<td align="right">108</td>
-<td align="right">2.16%</td>
+<td align="right">84</td>
+<td align="right">1.68%</td>
 <td align="right">5000</td>
 <td align="right">100.00%</td>
 </tr>

docs/articles/PCA.html

@@ -12,7 +12,7 @@
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 <link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
-<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
 <script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
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@@ -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">1.4.0.9044</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 

docs/articles/SPSS.html

@@ -12,7 +12,7 @@
 <link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
 <link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
 <link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
-<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
 <script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
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@@ -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">1.4.0.9044</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</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">24 December 2020</h4>
+            <h4 class="date">29 December 2020</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>

docs/articles/WHONET.html

@@ -12,7 +12,7 @@
 <link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
 <link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
 <link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
-<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
 <script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
@@ -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">1.4.0.9044</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 

docs/articles/benchmarks.html

@@ -12,7 +12,7 @@
 <link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
 <link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
 <link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
-<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
 <script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
@@ -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">1.4.0.9044</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 
@@ -227,20 +227,20 @@
   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">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</span>
-<span class="co">#                           as.mo("sau")   9.9  12.0   15.0   13.0   13.0   42.0</span>
-<span class="co">#                          as.mo("stau") 100.0 100.0  130.0  120.0  140.0  190.0</span>
-<span class="co">#                          as.mo("STAU") 110.0 110.0  130.0  130.0  140.0  150.0</span>
-<span class="co">#                        as.mo("staaur")   9.8  12.0   26.0   13.0   41.0   60.0</span>
-<span class="co">#                        as.mo("STAAUR")  11.0  11.0   15.0   13.0   13.0   41.0</span>
-<span class="co">#                     as.mo("S. aureus")  26.0  28.0   50.0   58.0   63.0   75.0</span>
-<span class="co">#                      as.mo("S aureus")  26.0  27.0   46.0   51.0   60.0   67.0</span>
-<span class="co">#         as.mo("Staphylococcus aureus")   1.9   2.2    2.5    2.5    2.8    3.1</span>
-<span class="co">#  as.mo("Staphylococcus aureus (MRSA)") 870.0 880.0 1100.0  910.0 1000.0 2400.0</span>
-<span class="co">#       as.mo("Sthafilokkockus aaureuz") 360.0 370.0  400.0  380.0  420.0  540.0</span>
-<span class="co">#                          as.mo("MRSA")   9.7  11.0   17.0   12.0   13.0   66.0</span>
-<span class="co">#                          as.mo("VISA")  19.0  19.0   36.0   35.0   53.0   56.0</span>
-<span class="co">#                          as.mo("VRSA")  17.0  20.0   20.0   21.0   21.0   23.0</span>
+<span class="co">#                                   expr    min     lq   mean median     uq  max</span>
+<span class="co">#                           as.mo("sau")   13.0   14.0   25.0   15.0   44.0   65</span>
+<span class="co">#                          as.mo("stau")  120.0  130.0  140.0  140.0  160.0  160</span>
+<span class="co">#                          as.mo("STAU")  120.0  130.0  150.0  160.0  160.0  180</span>
+<span class="co">#                        as.mo("staaur")   13.0   13.0   14.0   14.0   14.0   15</span>
+<span class="co">#                        as.mo("STAAUR")   13.0   14.0   17.0   15.0   15.0   43</span>
+<span class="co">#                     as.mo("S. aureus")   30.0   32.0   45.0   34.0   62.0   68</span>
+<span class="co">#                      as.mo("S aureus")   31.0   34.0   42.0   35.0   61.0   63</span>
+<span class="co">#         as.mo("Staphylococcus aureus")    2.5    2.6    2.8    2.8    2.9    3</span>
+<span class="co">#  as.mo("Staphylococcus aureus (MRSA)") 1200.0 1200.0 1200.0 1200.0 1200.0 1200</span>
+<span class="co">#       as.mo("Sthafilokkockus aaureuz")  550.0  560.0  570.0  560.0  570.0  610</span>
+<span class="co">#                          as.mo("MRSA")   13.0   13.0   17.0   15.0   15.0   42</span>
+<span class="co">#                          as.mo("VISA")   21.0   22.0   26.0   23.0   23.0   52</span>
+<span class="co">#                          as.mo("VRSA")   21.0   23.0   35.0   24.0   52.0   54</span>
 <span class="co">#  neval</span>
 <span class="co">#     10</span>
 <span class="co">#     10</span>
@@ -284,8 +284,8 @@
 <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) 134 167  201    179 207 310    10</span></code></pre></div>
-<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.179 seconds. You only lose time on your unique input values.</p>
+<span class="co">#  mo_name(x) 141 180  218    207 245 312    10</span></code></pre></div>
+<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.207 seconds. You only lose time on your unique input values.</p>
 </div>
 <div id="precalculated-results" class="section level3">
 <h3 class="hasAnchor">
@@ -299,10 +299,10 @@
 <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  7.59  7.93  8.24   8.09  8.66  9.06    10</span>
-<span class="co">#     B 23.60 23.70 29.20  24.30 27.10 66.10    10</span>
-<span class="co">#     C  1.84  2.13  2.22   2.19  2.35  2.62    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>
+<span class="co">#     A  8.76  8.96  9.39   9.31  9.86 10.10    10</span>
+<span class="co">#     B 27.60 28.20 33.00  28.90 29.40 71.20    10</span>
+<span class="co">#     C  2.28  2.32  2.47   2.45  2.48  2.85    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 0.0025 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">microbenchmark</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>,
@@ -316,14 +316,14 @@
 <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 1.69 1.77 1.82   1.83 1.86 1.92    10</span>
-<span class="co">#     B 1.78 1.79 1.89   1.91 1.95 2.06    10</span>
-<span class="co">#     C 1.74 1.79 1.88   1.87 1.94 2.06    10</span>
-<span class="co">#     D 1.75 1.77 1.94   1.95 1.99 2.41    10</span>
-<span class="co">#     E 1.70 1.75 1.84   1.81 1.87 2.08    10</span>
-<span class="co">#     F 1.66 1.70 1.76   1.74 1.80 1.89    10</span>
-<span class="co">#     G 1.68 1.70 1.82   1.75 1.93 2.09    10</span>
-<span class="co">#     H 1.66 1.69 1.75   1.74 1.80 1.92    10</span></code></pre></div>
+<span class="co">#     A 1.91 1.95 2.06   1.99 2.09 2.62    10</span>
+<span class="co">#     B 1.83 1.91 2.09   2.04 2.20 2.45    10</span>
+<span class="co">#     C 1.79 1.90 2.03   1.99 2.22 2.30    10</span>
+<span class="co">#     D 1.90 2.01 2.18   2.12 2.25 2.71    10</span>
+<span class="co">#     E 1.91 2.02 2.14   2.08 2.15 2.81    10</span>
+<span class="co">#     F 1.86 1.92 2.00   2.01 2.06 2.16    10</span>
+<span class="co">#     G 1.81 1.96 2.09   2.08 2.22 2.41    10</span>
+<span class="co">#     H 1.90 1.93 2.05   2.00 2.22 2.29    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 ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
 </div>
 <div id="results-in-other-languages" class="section level3">
@@ -350,14 +350,14 @@
                          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 15.91 16.98 21.87  17.54 18.34 168.50   100</span>
-<span class="co">#    de 18.98 20.14 26.30  20.74 22.64  66.68   100</span>
-<span class="co">#    nl 31.02 32.71 37.56  33.84 35.81  82.77   100</span>
-<span class="co">#    es 19.13 20.06 22.96  20.54 21.42  65.26   100</span>
-<span class="co">#    it 18.90 19.84 24.26  20.59 22.80  60.30   100</span>
-<span class="co">#    fr 18.89 19.92 23.46  20.49 21.72  62.85   100</span>
-<span class="co">#    pt 18.90 19.99 23.80  20.70 22.17  61.42   100</span></code></pre></div>
+<span class="co">#  expr   min    lq  mean median    uq   max neval</span>
+<span class="co">#    en 17.45 18.01 19.69  18.53 19.14 55.30   100</span>
+<span class="co">#    de 20.58 21.54 26.69  22.08 23.96 67.16   100</span>
+<span class="co">#    nl 33.79 34.67 39.13  35.39 36.72 74.60   100</span>
+<span class="co">#    es 20.71 21.42 24.36  21.88 22.65 58.57   100</span>
+<span class="co">#    it 20.65 21.18 26.50  21.53 22.68 61.96   100</span>
+<span class="co">#    fr 20.68 21.27 25.05  21.64 22.37 58.82   100</span>
+<span class="co">#    pt 20.69 21.44 24.36  21.94 22.99 59.66   100</span></code></pre></div>
 <p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
 </div>
   </div>

docs/articles/datasets.html

@@ -12,7 +12,7 @@
 <link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
 <link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
 <link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
-<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
 <script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
@@ -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">1.4.0.9044</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -19,8 +19,8 @@
 <!-- jquery -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
 <!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
 
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
 
@@ -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">1.4.0.9045</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 

docs/articles/resistance_predict.html

@@ -12,7 +12,7 @@
 <link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
 <link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
 <link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
-<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
 <script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
@@ -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">1.4.0.9044</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 

docs/articles/welcome_to_AMR.html

@@ -12,7 +12,7 @@
 <link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
 <link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
 <link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
-<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
 <script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
@@ -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">1.4.0.9044</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 

docs/authors.html

@@ -19,8 +19,8 @@
 <!-- jquery -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
 <!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
 
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
 
@@ -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">1.4.0.9045</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 
@@ -303,6 +303,10 @@
         <p><strong>Sofia Ny</strong>. Contributor. 
         </p>
       </li>
+      <li>
+        <p><strong>Rogier P. Schade</strong>. Contributor. 
+        </p>
+      </li>
       <li>
         <p><strong>Dennis Souverein</strong>. Contributor. 
         </p>

docs/extra.css

@@ -7,7 +7,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

docs/extra.js

@@ -7,7 +7,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -90,6 +90,7 @@ $(document).ready(function() {
       x = x.replace("Judith", "Dr. Judith");
       x = x.replace("Gwen", "Dr. Gwen");
       x = x.replace("Anthony", "Dr. Anthony");
+      x = x.replace("Rogier", "Dr. Rogier");
     }
     return(x);
   }

docs/index.html

@@ -12,7 +12,7 @@
 <link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png">
 <link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png">
 <link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png">
-<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css">
 <script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
@@ -43,7 +43,7 @@
       </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">1.4.0.9045</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 
@@ -197,6 +197,7 @@
 <div class="page-header"><h1 class="hasAnchor">
 <a href="#amr-for-r-" class="anchor"></a><code>AMR</code> (for R) <img src="./logo.png" align="right" height="120px">
 </h1></div>
+<p><em>Note: the rules of ‘EUCAST Clinical Breakpoints v11.0 (2021)’ will be added in the next release, to be expected in February/March 2021.</em></p>
 <blockquote>
 <p><span class="fa fa-clipboard-list" style="color: #128f76; font-size: 20pt; margin-right: 5px;"></span> <strong>PLEASE TAKE PART IN OUR SURVEY!</strong><br>
 Since you are one of our users, we would like to know how you use the package and what it brought you or your organisation. <strong>If you have a minute, please <a href="./survey.html">anonymously fill in this short questionnaire</a></strong>. Your valuable input will help to improve the package and its functionalities. You can answer the open questions in either English, Spanish, French, Dutch, or German. Thank you very much in advance! <br><a class="btn btn-info btn-amr" href="./survey.html">Take me to the 5-min survey!</a></p>
@@ -210,7 +211,7 @@ Since you are one of our users, we would like to know how you use the package an
 <p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell">fully independent of any other R package</a> and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl">Certe Medical Diagnostics and Advice</a> and <a href="https://www.umcg.nl">University Medical Center Groningen</a>. This R package is <a href="./news">actively maintained</a> and is free software (see <a href="#copyright">Copyright</a>).</p>
 <div class="main-content" style="display: inline-block;">
 <p>
-<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in 135 countries</strong><br> Since its first public release in early 2018, this package has been downloaded from 135 countries. Click the map to enlarge and to see the country names.
+<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in 138 countries</strong><br> Since its first public release in early 2018, this package has been downloaded from 138 countries. Click the map to enlarge and to see the country names.
 </p>
 </div>
 <div id="with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side" class="section level5">
@@ -227,6 +228,8 @@ Since you are one of our users, we would like to know how you use the package an
   <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"><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; NOTE: Using column 'mo' as input for mo_is_gram_negative()</span>
 <span class="co">#&gt; NOTE: Using column 'mo' as input for mo_is_intrinsic_resistant()</span>
+<span class="co">#&gt; NOTE: Determining intrinsic resistance based on 'EUCAST Expert Rules' and</span>
+<span class="co">#&gt;       'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2 from 2020.</span>
 <span class="co">#&gt; Selecting aminoglycosides: 'AMK' (amikacin), 'GEN' (gentamicin), </span>
 <span class="co">#&gt;                            'KAN' (kanamycin), 'TOB' (tobramycin)</span>
 <span class="co">#&gt; Selecting carbapenems: 'IPM' (imipenem), 'MEM' (meropenem)</span></code></pre></div>
@@ -298,6 +301,12 @@ Since you are one of our users, we would like to know how you use the package an
 </tr>
 </tbody>
 </table>
+<p>A base R equivalent would be:</p>
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">example_isolates</span><span class="op">$</span><span class="va">mo</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">mo</span><span class="op">)</span>
+<span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html">which</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</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="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"mo"</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="op">]</span></code></pre></div>
 </div>
 <div id="partners" class="section level4">
 <h4 class="hasAnchor">
@@ -327,7 +336,7 @@ Since you are one of our users, we would like to know how you use the package an
 <li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li>
 <li>Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li>
 <li>Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
-<li>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI (<a href="https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt">link</a>)</li>
+<li>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI (<a href="./articles/datasets.html">link</a>)</li>
 <li>Principal component analysis for AMR (<a href="./articles/PCA.html">tutorial</a>)</li>
 </ul>
 </div>
@@ -337,9 +346,9 @@ Since you are one of our users, we would like to know how you use the package an
 <div id="latest-released-version" class="section level4">
 <h4 class="hasAnchor">
 <a href="#latest-released-version" class="anchor"></a>Latest released version</h4>
-<p><img src="https://www.r-pkg.org/badges/version-ago/AMR"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR"></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>, which has a peer-reviewed submission process. Install this package in R from CRAN by using the command:</p>
-<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<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><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>
@@ -347,8 +356,9 @@ Since you are one of our users, we would like to know how you use the package an
 <div id="latest-development-version" class="section level4">
 <h4 class="hasAnchor">
 <a href="#latest-development-version" class="anchor"></a>Latest development version</h4>
+<p><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master" alt="R-code-check"><a href="https://www.codefactor.io/repository/github/msberends/amr"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=master"><img src="https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg" alt="Codecov"></a></p>
 <p>The latest and unpublished development version can be installed from GitHub using:</p>
-<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<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="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>
 </div>

docs/news/index.html

@@ -19,8 +19,8 @@
 <!-- jquery -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
 <!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
 
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
 
@@ -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">1.4.0.9045</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 
@@ -236,36 +236,34 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1409045" class="section level1">
-<h1 class="page-header" data-toc-text="1.4.0.9045">
-<a href="#amr-1409045" class="anchor"></a>AMR 1.4.0.9045<small> Unreleased </small>
+    <div id="amr-150" class="section level1">
+<h1 class="page-header" data-toc-text="1.5.0">
+<a href="#amr-150" class="anchor"></a>AMR 1.5.0<small> Unreleased </small>
 </h1>
-<div id="last-updated-25-december-2020" class="section level2">
-<h2 class="hasAnchor">
-<a href="#last-updated-25-december-2020" class="anchor"></a><small>Last updated: 25 December 2020</small>
-</h2>
+<p><em>Note: the rules of ‘EUCAST Clinical Breakpoints v11.0 (2021)’ will be added in the next release, to be expected in February/March 2021.</em></p>
 <div id="new" class="section level3">
 <h3 class="hasAnchor">
 <a href="#new" class="anchor"></a>New</h3>
 <ul>
 <li>
-<p>Function <code><a href="../reference/is_new_episode.html">is_new_episode()</a></code> to determine patient episodes which are not necessarily based on microorganisms. It also supports grouped variables with e.g. <code><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</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> of the <code>dplyr</code> package:</p>
+<p>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> to determine (patient) episodes which are not necessarily based on microorganisms. The <code><a href="../reference/get_episode.html">get_episode()</a></code> function returns the index number of the episode per group, while the <code><a href="../reference/get_episode.html">is_new_episode()</a></code> function returns values <code>TRUE</code>/<code>FALSE</code> to indicate whether an item in a vector is the start of a new episode. They also support <code>dplyr</code>s grouping (i.e. using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code>):</p>
 <div class="sourceCode" id="cb1"><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://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/group_by.html">group_by</a></span><span class="op">(</span><span class="va">patient_id</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/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/is_new_episode.html">is_new_episode</a></span><span class="op">(</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+  <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/get_episode.html">is_new_episode</a></span><span class="op">(</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span><span class="op">)</span></code></pre></div>
 </li>
 <li><p>Functions <code><a href="../reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="../reference/mo_property.html">mo_is_gram_positive()</a></code> as wrappers around <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>. They always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p></li>
 <li><p>Function <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> to test for intrinsic resistance, based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2</a> from 2020.</p></li>
-<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 number generation. They take microorganism names and antibiotic names as input to make generation more realistic.</p></li>
+<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" class="section level3">
 <h3 class="hasAnchor">
 <a href="#changed" 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>
 <p>Interpretation of antimicrobial resistance - <code><a href="../reference/as.rsi.html">as.rsi()</a></code>:</p>
 <ul>
@@ -279,7 +277,30 @@
 </ul>
 </li>
 <li>
-<p>Some functions are now context-aware when used inside <code>dplyr</code> verbs, such as <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>. This means that then the data argument does not need to be set anymore. This is the case for the new functions <code><a href="../reference/mo_property.html">mo_is_gram_negative()</a></code>, <code><a href="../reference/mo_property.html">mo_is_gram_positive()</a></code>, <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> and for the existing functions <code><a href="../reference/first_isolate.html">first_isolate()</a></code>, <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code>, <code><a href="../reference/mdro.html">mdro()</a></code>, <code><a href="../reference/mdro.html">brmo()</a></code>, <code><a href="../reference/mdro.html">mrgn()</a></code>, <code><a href="../reference/mdro.html">mdr_tb()</a></code>, <code><a href="../reference/mdro.html">mdr_cmi2012()</a></code>, <code><a href="../reference/mdro.html">eucast_exceptional_phenotypes()</a></code>. This was already the case for antibiotic selection functions (such as using <code><a href="../reference/antibiotic_class_selectors.html">penicillins()</a></code> in <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code>).</p>
+<p>Some functions are now context-aware when used inside <code>dplyr</code> verbs, such as <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>. This means that then the data argument does not need to be set anymore. This is the case for the new functions:</p>
+<ul>
+<li><code><a href="../reference/mo_property.html">mo_is_gram_negative()</a></code></li>
+<li><code><a href="../reference/mo_property.html">mo_is_gram_positive()</a></code></li>
+<li><code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code></li>
+</ul>
+<p>… and for the existing functions:</p>
+<ul>
+<li>
+<code><a href="../reference/first_isolate.html">first_isolate()</a></code>,</li>
+<li>
+<code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code>,</li>
+<li>
+<code><a href="../reference/mdro.html">mdro()</a></code>,</li>
+<li>
+<code><a href="../reference/mdro.html">brmo()</a></code>,</li>
+<li>
+<code><a href="../reference/mdro.html">mrgn()</a></code>,</li>
+<li>
+<code><a href="../reference/mdro.html">mdr_tb()</a></code>,</li>
+<li>
+<code><a href="../reference/mdro.html">mdr_cmi2012()</a></code>,</li>
+<li><code><a href="../reference/mdro.html">eucast_exceptional_phenotypes()</a></code></li>
+</ul>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># to select first isolates that are Gram-negative </span>
@@ -290,6 +311,14 @@
   <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"><a href="../reference/antibiotic_class_selectors.html">cephalosporins</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</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://tibble.tidyverse.org/reference/as_tibble.html">as_tibble</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
 </li>
+<li>
+<p>For antibiotic selection functions (such as <code><a href="../reference/antibiotic_class_selectors.html">cephalosporins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>) to select columns based on a certain antibiotic group, the dependency on the <code>tidyselect</code> package was removed, meaning that they can now also be used without the need to have this package installed and now also work in base R function calls (they rely on R 3.2 or later):</p>
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<code class="sourceCode R">
+<span class="co"># above example in base R:</span>
+<span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html">which</a></span><span class="op">(</span><span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</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="op">)</span>,
+                 <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"mo"</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">cephalosporins</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></code></pre></div>
+</li>
 <li><p>For all function arguments in the code, it is now defined what the exact type of user input should be (inspired by the <a href="https://github.com/moodymudskipper/typed"><code>typed</code></a> package). If the user input for a certain function does not meet the requirements for a specific argument (such as the class or length), an informative error will be thrown. This makes the package more robust and the use of it more reproducible and reliable. In total, more than 420 arguments were defined.</p></li>
 <li><p>Fix for <code><a href="../reference/mo_source.html">set_mo_source()</a></code>, that previously would not remember the file location of the original file</p></li>
 <li><p>Deprecated function <code><a href="../reference/AMR-deprecated.html">p_symbol()</a></code> that not really fits the scope of this package. It will be removed in a future version. See <a href="https://github.com/msberends/AMR/blob/v1.4.0/R/p_symbol.R">here</a> for the source code to preserve it.</p></li>
@@ -313,11 +342,14 @@
 <ul>
 <li>All messages and warnings thrown by this package now break sentences on whole words</li>
 <li>More extensive unit tests</li>
-<li>Internal calls to <code><a href="https://rdrr.io/r/base/options.html">options()</a></code> were all removed in favour of a new internal environment <code>mo_env</code>
+<li>Internal calls to <code><a href="https://rdrr.io/r/base/options.html">options()</a></code> were all removed in favour of a new internal environment <code>pkg_env</code>
 </li>
+<li>Improved internal type setting (among other things: replaced all <code><a href="https://rdrr.io/r/base/lapply.html">sapply()</a></code> calls with <code><a href="https://rdrr.io/r/base/lapply.html">vapply()</a></code>)</li>
+<li>Added CodeFactor as a continuous code review to this package: <a href="https://www.codefactor.io/repository/github/msberends/amr/" class="uri">https://www.codefactor.io/repository/github/msberends/amr/</a>
+</li>
+<li>Added Dr. Rogier Schade as contributor</li>
 </ul>
 </div>
-</div>
 </div>
     <div id="amr-140" class="section level1">
 <h1 class="page-header" data-toc-text="1.4.0">
@@ -332,7 +364,7 @@
 <li>
 <p>Data set <code>intrinsic_resistant</code>. This data set contains all bug-drug combinations where the ‘bug’ is intrinsic resistant to the ‘drug’ according to the latest EUCAST insights. It contains just two columns: <code>microorganism</code> and <code>antibiotic</code>.</p>
 <p>Curious about which enterococci are actually intrinsic resistant to vancomycin?</p>
-<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb4"><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://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
@@ -355,7 +387,7 @@
 <ul>
 <li>
 <p>Support for using <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/across.html">across()</a></code> to interpret MIC values or disk zone diameters, which also automatically determines the column with microorganism names or codes.</p>
-<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># until dplyr 1.0.0</span>
 <span class="va">your_data</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.rsi</span><span class="op">)</span>
@@ -373,7 +405,7 @@
 </li>
 <li>
 <p>Added intelligent data cleaning to <code><a href="../reference/as.disk.html">as.disk()</a></code>, so numbers can also be extracted from text and decimal numbers will always be rounded up:</p>
-<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/as.disk.html">as.disk</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="st">"disk zone: 23.4 mm"</span>, <span class="fl">23.4</span><span class="op">)</span><span class="op">)</span>
 <span class="co">#&gt; Class &lt;disk&gt;</span>
@@ -434,7 +466,7 @@
 <li><p>Function <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code> to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses <code><a href="../reference/as.ab.html">as.ab()</a></code> internally</p></li>
 <li>
 <p><a href="https://tidyselect.r-lib.org/reference/language.html">Tidyverse selection helpers</a> for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code> and <code><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html">tidyr::pivot_longer()</a></code>:</p>
-<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb7"><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://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
 
@@ -623,7 +655,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li>
 <li>
 <p>Interpretation from MIC values (and disk zones) to R/SI can now be used with <code><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at()</a></code> of the <code>dplyr</code> package:</p>
-<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">yourdata</span> <span class="op">%&gt;%</span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span><span class="op">(</span><span class="va">antibiotic1</span><span class="op">:</span><span class="va">antibiotic25</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span><span class="op">)</span>
@@ -652,7 +684,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>Support for LOINC codes in the <code>antibiotics</code> data set. Use <code><a href="../reference/ab_property.html">ab_loinc()</a></code> to retrieve LOINC codes, or use a LOINC code for input in any <code>ab_*</code> function:</p>
-<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/ab_property.html">ab_loinc</a></span><span class="op">(</span><span class="st">"ampicillin"</span><span class="op">)</span>
 <span class="co">#&gt; [1] "21066-6" "3355-5"  "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"</span>
@@ -663,7 +695,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 <li>
 <p>Support for SNOMED CT codes in the <code>microorganisms</code> data set. Use <code><a href="../reference/mo_property.html">mo_snomed()</a></code> to retrieve SNOMED codes, or use a SNOMED code for input in any <code>mo_*</code> function:</p>
-<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/mo_property.html">mo_snomed</a></span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>
 <span class="co">#&gt; [1] 115329001   3092008 113961008</span>
@@ -728,11 +760,11 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>If you were dependent on the old Enterobacteriaceae family e.g. by using in your code:</p>
-<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_family</a></span><span class="op">(</span><span class="va">somebugs</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Enterobacteriaceae"</span><span class="op">)</span> <span class="va">...</span></code></pre></div>
 <p>then please adjust this to:</p>
-<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_order</a></span><span class="op">(</span><span class="va">somebugs</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Enterobacterales"</span><span class="op">)</span> <span class="va">...</span></code></pre></div>
 </li>
@@ -746,7 +778,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>Functions <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> as aliases of <code><a href="../reference/proportion.html">proportion_SI()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code>, respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.</p>
-<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb13"><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://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
 <span class="va">example_isolates</span> <span class="op">%&gt;%</span>
@@ -775,7 +807,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>More intelligent way of coping with some consonants like “l” and “r”</p></li>
 <li>
 <p>Added a score (a certainty percentage) to <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code>, that is calculated using the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance">Levenshtein distance</a>:</p>
-<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/as.mo.html">as.mo</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="st">"Stafylococcus aureus"</span>,
         <span class="st">"staphylokok aureuz"</span><span class="op">)</span><span class="op">)</span>
@@ -834,14 +866,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>Determination of first isolates now <strong>excludes</strong> all ‘unknown’ microorganisms at default, i.e. microbial code <code>"UNKNOWN"</code>. They can be included with the new argument <code>include_unknown</code>:</p>
-<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="va">...</span>, include_unknown <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
 <p>For WHONET users, this means that all records/isolates with organism code <code>"con"</code> (<em>contamination</em>) will be excluded at default, since <code>as.mo("con") = "UNKNOWN"</code>. The function always shows a note with the number of ‘unknown’ microorganisms that were included or excluded.</p>
 </li>
 <li>
 <p>For code consistency, classes <code>ab</code> and <code>mo</code> will now be preserved in any subsetting or assignment. For the sake of data integrity, this means that invalid assignments will now result in <code>NA</code>:</p>
-<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># how it works in base R:</span>
 <span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html">factor</a></span><span class="op">(</span><span class="st">"A"</span><span class="op">)</span>
@@ -866,7 +898,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with <code><a href="../reference/mo_property.html">mo_shortname()</a></code> at default:</p>
-<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
 <span class="co">#&gt; NOTE: Using column `mo` as input for `col_mo`.</span>
@@ -889,13 +921,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <span class="co">#&gt; 4 Gram-negative AMX 227  0 405   632</span>
 <span class="co">#&gt; NOTE: Use 'format()' on this result to get a publicable/printable format.</span></code></pre></div>
 <p>You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R <code><a href="https://rdrr.io/r/base/format.html">format()</a></code> function:</p>
-<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="https://rdrr.io/r/base/format.html">format</a></span><span class="op">(</span><span class="va">x</span>, combine_IR <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
 </li>
 <li>
 <p>Additional way to calculate co-resistance, i.e. when using multiple antimicrobials as input for <code>portion_*</code> functions or <code>count_*</code> functions. This can be used to determine the empiric susceptibility of a combination therapy. A new argument <code>only_all_tested</code> (<strong>which defaults to <code>FALSE</code></strong>) replaces the old <code>also_single_tested</code> and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the <code>portion</code> and <code>count</code> help pages), where the %SI is being determined:</p>
-<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># --------------------------------------------------------------------</span>
 <span class="co">#                     only_all_tested = FALSE  only_all_tested = TRUE</span>
@@ -917,7 +949,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 <li>
 <p><code>tibble</code> printing support for classes <code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code> <code>mo</code>. When using <code>tibble</code>s containing antimicrobial columns, values <code>S</code> will print in green, values <code>I</code> will print in yellow and values <code>R</code> will print in red. Microbial IDs (class <code>mo</code>) will emphasise on the genus and species, not on the kingdom.</p>
-<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># (run this on your own console, as this page does not support colour printing)</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>
@@ -1000,7 +1032,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>Function <code><a href="../reference/proportion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code>portion_df()</code> to immediately show resistance percentages and number of available isolates:</p>
-<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb21"><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://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">AMX</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op">%&gt;%</span>
@@ -1027,7 +1059,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>UPEC (Uropathogenic <em>E. coli</em>)</li>
 </ul>
 <p>All these lead to the microbial ID of <em>E. coli</em>:</p>
-<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"UPEC"</span><span class="op">)</span>
 <span class="co"># B_ESCHR_COL</span>
@@ -1132,7 +1164,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>when all values are unique it now shows a message instead of a warning</p></li>
 <li>
 <p>support for boxplots:</p>
-<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</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> 
@@ -1227,7 +1259,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 <li>
 <p>New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:</p>
-<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>
 <span class="fu"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span><span class="op">(</span><span class="op">)</span>
@@ -1241,7 +1273,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <span class="fu"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span><span class="op">(</span><span class="op">)</span>
 <span class="fu"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
 <p>The <code>antibiotics</code> data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set. For example:</p>
-<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb25"><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="../reference/filter_ab_class.html">filter_glycopeptides</a></span><span class="op">(</span>result <span class="op">=</span> <span class="st">"R"</span><span class="op">)</span>
 <span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span>
@@ -1250,7 +1282,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 <li>
 <p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
-<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">ab_property</span> <span class="op">-&gt;</span> <span class="fu">atc_property</span><span class="op">(</span><span class="op">)</span>
 <span class="va">ab_name</span> <span class="op">-&gt;</span> <span class="fu">atc_name</span><span class="op">(</span><span class="op">)</span>
@@ -1271,7 +1303,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</p></li>
 <li>
 <p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="../reference/plot.html">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
-<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span><span class="va">septic_patients</span>, col_ab <span class="op">=</span> <span class="st">"amox"</span><span class="op">)</span>
 <span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
@@ -1279,13 +1311,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 <li>
 <p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
-<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb28"><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="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="va">...</span><span class="op">)</span>
 <span class="co"># or</span>
 <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="va">...</span><span class="op">)</span></code></pre></div>
 <p>is equal to:</p>
-<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
+<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://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>only_firsts <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="va">...</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
@@ -1318,7 +1350,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>Now handles incorrect spelling, like <code>i</code> instead of <code>y</code> and <code>f</code> instead of <code>ph</code>:</p>
-<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># mo_fullname() uses as.mo() internally</span>
 
@@ -1330,7 +1362,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 <li>
 <p>Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default <code>allow_uncertain = TRUE</code> is equal to uncertainty level 2. Run <code><a href="../reference/as.mo.html">?as.mo</a></code> for more info about these levels.</p>
-<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># equal:</span>
 <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">...</span>, allow_uncertain <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
@@ -1345,7 +1377,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>All microbial IDs that found are now saved to a local file <code>~/.Rhistory_mo</code>. Use the new function <code>clean_mo_history()</code> to delete this file, which resets the algorithms.</p></li>
 <li>
 <p>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</p>
-<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"qwerty"</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span>
 <span class="co"># Warning: </span>
@@ -1395,7 +1427,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
-<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span>
 <span class="co"># OLD WAY</span>
@@ -1479,7 +1511,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Fewer than 3 characters as input for <code>as.mo</code> will return NA</p></li>
 <li>
 <p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
-<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. species"</span><span class="op">)</span>        <span class="co"># B_ESCHR</span>
 <span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"E. spp."</span><span class="op">)</span>     <span class="co"># "Escherichia species"</span>
@@ -1496,7 +1528,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>Support for grouping variables, test with:</p>
-<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb35"><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://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> 
@@ -1504,7 +1536,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 <li>
 <p>Support for (un)selecting columns:</p>
-<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</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> 
@@ -1584,7 +1616,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 </ul>
 <p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
-<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
 <span class="co"># [1] "Gram negative"</span>
@@ -1595,7 +1627,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"S. group A"</span>, language <span class="op">=</span> <span class="st">"pt"</span><span class="op">)</span> <span class="co"># Portuguese</span>
 <span class="co"># [1] "Streptococcus grupo A"</span></code></pre></div>
 <p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
-<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"Esc blattae"</span><span class="op">)</span>
 <span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span>
@@ -1610,7 +1642,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Function <code>is.rsi.eligible</code> to check for columns that have valid antimicrobial results, but do not have the <code>rsi</code> class yet. Transform the columns of your raw data with: <code>data %&gt;% mutate_if(is.rsi.eligible, as.rsi)</code></p></li>
 <li>
 <p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using intelligent rules:</p>
-<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
 <span class="co"># [1] B_ESCHR_COL</span>
@@ -1619,7 +1651,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"S group A"</span><span class="op">)</span>
 <span class="co"># [1] B_STRPTC_GRA</span></code></pre></div>
 <p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p>
-<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">thousands_of_E_colis</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span><span class="op">(</span><span class="st">"E. coli"</span>, <span class="fl">25000</span><span class="op">)</span>
 <span class="fu">microbenchmark</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span><span class="op">(</span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">thousands_of_E_colis</span><span class="op">)</span>, unit <span class="op">=</span> <span class="st">"s"</span><span class="op">)</span>
@@ -1653,7 +1685,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</p></li>
 <li>
 <p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
-<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu">ab_official</span><span class="op">(</span><span class="st">"Bactroban"</span><span class="op">)</span>
 <span class="co"># [1] "Mupirocin"</span>
@@ -1670,7 +1702,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Added arguments <code>minimum</code> and <code>as_percent</code> to <code>portion_df</code></p></li>
 <li>
 <p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
-<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r">
+<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://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">amox</span>, <span class="va">cipr</span><span class="op">)</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span><span class="op">(</span><span class="op">)</span>
 <span class="co"># which is the same as:</span>
@@ -1690,12 +1722,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Added longest en shortest character length in the frequency table (<code>freq</code>) header of class <code>character</code></p></li>
 <li>
 <p>Support for types (classes) list and matrix for <code>freq</code></p>
-<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb43"><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">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="cb43"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb44"><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">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span>

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: 2020-12-24T23:05Z
+last_built: 2021-01-05T08:44Z
 urls:
   reference: https://msberends.github.io/AMR//reference
   article: https://msberends.github.io/AMR//articles

docs/reference/AMR-deprecated.html

@@ -19,8 +19,8 @@
 <!-- jquery -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
 <!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
 
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
 
@@ -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">1.4.0.9044</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 

docs/reference/AMR.html

@@ -19,8 +19,8 @@
 <!-- jquery -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
 <!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
 
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
 
@@ -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">1.4.0.9044</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 

docs/reference/WHOCC.html

@@ -19,8 +19,8 @@
 <!-- jquery -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
 <!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
 
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
 
@@ -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">1.4.0.9044</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 

docs/reference/WHONET.html

@@ -19,8 +19,8 @@
 <!-- jquery -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
 <!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
 
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
 
@@ -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">1.4.0.9044</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>