v1.5.0

.github/workflows/check.yaml

@@ -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: '3.4',     allowfail: false, 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: '3.3',     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: '3.2',     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: '3.1',     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 }}
@@ -80,21 +88,22 @@ 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') }}
+          key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-3-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-3-
+          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: |
@@ -102,12 +111,22 @@ jobs:
           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")
@@ -116,16 +135,27 @@ jobs:
       - name: Session info
         run: |
           options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
+          utils::sessionInfo()
-          sessioninfo::session_info(pkgs, include_base = TRUE)
+          as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
         shell: Rscript {0}
 
       - 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()
         run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
@@ -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

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.4.0.9052
+Version: 1.5.0
-Date: 2020-12-28
+Date: 2021-01-05
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 
@@ -57,7 +57,6 @@ Suggests:
     skimr,
     testthat,
     tidyr,
-    tidyselect,
     xml2
 VignetteBuilder: knitr,rmarkdown
 URL: https://msberends.github.io/AMR/, https://github.com/msberends/AMR

NEWS.md

@@ -1,5 +1,6 @@
-# AMR 1.4.0.9052
+# AMR 1.5.0
-## <small>Last updated: 28 December 2020</small>
+
+*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
 * 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()`):
@@ -11,7 +12,7 @@
   ```
 * 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
@@ -22,7 +23,21 @@
   * `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 
   # and view results of cephalosporins and aminoglycosides:
@@ -32,6 +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.
@@ -47,7 +68,6 @@
 * Fix for printing class <mo> in tibbles when all values are `NA`
 * Fix for `mo_shortname()` when the input contains `NA`
 * If `as.mo()` takes more than 30 seconds, some suggestions will be done to improve speed
-* Lost dependency on the `tidyselect` package for using antibiotic selectors such as `carbapenems()` and `aminoglycosides()`
 
 ### Other
 * All messages and warnings thrown by this package now break sentences on whole words

R/aa_helper_functions.R

@@ -458,7 +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())
   }
@@ -527,43 +527,87 @@ 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
+  if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2) {
-  cur_data_all_dplyr <- import_fn("cur_data_all", "dplyr", error_on_fail = FALSE)
+    if (is.na(arg_name)) {
-  if (is.null(cur_data_all_dplyr)) {
+      warning_("this function can only be used in R >= 3.2", call = call)
-    # dplyr not installed
+      return(data.frame())
-    stop_("argument `", arg_name, "` is missing, with no default", call = call)
+    } 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))
 }
 
-unique_call_id <- function() {
+unique_call_id <- function(entire_session = FALSE) {
-  # combination of environment ID (like "0x7fed4ee8c848")
+  if (entire_session == TRUE) {
-  # and highest system call
+    c(envir = "session",
-  c(envir = gsub("<environment: (.*)>", "\\1", utils::capture.output(sys.frames()[[1]])),
+      call = "session")
-    call = paste0(deparse(sys.calls()[[1]]), collapse = ""))
+  } 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) {
+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("uniquecall_", fn),
+  assign(x = paste0("thrown_msg_", fn),
-         value = unique_call_id(),
+         value = unique_call_id(entire_session = entire_session),
          envir = pkg_env)
 }
 
-message_not_thrown_before <- function(fn) {
+message_not_thrown_before <- function(fn, entire_session = FALSE) {
-  is.null(pkg_env[[paste0("uniquecall_", fn)]]) || !identical(pkg_env[[paste0("uniquecall_", fn)]], unique_call_id())
+  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% "^uniquecall_"],
+  rm(list = pkg_env_contents[pkg_env_contents %like% "^thrown_msg_"],
      envir = pkg_env)
 }
 
@@ -571,7 +615,7 @@ has_colour <- function() {
   # 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, only supports 8 colours
+    # disable on emacs, which only supports 8 colours
     return(FALSE)
   }
   enabled <- getOption("crayon.enabled")

R/ab_class_selectors.R

@@ -27,7 +27,9 @@
 #' 
 #' 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, "."), "")}}
+#' 
+#' 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
@@ -162,28 +164,14 @@ 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)
   
-  for (i in seq_len(length(sys.frames()))) {
+  if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2) {
-    # dplyr?
+    warning_("antibiotic class selectors such as ", function_name, 
-    if (".data" %in% names(sys.frames()[[i]])) {
+             "() require R version 3.2 or later - you have ", R.version.string,
-      vars_df <- sys.frames()[[i]]$`.data`
+             call = FALSE)
-      if (is.data.frame(vars_df)) {
+    return(NULL)
-        break
-      }
-    }
-    # then try base R - an element `x` will be in the system call stack
-    vars_df <- tryCatch(sys.frames()[[i]]$x, error = function(e) NULL)
-    if (!is.null(vars_df) && is.data.frame(vars_df)) {
-      # when using e.g. example_isolates[, carbapenems()] or example_isolates %>% select(carbapenems())
-      break
-    } else if (!is.null(vars_df) && is.list(vars_df)) {
-      # when using e.g. example_isolates %>% filter(across(carbapenems(), ~. == "R"))
-      vars_df <- tryCatch(as.data.frame(vars_df, stringsAsFactors = FALSE), error = function(e) NULL)
-      if (!is.null(vars_df)) {
-        break
-      }
-    }
   }
-  stop_ifnot(is.data.frame(vars_df), "this function must be used inside dplyr selection verbs or within a data.frame call.", call = -2)
+  
+  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) {
@@ -208,10 +196,11 @@ ab_selector <- function(ab_class, function_name) {
     if (length(agents) == 0) {
       message_("No antimicrobial agents of class ", ab_group, " found", examples, ".")
     } else {
-      message_("Selecting ", ab_group, ": ",
+      agents_formatted <- paste0("column '", font_bold(agents, collapse = NULL), "'")
-               paste(paste0("column '", font_bold(agents, collapse = NULL),
+      agents_names <- ab_name(names(agents), tolower = TRUE, language = NULL)
-                            "' (", ab_name(names(agents), tolower = TRUE, language = NULL), ")"),
+      agents_formatted[agents != agents_names] <- paste0(agents_formatted[agents != agents_names],
-                     collapse = ", "),
+                                                         " (", agents_names[agents != agents_names], ")")
+      message_("Selecting ", ab_group, ": ", paste(agents_formatted, collapse = ", "),
                as_note = FALSE,
                extra_indent = nchar(paste0("Selecting ", ab_group, ": ")))
     }

R/ab_from_text.R

@@ -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.

R/catalogue_of_life.R

@@ -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/data.R

@@ -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]

R/eucast_rules.R

@@ -83,7 +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.
 #'
@@ -96,7 +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)

R/mdro.R

@@ -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"`
 #'
@@ -193,7 +193,7 @@ 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_url <- "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$code == "eucast3.1") {
@@ -222,7 +222,7 @@ mdro <- function(x,
     guideline$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$source_url <- "Antimicrobial Resistance and Infection Control 4:7, 2015. DOI: 10.1186/s13756-015-0047-6"
+    guideline$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") {

R/mo.R

@@ -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>
+#' 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. <https://doi.org/10.1016/j.cmi.2019.02.028>
+#' 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. <https://dx.doi.org/10.1080/14787210.2020.1730813>
+#' 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. <https://dx.doi.org/10.1084/jem.57.4.571>
+#' 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`]
@@ -2006,5 +2006,3 @@ repair_reference_df <- function(reference_df) {
   reference_df[, "mo"] <- as.mo(reference_df[, "mo", drop = TRUE])
   reference_df
 }
-
-pkg_env <- new.env(hash = FALSE)

R/mo_property.R

@@ -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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_name")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_shortname")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_subspecies")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_species")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_genus")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_family")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_order")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_class")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_phylum")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_kingdom")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_type")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_gramstain")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_is_gram_negative")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_is_gram_positive")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_is_intrinsic_resistant")
+    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
+  # show used version number once per session (pkg_env will reload every session)
-  if (is.null(getOption("AMR_intrinsic_resistance_note", NULL))) {
+  if (message_not_thrown_before("intrinsic_resistant_version", entire_session = TRUE)) {
     message_("Determining intrinsic resistance based on ",
-             format_eucast_version_nr(3.2, FALSE), ". ",
+             format_eucast_version_nr(3.2, markdown = FALSE), ". ",
-             font_bold("This note is shown only once per session."))
+             font_red("This note will be shown once per session."))
-    options(AMR_intrinsic_resistance_note = "shown")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_snomed")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_ref")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_authors")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_year")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_rank")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_taxonomy")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_synonyms")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_info")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_url")
+    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"))
+    # this tries to find the data and an <mo> column
-    x <- find_mo_col("mo_property")
+    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/zzz.R

@@ -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)
+[![CRAN](https://www.r-pkg.org/badges/version-ago/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)
+[![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" />
 

data-raw/reproduction_of_intrinsic_resistant.R

@@ -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()

docs/404.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9052</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

@@ -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">1.4.0.9052</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

@@ -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">1.4.0.9046</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">26 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 26 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">2020-12-26</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">2020-12-26</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">2020-12-26</td>
+<td align="center">2020-12-29</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@@ -352,9 +352,9 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2011-10-28</td>
+<td align="center">2014-02-24</td>
-<td align="center">I1</td>
+<td align="center">H4</td>
-<td align="center">Hospital A</td>
+<td align="center">Hospital D</td>
 <td align="center">Staphylococcus aureus</td>
 <td align="center">R</td>
 <td align="center">S</td>
@@ -363,41 +363,19 @@
 <td align="center">M</td>
 </tr>
 <tr class="even">
-<td align="center">2011-06-05</td>
+<td align="center">2017-04-27</td>
-<td align="center">G5</td>
+<td align="center">Q3</td>
-<td align="center">Hospital A</td>
+<td align="center">Hospital B</td>
-<td align="center">Escherichia coli</td>
+<td align="center">Staphylococcus aureus</td>
+<td align="center">S</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">2014-05-12</td>
-<td align="center">X7</td>
-<td align="center">Hospital D</td>
-<td align="center">Streptococcus pneumoniae</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">2011-02-23</td>
-<td align="center">K5</td>
-<td align="center">Hospital A</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">S</td>
-<td align="center">M</td>
-</tr>
 <tr class="odd">
-<td align="center">2017-09-20</td>
+<td align="center">2013-03-12</td>
-<td align="center">T5</td>
+<td align="center">Q4</td>
 <td align="center">Hospital B</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
@@ -407,15 +385,37 @@
 <td align="center">F</td>
 </tr>
 <tr class="even">
-<td align="center">2017-02-10</td>
+<td align="center">2013-03-24</td>
-<td align="center">Y6</td>
+<td align="center">H9</td>
-<td align="center">Hospital D</td>
+<td align="center">Hospital A</td>
 <td align="center">Escherichia 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">F</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">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>
 </tr>
 </tbody>
 </table>
@@ -449,16 +449,16 @@ Longest: 1</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">M</td>
-<td align="right">10,426</td>
+<td align="right">10,444</td>
-<td align="right">52.13%</td>
+<td align="right">52.22%</td>
-<td align="right">10,426</td>
+<td align="right">10,444</td>
-<td align="right">52.13%</td>
+<td align="right">52.22%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">F</td>
-<td align="right">9,574</td>
+<td align="right">9,556</td>
-<td align="right">47.87%</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 F3, 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">2010-01-17</td>
+<td align="center">2010-07-01</td>
-<td align="center">F3</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">R</td>
+<td align="center">S</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">2</td>
-<td align="center">2010-03-13</td>
+<td align="center">2010-08-01</td>
-<td align="center">F3</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">R</td>
-<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="odd">
 <td align="center">3</td>
-<td align="center">2010-04-21</td>
+<td align="center">2010-08-18</td>
-<td align="center">F3</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">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">2010-06-24</td>
+<td align="center">2010-10-16</td>
-<td align="center">F3</td>
+<td align="center">Z4</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
@@ -575,19 +575,19 @@ Longest: 1</p>
 </tr>
 <tr class="odd">
 <td align="center">5</td>
-<td align="center">2010-08-02</td>
+<td align="center">2010-12-23</td>
-<td align="center">F3</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">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">6</td>
-<td align="center">2010-08-14</td>
+<td align="center">2010-12-25</td>
-<td align="center">F3</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">2010-10-06</td>
+<td align="center">2011-01-07</td>
-<td align="center">F3</td>
+<td align="center">Z4</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
+<td align="center">R</td>
-<td align="center">S</td>
+<td align="center">R</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="even">
 <td align="center">8</td>
-<td align="center">2010-10-17</td>
+<td align="center">2011-01-30</td>
-<td align="center">F3</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">2010-11-17</td>
+<td align="center">2011-05-19</td>
-<td align="center">F3</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>
 <tr class="even">
 <td align="center">10</td>
-<td align="center">2011-02-21</td>
+<td align="center">2011-06-21</td>
-<td align="center">F3</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">S</td>
 <td align="center">R</td>
-<td align="center">TRUE</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> 
@@ -665,46 +665,46 @@ Longest: 1</p>
 <tbody>
 <tr class="odd">
 <td align="center">1</td>
-<td align="center">2010-01-17</td>
+<td align="center">2010-07-01</td>
-<td align="center">F3</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">R</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">2010-03-13</td>
+<td align="center">2010-08-01</td>
-<td align="center">F3</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">R</td>
-<td align="center">S</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">2010-04-21</td>
+<td align="center">2010-08-18</td>
-<td align="center">F3</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">I</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
-<td align="center">TRUE</td>
+<td align="center">FALSE</td>
 </tr>
 <tr class="even">
 <td align="center">4</td>
-<td align="center">2010-06-24</td>
+<td align="center">2010-10-16</td>
-<td align="center">F3</td>
+<td align="center">Z4</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
@@ -713,47 +713,47 @@ Longest: 1</p>
 </tr>
 <tr class="odd">
 <td align="center">5</td>
-<td align="center">2010-08-02</td>
+<td align="center">2010-12-23</td>
-<td align="center">F3</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">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>
 <tr class="even">
 <td align="center">6</td>
-<td align="center">2010-08-14</td>
+<td align="center">2010-12-25</td>
-<td align="center">F3</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">S</td>
 <td align="center">FALSE</td>
-<td align="center">FALSE</td>
+<td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">7</td>
-<td align="center">2010-10-06</td>
+<td align="center">2011-01-07</td>
-<td align="center">F3</td>
+<td align="center">Z4</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
+<td align="center">R</td>
-<td align="center">S</td>
+<td align="center">R</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
-<td align="center">FALSE</td>
+<td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">8</td>
-<td align="center">2010-10-17</td>
+<td align="center">2011-01-30</td>
-<td align="center">F3</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">2010-11-17</td>
+<td align="center">2011-05-19</td>
-<td align="center">F3</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">I</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="even">
 <td align="center">10</td>
-<td align="center">2011-02-21</td>
+<td align="center">2011-06-21</td>
-<td align="center">F3</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">S</td>
 <td align="center">R</td>
-<td align="center">TRUE</td>
+<td align="center">S</td>
-<td align="center">TRUE</td>
+<td align="center">FALSE</td>
+<td align="center">FALSE</td>
 </tr>
 </tbody>
 </table>
-<p>Instead of 2, now 6 isolates are flagged. In total, 78.5% of all isolates are marked ‘first weighted’ - 50.1% 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 15,695 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>
@@ -833,10 +831,9 @@ Longest: 1</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="left">1</td>
+<td align="center">2014-02-24</td>
-<td align="center">2011-10-28</td>
+<td align="center">H4</td>
-<td align="center">I1</td>
+<td align="center">Hospital D</td>
-<td align="center">Hospital A</td>
 <td align="center">B_STPHY_AURS</td>
 <td align="center">R</td>
 <td align="center">S</td>
@@ -849,9 +846,38 @@ Longest: 1</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="left">2</td>
+<td align="center">2017-04-27</td>
-<td align="center">2011-06-05</td>
+<td align="center">Q3</td>
-<td align="center">G5</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>
@@ -865,67 +891,33 @@ Longest: 1</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
-<td align="left">3</td>
+<td align="center">2017-03-11</td>
-<td align="center">2014-05-12</td>
+<td align="center">M1</td>
-<td align="center">X7</td>
+<td align="center">Hospital A</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">F</td>
+<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="left">4</td>
+<td align="center">2011-12-21</td>
-<td align="center">2011-02-23</td>
+<td align="center">M5</td>
-<td align="center">K5</td>
 <td align="center">Hospital A</td>
-<td align="center">B_STPHY_AURS</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">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">5</td>
-<td align="center">2017-09-20</td>
-<td align="center">T5</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">M</td>
-<td align="center">F</td>
+<td align="center">Gram-positive</td>
-<td align="center">Gram-negative</td>
+<td align="center">Streptococcus</td>
-<td align="center">Escherichia</td>
+<td align="center">pneumoniae</td>
-<td align="center">coli</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="even">
-<td align="left">7</td>
-<td align="center">2017-12-17</td>
-<td align="center">Z3</td>
-<td align="center">Hospital B</td>
-<td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">F</td>
-<td align="center">Gram-negative</td>
-<td align="center">Escherichia</td>
-<td align="center">coli</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: 15,695<br>
+Length: 15,805<br>
-Available: 15,695 (100%, NA: 0 = 0%)<br>
+Available: 15,805 (100%, NA: 0 = 0%)<br>
 Unique: 4</p>
 <p>Shortest: 16<br>
 Longest: 24</p>
@@ -968,32 +960,32 @@ Longest: 24</p>
 <td align="left">1</td>
 <td align="left">Escherichia coli</td>
 <td align="right">7,828</td>
-<td align="right">49.88%</td>
+<td align="right">49.53%</td>
 <td align="right">7,828</td>
-<td align="right">49.88%</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">3,977</td>
+<td align="right">3,963</td>
-<td align="right">25.34%</td>
+<td align="right">25.07%</td>
-<td align="right">11,805</td>
+<td align="right">11,791</td>
-<td align="right">75.22%</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">2,320</td>
+<td align="right">2,392</td>
-<td align="right">14.78%</td>
+<td align="right">15.13%</td>
-<td align="right">14,125</td>
+<td align="right">14,183</td>
-<td align="right">90.00%</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">1,570</td>
+<td align="right">1,622</td>
-<td align="right">10.00%</td>
+<td align="right">10.26%</td>
-<td align="right">15,695</td>
+<td align="right">15,805</td>
 <td align="right">100.00%</td>
 </tr>
 </tbody>
@@ -1020,33 +1012,33 @@ Longest: 24</p>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">AMX</td>
-<td align="center">3731</td>
+<td align="center">3777</td>
-<td align="center">275</td>
+<td align="center">245</td>
-<td align="center">3822</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">6146</td>
+<td align="center">6159</td>
-<td align="center">297</td>
+<td align="center">278</td>
-<td align="center">1385</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">5918</td>
+<td align="center">5997</td>
 <td align="center">0</td>
-<td align="center">1910</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">7087</td>
+<td align="center">6984</td>
 <td align="center">0</td>
-<td align="center">741</td>
+<td align="center">844</td>
 <td align="center">7828</td>
 </tr>
 <tr class="odd">
@@ -1054,16 +1046,16 @@ Longest: 24</p>
 <td align="center">AMX</td>
 <td align="center">0</td>
 <td align="center">0</td>
-<td align="center">1570</td>
+<td align="center">1622</td>
-<td align="center">1570</td>
+<td align="center">1622</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMC</td>
-<td align="center">1231</td>
+<td align="center">1271</td>
-<td align="center">57</td>
+<td align="center">63</td>
-<td align="center">282</td>
+<td align="center">288</td>
-<td align="center">1570</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">5918</td>
+<td align="center">5997</td>
 <td align="center">0</td>
-<td align="center">1910</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">1191</td>
+<td align="center">1266</td>
 <td align="center">0</td>
-<td align="center">379</td>
+<td align="center">356</td>
-<td align="center">1570</td>
+<td align="center">1622</td>
 </tr>
 <tr class="odd">
 <td align="center">S. aureus</td>
 <td align="center">CIP</td>
-<td align="center">3045</td>
+<td align="center">3017</td>
 <td align="center">0</td>
-<td align="center">932</td>
+<td align="center">946</td>
-<td align="center">3977</td>
+<td align="center">3963</td>
 </tr>
 <tr class="even">
 <td align="center">S. pneumoniae</td>
 <td align="center">CIP</td>
-<td align="center">1785</td>
+<td align="center">1844</td>
 <td align="center">0</td>
-<td align="center">535</td>
+<td align="center">548</td>
-<td align="center">2320</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] 0.536604</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">0.5429950</td>
+<td align="center">0.5273258</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5429998</td>
+<td align="center">0.5421512</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5283993</td>
+<td align="center">0.5394139</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5222153</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">0.5429950</td>
+<td align="center">0.5273258</td>
-<td align="center">4768</td>
+<td align="center">4794</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5429998</td>
+<td align="center">0.5421512</td>
-<td align="center">5407</td>
+<td align="center">5504</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5283993</td>
+<td align="center">0.5394139</td>
-<td align="center">2324</td>
+<td align="center">2423</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5222153</td>
+<td align="center">0.5350195</td>
-<td align="center">3196</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">0.8230710</td>
+<td align="center">0.8223045</td>
-<td align="center">0.9053398</td>
+<td align="center">0.8921819</td>
-<td align="center">0.9872253</td>
+<td align="center">0.9842872</td>
 </tr>
 <tr class="even">
 <td align="center">Klebsiella</td>
-<td align="center">0.8203822</td>
+<td align="center">0.8224414</td>
-<td align="center">0.9076433</td>
+<td align="center">0.8927250</td>
-<td align="center">0.9847134</td>
+<td align="center">0.9833539</td>
 </tr>
 <tr class="odd">
 <td align="center">Staphylococcus</td>
-<td align="center">0.8287654</td>
+<td align="center">0.8268988</td>
-<td align="center">0.9192859</td>
+<td align="center">0.9192531</td>
-<td align="center">0.9894393</td>
+<td align="center">0.9861216</td>
 </tr>
 <tr class="even">
 <td align="center">Streptococcus</td>
-<td align="center">0.5379310</td>
+<td align="center">0.5447324</td>
 <td align="center">0.0000000</td>
-<td align="center">0.5379310</td>
+<td align="center">0.5447324</td>
 </tr>
 </tbody>
 </table>

docs/articles/EUCAST.html

@@ -39,7 +39,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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

@@ -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">1.4.0.9046</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          R         I            R          S            I            S</span>
+<span class="co"># 1          S         R            S          S            I            R</span>
-<span class="co"># 2          I         S            I          S            S            R</span>
+<span class="co"># 2          R         I            S          I            S            I</span>
-<span class="co"># 3          I         I            I          R            I            R</span>
+<span class="co"># 3          I         I            R          S            I            S</span>
-<span class="co"># 4          S         S            I          S            R            I</span>
+<span class="co"># 4          R         S            R          I            R            S</span>
-<span class="co"># 5          I         R            S          R            S            R</span>
+<span class="co"># 5          I         R            I          I            I            R</span>
-<span class="co"># 6          I         I            I          R            S            I</span>
+<span class="co"># 6          I         R            I          R            S            R</span>
 <span class="co">#   kanamycin</span>
-<span class="co"># 1         S</span>
+<span class="co"># 1         R</span>
 <span class="co"># 2         I</span>
 <span class="co"># 3         I</span>
-<span class="co"># 4         S</span>
+<span class="co"># 4         I</span>
-<span class="co"># 5         I</span>
+<span class="co"># 5         S</span>
-<span class="co"># 6         R</span></code></pre></div>
+<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">3219</td>
+<td align="right">3286</td>
-<td align="right">64.38%</td>
+<td align="right">65.72%</td>
-<td align="right">3219</td>
+<td align="right">3286</td>
-<td align="right">64.38%</td>
+<td align="right">65.72%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">982</td>
+<td align="right">992</td>
-<td align="right">19.64%</td>
+<td align="right">19.84%</td>
-<td align="right">4201</td>
+<td align="right">4278</td>
-<td align="right">84.02%</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">434</td>
+<td align="right">424</td>
-<td align="right">8.68%</td>
+<td align="right">8.48%</td>
-<td align="right">4635</td>
+<td align="right">4702</td>
-<td align="right">92.70%</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">251</td>
+<td align="right">214</td>
-<td align="right">5.02%</td>
+<td align="right">4.28%</td>
-<td align="right">4886</td>
+<td align="right">4916</td>
-<td align="right">97.72%</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">114</td>
+<td align="right">84</td>
-<td align="right">2.28%</td>
+<td align="right">1.68%</td>
 <td align="right">5000</td>
 <td align="right">100.00%</td>
 </tr>

docs/articles/PCA.html

@@ -39,7 +39,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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

@@ -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">1.4.0.9046</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">26 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

@@ -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">1.4.0.9046</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

@@ -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">1.4.0.9046</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 +227,34 @@
   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 neval</span>
+<span class="co">#                                   expr    min     lq   mean median     uq  max</span>
-<span class="co">#                           as.mo("sau")   9.9  11  19.0   12.0  13.0  47.0    10</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") 100.0 110 130.0  130.0 140.0 150.0    10</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") 110.0 110 130.0  140.0 140.0 150.0    10</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")  11.0  11  15.0   12.0  13.0  40.0    10</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")  12.0  12  21.0   13.0  40.0  46.0    10</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")  26.0  31  45.0   34.0  60.0  86.0    10</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")  26.0  29  36.0   31.0  33.0  58.0    10</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")   1.6   2   2.3    2.3   2.7   2.8    10</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)") 880.0 900 910.0  910.0 920.0 950.0    10</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") 370.0 370 380.0  380.0 380.0 400.0    10</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")   9.9  11  18.0   13.0  14.0  47.0    10</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")  17.0  19  29.0   21.0  48.0  50.0    10</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")  16.0  19  29.0   20.0  47.0  55.0    10</span></code></pre></div>
+<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>
+<span class="co">#     10</span>
+<span class="co">#     10</span>
+<span class="co">#     10</span>
+<span class="co">#     10</span>
+<span class="co">#     10</span>
+<span class="co">#     10</span>
+<span class="co">#     10</span>
+<span class="co">#     10</span>
+<span class="co">#     10</span>
+<span class="co">#     10</span>
+<span class="co">#     10</span></code></pre></div>
 <p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="562.5"></p>
 <p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations can take up to 500-1000 times as much time.</p>
 <p>To improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
@@ -270,8 +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) 136 169  210    198 247 317    10</span></code></pre></div>
+<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 0.198 seconds. You only lose time on your unique input values.</p>
+<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">
@@ -285,10 +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  7.21  7.32  7.92   7.69  8.49  9.43    10</span>
+<span class="co">#     A  8.76  8.96  9.39   9.31  9.86 10.10    10</span>
-<span class="co">#     B 22.60 23.50 28.90  24.70 26.10 69.20    10</span>
+<span class="co">#     B 27.60 28.20 33.00  28.90 29.40 71.20    10</span>
-<span class="co">#     C  1.87  1.92  2.10   2.08  2.27  2.34    10</span></code></pre></div>
+<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 0.0021 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>
+<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>,
@@ -302,14 +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 1.34 1.59 1.66   1.65 1.74 2.18    10</span>
+<span class="co">#     A 1.91 1.95 2.06   1.99 2.09 2.62    10</span>
-<span class="co">#     B 1.34 1.63 1.73   1.72 1.85 2.31    10</span>
+<span class="co">#     B 1.83 1.91 2.09   2.04 2.20 2.45    10</span>
-<span class="co">#     C 1.41 1.61 1.65   1.65 1.72 1.83    10</span>
+<span class="co">#     C 1.79 1.90 2.03   1.99 2.22 2.30    10</span>
-<span class="co">#     D 1.59 1.63 1.77   1.77 1.89 2.03    10</span>
+<span class="co">#     D 1.90 2.01 2.18   2.12 2.25 2.71    10</span>
-<span class="co">#     E 1.33 1.60 1.68   1.65 1.73 2.08    10</span>
+<span class="co">#     E 1.91 2.02 2.14   2.08 2.15 2.81    10</span>
-<span class="co">#     F 1.31 1.34 1.56   1.52 1.71 2.11    10</span>
+<span class="co">#     F 1.86 1.92 2.00   2.01 2.06 2.16    10</span>
-<span class="co">#     G 1.34 1.60 1.75   1.64 1.76 2.74    10</span>
+<span class="co">#     G 1.81 1.96 2.09   2.08 2.22 2.41    10</span>
-<span class="co">#     H 1.32 1.38 1.57   1.63 1.71 1.78    10</span></code></pre></div>
+<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">
@@ -337,13 +351,13 @@
 <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 15.73 16.35 20.85  16.74 17.71 56.56   100</span>
+<span class="co">#    en 17.45 18.01 19.69  18.53 19.14 55.30   100</span>
-<span class="co">#    de 18.96 19.62 22.32  19.86 20.46 59.58   100</span>
+<span class="co">#    de 20.58 21.54 26.69  22.08 23.96 67.16   100</span>
-<span class="co">#    nl 31.06 31.91 37.31  32.78 34.57 75.58   100</span>
+<span class="co">#    nl 33.79 34.67 39.13  35.39 36.72 74.60   100</span>
-<span class="co">#    es 18.92 19.59 23.43  19.92 20.42 62.72   100</span>
+<span class="co">#    es 20.71 21.42 24.36  21.88 22.65 58.57   100</span>
-<span class="co">#    it 18.80 19.36 22.59  19.74 20.54 62.72   100</span>
+<span class="co">#    it 20.65 21.18 26.50  21.53 22.68 61.96   100</span>
-<span class="co">#    fr 18.88 19.53 23.89  19.85 20.91 61.56   100</span>
+<span class="co">#    fr 20.68 21.27 25.05  21.64 22.37 58.82   100</span>
-<span class="co">#    pt 18.89 19.51 21.46  19.87 20.29 59.12   100</span></code></pre></div>
+<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

@@ -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">1.4.0.9046</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

@@ -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">1.4.0.9052</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

@@ -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">1.4.0.9046</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

@@ -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">1.4.0.9046</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

@@ -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">1.4.0.9052</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 

docs/index.html

@@ -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">1.4.0.9052</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>
@@ -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">
@@ -339,7 +348,7 @@ Since you are one of our users, we would like to know how you use the package an
 <a href="#latest-released-version" class="anchor"></a>Latest released version</h4>
 <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>
@@ -349,7 +358,7 @@ Since you are one of our users, we would like to know how you use the package an
 <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

@@ -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">1.4.0.9052</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 
@@ -236,14 +236,11 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1409052" class="section level1">
+    <div id="amr-150" class="section level1">
-<h1 class="page-header" data-toc-text="1.4.0.9052">
+<h1 class="page-header" data-toc-text="1.5.0">
-<a href="#amr-1409052" class="anchor"></a>AMR 1.4.0.9052<small> Unreleased </small>
+<a href="#amr-150" class="anchor"></a>AMR 1.5.0<small> Unreleased </small>
 </h1>
-<div id="last-updated-28-december-2020" class="section level2">
+<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>
-<h2 class="hasAnchor">
-<a href="#last-updated-28-december-2020" class="anchor"></a><small>Last updated: 28 December 2020</small>
-</h2>
 <div id="new" class="section level3">
 <h3 class="hasAnchor">
 <a href="#new" class="anchor"></a>New</h3>
@@ -259,7 +256,7 @@
 </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">
@@ -280,7 +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>
@@ -291,6 +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>
@@ -306,7 +334,6 @@
 <li><p>Fix for printing class <mo> in tibbles when all values are <code>NA</code></mo></p></li>
 <li><p>Fix for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> when the input contains <code>NA</code></p></li>
 <li><p>If <code><a href="../reference/as.mo.html">as.mo()</a></code> takes more than 30 seconds, some suggestions will be done to improve speed</p></li>
-<li><p>Lost dependency on the <code>tidyselect</code> package for using antibiotic selectors such as <code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code></p></li>
 </ul>
 </div>
 <div id="other" class="section level3">
@@ -323,7 +350,6 @@
 <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">
@@ -338,7 +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>
@@ -361,7 +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>
@@ -379,7 +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>
@@ -440,7 +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>
 
@@ -629,7 +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>
@@ -658,7 +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>
@@ -669,7 +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>
@@ -734,11 +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>
@@ -752,7 +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>
@@ -781,7 +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>
@@ -840,14 +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>
@@ -872,7 +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>
@@ -895,13 +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>
@@ -923,7 +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>
@@ -1006,7 +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>
@@ -1033,7 +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>
@@ -1138,7 +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> 
@@ -1233,7 +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>
@@ -1247,7 +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>
@@ -1256,7 +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>
@@ -1277,7 +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>
@@ -1285,13 +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>
@@ -1324,7 +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>
 
@@ -1336,7 +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>
@@ -1351,7 +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>
@@ -1401,7 +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>
@@ -1485,7 +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>
@@ -1502,7 +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> 
@@ -1510,7 +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> 
@@ -1590,7 +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>
@@ -1601,7 +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>
@@ -1616,7 +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>
@@ -1625,7 +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>
@@ -1659,7 +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>
@@ -1676,7 +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>
@@ -1696,12 +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: 2020-12-28T21:24Z
+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

@@ -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">1.4.0.9046</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

@@ -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">1.4.0.9046</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

@@ -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">1.4.0.9046</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

@@ -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">1.4.0.9046</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/ab_from_text.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9053</span>
       </span>
     </div>
 
@@ -285,7 +285,7 @@
     <p>A <a href='https://rdrr.io/r/base/list.html'>list</a>, or a  <a href='https://rdrr.io/r/base/character.html'>character</a> if <code>collapse</code> is not <code>NULL</code></p>
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
-    <p>This function is also internally used by <code><a href='as.ab.html'>as.ab()</a></code>, although it then only searches for the first drug name and will throw a note if more drug names could have been returned.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Argument <code>type</code></h3>
+    <p>This function is also internally used by <code><a href='as.ab.html'>as.ab()</a></code>, 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 <code><a href='as.ab.html'>as.ab()</a></code> function may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Argument <code>type</code></h3>
 
 
 <p>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 <code><a href='as.ab.html'>as.ab()</a></code> internally, it will correct for misspelling.</p>

docs/reference/ab_property.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/age.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/age_groups.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/antibiotic_class_selectors.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 
@@ -281,7 +281,9 @@
 
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
-    <p>All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.) in the <a href='antibiotics.html'>antibiotics</a> data set. This means that a selector like e.g. <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.</p>
+    <p><strong>
+</strong></p>
+<p>All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.) in the <a href='antibiotics.html'>antibiotics</a> data set. This means that a selector like e.g. <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.</p>
     <h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference data publicly available</h2>
 
     

docs/reference/antibiotics.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/as.ab.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/as.disk.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/as.mic.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/as.mo.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 
@@ -368,10 +368,10 @@
     
 
 <ol>
-<li><p>Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870–926. <a href='https://dx.doi.org/10.1128/CMR.00109-13'>https://dx.doi.org/10.1128/CMR.00109-13</a></p></li>
+<li><p>Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870–926; doi: <a href='https://doi.org/10.1128/CMR.00109-13'>10.1128/CMR.00109-13</a></p></li>
-<li><p>Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect. <a href='https://doi.org/10.1016/j.cmi.2019.02.028'>https://doi.org/10.1016/j.cmi.2019.02.028</a></p></li>
+<li><p>Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect; doi: <a href='https://doi.org/10.1016/j.cmi.2019.02.028'>10.1016/j.cmi.2019.02.028</a></p></li>
-<li><p>Becker K <em>et al.</em> <strong>Emergence of coagulase-negative staphylococci</strong> 2020. Expert Rev Anti Infect Ther. 18(4):349-366. <a href='https://dx.doi.org/10.1080/14787210.2020.1730813'>https://dx.doi.org/10.1080/14787210.2020.1730813</a></p></li>
+<li><p>Becker K <em>et al.</em> <strong>Emergence of coagulase-negative staphylococci</strong> 2020. Expert Rev Anti Infect Ther. 18(4):349-366; doi: <a href='https://doi.org/10.1080/14787210.2020.1730813'>10.1080/14787210.2020.1730813</a></p></li>
-<li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95. <a href='https://dx.doi.org/10.1084/jem.57.4.571'>https://dx.doi.org/10.1084/jem.57.4.571</a></p></li>
+<li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95; doi: <a href='https://doi.org/10.1084/jem.57.4.571'>10.1084/jem.57.4.571</a></p></li>
 <li><p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p></li>
 </ol>
 
@@ -404,7 +404,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
     
 
 <p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
-This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). 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, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/Sp2000/colplus'>CoL+ project</a> is finished, which we await.</p>
+This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). 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, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
 <p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which versions of the CoL and LSPN were included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>.</p>
     <h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference data publicly available</h2>
 

docs/reference/as.rsi.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/atc_online.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/availability.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/bug_drug_combinations.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/catalogue_of_life.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 
@@ -249,7 +249,7 @@
     
 
 <p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
-This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). 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, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/Sp2000/colplus'>CoL+ project</a> is finished, which we await.</p>
+This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). 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, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
 <p>Click here for more information about the included taxa. Check which versions of the CoL and LSPN were included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>.</p>
     <h2 class="hasAnchor" id="included-taxa"><a class="anchor" href="#included-taxa"></a>Included taxa</h2>
 

docs/reference/catalogue_of_life_version.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 
@@ -256,7 +256,7 @@
     
 
 <p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
-This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). 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, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/Sp2000/colplus'>CoL+ project</a> is finished, which we await.</p>
+This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). 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, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
 <p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which versions of the CoL and LSPN were included in this package with <code>catalogue_of_life_version()</code>.</p>
     <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
 

docs/reference/count.html

@@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/eucast_rules.html

@@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
       </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">1.4.0.9052</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 
@@ -289,7 +289,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
     </tr>
     <tr>
       <th>ampc_cephalosporin_resistance</th>
-      <td><p>a character value that should be applied for AmpC de-repressed cephalosporin-resistant mutants, defaults to <code>NA</code>. Currently only works when <code>version_expertrules</code> is <code>3.2</code>; '<em>EUCAST Expert Rules v3.2 on Enterobacterales</em>' 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 <code>NA</code> for this argument will remove results for these agents, while e.g. a value of <code>"R"</code> will make the results for these agents resistant. Use <code>NULL</code> to not alter the results for AmpC de-repressed cephalosporin-resistant mutants. <br /> For <em>EUCAST Expert Rules</em> v3.2, this rule applies to: <em>Enterobacter, Klebsiella aerogenes, Citrobacter freundii, Hafnia alvei, Serratia, Morganella morganii, Providencia</em>.</p></td>
+      <td><p>a character value that should be applied for AmpC de-repressed cephalosporin-resistant mutants, defaults to <code>NA</code>. Currently only works when <code>version_expertrules</code> is <code>3.2</code>; '<em>EUCAST Expert Rules v3.2 on Enterobacterales</em>' 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 <code>NA</code> for this argument will remove results for these agents, while e.g. a value of <code>"R"</code> will make the results for these agents resistant. Use <code>NULL</code> to not alter the results for AmpC de-repressed cephalosporin-resistant mutants. <br /> For <em>EUCAST Expert Rules</em> v3.2, this rule applies to: <em>Enterobacter, Klebsiella aerogenes, Citrobacter braakii, freundii, gillenii, murliniae, rodenticum, sedlakii, werkmanii, youngae, Hafnia alvei, Serratia, Morganella morganii, Providencia</em>.</p></td>
     </tr>
     <tr>
       <th>...</th>
@@ -302,7 +302,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
     
 <ul>
 <li><p>EUCAST Expert Rules. Version 2.0, 2012.<br />
-Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility testing.</strong> <em>Clin Microbiol Infect.</em> 2013;19(2):141-60.  <a href='https://doi.org/10.1111/j.1469-0691.2011.03703.x'>(link)</a></p></li>
+Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility testing.</strong> <em>Clin Microbiol Infect.</em> 2013;19(2):141-60; doi: <a href='https://doi.org/10.1111/j.1469-0691.2011.03703.x'>10.1111/j.1469-0691.2011.03703.x</a></p></li>
 <li><p>EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>(link)</a></p></li>
 <li><p>EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf'>(link)</a></p></li>
 <li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx'>(link)</a></p></li>
@@ -325,7 +325,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
 </ol>
 
 <p>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.</p>
-<p>Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include <code>"other"</code> to the <code>rules</code> argument, or use <code>eucast_rules(..., rules = "all")</code>.</p>
+<p>Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include <code>"other"</code> to the <code>rules</code> argument, or use <code>eucast_rules(..., rules = "all")</code>. You can also set the option <code>AMR_eucastrules</code>, i.e. run <code><a href='https://rdrr.io/r/base/options.html'>options(AMR_eucastrules = "all")</a></code>.</p>
 
     <h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
 

docs/reference/example_isolates.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/example_isolates_unclean.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/filter_ab_class.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</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/first_isolate.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9050</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/g.test.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/get_episode.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9050</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/ggplot_pca.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/ggplot_rsi.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/guess_ab_col.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9052</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/intrinsic_resistant.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/join.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/key_antibiotics.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9050</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/kurtosis.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/lifecycle.html

@@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
       </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">1.4.0.9046</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/like.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/mdro.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9050</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 
@@ -331,7 +331,7 @@ Ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with levels <cod
 <li><p><code>guideline = "TB"</code></p>
 <p>The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (<a href='https://www.who.int/tb/publications/pmdt_companionhandbook/en/'>link</a>)</p></li>
 <li><p><code>guideline = "MRGN"</code></p>
-<p>The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6</p></li>
+<p>The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7; doi: <a href='https://doi.org/10.1186/s13756-015-0047-6'>10.1186/s13756-015-0047-6</a></p></li>
 <li><p><code>guideline = "BRMO"</code></p>
 <p>The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)" (<a href='https://www.rivm.nl/wip-richtlijn-brmo-bijzonder-resistente-micro-organismen-zkh'>link</a>)</p></li>
 </ul>

docs/reference/microorganisms.codes.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 
@@ -262,7 +262,7 @@
     
 
 <p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
-This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). 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, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/Sp2000/colplus'>CoL+ project</a> is finished, which we await.</p>
+This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). 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, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
 <p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which versions of the CoL and LSPN were included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>.</p>
     <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
 

docs/reference/microorganisms.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 
@@ -262,7 +262,7 @@
     <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
 
     <p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p>
-<p>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</p>
+<p>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: <a href='https://doi.org/10.1099/ijsem.0.002786'>10.1099/ijsem.0.002786</a></p>
 <p>Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, <a href='https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date'>https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date</a> and <a href='https://lpsn.dsmz.de'>https://lpsn.dsmz.de</a> (check included version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p>
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
@@ -300,7 +300,7 @@
     
 
 <p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
-This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). 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, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/Sp2000/colplus'>CoL+ project</a> is finished, which we await.</p>
+This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). 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, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
 <p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which versions of the CoL and LSPN were included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>.</p>
     <h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference data publicly available</h2>
 

docs/reference/microorganisms.old.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 
@@ -257,13 +257,13 @@
     <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
 
     <p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p>
-<p>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</p>
+<p>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: <a href='https://doi.org/10.1099/ijsem.0.002786'>10.1099/ijsem.0.002786</a></p>
     <h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
 
     
 
 <p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
-This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). 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, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/Sp2000/colplus'>CoL+ project</a> is finished, which we await.</p>
+This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). 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, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
 <p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which versions of the CoL and LSPN were included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>.</p>
     <h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference data publicly available</h2>
 

docs/reference/mo_matching_score.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/mo_property.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9050</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 
@@ -379,17 +379,17 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
     
 
 <p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
-This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). 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, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/Sp2000/colplus'>CoL+ project</a> is finished, which we await.</p>
+This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). 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, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
 <p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which versions of the CoL and LSPN were included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>.</p>
     <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
 
     
 
 <ol>
-<li><p>Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870–926. <a href='https://dx.doi.org/10.1128/CMR.00109-13'>https://dx.doi.org/10.1128/CMR.00109-13</a></p></li>
+<li><p>Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870–926; doi: <a href='https://doi.org/10.1128/CMR.00109-13'>10.1128/CMR.00109-13</a></p></li>
-<li><p>Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect. <a href='https://doi.org/10.1016/j.cmi.2019.02.028'>https://doi.org/10.1016/j.cmi.2019.02.028</a></p></li>
+<li><p>Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect; doi: <a href='https://doi.org/10.1016/j.cmi.2019.02.028'>10.1016/j.cmi.2019.02.028</a></p></li>
-<li><p>Becker K <em>et al.</em> <strong>Emergence of coagulase-negative staphylococci</strong> 2020. Expert Rev Anti Infect Ther. 18(4):349-366. <a href='https://dx.doi.org/10.1080/14787210.2020.1730813'>https://dx.doi.org/10.1080/14787210.2020.1730813</a></p></li>
+<li><p>Becker K <em>et al.</em> <strong>Emergence of coagulase-negative staphylococci</strong> 2020. Expert Rev Anti Infect Ther. 18(4):349-366; doi: <a href='https://doi.org/10.1080/14787210.2020.1730813'>10.1080/14787210.2020.1730813</a></p></li>
-<li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95. <a href='https://dx.doi.org/10.1084/jem.57.4.571'>https://dx.doi.org/10.1084/jem.57.4.571</a></p></li>
+<li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95; doi: <a href='https://doi.org/10.1084/jem.57.4.571'>10.1084/jem.57.4.571</a></p></li>
 <li><p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p></li>
 </ol>
 

docs/reference/mo_source.html

@@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
       </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">1.4.0.9046</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/pca.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/plot.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/proportion.html

@@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
       </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">1.4.0.9046</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/random.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/resistance_predict.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9050</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/rsi_translation.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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/skewness.html

@@ -83,7 +83,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
       </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">1.4.0.9046</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/translate.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 

docs/survey.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9052</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
       </span>
     </div>
 

git_premaster.sh

@@ -120,13 +120,21 @@ echo "• Updating internal data •"
 echo "••••••••••••••••••••••••••"
 Rscript -e "source('data-raw/internals.R')"
 echo
+echo "••••••••••••••••••••"
+echo "• Building package •"
+echo "••••••••••••••••••••"
+echo "• Removing old build from 'data-raw/'..."
+rm data-raw/AMR_*.tar.gz
+echo "• Building 'data-raw/AMR_${new_version}.tar.gz'..."
+Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = FALSE, manual = FALSE, binary = FALSE, quiet = TRUE)"
+echo "• Installing..."
+Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
+echo
 echo "•••••••••••••••••"
 echo "• Building site •"
 echo "•••••••••••••••••"
-echo "• Installing..."
-Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
 Rscript -e "suppressMessages(pkgdown::build_site(lazy = $lazy, examples = FALSE))"
-# add the survey
+# add the survey page
 Rscript -e "source('data-raw/create_survey_page.R')"
 echo
 echo "•••••••••••••••••••••••••"
@@ -148,7 +156,7 @@ echo "••••••••••••••••••••••••
 # save latest changes as well
 git add .
 # and commit
-git commit -a -m "(v$new_version) $1" --quiet
+git commit -a -m "(v${new_version}) $1" --quiet
 git push --quiet
 echo "Comparison:"
 echo "https://github.com/msberends/AMR/compare/master...premaster?view=inline"

index.md

@@ -1,5 +1,7 @@
 # `AMR` (for R) <img src="./logo.png" align="right" height="120px" />
 
+*Note: the rules of 'EUCAST Clinical Breakpoints v11.0 (2021)' will be added in the next release, to be expected in February/March 2021.*
+
 > <span class="fa fa-clipboard-list" style="color: #128f76; font-size: 20pt; margin-right: 5px;"></span> **PLEASE TAKE PART IN OUR SURVEY!**  
 > 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. **If you have a minute, please [anonymously fill in this short questionnaire](./survey.html)**. 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>
@@ -35,6 +37,8 @@ example_isolates %>%
   select(mo, aminoglycosides(), carbapenems())
 #> NOTE: Using column 'mo' as input for mo_is_gram_negative()
 #> NOTE: Using column 'mo' as input for mo_is_intrinsic_resistant()
+#> NOTE: Determining intrinsic resistance based on 'EUCAST Expert Rules' and
+#>       'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2 from 2020.
 #> Selecting aminoglycosides: 'AMK' (amikacin), 'GEN' (gentamicin), 
 #>                            'KAN' (kanamycin), 'TOB' (tobramycin)
 #> Selecting carbapenems: 'IPM' (imipenem), 'MEM' (meropenem)
@@ -52,6 +56,15 @@ With only having defined a row filter on Gram-negative bacteria with intrinsic r
 |*Stenotrophomonas maltophilia* |     R     |     R     |     R     |     R     |     R     |     R     |
 |*Pseudomonas aeruginosa*       |     S     |     S     |     R     |     S     |           |     S     |
 
+A base R equivalent would be:
+
+```r
+example_isolates$mo <- mo_fullname(example_isolates$mo)
+example_isolates[which(mo_is_gram_negative() &
+                         mo_is_intrinsic_resistant(ab = "cefotax")),
+                 c("mo", aminoglycosides(), carbapenems())]
+```
+
 #### Partners
 
 The development of this package is part of, related to, or made possible by:

man/ab_from_text.Rd

@@ -33,7 +33,7 @@ A \link{list}, or a  \link{character} if \code{collapse} is not \code{NULL}
 Use this function on e.g. clinical texts from health care records. It returns a \link{list} with all antimicrobial drugs, doses and forms of administration found in the texts.
 }
 \details{
-This function is also internally used by \code{\link[=as.ab]{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.
+This function is also internally used by \code{\link[=as.ab]{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 \code{\link[=as.ab]{as.ab()}} function may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems.
 \subsection{Argument \code{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 \code{\link[=as.ab]{as.ab()}} internally, it will correct for misspelling.

man/antibiotic_class_selectors.Rd

@@ -53,6 +53,8 @@ tetracyclines()
 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.
 }
 \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, "."), "")}}
+
 All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.) in the \link{antibiotics} data set. This means that a selector like e.g. \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
 }
 \section{Reference data publicly available}{

man/as.mo.Rd

@@ -123,10 +123,10 @@ The intelligent rules consider the prevalence of microorganisms in humans groupe
 \section{Source}{
 
 \enumerate{
-\item Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13}
+\item Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926; \doi{10.1128/CMR.00109-13}
-\item Becker K \emph{et al.} \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} 2019. Clin Microbiol Infect. \url{https://doi.org/10.1016/j.cmi.2019.02.028}
+\item Becker K \emph{et al.} \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{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}
-\item Becker K \emph{et al.} \strong{Emergence of coagulase-negative staphylococci} 2020. Expert Rev Anti Infect Ther. 18(4):349-366. \url{https://dx.doi.org/10.1080/14787210.2020.1730813}
+\item Becker K \emph{et al.} \strong{Emergence of coagulase-negative staphylococci} 2020. Expert Rev Anti Infect Ther. 18(4):349-366; \doi{10.1080/14787210.2020.1730813}
-\item Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
+\item Lancefield RC \strong{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}
 \item Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}).
 }
 }
@@ -163,7 +163,7 @@ All matches are sorted descending on their matching score and for all user input
 \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, \url{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, \href{https://lpsn.dsmz.de}{lpsn.dsmz.de}). This supplementation is needed until the \href{https://github.com/Sp2000/colplus}{CoL+ project} 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, \url{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, \href{https://lpsn.dsmz.de}{lpsn.dsmz.de}). This supplementation is needed until the \href{https://github.com/CatalogueOfLife/general}{CoL+ project} is finished, which we await.
 
 \link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which versions of the CoL and LSPN were included in this package with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}.
 }

man/catalogue_of_life.Rd

@@ -9,7 +9,7 @@ This package contains the complete taxonomic tree of almost all microorganisms f
 \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, \url{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, \href{https://lpsn.dsmz.de}{lpsn.dsmz.de}). This supplementation is needed until the \href{https://github.com/Sp2000/colplus}{CoL+ project} 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, \url{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, \href{https://lpsn.dsmz.de}{lpsn.dsmz.de}). This supplementation is needed until the \href{https://github.com/CatalogueOfLife/general}{CoL+ project} is finished, which we await.
 
 \link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which versions of the CoL and LSPN were included in this package with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}.
 }

man/catalogue_of_life_version.Rd

@@ -18,7 +18,7 @@ For DSMZ, see \link{microorganisms}.
 \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, \url{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, \href{https://lpsn.dsmz.de}{lpsn.dsmz.de}). This supplementation is needed until the \href{https://github.com/Sp2000/colplus}{CoL+ project} 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, \url{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, \href{https://lpsn.dsmz.de}{lpsn.dsmz.de}). This supplementation is needed until the \href{https://github.com/CatalogueOfLife/general}{CoL+ project} is finished, which we await.
 
 \link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which versions of the CoL and LSPN were included in this package with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}.
 }

man/eucast_rules.Rd

@@ -7,7 +7,7 @@
 \source{
 \itemize{
 \item EUCAST Expert Rules. Version 2.0, 2012.\cr
-Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility testing.} \emph{Clin Microbiol Infect.} 2013;19(2):141-60.  \href{https://doi.org/10.1111/j.1469-0691.2011.03703.x}{(link)}
+Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility testing.} \emph{Clin Microbiol Infect.} 2013;19(2):141-60; \doi{https://doi.org/10.1111/j.1469-0691.2011.03703.x}
 \item EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{(link)}
 \item EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf}{(link)}
 \item EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx}{(link)}
@@ -42,7 +42,7 @@ eucast_rules(
 
 \item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Currently supported: 3.1, 3.2.}
 
-\item{ampc_cephalosporin_resistance}{a character value that should be applied for AmpC de-repressed cephalosporin-resistant mutants, defaults to \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2}; '\emph{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 \code{NA} for this argument will remove results for these agents, while e.g. a value of \code{"R"} will make the results for these agents resistant. Use \code{NULL} to not alter the results for AmpC de-repressed cephalosporin-resistant mutants. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Enterobacter, Klebsiella aerogenes, Citrobacter freundii, Hafnia alvei, Serratia, Morganella morganii, Providencia}.}
+\item{ampc_cephalosporin_resistance}{a character value that should be applied for AmpC de-repressed cephalosporin-resistant mutants, defaults to \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2}; '\emph{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 \code{NA} for this argument will remove results for these agents, while e.g. a value of \code{"R"} will make the results for these agents resistant. Use \code{NULL} to not alter the results for AmpC de-repressed cephalosporin-resistant mutants. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Enterobacter, Klebsiella aerogenes, Citrobacter braakii, freundii, gillenii, murliniae, rodenticum, sedlakii, werkmanii, youngae, Hafnia alvei, Serratia, Morganella morganii, Providencia}.}
 
 \item{...}{column name of an antibiotic, please see section \emph{Antibiotics} below}
 }
@@ -69,7 +69,7 @@ Before further processing, two non-EUCAST rules about drug combinations can be a
 
 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 \code{"other"} to the \code{rules} argument, or use \code{eucast_rules(..., rules = "all")}.
+Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include \code{"other"} to the \code{rules} argument, or use \code{eucast_rules(..., rules = "all")}. You can also set the option \code{AMR_eucastrules}, i.e. run \code{options(AMR_eucastrules = "all")}.
 }
 }
 \section{Antibiotics}{