(v1.7.0) v1.7.0

doc update
v1.7.0
2025-07-05 01:08:38 +02:00 · 2021-05-26 11:10:34 +02:00 · 2021-05-26 11:00:32 +02:00 · 2021-05-26 10:59:54 +02:00 · 2021-05-25 10:00:11 +02:00 · 2021-05-24 15:29:31 +02:00
165 changed files with 1794 additions and 1772 deletions
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@ -50,17 +50,22 @@ jobs:
      fail-fast: false
      matrix:
        config:
+          # these are the developmental version of R - we allow those tests to fail
          - {os: macOS-latest,   r: 'devel',   allowfail: true}
-          - {os: macOS-latest,   r: 'release', allowfail: false}
-          - {os: macOS-latest,   r: 'oldrel',  allowfail: false}
-          
          - {os: windows-latest, r: 'devel',   allowfail: true}
-          - {os: windows-latest, r: 'release', allowfail: false}
-          - {os: windows-latest, r: 'oldrel',  allowfail: false}
-          
          - {os: ubuntu-20.04,   r: 'devel',   allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          
+          # these are the current release of R
+          - {os: macOS-latest,   r: 'release', allowfail: false}
+          - {os: windows-latest, r: 'release', allowfail: false}
          - {os: ubuntu-20.04,   r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          
+          # these are the previous release of R
+          - {os: macOS-latest,   r: 'oldrel',  allowfail: false}
+          - {os: windows-latest, r: 'oldrel',  allowfail: false}
          - {os: ubuntu-20.04,   r: 'oldrel',  allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          
+          # test against all released versions of R >= 3.0, we support them all!
          - {os: ubuntu-20.04,   r: '4.1',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
          - {os: ubuntu-20.04,   r: '4.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
          - {os: ubuntu-20.04,   r: '3.6',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
@ -116,6 +121,7 @@ jobs:
      # - name: Only keep vignettes on release version
      - name: Remove vignettes
        # if: matrix.config.r != 'release'
+        if: always()
        # writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R < 3.3 as writeLines() cannot overwrite
        run: |
          rm -rf AMR/vignettes
@ -136,7 +142,7 @@ jobs:
          R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
          R_RUN_TINYTEST: true
        run: |
-          R CMD check --no-manual AMR
+          R CMD check --no-manual --run-donttest --run-dontrun AMR
        shell: bash

      - name: Show unit tests output
--- a/.github/workflows/codecovr.yaml
+++ b/.github/workflows/codecovr.yaml
@ -30,7 +30,6 @@ on:
      - master
  pull_request:
    branches:
-      - premaster
      - master

 name: code-coverage
@ -69,17 +68,28 @@ jobs:
          as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
        shell: Rscript {0}

+      # - name: Test coverage
+      #   env:
+      #     CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      #   run: |
+      #     library(AMR)
+      #     library(tinytest)
+      #     library(covr)
+      #     source_files <- list.files("R", pattern = ".R$", full.names = TRUE)
+      #     test_files <- list.files("inst/tinytest", full.names = TRUE)
+      #     cov <- file_coverage(source_files = source_files, test_files = test_files, parent_env = asNamespace("AMR"), line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
+      #     attr(cov, which = "package") <- list(path = ".") # until https://github.com/r-lib/covr/issues/478 is solved
+      #     codecov(coverage = cov, quiet = FALSE)
+      #   shell: Rscript {0}
+      
      - name: Test coverage
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          R_RUN_TINYTEST: true
        run: |
          library(AMR)
          library(tinytest)
-          library(covr)
-          source_files <- list.files("AMR/R", pattern = ".R$", full.names = TRUE)
-          test_files <- list.files("AMR/inst/tinytest", full.names = TRUE)
-          cov <- file_coverage(source_files = source_files, test_files = test_files, parent_env = asNamespace("AMR"), line_exclusions = list("AMR/R/atc_online.R", "AMR/R/mo_source.R", "AMR/R/translate.R", "AMR/R/resistance_predict.R", "AMR/R/aa_helper_functions.R", "AMR/R/aa_helper_pm_functions.R", "AMR/R/zzz.R"))
-          print(cov)
-          attr(cov, which = "package") <- list(path = ".") # until https://github.com/r-lib/covr/issues/478 is solved
-          codecov(coverage = cov, quiet = FALSE)
+          covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
        shell: Rscript {0}
+      
+      
--- a/4
+++ b/4
@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.6.0.9060
-Date: 2021-05-22
+Version: 1.7.0
+Date: 2021-05-26
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(
    person(role = c("aut", "cre"), 
--- a/NEWS.md
+++ b/NEWS.md
@ -1,5 +1,5 @@
-# `AMR` 1.6.0.9060
-## <small>Last updated: 22 May 2021</small>
+# `AMR` 1.7.0
+

 ### Breaking change
 * All antibiotic class selectors (such as `carbapenems()`, `aminoglycosides()`) can now be used for filtering as well, making all their accompanying `filter_*()` functions redundant (such as `filter_carbapenems()`, `filter_aminoglycosides()`). These functions are now deprecated and will be removed in a next release.
@ -64,6 +64,7 @@
 * Updated join functions to always use `dplyr` join functions if the `dplyr` package is installed - now also preserving grouped variables
 * Antibiotic class selectors (such as `cephalosporins()`) now maintain the column order from the original data
 * Fix for selecting columns using `fluoroquinolones()`
+* `age()` now vectorises over both `x` and `reference`

 ### Other
 * All unit tests are now processed by the `tinytest` package, instead of the `testthat` package. The `testthat` package unfortunately requires tons of dependencies that are also heavy and only usable for recent R versions, disallowing developers to test a package under any R 3.* version. On the contrary, the `tinytest` package is very lightweight and dependency-free.
@ -905,7 +906,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
  * Emphasised in manual that penicillin is meant as benzylpenicillin (ATC [J01CE01](https://www.whocc.no/atc_ddd_index/?code=J01CE01))
  * New info is returned when running this function, stating exactly what has been changed or added. Use `eucast_rules(..., verbose = TRUE)` to get a data set with all changed per bug and drug combination.
 * Removed data sets `microorganisms.oldDT`, `microorganisms.prevDT`, `microorganisms.unprevDT` and `microorganismsDT` since they were no longer needed and only contained info already available in the `microorganisms` data set
-* Added 65 antibiotics to the `antibiotics` data set, from the [Pharmaceuticals Community Register](http://ec.europa.eu/health/documents/community-register/html/atc.htm) of the European Commission
+* Added 65 antibiotics to the `antibiotics` data set, from the [Pharmaceuticals Community Register](https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm) of the European Commission
 * Removed columns `atc_group1_nl` and `atc_group2_nl` from the `antibiotics` data set
 * Functions `atc_ddd()` and `atc_groups()` have been renamed `atc_online_ddd()` and `atc_online_groups()`. The old functions are deprecated and will be removed in a future version.
 * Function `guess_mo()` is now deprecated in favour of `as.mo()` and will be removed in future versions
--- a/R/aa_helper_functions.R
+++ b/R/aa_helper_functions.R
@ -192,7 +192,7 @@ search_type_in_df <- function(x, type, info = TRUE) {

  }
  # -- key antibiotics
-  if (type == "keyantibiotics") {
+  if (type %in% c("keyantibiotics", "keyantimicrobials")) {
    if (any(colnames(x) %like% "^key.*(ab|antibiotics|antimicrobials)")) {
      found <- sort(colnames(x)[colnames(x) %like% "^key.*(ab|antibiotics|antimicrobials)"])[1]
    }
@ -716,6 +716,11 @@ meet_criteria <- function(object,
 }

 get_current_data <- function(arg_name, call) {
+  # check if retrieved before, then get it from package environment
+  if (identical(unique_call_id(entire_session = FALSE), pkg_env$get_current_data.call)) {
+    return(pkg_env$get_current_data.out)
+  }
+  
  # try dplyr::cur_data_all() first to support dplyr groups
  # only useful for e.g. dplyr::filter(), dplyr::mutate() and dplyr::summarise()
  # not useful (throws error) with e.g. dplyr::select() - but that will be caught later in this function
@ -723,11 +728,14 @@ get_current_data <- function(arg_name, call) {
  if (!is.null(cur_data_all)) {
    out <- tryCatch(cur_data_all(), error = function(e) NULL)
    if (is.data.frame(out)) {
-      return(structure(out, type = "dplyr_cur_data_all"))
+      out <- structure(out, type = "dplyr_cur_data_all")
+      pkg_env$get_current_data.call <- unique_call_id(entire_session = FALSE)
+      pkg_env$get_current_data.out <- out
+      return(out)
    }
  }

-  if (current_R_older_than(3.2)) {
+  if (getRversion() < "3.2") {
    # R-3.0 and R-3.1 do not have an `x` element in the call stack, rendering this function useless
    if (is.na(arg_name)) {
      # like in carbapenems() etc.
@ -779,7 +787,10 @@ get_current_data <- function(arg_name, call) {
  # lookup the matched frame and return its value: a data.frame
  vars_df <- tryCatch(frms[[which(!vapply(FUN.VALUE = logical(1), frms, is.null))]], error = function(e) NULL)
  if (is.data.frame(vars_df)) {
-    return(structure(vars_df, type = source))
+    out <- structure(vars_df, type = source)
+    pkg_env$get_current_data.call <- unique_call_id(entire_session = FALSE)
+    pkg_env$get_current_data.out <- out
+    return(out)
  }
  
  # nothing worked, so:
@ -853,8 +864,13 @@ unique_call_id <- function(entire_session = FALSE) {
  } else {
    # combination of environment ID (like "0x7fed4ee8c848")
    # and highest system call
+    call <- paste0(deparse(sys.calls()[[1]]), collapse = "")
+    if (!interactive() || call %like% "run_test_dir|test_all|tinytest|test_package|testthat") {
+      # unit tests will keep the same call and environment - give them a unique ID
+      call <- paste0(sample(c(c(0:9), letters[1:6]), size = 64, replace = TRUE), collapse = "")
+    }
    c(envir = gsub("<environment: (.*)>", "\\1", utils::capture.output(sys.frames()[[1]])),
-      call = paste0(deparse(sys.calls()[[1]]), collapse = ""))
+      call = call)
  }
 }

@ -870,14 +886,6 @@ message_not_thrown_before <- function(fn, entire_session = FALSE) {
  is.null(pkg_env[[paste0("thrown_msg.", fn)]]) || !identical(pkg_env[[paste0("thrown_msg.", fn)]], unique_call_id(entire_session))
 }

-reset_all_thrown_messages <- function() {
-  # for unit tests, where the environment and highest system call do not change
-  # can be found in tests/testthat/*.R
-  pkg_env_contents <- ls(envir = pkg_env)
-  rm(list = pkg_env_contents[pkg_env_contents %like% "^thrown_msg."],
-     envir = pkg_env)
-}
-
 has_colour <- function() {
  # this is a base R version of crayon::has_color, but disables colours on emacs
  
@ -893,7 +901,7 @@ has_colour <- function() {
    if (Sys.getenv("RSTUDIO", "") == "") {
      return(FALSE)
    }
-    if ((cols <- Sys.getenv("RSTUDIO_CONSOLE_COLOR", "")) != "" && !is.na(as.numeric(cols))) {
+    if ((cols <- Sys.getenv("RSTUDIO_CONSOLE_COLOR", "")) != "" && !is.na(as.double(cols))) {
      return(TRUE)
    }
    tryCatch(get("isAvailable", envir = asNamespace("rstudioapi"))(), error = function(e) return(FALSE)) &&
@ -1114,7 +1122,7 @@ s3_register <- function(generic, class, method = NULL) {

 # works exactly like round(), but rounds `round2(44.55, 1)` to 44.6 instead of 44.5
 # and adds decimal zeroes until `digits` is reached when force_zero = TRUE
-round2 <- function(x, digits = 0, force_zero = TRUE) {
+round2 <- function(x, digits = 1, force_zero = TRUE) {
  x <- as.double(x)
  # https://stackoverflow.com/a/12688836/4575331
  val <- (trunc((abs(x) * 10 ^ digits) + 0.5) / 10 ^ digits) * sign(x)
@ -1166,7 +1174,7 @@ percentage <- function(x, digits = NULL, ...) {
    # round right: percentage(0.4455) and format(as.percentage(0.4455), 1) should return "44.6%", not "44.5%"
    x_formatted <- format(round2(as.double(x), digits = digits + 2) * 100,
                          scientific = FALSE,
-                          digits = digits,
+                          digits = max(1, digits),
                          nsmall = digits,
                          ...)
    x_formatted <- paste0(x_formatted, "%")
@ -1186,15 +1194,11 @@ percentage <- function(x, digits = NULL, ...) {
 }

 time_start_tracking <- function() {
-  pkg_env$time_start <- round(as.numeric(Sys.time()) * 1000)
+  pkg_env$time_start <- round(as.double(Sys.time()) * 1000)
 }

 time_track <- function(name = NULL) {
-  paste("(until now:", trimws(round(as.numeric(Sys.time()) * 1000) - pkg_env$time_start), "ms)")
-}
-
-current_R_older_than <- function(version) {
-  as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < version
+  paste("(until now:", trimws(round(as.double(Sys.time()) * 1000) - pkg_env$time_start), "ms)")
 }

 # prevent dependency on package 'backports' ----
@ -1245,7 +1249,7 @@ lengths <- function(x, use.names = TRUE) {
  vapply(x, length, FUN.VALUE = NA_integer_, USE.NAMES = use.names)
 }

-if (current_R_older_than(3.1)) {
+if (getRversion() < "3.1") {
  # R-3.0 does not contain these functions, set them here to prevent installation failure
  # (required for extension of the <mic> class)
  cospi <- function(...) 1
--- a/R/ab.R
+++ b/R/ab.R
@ -50,7 +50,7 @@
 #'
 #' WHONET 2019 software: \url{http://www.whonet.org/software.html}
 #'
-#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}
+#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
 #' @aliases ab
 #' @return A [character] [vector] with additional class [`ab`]
 #' @seealso 
@ -82,7 +82,7 @@
 #' # they use as.ab() internally:
 #' ab_name("J01FA01")    # "Erythromycin"
 #' ab_name("eryt")       # "Erythromycin"
-#' 
+#' \donttest{
 #' if (require("dplyr")) {
 #' 
 #'   # you can quickly rename <rsi> columns using dplyr >= 1.0.0:
@ -90,6 +90,7 @@
 #'     rename_with(as.ab, where(is.rsi))
 #'    
 #' }
+#' }
 as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
  meet_criteria(x, allow_class = c("character", "numeric", "integer", "factor"), allow_NA = TRUE)
  meet_criteria(flag_multiple_results, allow_class = "logical", has_length = 1)
--- a/R/ab_class_selectors.R
+++ b/R/ab_class_selectors.R
@ -25,11 +25,11 @@

 #' Antibiotic Class Selectors
 #' 
-#' These functions help to filter and select columns with antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(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, "."), "")}}
+#' These functions help to filter and select columns with antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(getRversion() < "3.2", paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
 #' @inheritSection lifecycle Stable Lifecycle
-#' @param ab_class an antimicrobial class, like `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value.
+#' @param ab_class an antimicrobial class, such as `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value.
 #' @param only_rsi_columns a [logical] to indicate whether only columns of class `<rsi>` must be selected (defaults to `FALSE`), see [as.rsi()]
-#' @details \strong{\Sexpr{ifelse(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, "."), "")}}
+#' @details \strong{\Sexpr{ifelse(getRversion() < "3.2", paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
 #' 
 #' 
 #' These functions can be used in data set calls for selecting columns and filtering rows, see *Examples*. They support base R, but work more convenient in dplyr functions such as [`select()`][dplyr::select()], [`filter()`][dplyr::filter()] and [`summarise()`][dplyr::summarise()].
@ -70,7 +70,7 @@
 #' 
 #' 
 #' # dplyr -------------------------------------------------------------------
-#' 
+#' \donttest{
 #' if (require("dplyr")) {
 #' 
 #'   # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
@ -119,6 +119,7 @@
 #'   example_isolates %>% filter(carbapenems() == "R")
 #'   example_isolates %>% filter(across(carbapenems(), ~.x == "R"))
 #' }
+#' }
 ab_class <- function(ab_class, 
                     only_rsi_columns = FALSE) {
  ab_selector(ab_class, function_name = "ab_class", only_rsi_columns = only_rsi_columns)
@ -220,23 +221,16 @@ ab_selector <- function(ab_class,
  meet_criteria(function_name, allow_class = "character", has_length = 1, .call_depth = 1)
  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1, .call_depth = 1)
  
-  if (current_R_older_than(3.2)) {
+  if (getRversion() < "3.2") {
    warning_("antibiotic class selectors such as ", function_name, 
             "() require R version 3.2 or later - you have ", R.version.string,
             call = FALSE)
    return(NULL)
  }
  
+  # to improve speed, get_current_data() and get_column_abx() only run once when e.g. in a select or group call
  vars_df <- get_current_data(arg_name = NA, call = -3)
-
-  # improve speed here so it will only run once when e.g. in one select call
-  if (!identical(pkg_env$ab_selector, unique_call_id())) {
-    ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE)
-    pkg_env$ab_selector <- unique_call_id()
-    pkg_env$ab_selector_cols <- ab_in_data
-  } else {
-    ab_in_data <- pkg_env$ab_selector_cols
-  }
+  ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE)
  
  if (length(ab_in_data) == 0) {
    message_("No antimicrobial agents found.")
--- a/R/age.R
+++ b/R/age.R
@ -27,12 +27,14 @@
 #'
 #' Calculates age in years based on a reference date, which is the sytem date at default.
 #' @inheritSection lifecycle Stable Lifecycle
-#' @param x date(s), will be coerced with [as.POSIXlt()]
-#' @param reference reference date(s) (defaults to today), will be coerced with [as.POSIXlt()]
+#' @param x date(s), [character] (vectors) will be coerced with [as.POSIXlt()]
+#' @param reference reference date(s) (defaults to today), [character] (vectors) will be coerced with [as.POSIXlt()]
 #' @param exact a [logical] to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of [year-to-date](https://en.wikipedia.org/wiki/Year-to-date) (YTD) of `x` by the number of days in the year of `reference` (either 365 or 366).
 #' @param na.rm a [logical] to indicate whether missing values should be removed
 #' @param ... arguments passed on to [as.POSIXlt()], such as `origin`
 #' @details Ages below 0 will be returned as `NA` with a warning. Ages above 120 will only give a warning.
+#' 
+#' This function vectorises over both `x` and `reference`, meaning that either can have a length of 1 while the other argument has a larger length.
 #' @return An [integer] (no decimals) if `exact = FALSE`, a [double] (with decimals) otherwise
 #' @seealso To split ages into groups, use the [age_groups()] function.
 #' @inheritSection AMR Read more on Our Website!
@ -53,8 +55,13 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
  meet_criteria(na.rm, allow_class = "logical", has_length = 1)
  
  if (length(x) != length(reference)) {
-    stop_if(length(reference) != 1, "`x` and `reference` must be of same length, or `reference` must be of length 1.")
-    reference <- rep(reference, length(x))
+    if (length(x) == 1) {
+      x <- rep(x, length(reference))
+    } else if (length(reference) == 1) {
+      reference <- rep(reference, length(x))
+    } else {
+      stop_("`x` and `reference` must be of same length, or `reference` must be of length 1.")
+    }
  }
  x <- as.POSIXlt(x, ...)
  reference <- as.POSIXlt(reference, ...)
@ -68,21 +75,26 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
  # add decimals
  if (exact == TRUE) {
    # get dates of `x` when `x` would have the year of `reference`
-    x_in_reference_year <- as.POSIXlt(paste0(format(reference, "%Y"), format(x, "-%m-%d")))
+    x_in_reference_year <- as.POSIXlt(paste0(format(as.Date(reference), "%Y"),
+                                             format(as.Date(x), "-%m-%d")),
+                                      format = "%Y-%m-%d")
    # get differences in days
-    n_days_x_rest <- as.double(difftime(reference, x_in_reference_year, units = "days"))
+    n_days_x_rest <- as.double(difftime(as.Date(reference), 
+                                        as.Date(x_in_reference_year),
+                                        units = "days"))
    # get numbers of days the years of `reference` has for a reliable denominator
-    n_days_reference_year <- as.POSIXlt(paste0(format(reference, "%Y"), "-12-31"))$yday + 1
+    n_days_reference_year <- as.POSIXlt(paste0(format(as.Date(reference), "%Y"), "-12-31"),
+                                        format = "%Y-%m-%d")$yday + 1
    # add decimal parts of year
    mod <- n_days_x_rest / n_days_reference_year
    # negative mods are cases where `x_in_reference_year` > `reference` - so 'add' a year
-    mod[mod < 0] <- 1 + mod[mod < 0]
+    mod[!is.na(mod) & mod < 0] <- mod[!is.na(mod) & mod < 0] + 1
    # and finally add to ages
    ages <- ages + mod
  }
  
  if (any(ages < 0, na.rm = TRUE)) {
-    ages[ages < 0] <- NA
+    ages[!is.na(ages) & ages < 0] <- NA
    warning_("NAs introduced for ages below 0.", call = TRUE)
  }
  if (any(ages > 120, na.rm = TRUE)) {
@ -93,7 +105,11 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
    ages <- ages[!is.na(ages)]
  }
  
-  ages
+  if (exact == TRUE) {
+    as.double(ages)
+  } else {
+    as.integer(ages)
+  }
 }

 #' Split Ages into Age Groups
--- a/R/atc_online.R
+++ b/R/atc_online.R
@ -65,13 +65,15 @@
 #' @source <https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/>
 #' @examples
 #' \donttest{
-#' # oral DDD (Defined Daily Dose) of amoxicillin
-#' atc_online_property("J01CA04", "DDD", "O")
+#' if (requireNamespace("curl") && requireNamespace("rvest") && requireNamespace("xml2")) { 
+#'   # oral DDD (Defined Daily Dose) of amoxicillin
+#'   atc_online_property("J01CA04", "DDD", "O")
 #' 
-#' # parenteral DDD (Defined Daily Dose) of amoxicillin
-#' atc_online_property("J01CA04", "DDD", "P")
+#'   # parenteral DDD (Defined Daily Dose) of amoxicillin
+#'   atc_online_property("J01CA04", "DDD", "P")
 #'
-#' atc_online_property("J01CA04", property = "groups") # search hierarchical groups of amoxicillin
+#'   atc_online_property("J01CA04", property = "groups") # search hierarchical groups of amoxicillin
+#' }
 #' }
 atc_online_property <- function(atc_code,
                                property,
--- a/R/availability.R
+++ b/R/availability.R
@ -35,13 +35,14 @@
 #' @export
 #' @examples
 #' availability(example_isolates)
-#'
+#' \donttest{
 #' if (require("dplyr")) {
 #'   example_isolates %>%
 #'     filter(mo == as.mo("E. coli")) %>%
 #'     select_if(is.rsi) %>%
 #'     availability()
 #' }
+#' }
 availability <- function(tbl, width = NULL) {
  meet_criteria(tbl, allow_class = "data.frame")
  meet_criteria(width, allow_class = c("numeric", "integer"), has_length = 1, allow_NULL = TRUE, is_positive = TRUE, is_finite = TRUE)
--- a/R/count.R
+++ b/R/count.R
@ -72,7 +72,7 @@
 #' count_susceptible(example_isolates$AMX)
 #' susceptibility(example_isolates$AMX) * n_rsi(example_isolates$AMX)
 #'
-#' 
+#' \donttest{
 #' if (require("dplyr")) {
 #'   example_isolates %>%
 #'     group_by(hospital_id) %>%
@ -106,6 +106,7 @@
 #'     group_by(hospital_id) %>%
 #'     count_df(translate = FALSE)
 #' }
+#' }
 count_resistant <- function(..., only_all_tested = FALSE) {
  rsi_calc(...,
           ab_result = "R",
--- a/R/data.R
+++ b/R/data.R
@ -71,7 +71,7 @@
 #'
 #' WHONET 2019 software: <http://www.whonet.org/software.html>
 #'
-#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <http://ec.europa.eu/health/documents/community-register/html/atc.htm>
+#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm>
 #' @inheritSection AMR Reference Data Publicly Available
 #' @inheritSection WHOCC WHOCC
 #' @inheritSection AMR Read more on Our Website!
@ -269,12 +269,14 @@
 #' @inheritSection AMR Reference Data Publicly Available
 #' @inheritSection AMR Read more on Our Website!
 #' @examples
+#' \donttest{
 #' if (require("dplyr")) {
 #'   intrinsic_resistant %>%
 #'     filter(antibiotic == "Vancomycin", microorganism %like% "Enterococcus") %>% 
 #'     pull(microorganism)
 #'   # [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
 #' }
+#' }
 "intrinsic_resistant"

 #' Data Set with Treatment Dosages as Defined by EUCAST
--- a/R/disk.R
+++ b/R/disk.R
@ -85,7 +85,7 @@ as.disk <- function(x, na.rm = FALSE) {
               fixed = TRUE)
      x_clean <- gsub(remove, "", x, ignore.case = TRUE, fixed = fixed)
      # remove everything that is not a number or dot
-      as.numeric(gsub("[^0-9.]+", "", x_clean))
+      as.double(gsub("[^0-9.]+", "", x_clean))
    }
    
    # round up and make it an integer
--- a/R/first_isolate.R
+++ b/R/first_isolate.R
@ -273,7 +273,7 @@ first_isolate <- function(x = NULL,
  # try to find columns based on type
  # -- mo
  if (is.null(col_mo)) {
-    col_mo <- search_type_in_df(x = x, type = "mo")
+    col_mo <- search_type_in_df(x = x, type = "mo", info = info)
    stop_if(is.null(col_mo), "`col_mo` must be set")
  }
  
@ -299,7 +299,7 @@ first_isolate <- function(x = NULL,
      x$keyantimicrobials <- all_antimicrobials(x, only_rsi_columns = FALSE)
      col_keyantimicrobials <- "keyantimicrobials"
    } else if (type == "keyantimicrobials" & is.null(col_keyantimicrobials)) {
-      col_keyantimicrobials <- search_type_in_df(x = x, type = "keyantibiotics")
+      col_keyantimicrobials <- search_type_in_df(x = x, type = "keyantimicrobials", info = info)
      if (is.null(col_keyantimicrobials)) {
        # still not found as a column, create it ourselves
        x$keyantimicrobials <- key_antimicrobials(x, only_rsi_columns = FALSE, col_mo = col_mo, ...)
@ -310,7 +310,7 @@ first_isolate <- function(x = NULL,
  
  # -- date
  if (is.null(col_date)) {
-    col_date <- search_type_in_df(x = x, type = "date")
+    col_date <- search_type_in_df(x = x, type = "date", info = info)
    stop_if(is.null(col_date), "`col_date` must be set")
  }
  
@ -322,14 +322,14 @@ first_isolate <- function(x = NULL,
      col_patient_id <- "patient_id"
      message_("Using combined columns '", font_bold("First name"), "', '", font_bold("Last name"), "' and '", font_bold("Sex"), "' as input for `col_patient_id`")
    } else {
-      col_patient_id <- search_type_in_df(x = x, type = "patient_id")
+      col_patient_id <- search_type_in_df(x = x, type = "patient_id", info = info)
    }
    stop_if(is.null(col_patient_id), "`col_patient_id` must be set")
  }

  # -- specimen
  if (is.null(col_specimen) & !is.null(specimen_group)) {
-    col_specimen <- search_type_in_df(x = x, type = "specimen")
+    col_specimen <- search_type_in_df(x = x, type = "specimen", info = info)
  }
  
  # check if columns exist
--- a/R/ggplot_pca.R
+++ b/R/ggplot_pca.R
@ -65,6 +65,7 @@
 #' # See ?example_isolates.
 #'
 #' # See ?pca for more info about Principal Component Analysis (PCA).
+#' \donttest{
 #' if (require("dplyr")) {
 #'   pca_model <- example_isolates %>% 
 #'     filter(mo_genus(mo) == "Staphylococcus") %>% 
@ -84,6 +85,7 @@
 #'       labs(title = "Title here")
 #'   }
 #' }
+#' }
 ggplot_pca <- function(x,
                       choices = 1:2,
                       scale = 1,
--- a/R/ggplot_rsi.R
+++ b/R/ggplot_rsi.R
@ -67,6 +67,7 @@
 #' @export
 #' @inheritSection AMR Read more on Our Website!
 #' @examples
+#' \donttest{
 #' if (require("ggplot2") & require("dplyr")) {
 #'  
 #'   # get antimicrobial results for drugs against a UTI:
@ -114,36 +115,35 @@
 #'     ggplot() +
 #'     geom_col(aes(x = x, y = y, fill = z)) +
 #'     scale_rsi_colours(Value4 = "S", Value5 = "I", Value6 = "R")
+#'   
+#'   # resistance of ciprofloxacine per age group
+#'   example_isolates %>%
+#'     mutate(first_isolate = first_isolate()) %>%
+#'     filter(first_isolate == TRUE,
+#'            mo == as.mo("E. coli")) %>%
+#'     # age_groups() is also a function in this AMR package:
+#'     group_by(age_group = age_groups(age)) %>%
+#'     select(age_group,
+#'            CIP) %>%
+#'     ggplot_rsi(x = "age_group")
+#'   
+#'   # a shorter version which also adjusts data label colours:
+#'   example_isolates %>%
+#'     select(AMX, NIT, FOS, TMP, CIP) %>%
+#'     ggplot_rsi(colours = FALSE)
+#'
+#'
+#'   # it also supports groups (don't forget to use the group var on `x` or `facet`):
+#'   example_isolates %>%
+#'     select(hospital_id, AMX, NIT, FOS, TMP, CIP) %>%
+#'     group_by(hospital_id) %>%
+#'     ggplot_rsi(x = "hospital_id",
+#'                facet = "antibiotic",
+#'                nrow = 1,
+#'                title = "AMR of Anti-UTI Drugs Per Hospital",
+#'                x.title = "Hospital",
+#'                datalabels = FALSE)
 #' }
-#'   
-#' \donttest{
-#' # resistance of ciprofloxacine per age group
-#' example_isolates %>%
-#'   mutate(first_isolate = first_isolate(.)) %>%
-#'   filter(first_isolate == TRUE,
-#'          mo == as.mo("E. coli")) %>%
-#'   # age_groups() is also a function in this AMR package:
-#'   group_by(age_group = age_groups(age)) %>%
-#'   select(age_group,
-#'          CIP) %>%
-#'   ggplot_rsi(x = "age_group")
-#'   
-#' # a shorter version which also adjusts data label colours:
-#' example_isolates %>%
-#'   select(AMX, NIT, FOS, TMP, CIP) %>%
-#'   ggplot_rsi(colours = FALSE)
-#'
-#'
-#' # it also supports groups (don't forget to use the group var on `x` or `facet`):
-#' example_isolates %>%
-#'   select(hospital_id, AMX, NIT, FOS, TMP, CIP) %>%
-#'   group_by(hospital_id) %>%
-#'   ggplot_rsi(x = "hospital_id",
-#'              facet = "antibiotic",
-#'              nrow = 1,
-#'              title = "AMR of Anti-UTI Drugs Per Hospital",
-#'              x.title = "Hospital",
-#'              datalabels = FALSE)
 #' }
 ggplot_rsi <- function(data,
                       position = NULL,
--- a/R/guess_ab_col.R
+++ b/R/guess_ab_col.R
@ -104,6 +104,12 @@ get_column_abx <- function(x,
                           only_rsi_columns = FALSE,
                           sort = TRUE,
                           ...) {
+  
+  # check if retrieved before, then get it from package environment
+  if (identical(unique_call_id(entire_session = FALSE), pkg_env$get_column_abx.call)) {
+    return(pkg_env$get_column_abx.out)
+  }
+  
  meet_criteria(x, allow_class = "data.frame")
  meet_criteria(soft_dependencies, allow_class = "character", allow_NULL = TRUE)
  meet_criteria(hard_dependencies, allow_class = "character", allow_NULL = TRUE)
@ -184,6 +190,8 @@ get_column_abx <- function(x,
    if (info == TRUE) {
      message_("No columns found.")
    }
+    pkg_env$get_column_abx.call <- unique_call_id(entire_session = FALSE)
+    pkg_env$get_column_abx.out <- x
    return(x)
  }
  
@ -239,6 +247,9 @@ get_column_abx <- function(x,
               missing_msg)
    }
  }
+  
+  pkg_env$get_column_abx.call <- unique_call_id(entire_session = FALSE)
+  pkg_env$get_column_abx.out <- x
  x
 }

--- a/R/italicise_taxonomy.R
+++ b/R/italicise_taxonomy.R
@ -45,12 +45,13 @@
 #' 
 #' # since ggplot2 supports no markdown (yet), use
 #' # italicise_taxonomy() and the `ggtext` pkg for titles:
-#' 
+#' \donttest{
 #' if (require("ggplot2") && require("ggtext")) {
 #'   ggplot(example_isolates$AMC,
 #'          title = italicise_taxonomy("Amoxi/clav in E. coli")) +
 #'     theme(plot.title = ggtext::element_markdown())
 #' }
+#' }
 italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
  if (missing(type)) {
    type <- "markdown"
--- a/R/mo_property.R
+++ b/R/mo_property.R
@ -152,6 +152,7 @@
 #' mo_is_yeast(c("Candida", "E. coli"))      # TRUE, FALSE
 #' 
 #' # gram stains and intrinsic resistance can also be used as a filter in dplyr verbs
+#' \donttest{
 #' if (require("dplyr")) {
 #'   example_isolates %>%
 #'     filter(mo_is_gram_positive())
@ -167,6 +168,7 @@
 #' #   SNOMED codes, and URL to the online database
 #' mo_info("E. coli")
 #' }
+#' }
 mo_name <- function(x, language = get_locale(), ...) {
  if (missing(x)) {
    # this tries to find the data and an <mo> column
--- a/R/pca.R
+++ b/R/pca.R
@ -42,7 +42,6 @@
 #' # See ?example_isolates.
 #'
 #' \donttest{
-#' 
 #' if (require("dplyr")) {
 #'   # calculate the resistance per group first 
 #'   resistance_data <- example_isolates %>% 
@ -120,7 +119,7 @@ pca <- function(x,
  message_("Columns selected for PCA: ", vector_and(font_bold(colnames(pca_data), collapse = NULL), quotes = TRUE),
           ". Total observations available: ", nrow(pca_data), ".")
  
-  if (current_R_older_than(3.4)) {
+  if (getRversion() < "3.4.0") {
    # stats::prcomp prior to 3.4.0 does not have the 'rank.' argument
    pca_model <- prcomp(pca_data, retx = retx, center = center, scale. = scale., tol = tol)
  } else {
--- a/R/plot.R
+++ b/R/plot.R
@ -61,11 +61,13 @@
 #' plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")
 #' plot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
 #' 
+#' \donttest{
 #' if (require("ggplot2")) {
 #'   ggplot(some_mic_values)
 #'   ggplot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
 #'   ggplot(some_rsi_values)
 #' }
+#' }
 NULL

 #' @method plot mic
--- a/R/proportion.R
+++ b/R/proportion.R
@ -103,6 +103,7 @@
 #' proportion_IR(example_isolates$AMX)
 #' proportion_R(example_isolates$AMX)
 #'
+#' \donttest{
 #' if (require("dplyr")) {
 #'   example_isolates %>%
 #'     group_by(hospital_id) %>%
@ -161,6 +162,7 @@
 #'     group_by(hospital_id) %>%
 #'     proportion_df(translate = FALSE)
 #' }
+#' }
 resistance <- function(...,
                       minimum = 30,
                       as_percent = FALSE,
--- a/R/resistance_predict.R
+++ b/R/resistance_predict.R
@ -70,6 +70,7 @@
 #'                         year_min = 2010,
 #'                         model = "binomial")
 #' plot(x)
+#' \donttest{
 #' if (require("ggplot2")) {
 #'   ggplot_rsi_predict(x)
 #' }
@ -98,7 +99,9 @@
 #'                        info = FALSE,
 #'                        minimum = 15)
 #'                        
-#'   ggplot(data,
+#'   ggplot(data)
+#'
+#'   ggplot(as.data.frame(data),
 #'          aes(x = year)) +
 #'     geom_col(aes(y = value),
 #'              fill = "grey75") +
@ -114,6 +117,7 @@
 #'          x = "Year") +
 #'     theme_minimal(base_size = 13)
 #' }
+#' }
 resistance_predict <- function(x,
                               col_ab,
                               col_date = NULL,
--- a/R/rsi.R
+++ b/R/rsi.R
@ -101,12 +101,12 @@
 #' @inheritSection AMR Read more on Our Website!
 #' @examples
 #' summary(example_isolates) # see all R/SI results at a glance
-#' 
+#' \donttest{
 #' if (require("skimr")) {
 #'   # class <rsi> supported in skim() too:
 #'   skim(example_isolates)
 #' }
-#' 
+#' }
 #' # For INTERPRETING disk diffusion and MIC values -----------------------
 #'        
 #' # a whole data set, even with combined MIC values and disk zones
@ -215,7 +215,6 @@ is.rsi.eligible <- function(x, threshold = 0.05) {
            "ab",
            "Date",
            "POSIXt",
-            "rsi",
            "raw",
            "hms",
            "mic",
--- a/R/whocc.R
+++ b/R/whocc.R
@ -28,7 +28,7 @@
 #' All antimicrobial drugs and their official names, ATC codes, ATC groups and defined daily dose (DDD) are included in this package, using the WHO Collaborating Centre for Drug Statistics Methodology.
 #' @section WHOCC:
 #' \if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
-#' This package contains **all ~550 antibiotic, antimycotic and antiviral drugs** and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <https://www.whocc.no>) and the Pharmaceuticals Community Register of the European Commission (<http://ec.europa.eu/health/documents/community-register/html/atc.htm>). 
+#' This package contains **all ~550 antibiotic, antimycotic and antiviral drugs** and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <https://www.whocc.no>) and the Pharmaceuticals Community Register of the European Commission (<https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm>). 
 #'
 #' These have become the gold standard for international drug utilisation monitoring and research.
 #'
--- a/cran-comments.md
+++ b/cran-comments.md
@ -1 +1,3 @@
-* This package has a tarball size of over 7 MB and an installation size of over 5 MB, which will return a NOTE on R CMD CHECK. The package size is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package. This was written and explained in a manuscript that was accepted for publication in the Journal of Statistical Software 4 weeks ago. We will add the paper as a vignette in the next version. Please allow this exception in package size for CRAN. We already compressed all data sets using `compression = "xz"` to make them as small as possible.
+* This package has been archived on 22 May 2021 because of errors in the dplyr package, causing the skimr package to fail: <https://github.com/tidyverse/dplyr/issues/5881>. This AMR package contains a fix around this error. Perhaps an idea for future development of CRAN to send an automated email to a maintainer with a warning that a package will be archived in due time?
+
+* This package continuously has a tarball size of over 7 MB and an installation size of over 5 MB, which will return a NOTE on R CMD CHECK. This has been the case in the last releases as well. The package size is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package. This was written and explained in a manuscript that was accepted for publication in the Journal of Statistical Software earlier this year. We will add the paper as a vignette after publication in a next version. All data sets were compressed using `compression = "xz"` to make them as small as possible.
--- a/data-raw/AMR_latest.tar.gz
+++ b/data-raw/AMR_latest.tar.gz
--- a/data-raw/_install_deps.R
+++ b/data-raw/_install_deps.R
@ -24,7 +24,7 @@
 # ==================================================================== #

 # some old R instances have trouble installing tinytest, so we ship it too
-install.packages("data-raw/tinytest_1.2.4.patched.tar.gz")
+install.packages("data-raw/tinytest_1.2.4.10.tar.gz")
 install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)

 pkg_suggests <- gsub("[^a-zA-Z0-9]+", "", unlist(strsplit(packageDescription("AMR", fields = "Suggests"), ", ?")))
--- a/data-raw/tinytest_1.2.4.10.tar.gz
+++ b/data-raw/tinytest_1.2.4.10.tar.gz
--- a/data-raw/tinytest_1.2.4.patched.tar.gz
+++ b/data-raw/tinytest_1.2.4.patched.tar.gz
--- a/docs/404.html
+++ b/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">1.6.0.9060</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

--- a/docs/LICENSE-text.html
+++ b/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">1.6.0.9060</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

--- a/docs/articles/AMR.html
+++ b/docs/articles/AMR.html
--- a/docs/articles/AMR_files/figure-html/disk_plots-1.png
+++ b/docs/articles/AMR_files/figure-html/disk_plots-1.png
--- a/docs/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png
+++ b/docs/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png
--- a/docs/articles/AMR_files/figure-html/mic_plots-1.png
+++ b/docs/articles/AMR_files/figure-html/mic_plots-1.png
--- a/docs/articles/AMR_files/figure-html/mic_plots-2.png
+++ b/docs/articles/AMR_files/figure-html/mic_plots-2.png
--- a/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png
+++ b/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png
--- a/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png
+++ b/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png
--- a/docs/articles/AMR_files/figure-html/plot
+++ b/docs/articles/AMR_files/figure-html/plot
--- a/docs/articles/AMR_files/figure-html/plot
+++ b/docs/articles/AMR_files/figure-html/plot
--- a/docs/articles/AMR_files/figure-html/plot
+++ b/docs/articles/AMR_files/figure-html/plot
--- a/docs/articles/AMR_files/figure-html/plot
+++ b/docs/articles/AMR_files/figure-html/plot
--- a/docs/articles/AMR_files/header-attrs-2.8/header-attrs.js
+++ b/docs/articles/AMR_files/header-attrs-2.8/header-attrs.js
@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
--- a/docs/articles/EUCAST.html
+++ b/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">1.6.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -47,14 +47,14 @@
      <ul class="nav navbar-nav">
 <li>
  <a href="../index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -63,77 +63,77 @@
  <ul class="dropdown-menu" role="menu">
 <li>
      <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="../articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="../articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="../articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="../reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="../articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -142,21 +142,21 @@
 </li>
 <li>
  <a href="../reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="../authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="../news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -165,14 +165,14 @@
 <ul class="nav navbar-nav navbar-right">
 <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
@ -187,8 +187,7 @@

      

-      </header><link href="EUCAST_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
-<script src="EUCAST_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
+      </header><script src="EUCAST_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
  <div class="col-md-9 contents">
    <div class="page-header toc-ignore">
      <h1 data-toc-skip>How to apply EUCAST rules</h1>
@ -216,8 +215,8 @@
 <a href="#examples" class="anchor"></a>Examples</h2>
 <p>These rules can be used to discard impossible bug-drug combinations in your data. For example, <em>Klebsiella</em> produces beta-lactamase that prevents ampicillin (or amoxicillin) from working against it. In other words, practically every strain of <em>Klebsiella</em> is resistant to ampicillin.</p>
 <p>Sometimes, laboratory data can still contain such strains with ampicillin being susceptible to ampicillin. This could be because an antibiogram is available before an identification is available, and the antibiogram is then not re-interpreted based on the identification (namely, <em>Klebsiella</em>). EUCAST expert rules solve this, that can be applied using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:</p>
-<div class="sourceCode" id="cb1"><pre class="downlit">
-<span class="va">oops</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>mo <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">"Klebsiella"</span>, 
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">oops</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>mo <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">"Klebsiella"</span>, 
                          <span class="st">"Escherichia"</span><span class="op">)</span>,
                   ampicillin <span class="op">=</span> <span class="st">"S"</span><span class="op">)</span>
 <span class="va">oops</span>
@ -228,19 +227,19 @@
 <span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">oops</span>, info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
 <span class="co">#            mo ampicillin</span>
 <span class="co"># 1  Klebsiella          R</span>
-<span class="co"># 2 Escherichia          S</span></pre></div>
+<span class="co"># 2 Escherichia          S</span></code></pre></div>
 <p>A more convenient function is <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> that uses the same guideline, but allows to check for one or more specific microorganisms or antibiotics:</p>
-<div class="sourceCode" id="cb2"><pre class="downlit">
-<span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</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">"Klebsiella"</span>, <span class="st">"Escherichia"</span><span class="op">)</span>,
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</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">"Klebsiella"</span>, <span class="st">"Escherichia"</span><span class="op">)</span>,
                          <span class="st">"ampicillin"</span><span class="op">)</span>
 <span class="co"># [1]  TRUE FALSE</span>

 <span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>,
                          <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"ampicillin"</span>, <span class="st">"kanamycin"</span><span class="op">)</span><span class="op">)</span>
-<span class="co"># [1]  TRUE FALSE</span></pre></div>
+<span class="co"># [1]  TRUE FALSE</span></code></pre></div>
 <p>EUCAST rules can not only be used for correction, they can also be used for filling in known resistance and susceptibility based on results of other antimicrobials drugs. This process is called <em>interpretive reading</em>, is basically a form of imputation, and is part of the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function as well:</p>
-<div class="sourceCode" id="cb3"><pre class="downlit">
-<span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>mo <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">"Staphylococcus aureus"</span>,
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>mo <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">"Staphylococcus aureus"</span>,
                          <span class="st">"Enterococcus faecalis"</span>,
                          <span class="st">"Escherichia coli"</span>,
                          <span class="st">"Klebsiella pneumoniae"</span>,
@ -252,9 +251,9 @@
                   CXM <span class="op">=</span> <span class="st">"-"</span>,       <span class="co"># Cefuroxime</span>
                   PEN <span class="op">=</span> <span class="st">"S"</span>,       <span class="co"># Benzylenicillin</span>
                   FOX <span class="op">=</span> <span class="st">"S"</span>,       <span class="co"># Cefoxitin</span>
-                   stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></pre></div>
-<div class="sourceCode" id="cb4"><pre class="downlit">
-<span class="va">data</span></pre></div>
+                   stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">data</span></code></pre></div>
 <table class="table">
 <thead><tr class="header">
 <th align="left">mo</th>
@ -319,8 +318,8 @@
 </tr>
 </tbody>
 </table>
-<div class="sourceCode" id="cb5"><pre class="downlit">
-<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">data</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">data</span><span class="op">)</span></code></pre></div>
 <table class="table">
 <thead><tr class="header">
 <th align="left">mo</th>
--- a/docs/articles/EUCAST_files/header-attrs-2.8/header-attrs.js
+++ b/docs/articles/EUCAST_files/header-attrs-2.8/header-attrs.js
@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
--- a/docs/articles/MDR.html
+++ b/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">1.6.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -47,14 +47,14 @@
      <ul class="nav navbar-nav">
 <li>
  <a href="../index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -63,77 +63,77 @@
  <ul class="dropdown-menu" role="menu">
 <li>
      <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="../articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="../articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="../articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="../reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="../articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -142,21 +142,21 @@
 </li>
 <li>
  <a href="../reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="../authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="../news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -165,14 +165,14 @@
 <ul class="nav navbar-nav navbar-right">
 <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
@ -187,8 +187,7 @@

      

-      </header><link href="MDR_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
-<script src="MDR_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
+      </header><script src="MDR_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
  <div class="col-md-9 contents">
    <div class="page-header toc-ignore">
      <h1 data-toc-skip>How to determine multi-drug resistance (MDR)</h1>
@ -244,27 +243,27 @@
 <a href="#custom-guidelines" class="anchor"></a>Custom Guidelines</h4>
 <p>You can also use your own custom guideline. Custom guidelines can be set with the <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function. This is of great importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.</p>
 <p>If you are familiar with <code><a href="https://dplyr.tidyverse.org/reference/case_when.html">case_when()</a></code> of the <code>dplyr</code> package, you will recognise the input method to set your own rules. Rules must be set using what considers to be the ‘formula notation’:</p>
-<div class="sourceCode" id="cb1"><pre class="downlit">
-<span class="va">custom</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">custom_mdro_guideline</a></span><span class="op">(</span><span class="va">CIP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">age</span> <span class="op">&gt;</span> <span class="fl">60</span> <span class="op">~</span> <span class="st">"Elderly Type A"</span>,
-                                <span class="va">ERY</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">age</span> <span class="op">&gt;</span> <span class="fl">60</span> <span class="op">~</span> <span class="st">"Elderly Type B"</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">custom</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">custom_mdro_guideline</a></span><span class="op">(</span><span class="va">CIP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">age</span> <span class="op">&gt;</span> <span class="fl">60</span> <span class="op">~</span> <span class="st">"Elderly Type A"</span>,
+                                <span class="va">ERY</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">age</span> <span class="op">&gt;</span> <span class="fl">60</span> <span class="op">~</span> <span class="st">"Elderly Type B"</span><span class="op">)</span></code></pre></div>
 <p>If a row/an isolate matches the first rule, the value after the first <code><a href="https://rdrr.io/r/base/tilde.html">~</a></code> (in this case <em>‘Elderly Type A’</em>) will be set as MDRO value. Otherwise, the second rule will be tried and so on. The number of rules is unlimited.</p>
 <p>You can print the rules set in the console for an overview. Colours will help reading it if your console supports colours.</p>
-<div class="sourceCode" id="cb2"><pre class="downlit">
-<span class="va">custom</span>
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">custom</span>
 <span class="co"># A set of custom MDRO rules:</span>
 <span class="co">#   1. If CIP is "R" and age is higher than 60 then: Elderly Type A</span>
 <span class="co">#   2. If ERY is "R" and age is higher than 60 then: Elderly Type B</span>
 <span class="co">#   3. Otherwise: Negative</span>
 <span class="co"># </span>
 <span class="co"># Unmatched rows will return NA.</span>
-<span class="co"># Results will be of class &lt;factor&gt;, with ordered levels: Negative &lt; Elderly Type A &lt; Elderly Type B</span></pre></div>
+<span class="co"># Results will be of class &lt;factor&gt;, with ordered levels: Negative &lt; Elderly Type A &lt; Elderly Type B</span></code></pre></div>
 <p>The outcome of the function can be used for the <code>guideline</code> argument in the [mdro()] function:</p>
-<div class="sourceCode" id="cb3"><pre class="downlit">
-<span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">example_isolates</span>, guideline <span class="op">=</span> <span class="va">custom</span><span class="op">)</span>
+<div class="sourceCode" id="cb3"><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/mdro.html">mdro</a></span><span class="op">(</span><span class="va">example_isolates</span>, guideline <span class="op">=</span> <span class="va">custom</span><span class="op">)</span>
 <span class="fu"><a href="https://rdrr.io/r/base/table.html">table</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
 <span class="co"># x</span>
 <span class="co">#       Negative Elderly Type A Elderly Type B </span>
-<span class="co">#           1070            198            732</span></pre></div>
+<span class="co">#           1070            198            732</span></code></pre></div>
 <p>The rules set (the <code>custom</code> object in this case) could be exported to a shared file location using <code><a href="https://rdrr.io/r/base/readRDS.html">saveRDS()</a></code> if you collaborate with multiple users. The custom rules set could then be imported using <code><a href="https://rdrr.io/r/base/readRDS.html">readRDS()</a></code>.</p>
 </div>
 </div>
@ -273,15 +272,15 @@
 <a href="#examples" class="anchor"></a>Examples</h3>
 <p>The <code><a href="../reference/mdro.html">mdro()</a></code> function always returns an ordered <code>factor</code>. For example, the output of the default guideline by Magiorakos <em>et al.</em> returns a <code>factor</code> with levels ‘Negative’, ‘MDR’, ‘XDR’ or ‘PDR’ in that order.</p>
 <p>The next example uses the <code>example_isolates</code> data set. This is a data set included with this package and contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practice AMR data analysis. If we test the MDR/XDR/PDR guideline on this data set, we get:</p>
-<div class="sourceCode" id="cb4"><pre class="downlit">
-<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="co"># to support pipes: %&gt;%</span>
-<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/cleaner">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></pre></div>
-<div class="sourceCode" id="cb5"><pre class="downlit">
-<span class="va">example_isolates</span> <span class="op">%&gt;%</span> 
+<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://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>   <span class="co"># to support pipes: %&gt;%</span>
+<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/cleaner">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></code></pre></div>
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">example_isolates</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="op">)</span> <span class="co"># show frequency table of the result</span>
 <span class="co"># Warning: NA introduced for isolates where the available percentage of antimicrobial</span>
-<span class="co"># classes was below 50% (set with `pct_required_classes`)</span></pre></div>
+<span class="co"># classes was below 50% (set with `pct_required_classes`)</span></code></pre></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: factor &gt; ordered (numeric)<br>
 Length: 2,000<br>
@ -317,8 +316,8 @@ Unique: 2</p>
 </tbody>
 </table>
 <p>For another example, I will create a data set to determine multi-drug resistant TB:</p>
-<div class="sourceCode" id="cb6"><pre class="downlit">
-<span class="co"># random_rsi() is a helper function to generate</span>
+<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="co"># random_rsi() is a helper function to generate</span>
 <span class="co"># a random vector with values S, I and R</span>
 <span class="va">my_TB_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>rifampicin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
                         isoniazid <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
@ -326,44 +325,44 @@ Unique: 2</p>
                         ethambutol <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
                         pyrazinamide <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
                         moxifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
-                         kanamycin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span><span class="op">)</span></pre></div>
+                         kanamycin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span><span class="op">)</span></code></pre></div>
 <p>Because all column names are automatically verified for valid drug names or codes, this would have worked exactly the same:</p>
-<div class="sourceCode" id="cb7"><pre class="downlit">
-<span class="va">my_TB_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>RIF <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
+<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">my_TB_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>RIF <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
                         INH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
                         GAT <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
                         ETH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
                         PZA <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
                         MFX <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
-                         KAN <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span><span class="op">)</span></pre></div>
+                         KAN <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span><span class="op">)</span></code></pre></div>
 <p>The data set now looks like this:</p>
-<div class="sourceCode" id="cb8"><pre class="downlit">
-<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>
+<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
 <span class="co">#   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
-<span class="co"># 1          S         S            S          S            R            R</span>
-<span class="co"># 2          R         S            S          S            I            R</span>
-<span class="co"># 3          R         R            I          R            I            R</span>
-<span class="co"># 4          R         R            S          S            R            I</span>
-<span class="co"># 5          R         R            R          I            I            I</span>
-<span class="co"># 6          R         I            R          R            I            I</span>
+<span class="co"># 1          R         I            I          I            S            R</span>
+<span class="co"># 2          R         R            S          R            S            S</span>
+<span class="co"># 3          I         R            S          S            S            R</span>
+<span class="co"># 4          I         I            I          R            S            I</span>
+<span class="co"># 5          I         R            R          I            R            S</span>
+<span class="co"># 6          R         R            R          R            I            S</span>
 <span class="co">#   kanamycin</span>
-<span class="co"># 1         I</span>
-<span class="co"># 2         R</span>
-<span class="co"># 3         I</span>
-<span class="co"># 4         I</span>
-<span class="co"># 5         S</span>
-<span class="co"># 6         I</span></pre></div>
+<span class="co"># 1         S</span>
+<span class="co"># 2         I</span>
+<span class="co"># 3         R</span>
+<span class="co"># 4         S</span>
+<span class="co"># 5         I</span>
+<span class="co"># 6         I</span></code></pre></div>
 <p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
-<div class="sourceCode" id="cb9"><pre class="downlit">
-<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></pre></div>
+<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></code></pre></div>
 <p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
-<div class="sourceCode" id="cb10"><pre class="downlit">
-<span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">mdr_tb</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
-<span class="co"># ℹ No column found as input for `col_mo`, assuming all records</span>
-<span class="co">#   containMycobacterium tuberculosis.</span></pre></div>
+<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">mdr_tb</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
+<span class="co"># ℹ No column found as input for `col_mo`, assuming all rows contain</span>
+<span class="co">#   Mycobacterium tuberculosis.</span></code></pre></div>
 <p>Create a frequency table of the results:</p>
-<div class="sourceCode" id="cb11"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span><span class="op">)</span></code></pre></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: factor &gt; ordered (numeric)<br>
 Length: 5,000<br>
@ -383,40 +382,40 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistant</td>
-<td align="right">3165</td>
-<td align="right">63.30%</td>
-<td align="right">3165</td>
-<td align="right">63.30%</td>
+<td align="right">3200</td>
+<td align="right">64.00%</td>
+<td align="right">3200</td>
+<td align="right">64.00%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">1000</td>
-<td align="right">20.00%</td>
-<td align="right">4165</td>
-<td align="right">83.30%</td>
+<td align="right">1014</td>
+<td align="right">20.28%</td>
+<td align="right">4214</td>
+<td align="right">84.28%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Multi-drug-resistant</td>
-<td align="right">463</td>
-<td align="right">9.26%</td>
-<td align="right">4628</td>
-<td align="right">92.56%</td>
+<td align="right">455</td>
+<td align="right">9.10%</td>
+<td align="right">4669</td>
+<td align="right">93.38%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistant</td>
-<td align="right">255</td>
-<td align="right">5.10%</td>
-<td align="right">4883</td>
-<td align="right">97.66%</td>
+<td align="right">252</td>
+<td align="right">5.04%</td>
+<td align="right">4921</td>
+<td align="right">98.42%</td>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
 <td align="left">Extensively drug-resistant</td>
-<td align="right">117</td>
-<td align="right">2.34%</td>
+<td align="right">79</td>
+<td align="right">1.58%</td>
 <td align="right">5000</td>
 <td align="right">100.00%</td>
 </tr>
--- a/docs/articles/MDR_files/header-attrs-2.8/header-attrs.js
+++ b/docs/articles/MDR_files/header-attrs-2.8/header-attrs.js
@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
--- a/docs/articles/PCA.html
+++ b/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">1.6.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -47,14 +47,14 @@
      <ul class="nav navbar-nav">
 <li>
  <a href="../index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -63,77 +63,77 @@
  <ul class="dropdown-menu" role="menu">
 <li>
      <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="../articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="../articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="../articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="../reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="../articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -142,21 +142,21 @@
 </li>
 <li>
  <a href="../reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="../authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="../news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -165,14 +165,14 @@
 <ul class="nav navbar-nav navbar-right">
 <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
@ -187,8 +187,7 @@

      

-      </header><link href="PCA_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
-<script src="PCA_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
+      </header><script src="PCA_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
  <div class="col-md-9 contents">
    <div class="page-header toc-ignore">
      <h1 data-toc-skip>How to conduct principal component analysis (PCA) for AMR</h1>
@ -210,64 +209,64 @@
 <h1 class="hasAnchor">
 <a href="#transforming" class="anchor"></a>Transforming</h1>
 <p>For PCA, we need to transform our AMR data first. This is what the <code>example_isolates</code> data set in this package looks like:</p>
-<div class="sourceCode" id="cb1"><pre class="downlit">
-<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>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://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>
-<span class="fu"><a href="https://tibble.tidyverse.org/reference/glimpse.html">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
+<span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
 <span class="co"># Rows: 2,000</span>
 <span class="co"># Columns: 49</span>
-<span class="co"># $ date            &lt;date&gt; 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002…</span>
-<span class="co"># $ hospital_id     &lt;fct&gt; D, D, B, B, B, B, D, D, B, B, D, D, D, D, D, B, B, B,…</span>
-<span class="co"># $ ward_icu        &lt;lgl&gt; FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, T…</span>
-<span class="co"># $ ward_clinical   &lt;lgl&gt; TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, F…</span>
-<span class="co"># $ ward_outpatient &lt;lgl&gt; FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALS…</span>
-<span class="co"># $ age             &lt;dbl&gt; 65, 65, 45, 45, 45, 45, 78, 78, 45, 79, 67, 67, 71, 7…</span>
-<span class="co"># $ gender          &lt;chr&gt; "F", "F", "F", "F", "F", "F", "M", "M", "F", "F", "M"…</span>
-<span class="co"># $ patient_id      &lt;chr&gt; "A77334", "A77334", "067927", "067927", "067927", "06…</span>
-<span class="co"># $ mo              &lt;mo&gt; "B_ESCHR_COLI", "B_ESCHR_COLI", "B_STPHY_EPDR", "B_STP…</span>
-<span class="co"># $ PEN             &lt;rsi&gt; R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R,…</span>
-<span class="co"># $ OXA             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
-<span class="co"># $ FLC             &lt;rsi&gt; NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA,…</span>
-<span class="co"># $ AMX             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA,…</span>
-<span class="co"># $ AMC             &lt;rsi&gt; I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I,…</span>
-<span class="co"># $ AMP             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA,…</span>
-<span class="co"># $ TZP             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
-<span class="co"># $ CZO             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
-<span class="co"># $ FEP             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
-<span class="co"># $ CXM             &lt;rsi&gt; I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R…</span>
-<span class="co"># $ FOX             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
-<span class="co"># $ CTX             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
-<span class="co"># $ CAZ             &lt;rsi&gt; NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, …</span>
-<span class="co"># $ CRO             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
-<span class="co"># $ GEN             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
-<span class="co"># $ TOB             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, N…</span>
-<span class="co"># $ AMK             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
-<span class="co"># $ KAN             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
-<span class="co"># $ TMP             &lt;rsi&gt; R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, …</span>
-<span class="co"># $ SXT             &lt;rsi&gt; R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S,…</span>
-<span class="co"># $ NIT             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
-<span class="co"># $ FOS             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
-<span class="co"># $ LNZ             &lt;rsi&gt; R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
-<span class="co"># $ CIP             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA,…</span>
-<span class="co"># $ MFX             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
-<span class="co"># $ VAN             &lt;rsi&gt; R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, …</span>
-<span class="co"># $ TEC             &lt;rsi&gt; R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
-<span class="co"># $ TCY             &lt;rsi&gt; R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, …</span>
-<span class="co"># $ TGC             &lt;rsi&gt; NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R,…</span>
-<span class="co"># $ DOX             &lt;rsi&gt; NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R,…</span>
-<span class="co"># $ ERY             &lt;rsi&gt; R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span>
-<span class="co"># $ CLI             &lt;rsi&gt; R, R, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, R, R, R,…</span>
-<span class="co"># $ AZM             &lt;rsi&gt; R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span>
-<span class="co"># $ IPM             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
-<span class="co"># $ MEM             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
-<span class="co"># $ MTR             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
-<span class="co"># $ CHL             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
-<span class="co"># $ COL             &lt;rsi&gt; NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, …</span>
-<span class="co"># $ MUP             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
-<span class="co"># $ RIF             &lt;rsi&gt; R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span></pre></div>
+<span class="co"># $ date            &lt;date&gt; 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-…</span>
+<span class="co"># $ hospital_id     &lt;fct&gt; D, D, B, B, B, B, D, D, B, B, D, D, D, D, D, B, B, B, …</span>
+<span class="co"># $ ward_icu        &lt;lgl&gt; FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TR…</span>
+<span class="co"># $ ward_clinical   &lt;lgl&gt; TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, FA…</span>
+<span class="co"># $ ward_outpatient &lt;lgl&gt; FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE…</span>
+<span class="co"># $ age             &lt;dbl&gt; 65, 65, 45, 45, 45, 45, 78, 78, 45, 79, 67, 67, 71, 71…</span>
+<span class="co"># $ gender          &lt;chr&gt; "F", "F", "F", "F", "F", "F", "M", "M", "F", "F", "M",…</span>
+<span class="co"># $ patient_id      &lt;chr&gt; "A77334", "A77334", "067927", "067927", "067927", "067…</span>
+<span class="co"># $ mo              &lt;mo&gt; "B_ESCHR_COLI", "B_ESCHR_COLI", "B_STPHY_EPDR", "B_STPH…</span>
+<span class="co"># $ PEN             &lt;rsi&gt; R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, …</span>
+<span class="co"># $ OXA             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
+<span class="co"># $ FLC             &lt;rsi&gt; NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA, …</span>
+<span class="co"># $ AMX             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, …</span>
+<span class="co"># $ AMC             &lt;rsi&gt; I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I, …</span>
+<span class="co"># $ AMP             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, …</span>
+<span class="co"># $ TZP             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
+<span class="co"># $ CZO             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
+<span class="co"># $ FEP             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
+<span class="co"># $ CXM             &lt;rsi&gt; I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R,…</span>
+<span class="co"># $ FOX             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
+<span class="co"># $ CTX             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, …</span>
+<span class="co"># $ CAZ             &lt;rsi&gt; NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, S…</span>
+<span class="co"># $ CRO             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, …</span>
+<span class="co"># $ GEN             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
+<span class="co"># $ TOB             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, NA…</span>
+<span class="co"># $ AMK             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
+<span class="co"># $ KAN             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
+<span class="co"># $ TMP             &lt;rsi&gt; R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, R…</span>
+<span class="co"># $ SXT             &lt;rsi&gt; R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S, …</span>
+<span class="co"># $ NIT             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
+<span class="co"># $ FOS             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
+<span class="co"># $ LNZ             &lt;rsi&gt; R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R,…</span>
+<span class="co"># $ CIP             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, …</span>
+<span class="co"># $ MFX             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
+<span class="co"># $ VAN             &lt;rsi&gt; R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, S…</span>
+<span class="co"># $ TEC             &lt;rsi&gt; R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R,…</span>
+<span class="co"># $ TCY             &lt;rsi&gt; R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, S…</span>
+<span class="co"># $ TGC             &lt;rsi&gt; NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, …</span>
+<span class="co"># $ DOX             &lt;rsi&gt; NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, …</span>
+<span class="co"># $ ERY             &lt;rsi&gt; R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, …</span>
+<span class="co"># $ CLI             &lt;rsi&gt; R, R, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, R, R, R, …</span>
+<span class="co"># $ AZM             &lt;rsi&gt; R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, …</span>
+<span class="co"># $ IPM             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, …</span>
+<span class="co"># $ MEM             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
+<span class="co"># $ MTR             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
+<span class="co"># $ CHL             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
+<span class="co"># $ COL             &lt;rsi&gt; NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, R…</span>
+<span class="co"># $ MUP             &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
+<span class="co"># $ RIF             &lt;rsi&gt; R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R,…</span></code></pre></div>
 <p>Now to transform this to a data set with only resistance percentages per taxonomic order and genus:</p>
-<div class="sourceCode" id="cb2"><pre class="downlit">
-<span class="va">resistance_data</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op">%&gt;%</span> 
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">resistance_data</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span>order <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_order</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span>,       <span class="co"># group on anything, like order</span>
           genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>   <span class="co">#  and genus as we do here</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html">summarise_if</a></span><span class="op">(</span><span class="va">is.rsi</span>, <span class="va">resistance</span><span class="op">)</span> <span class="op">%&gt;%</span> <span class="co"># then get resistance of all drugs</span>
@ -284,26 +283,26 @@
 <span class="co"># 3 Bacteroidales    Bacteroides      NA    NA    NA    NA    NA    NA    NA    NA</span>
 <span class="co"># 4 Campylobacteral… Campylobacter    NA    NA    NA    NA    NA    NA    NA    NA</span>
 <span class="co"># 5 Caryophanales    Gemella          NA    NA    NA    NA    NA    NA    NA    NA</span>
-<span class="co"># 6 Caryophanales    Listeria         NA    NA    NA    NA    NA    NA    NA    NA</span></pre></div>
+<span class="co"># 6 Caryophanales    Listeria         NA    NA    NA    NA    NA    NA    NA    NA</span></code></pre></div>
 </div>
 <div id="perform-principal-component-analysis" class="section level1">
 <h1 class="hasAnchor">
 <a href="#perform-principal-component-analysis" class="anchor"></a>Perform principal component analysis</h1>
 <p>The new <code><a href="../reference/pca.html">pca()</a></code> function will automatically filter on rows that contain numeric values in all selected variables, so we now only need to do:</p>
-<div class="sourceCode" id="cb3"><pre class="downlit">
-<span class="va">pca_result</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/pca.html">pca</a></span><span class="op">(</span><span class="va">resistance_data</span><span class="op">)</span>
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">pca_result</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/pca.html">pca</a></span><span class="op">(</span><span class="va">resistance_data</span><span class="op">)</span>
 <span class="co"># ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", "TMP"</span>
-<span class="co">#   and "TOB". Total observations available: 7.</span></pre></div>
+<span class="co">#   and "TOB". Total observations available: 7.</span></code></pre></div>
 <p>The result can be reviewed with the good old <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> function:</p>
-<div class="sourceCode" id="cb4"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span>
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span>
 <span class="co"># Groups (n=4, named as 'order'):</span>
 <span class="co"># [1] "Caryophanales"    "Enterobacterales" "Lactobacillales"  "Pseudomonadales"</span>
 <span class="co"># Importance of components:</span>
 <span class="co">#                           PC1    PC2    PC3     PC4     PC5     PC6       PC7</span>
 <span class="co"># Standard deviation     2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 5.121e-17</span>
 <span class="co"># Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span>
-<span class="co"># Cumulative Proportion  0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></pre></div>
+<span class="co"># Cumulative Proportion  0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></code></pre></div>
 <pre><code># Groups (n=4, named as 'order'):
 # [1] "Caryophanales"    "Enterobacterales" "Lactobacillales"  "Pseudomonadales"</code></pre>
 <p>Good news. The first two components explain a total of 93.3% of the variance (see the PC1 and PC2 values of the <em>Proportion of Variance</em>. We can create a so-called biplot with the base R <code><a href="https://rdrr.io/r/stats/biplot.html">biplot()</a></code> function, to see which antimicrobial resistance per drug explain the difference per microorganism.</p>
@ -311,17 +310,17 @@
 <div id="plotting-the-results" class="section level1">
 <h1 class="hasAnchor">
 <a href="#plotting-the-results" class="anchor"></a>Plotting the results</h1>
-<div class="sourceCode" id="cb6"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/stats/biplot.html">biplot</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/stats/biplot.html">biplot</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></code></pre></div>
 <p><img src="PCA_files/figure-html/unnamed-chunk-5-1.png" width="750"></p>
 <p>But we can’t see the explanation of the points. Perhaps this works better with our new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function, that automatically adds the right labels and even groups:</p>
-<div class="sourceCode" id="cb7"><pre class="downlit">
-<span class="fu"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></code></pre></div>
 <p><img src="PCA_files/figure-html/unnamed-chunk-6-1.png" width="750"></p>
 <p>You can also print an ellipse per group, and edit the appearance:</p>
-<div class="sourceCode" id="cb8"><pre class="downlit">
-<span class="fu"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span><span class="op">(</span><span class="va">pca_result</span>, ellipse <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">+</span>
-  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"An AMR/PCA biplot!"</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span><span class="op">(</span><span class="va">pca_result</span>, ellipse <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">+</span>
+  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"An AMR/PCA biplot!"</span><span class="op">)</span></code></pre></div>
 <p><img src="PCA_files/figure-html/unnamed-chunk-7-1.png" width="750"></p>
 </div>
  </div>
--- a/docs/articles/PCA_files/figure-html/unnamed-chunk-5-1.png
+++ b/docs/articles/PCA_files/figure-html/unnamed-chunk-5-1.png
--- a/docs/articles/PCA_files/figure-html/unnamed-chunk-6-1.png
+++ b/docs/articles/PCA_files/figure-html/unnamed-chunk-6-1.png
--- a/docs/articles/PCA_files/figure-html/unnamed-chunk-7-1.png
+++ b/docs/articles/PCA_files/figure-html/unnamed-chunk-7-1.png
--- a/docs/articles/PCA_files/header-attrs-2.8/header-attrs.js
+++ b/docs/articles/PCA_files/header-attrs-2.8/header-attrs.js
@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
--- a/docs/articles/SPSS.html
+++ b/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">1.6.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -47,14 +47,14 @@
      <ul class="nav navbar-nav">
 <li>
  <a href="../index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -63,77 +63,77 @@
  <ul class="dropdown-menu" role="menu">
 <li>
      <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="../articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="../articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="../articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="../reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="../articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -142,21 +142,21 @@
 </li>
 <li>
  <a href="../reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="../authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="../news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -165,14 +165,14 @@
 <ul class="nav navbar-nav navbar-right">
 <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
@ -187,14 +187,13 @@

      

-      </header><link href="SPSS_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
-<script src="SPSS_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
+      </header><script src="SPSS_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
  <div class="col-md-9 contents">
    <div class="page-header toc-ignore">
      <h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
                        <h4 class="author">Matthijs S. Berends</h4>
            
-            <h4 class="date">27 April 2021</h4>
+            <h4 class="date">24 May 2021</h4>
      
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd"><code>vignettes/SPSS.Rmd</code></a></small>
      <div class="hidden name"><code>SPSS.Rmd</code></div>
@ -229,7 +228,7 @@
 </li>
 <li>
 <p><strong>R has a huge community.</strong></p>
-<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes">398,952 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
+<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes">403,383 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
 </li>
 <li>
 <p><strong>R understands any data type, including SPSS/SAS/Stata.</strong></p>
@ -248,8 +247,8 @@
 </li>
 </ul>
 <p>To demonstrate the first point:</p>
-<div class="sourceCode" id="cb1"><pre class="downlit">
-<span class="co"># not all values are valid MIC values:</span>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="co"># not all values are valid MIC values:</span>
 <span class="fu"><a href="../reference/as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">0.125</span><span class="op">)</span>
 <span class="co"># Class &lt;mic&gt;</span>
 <span class="co"># [1] 0.125</span>
@ -280,7 +279,7 @@
 <span class="co"># [4] "fluclox"              "flucloxacilina"       "flucloxacillin"      </span>
 <span class="co"># [7] "flucloxacilline"      "flucloxacillinum"     "fluorochloroxacillin"</span>
 <span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"floxapen"</span><span class="op">)</span>
-<span class="co"># [1] "J01CF05"</span></pre></div>
+<span class="co"># [1] "J01CF05"</span></code></pre></div>
 </div>
 <div id="import-data-from-spsssasstata" class="section level2">
 <h2 class="hasAnchor">
@ -296,8 +295,8 @@
 <p><img src="https://github.com/msberends/AMR/raw/master/docs/import2.png"></p>
 <p>If you want named variables to be imported as factors so it resembles SPSS more, use <code><a href="https://haven.tidyverse.org/reference/as_factor.html">as_factor()</a></code>.</p>
 <p>The difference is this:</p>
-<div class="sourceCode" id="cb2"><pre class="downlit">
-<span class="va">SPSS_data</span>
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">SPSS_data</span>
 <span class="co"># # A tibble: 4,203 x 4</span>
 <span class="co">#     v001 sex       status    statusage</span>
 <span class="co">#    &lt;dbl&gt; &lt;dbl+lbl&gt; &lt;dbl+lbl&gt;     &lt;dbl&gt;</span>
@ -327,74 +326,74 @@
 <span class="co">#  8 10011 Male   alive       73.1</span>
 <span class="co">#  9 10017 Male   alive       56.7</span>
 <span class="co"># 10 10018 Female alive       66.6</span>
-<span class="co"># # … with 4,193 more rows</span></pre></div>
+<span class="co"># # … with 4,193 more rows</span></code></pre></div>
 </div>
 <div id="base-r" class="section level3">
 <h3 class="hasAnchor">
 <a href="#base-r" class="anchor"></a>Base R</h3>
 <p>To import data from SPSS, SAS or Stata, you can use the <a href="https://haven.tidyverse.org/">great <code>haven</code> package</a> yourself:</p>
-<div class="sourceCode" id="cb3"><pre class="downlit">
-<span class="co"># download and install the latest version:</span>
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="co"># download and install the latest version:</span>
 <span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"haven"</span><span class="op">)</span>
 <span class="co"># load the package you just installed:</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="http://haven.tidyverse.org">haven</a></span><span class="op">)</span> </pre></div>
+<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://haven.tidyverse.org">haven</a></span><span class="op">)</span> </code></pre></div>
 <p>You can now import files as follows:</p>
 <div id="spss" class="section level4">
 <h4 class="hasAnchor">
 <a href="#spss" class="anchor"></a>SPSS</h4>
 <p>To read files from SPSS into R:</p>
-<div class="sourceCode" id="cb4"><pre class="downlit">
-<span class="co"># read any SPSS file based on file extension (best way):</span>
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="co"># read any SPSS file based on file extension (best way):</span>
 <span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_spss</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>

 <span class="co"># read .sav or .zsav file:</span>
 <span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_sav</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>

 <span class="co"># read .por file:</span>
-<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_por</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span></pre></div>
+<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_por</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span></code></pre></div>
 <p>Do not forget about <code><a href="https://haven.tidyverse.org/reference/as_factor.html">as_factor()</a></code>, as mentioned above.</p>
 <p>To export your R objects to the SPSS file format:</p>
-<div class="sourceCode" id="cb5"><pre class="downlit">
-<span class="co"># save as .sav file:</span>
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="co"># save as .sav file:</span>
 <span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>

 <span class="co"># save as compressed .zsav file:</span>
-<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span>, compress <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></pre></div>
+<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span>, compress <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
 </div>
 <div id="sas" class="section level4">
 <h4 class="hasAnchor">
 <a href="#sas" class="anchor"></a>SAS</h4>
 <p>To read files from SAS into R:</p>
-<div class="sourceCode" id="cb6"><pre class="downlit">
-<span class="co"># read .sas7bdat + .sas7bcat files:</span>
+<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="co"># read .sas7bdat + .sas7bcat files:</span>
 <span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html">read_sas</a></span><span class="op">(</span>data_file <span class="op">=</span> <span class="st">"path/to/file"</span>, catalog_file <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span>

 <span class="co"># read SAS transport files (version 5 and version 8):</span>
-<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html">read_xpt</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span></pre></div>
+<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html">read_xpt</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span></code></pre></div>
 <p>To export your R objects to the SAS file format:</p>
-<div class="sourceCode" id="cb7"><pre class="downlit">
-<span class="co"># save as regular SAS file:</span>
+<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="co"># save as regular SAS file:</span>
 <span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html">write_sas</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>

 <span class="co"># the SAS transport format is an open format </span>
 <span class="co"># (required for submission of the data to the FDA)</span>
-<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html">write_xpt</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span>, version <span class="op">=</span> <span class="fl">8</span><span class="op">)</span></pre></div>
+<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html">write_xpt</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span>, version <span class="op">=</span> <span class="fl">8</span><span class="op">)</span></code></pre></div>
 </div>
 <div id="stata" class="section level4">
 <h4 class="hasAnchor">
 <a href="#stata" class="anchor"></a>Stata</h4>
 <p>To read files from Stata into R:</p>
-<div class="sourceCode" id="cb8"><pre class="downlit">
-<span class="co"># read .dta file:</span>
+<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="co"># read .dta file:</span>
 <span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_stata</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"/path/to/file"</span><span class="op">)</span>

 <span class="co"># works exactly the same:</span>
-<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_dta</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"/path/to/file"</span><span class="op">)</span></pre></div>
+<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_dta</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"/path/to/file"</span><span class="op">)</span></code></pre></div>
 <p>To export your R objects to the Stata file format:</p>
-<div class="sourceCode" id="cb9"><pre class="downlit">
-<span class="co"># save as .dta file, Stata version 14:</span>
+<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="co"># save as .dta file, Stata version 14:</span>
 <span class="co"># (supports Stata v8 until v15 at the time of writing)</span>
-<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">write_dta</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"/path/to/file"</span>, version <span class="op">=</span> <span class="fl">14</span><span class="op">)</span></pre></div>
+<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">write_dta</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"/path/to/file"</span>, version <span class="op">=</span> <span class="fl">14</span><span class="op">)</span></code></pre></div>
 </div>
 </div>
 </div>
--- a/docs/articles/SPSS_files/header-attrs-2.8/header-attrs.js
+++ b/docs/articles/SPSS_files/header-attrs-2.8/header-attrs.js
@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
--- a/docs/articles/WHONET.html
+++ b/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">1.6.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -47,14 +47,14 @@
      <ul class="nav navbar-nav">
 <li>
  <a href="../index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -63,77 +63,77 @@
  <ul class="dropdown-menu" role="menu">
 <li>
      <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="../articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="../articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="../articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="../reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="../articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -142,21 +142,21 @@
 </li>
 <li>
  <a href="../reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="../authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="../news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -165,14 +165,14 @@
 <ul class="nav navbar-nav navbar-right">
 <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
@ -187,8 +187,7 @@

      

-      </header><link href="WHONET_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
-<script src="WHONET_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
+      </header><script src="WHONET_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
  <div class="col-md-9 contents">
    <div class="page-header toc-ignore">
      <h1 data-toc-skip>How to work with WHONET data</h1>
@ -206,38 +205,38 @@
 <a href="#import-of-data" class="anchor"></a>Import of data</h3>
 <p>This tutorial assumes you already imported the WHONET data with e.g. the <a href="https://readxl.tidyverse.org/"><code>readxl</code> package</a>. In RStudio, this can be done using the menu button ‘Import Dataset’ in the tab ‘Environment’. Choose the option ‘From Excel’ and select your exported file. Make sure date fields are imported correctly.</p>
 <p>An example syntax could look like this:</p>
-<div class="sourceCode" id="cb1"><pre class="downlit">
-<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://readxl.tidyverse.org">readxl</a></span><span class="op">)</span>
-<span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://readxl.tidyverse.org/reference/read_excel.html">read_excel</a></span><span class="op">(</span>path <span class="op">=</span> <span class="st">"path/to/your/file.xlsx"</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://readxl.tidyverse.org">readxl</a></span><span class="op">)</span>
+<span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://readxl.tidyverse.org/reference/read_excel.html">read_excel</a></span><span class="op">(</span>path <span class="op">=</span> <span class="st">"path/to/your/file.xlsx"</span><span class="op">)</span></code></pre></div>
 <p>This package comes with an <a href="https://msberends.github.io/AMR/reference/WHONET.html">example data set <code>WHONET</code></a>. We will use it for this analysis.</p>
 </div>
 <div id="preparation" class="section level3">
 <h3 class="hasAnchor">
 <a href="#preparation" class="anchor"></a>Preparation</h3>
 <p>First, load the relevant packages if you did not yet did this. I use the tidyverse for all of my analyses. All of them. If you don’t know it yet, I suggest you read about it on their website: <a href="https://www.tidyverse.org/" class="uri">https://www.tidyverse.org/</a>.</p>
-<div class="sourceCode" id="cb2"><pre class="downlit">
-<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="co"># part of tidyverse</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="http://ggplot2.tidyverse.org">ggplot2</a></span><span class="op">)</span> <span class="co"># part of tidyverse</span>
+<div class="sourceCode" id="cb2"><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="co"># part of tidyverse</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://ggplot2.tidyverse.org">ggplot2</a></span><span class="op">)</span> <span class="co"># part of tidyverse</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>     <span class="co"># this package</span>
-<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/cleaner">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></pre></div>
+<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/cleaner">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></code></pre></div>
 <p>We will have to transform some variables to simplify and automate the analysis:</p>
 <ul>
 <li>Microorganisms should be transformed to our own microorganism IDs (called an <code>mo</code>) using <a href="https://msberends.github.io/AMR/reference/catalogue_of_life">our Catalogue of Life reference data set</a>, which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with <code><a href="../reference/as.mo.html">as.mo()</a></code>. This function also recognises almost all WHONET abbreviations of microorganisms.</li>
 <li>Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values <code>"S"</code>, <code>"I"</code> or <code>"R"</code>. That is exactly where the <code><a href="../reference/as.rsi.html">as.rsi()</a></code> function is for.</li>
 </ul>
-<div class="sourceCode" id="cb3"><pre class="downlit">
-<span class="co"># transform variables</span>
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="co"># transform variables</span>
 <span class="va">data</span> <span class="op">&lt;-</span> <span class="va">WHONET</span> <span class="op">%&gt;%</span>
  <span class="co"># get microbial ID based on given organism</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">Organism</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span> 
  <span class="co"># transform everything from "AMP_ND10" to "CIP_EE" to the new `rsi` class</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">AMP_ND10</span><span class="op">:</span><span class="va">CIP_EE</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span></pre></div>
+  <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">AMP_ND10</span><span class="op">:</span><span class="va">CIP_EE</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span></code></pre></div>
 <p>No errors or warnings, so all values are transformed succesfully.</p>
 <p>We also created a package dedicated to data cleaning and checking, called the <code>cleaner</code> package. Its <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function can be used to create frequency tables.</p>
 <p>So let’s check our data, with a couple of frequency tables:</p>
-<div class="sourceCode" id="cb4"><pre class="downlit">
-<span class="co"># our newly created `mo` variable, put in the mo_name() function</span>
-<span class="va">data</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span>, nmax <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="co"># our newly created `mo` variable, put in the mo_name() function</span>
+<span class="va">data</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span>, nmax <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></code></pre></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: character<br>
 Length: 500<br>
@ -338,10 +337,10 @@ Longest: 40</p>
 </tbody>
 </table>
 <p>(omitted 27 entries, n = 56 [11.20%])</p>
-<div class="sourceCode" id="cb5"><pre class="downlit">
-<span class="co"># our transformed antibiotic columns</span>
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="co"># our transformed antibiotic columns</span>
 <span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span>
-<span class="va">data</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">AMC_ND2</span><span class="op">)</span></pre></div>
+<span class="va">data</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">AMC_ND2</span><span class="op">)</span></code></pre></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: factor &gt; ordered &gt; rsi (numeric)<br>
 Length: 500<br>
@ -392,11 +391,11 @@ Drug group: Beta-lactams/penicillins<br>
 <h3 class="hasAnchor">
 <a href="#a-first-glimpse-at-results" class="anchor"></a>A first glimpse at results</h3>
 <p>An easy <code>ggplot</code> will already give a lot of information, using the included <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> function:</p>
-<div class="sourceCode" id="cb6"><pre class="downlit">
-<span class="va">data</span> <span class="op">%&gt;%</span>
+<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">data</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">Country</span><span class="op">)</span> <span class="op">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">Country</span>, <span class="va">AMP_ND2</span>, <span class="va">AMC_ED20</span>, <span class="va">CAZ_ED10</span>, <span class="va">CIP_ED5</span><span class="op">)</span> <span class="op">%&gt;%</span>
-  <span class="fu"><a href="../reference/ggplot_rsi.html">ggplot_rsi</a></span><span class="op">(</span>translate_ab <span class="op">=</span> <span class="st">'ab'</span>, facet <span class="op">=</span> <span class="st">"Country"</span>, datalabels <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></pre></div>
+  <span class="fu"><a href="../reference/ggplot_rsi.html">ggplot_rsi</a></span><span class="op">(</span>translate_ab <span class="op">=</span> <span class="st">'ab'</span>, facet <span class="op">=</span> <span class="st">"Country"</span>, datalabels <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
 <p><img src="WHONET_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
 </div>
  </div>
--- a/docs/articles/WHONET_files/figure-html/unnamed-chunk-7-1.png
+++ b/docs/articles/WHONET_files/figure-html/unnamed-chunk-7-1.png
--- a/docs/articles/WHONET_files/header-attrs-2.8/header-attrs.js
+++ b/docs/articles/WHONET_files/header-attrs-2.8/header-attrs.js
@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
--- a/docs/articles/benchmarks.html
+++ b/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">1.6.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -187,7 +187,7 @@

      

-      </header><script src="benchmarks_files/header-attrs-2.7/header-attrs.js"></script><div class="row">
+      </header><script src="benchmarks_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
  <div class="col-md-9 contents">
    <div class="page-header toc-ignore">
      <h1 data-toc-skip>Benchmarks</h1>
@ -224,21 +224,34 @@
  <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>, <span class="co"># Methicillin Resistant S. aureus</span>
  <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span>, <span class="co"># Vancomycin Intermediate S. aureus</span>
  times <span class="op">=</span> <span class="fl">25</span><span class="op">)</span>
-<span class="fu"><a href="https://rdrr.io/r/base/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="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
-<span class="co">#                                   expr   min    lq  mean median    uq max neval</span>
-<span class="co">#                           as.mo("sau")   9.6  10.0  12.0     10  11.0  42    25</span>
-<span class="co">#                          as.mo("stau")  52.0  55.0  74.0     59  94.0 110    25</span>
-<span class="co">#                          as.mo("STAU")  51.0  53.0  73.0     57  91.0 100    25</span>
-<span class="co">#                        as.mo("staaur")   9.5   9.9  11.0     10  12.0  13    25</span>
-<span class="co">#                        as.mo("STAAUR")   9.4  10.0  18.0     10  12.0  52    25</span>
-<span class="co">#                     as.mo("S. aureus")  24.0  26.0  31.0     26  29.0  62    25</span>
-<span class="co">#                      as.mo("S aureus")  25.0  25.0  42.0     29  62.0  68    25</span>
-<span class="co">#         as.mo("Staphylococcus aureus")   2.5   2.9   3.2      3   3.5   4    25</span>
-<span class="co">#  as.mo("Staphylococcus aureus (MRSA)") 240.0 240.0 260.0    250 260.0 390    25</span>
-<span class="co">#       as.mo("Sthafilokkockus aaureuz") 150.0 190.0 190.0    190 190.0 250    25</span>
-<span class="co">#                          as.mo("MRSA")   8.7  10.0  15.0     11  12.0  49    25</span>
-<span class="co">#                          as.mo("VISA")  17.0  19.0  25.0     21  22.0  57    25</span></code></pre></div>
+<span class="co">#                                   expr   min    lq  mean median    uq   max</span>
+<span class="co">#                           as.mo("sau")  10.0  11.0  14.0   12.0  13.0  47.0</span>
+<span class="co">#                          as.mo("stau")  53.0  56.0  78.0   58.0  94.0 220.0</span>
+<span class="co">#                          as.mo("STAU")  53.0  54.0  69.0   58.0  92.0  99.0</span>
+<span class="co">#                        as.mo("staaur")  10.0  11.0  15.0   11.0  12.0  47.0</span>
+<span class="co">#                        as.mo("STAAUR")   9.4  11.0  14.0   11.0  12.0  64.0</span>
+<span class="co">#                     as.mo("S. aureus")  24.0  26.0  44.0   33.0  63.0  69.0</span>
+<span class="co">#                      as.mo("S aureus")  24.0  27.0  40.0   30.0  61.0  70.0</span>
+<span class="co">#         as.mo("Staphylococcus aureus")   2.6   3.1   3.2    3.2   3.3   3.8</span>
+<span class="co">#  as.mo("Staphylococcus aureus (MRSA)") 230.0 250.0 250.0  250.0 250.0 280.0</span>
+<span class="co">#       as.mo("Sthafilokkockus aaureuz") 180.0 190.0 200.0  190.0 200.0 330.0</span>
+<span class="co">#                          as.mo("MRSA")  10.0  11.0  16.0   12.0  13.0  47.0</span>
+<span class="co">#                          as.mo("VISA")  17.0  19.0  22.0   19.0  22.0  63.0</span>
+<span class="co">#  neval</span>
+<span class="co">#     25</span>
+<span class="co">#     25</span>
+<span class="co">#     25</span>
+<span class="co">#     25</span>
+<span class="co">#     25</span>
+<span class="co">#     25</span>
+<span class="co">#     25</span>
+<span class="co">#     25</span>
+<span class="co">#     25</span>
+<span class="co">#     25</span>
+<span class="co">#     25</span>
+<span class="co">#     25</span></code></pre></div>
 <p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="750"></p>
 <p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 200 times slower to determine.</p>
 <p>To improve performance, we implemented two important algorithms to save unnecessary calculations: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
@ -260,8 +273,8 @@
 <span class="co"># what do these values look like? They are of class &lt;mo&gt;:</span>
 <span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
 <span class="co"># Class &lt;mo&gt;</span>
-<span class="co"># [1] B_KLBSL_PNMN B_STPHY_EPDR B_STRPT_PNMN B_STRPT_EQNS B_ESCHR_COLI</span>
-<span class="co"># [6] B_KLBSL_PNMN</span>
+<span class="co"># [1] B_STRPT_PNMN B_STPHY_CONS B_ESCHR_COLI B_STRPT_PNMN B_ESCHR_COLI</span>
+<span class="co"># [6] B_ENTRC_FCLS</span>
  
 <span class="co"># as the example_isolates data set has 2,000 rows, we should have 2 million items</span>
 <span class="fu"><a href="https://rdrr.io/r/base/length.html">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
@ -274,11 +287,11 @@
 <span class="co"># now let's see:</span>
 <span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>,
                         times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
-<span class="fu"><a href="https://rdrr.io/r/base/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="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) 155 182  233    228 242 350    10</span></code></pre></div>
-<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.228 seconds. That is 114 nanoseconds on average. You only lose time on your unique input values.</p>
+<span class="co">#  mo_name(x) 180 186  215    221 222 281    10</span></code></pre></div>
+<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.221 seconds. That is 110 nanoseconds on average. You only lose time on your unique input values.</p>
 </div>
 <div id="precalculated-results" class="section level3">
 <h3 class="hasAnchor">
@ -289,13 +302,13 @@
                         B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>,
                         C <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span>,
                         times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
-<span class="fu"><a href="https://rdrr.io/r/base/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="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  6.62  6.84  7.30   6.91  8.10  8.74    10</span>
-<span class="co">#     B 22.20 23.10 33.20  24.50 27.70 70.80    10</span>
-<span class="co">#     C  1.37  1.50  1.66   1.71  1.81  1.84    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 0.0017 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
+<span class="co">#     A  7.45  7.68  8.13   8.23  8.39  8.95    10</span>
+<span class="co">#     B 22.70 22.90 31.30  23.90 26.50 62.00    10</span>
+<span class="co">#     C  1.51  1.58  1.79   1.84  1.97  1.99    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 0.0018 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
                         B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"Staphylococcus"</span><span class="op">)</span>,
@ -306,17 +319,17 @@
                         G <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_phylum</a></span><span class="op">(</span><span class="st">"Firmicutes"</span><span class="op">)</span>,
                         H <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span><span class="op">(</span><span class="st">"Bacteria"</span><span class="op">)</span>,
                         times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
-<span class="fu"><a href="https://rdrr.io/r/base/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="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 1.19 1.21 1.43   1.28 1.65 2.03    10</span>
-<span class="co">#     B 1.19 1.24 1.38   1.26 1.53 1.83    10</span>
-<span class="co">#     C 1.24 1.28 1.45   1.36 1.41 2.24    10</span>
-<span class="co">#     D 1.20 1.22 1.33   1.23 1.41 1.77    10</span>
-<span class="co">#     E 1.21 1.22 1.35   1.27 1.38 1.69    10</span>
-<span class="co">#     F 1.20 1.21 1.34   1.26 1.37 1.71    10</span>
-<span class="co">#     G 1.17 1.22 1.31   1.27 1.31 1.71    10</span>
-<span class="co">#     H 1.21 1.27 1.42   1.37 1.47 1.84    10</span></code></pre></div>
+<span class="co">#     A 1.44 1.44 1.51   1.46 1.56 1.68    10</span>
+<span class="co">#     B 1.37 1.40 1.53   1.48 1.67 1.81    10</span>
+<span class="co">#     C 1.42 1.47 1.61   1.59 1.68 1.84    10</span>
+<span class="co">#     D 1.39 1.43 1.52   1.46 1.53 1.92    10</span>
+<span class="co">#     E 1.41 1.46 1.58   1.50 1.70 1.91    10</span>
+<span class="co">#     F 1.36 1.44 1.49   1.46 1.57 1.64    10</span>
+<span class="co">#     G 1.37 1.44 1.64   1.48 1.82 2.40    10</span>
+<span class="co">#     H 1.41 1.43 1.52   1.48 1.54 1.87    10</span></code></pre></div>
 <p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package contains all phyla of all known bacteria, it can just return the initial value immediately.</p>
 </div>
 <div id="results-in-other-languages" class="section level3">
@ -341,16 +354,16 @@
                         fr <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"fr"</span><span class="op">)</span>,
                         pt <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"pt"</span><span class="op">)</span>,
                         times <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
-<span class="fu"><a href="https://rdrr.io/r/base/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="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
 <span class="co">#  expr   min    lq  mean median    uq    max neval</span>
-<span class="co">#    en 17.19 17.50 22.00  17.76 18.54  61.02   100</span>
-<span class="co">#    de 31.08 31.53 39.66  32.04 35.34  76.23   100</span>
-<span class="co">#    nl 30.19 31.41 40.64  32.30 35.93  79.53   100</span>
-<span class="co">#    es 30.50 31.33 41.70  31.84 35.90 181.80   100</span>
-<span class="co">#    it 20.94 21.37 25.27  21.63 22.44  69.84   100</span>
-<span class="co">#    fr 20.62 21.00 27.09  21.41 23.12  79.50   100</span>
-<span class="co">#    pt 20.41 21.23 25.33  21.56 22.22  70.65   100</span></code></pre></div>
+<span class="co">#    en 17.63 17.96 22.55  18.30 18.78  68.16   100</span>
+<span class="co">#    de 28.48 28.93 33.83  29.18 29.85  76.90   100</span>
+<span class="co">#    nl 32.10 33.11 43.48  33.70 35.84 202.50   100</span>
+<span class="co">#    es 32.17 32.67 43.51  33.33 66.07  78.29   100</span>
+<span class="co">#    it 21.95 22.29 26.55  22.59 23.13  70.41   100</span>
+<span class="co">#    fr 21.59 21.94 25.36  22.31 22.88  63.46   100</span>
+<span class="co">#    pt 21.75 22.15 28.50  22.48 23.01  68.10   100</span></code></pre></div>
 <p>Currently supported non-English languages are German, Dutch, Spanish, Italian, French and Portuguese.</p>
 </div>
  </div>
--- a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png
+++ b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png
--- a/docs/articles/benchmarks_files/header-attrs-2.8/header-attrs.js
+++ b/docs/articles/benchmarks_files/header-attrs-2.8/header-attrs.js
@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
--- a/docs/articles/datasets.html
+++ b/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">1.6.0.9060</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -192,7 +192,7 @@
    <div class="page-header toc-ignore">
      <h1 data-toc-skip>Data sets for download / own use</h1>
            
-            <h4 class="date">22 May 2021</h4>
+            <h4 class="date">26 May 2021</h4>
      
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
      <div class="hidden name"><code>datasets.Rmd</code></div>
--- a/docs/articles/index.html
+++ b/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">1.6.0.9060</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

--- a/docs/articles/resistance_predict.html
+++ b/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">1.6.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -47,14 +47,14 @@
      <ul class="nav navbar-nav">
 <li>
  <a href="../index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -63,77 +63,77 @@
  <ul class="dropdown-menu" role="menu">
 <li>
      <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="../articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="../articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="../articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="../reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="../articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -142,21 +142,21 @@
 </li>
 <li>
  <a href="../reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="../authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="../news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -165,14 +165,14 @@
 <ul class="nav navbar-nav navbar-right">
 <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
@ -187,8 +187,7 @@

      

-      </header><link href="resistance_predict_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
-<script src="resistance_predict_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
+      </header><script src="resistance_predict_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
  <div class="col-md-9 contents">
    <div class="page-header toc-ignore">
      <h1 data-toc-skip>How to predict antimicrobial resistance</h1>
@ -206,37 +205,37 @@
 <a href="#needed-r-packages" class="anchor"></a>Needed R packages</h2>
 <p>As with many uses in R, we need some additional packages for AMR data analysis. Our package works closely together with the <a href="https://www.tidyverse.org">tidyverse packages</a> <a href="https://dplyr.tidyverse.org/"><code>dplyr</code></a> and <a href="https://ggplot2.tidyverse.org"><code>ggplot2</code></a> by Dr Hadley Wickham. The tidyverse tremendously improves the way we conduct data science - it allows for a very natural way of writing syntaxes and creating beautiful plots in R.</p>
 <p>Our <code>AMR</code> package depends on these packages and even extends their use and functions.</p>
-<div class="sourceCode" id="cb1"><pre class="downlit">
-<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="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="http://ggplot2.tidyverse.org">ggplot2</a></span><span class="op">)</span>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
+<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org">ggplot2</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://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>

 <span class="co"># (if not yet installed, install with:)</span>
-<span class="co"># install.packages(c("tidyverse", "AMR"))</span></pre></div>
+<span class="co"># install.packages(c("tidyverse", "AMR"))</span></code></pre></div>
 </div>
 <div id="prediction-analysis" class="section level2">
 <h2 class="hasAnchor">
 <a href="#prediction-analysis" class="anchor"></a>Prediction analysis</h2>
 <p>Our package contains a function <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>, which takes the same input as functions for <a href="./AMR.html">other AMR data analysis</a>. Based on a date column, it calculates cases per year and uses a regression model to predict antimicrobial resistance.</p>
 <p>It is basically as easy as:</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="co"># resistance prediction of piperacillin/tazobactam (TZP):</span></a>
-<a class="sourceLine" id="cb2-2" title="2"><span class="kw">resistance_predict</span>(<span class="dt">tbl =</span> example_isolates, <span class="dt">col_date =</span> <span class="st">"date"</span>, <span class="dt">col_ab =</span> <span class="st">"TZP"</span>, <span class="dt">model =</span> <span class="st">"binomial"</span>)</a>
-<a class="sourceLine" id="cb2-3" title="3"></a>
-<a class="sourceLine" id="cb2-4" title="4"><span class="co"># or:</span></a>
-<a class="sourceLine" id="cb2-5" title="5">example_isolates <span class="op">%&gt;%</span><span class="st"> </span></a>
-<a class="sourceLine" id="cb2-6" title="6"><span class="st">  </span><span class="kw">resistance_predict</span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>,</a>
-<a class="sourceLine" id="cb2-7" title="7">                     model  <span class="st">"binomial"</span>)</a>
-<a class="sourceLine" id="cb2-8" title="8"></a>
-<a class="sourceLine" id="cb2-9" title="9"><span class="co"># to bind it to object 'predict_TZP' for example:</span></a>
-<a class="sourceLine" id="cb2-10" title="10">predict_TZP &lt;-<span class="st"> </span>example_isolates <span class="op">%&gt;%</span><span class="st"> </span></a>
-<a class="sourceLine" id="cb2-11" title="11"><span class="st">  </span><span class="kw">resistance_predict</span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>,</a>
-<a class="sourceLine" id="cb2-12" title="12">                     <span class="dt">model =</span> <span class="st">"binomial"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="co"># resistance prediction of piperacillin/tazobactam (TZP):</span></span>
+<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="fu">resistance_predict</span>(<span class="at">tbl =</span> example_isolates, <span class="at">col_date =</span> <span class="st">"date"</span>, <span class="at">col_ab =</span> <span class="st">"TZP"</span>, <span class="at">model =</span> <span class="st">"binomial"</span>)</span>
+<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a><span class="co"># or:</span></span>
+<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a>example_isolates <span class="sc">%&gt;%</span> </span>
+<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a>  <span class="fu">resistance_predict</span>(<span class="at">col_ab =</span> <span class="st">"TZP"</span>,</span>
+<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a>                     model  <span class="st">"binomial"</span>)</span>
+<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a><span class="co"># to bind it to object 'predict_TZP' for example:</span></span>
+<span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a>predict_TZP <span class="ot">&lt;-</span> example_isolates <span class="sc">%&gt;%</span> </span>
+<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a>  <span class="fu">resistance_predict</span>(<span class="at">col_ab =</span> <span class="st">"TZP"</span>,</span>
+<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a>                     <span class="at">model =</span> <span class="st">"binomial"</span>)</span></code></pre></div>
 <p>The function will look for a date column itself if <code>col_date</code> is not set.</p>
 <p>When running any of these commands, a summary of the regression model will be printed unless using <code><a href="../reference/resistance_predict.html">resistance_predict(..., info = FALSE)</a></code>.</p>
 <pre><code># ℹ Using column 'date' as input for `col_date`.</code></pre>
 <p>This text is only a printed summary - the actual result (output) of the function is a <code>data.frame</code> containing for each year: the number of observations, the actual observed resistance, the estimated resistance and the standard error below and above the estimation:</p>
-<div class="sourceCode" id="cb4"><pre class="downlit">
-<span class="va">predict_TZP</span>
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">predict_TZP</span>
 <span class="co">#    year      value    se_min    se_max observations   observed  estimated</span>
 <span class="co"># 1  2002 0.20000000        NA        NA           15 0.20000000 0.05616378</span>
 <span class="co"># 2  2003 0.06250000        NA        NA           32 0.06250000 0.06163839</span>
@ -267,30 +266,31 @@
 <span class="co"># 27 2028 0.43730688 0.3418075 0.5328063           NA         NA 0.43730688</span>
 <span class="co"># 28 2029 0.46175755 0.3597639 0.5637512           NA         NA 0.46175755</span>
 <span class="co"># 29 2030 0.48639359 0.3782932 0.5944939           NA         NA 0.48639359</span>
-<span class="co"># 30 2031 0.51109592 0.3973697 0.6248221           NA         NA 0.51109592</span></pre></div>
+<span class="co"># 30 2031 0.51109592 0.3973697 0.6248221           NA         NA 0.51109592</span></code></pre></div>
 <p>The function <code>plot</code> is available in base R, and can be extended by other packages to depend the output based on the type of input. We extended its function to cope with resistance predictions:</p>
-<div class="sourceCode" id="cb5"><pre class="downlit">
-<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span></code></pre></div>
 <p><img src="resistance_predict_files/figure-html/unnamed-chunk-4-1.png" width="720"></p>
 <p>This is the fastest way to plot the result. It automatically adds the right axes, error bars, titles, number of available observations and type of model.</p>
 <p>We also support the <code>ggplot2</code> package with our custom function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> to create more appealing plots:</p>
-<div class="sourceCode" id="cb6"><pre class="downlit">
-<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span></code></pre></div>
 <p><img src="resistance_predict_files/figure-html/unnamed-chunk-5-1.png" width="720"></p>
-<div class="sourceCode" id="cb7"><pre class="downlit">
-
+<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
+<code class="sourceCode R">
 <span class="co"># choose for error bars instead of a ribbon</span>
-<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="va">predict_TZP</span>, ribbon <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></pre></div>
+<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="va">predict_TZP</span>, ribbon <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
 <p><img src="resistance_predict_files/figure-html/unnamed-chunk-5-2.png" width="720"></p>
 <div id="choosing-the-right-model" class="section level3">
 <h3 class="hasAnchor">
 <a href="#choosing-the-right-model" class="anchor"></a>Choosing the right model</h3>
 <p>Resistance is not easily predicted; if we look at vancomycin resistance in Gram-positive bacteria, the spread (i.e. standard error) is enormous:</p>
-<div class="sourceCode" id="cb8"><pre class="downlit">
-<span class="va">example_isolates</span> <span class="op">%&gt;%</span>
+<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">example_isolates</span> <span class="op">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op">%&gt;%</span>
  <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"binomial"</span><span class="op">)</span> <span class="op">%&gt;%</span> 
-  <span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span></pre></div>
+  <span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span>
+<span class="co"># ℹ Using column 'date' as input for `col_date`.</span></code></pre></div>
 <p><img src="resistance_predict_files/figure-html/unnamed-chunk-6-1.png" width="720"></p>
 <p>Vancomycin resistance could be 100% in ten years, but might also stay around 0%.</p>
 <p>You can define the model with the <code>model</code> parameter. The model chosen above is a generalised linear regression model using a binomial distribution, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance.</p>
@ -331,16 +331,17 @@
 </tbody>
 </table>
 <p>For the vancomycin resistance in Gram-positive bacteria, a linear model might be more appropriate since no binomial distribution is to be expected based on the observed years:</p>
-<div class="sourceCode" id="cb9"><pre class="downlit">
-<span class="va">example_isolates</span> <span class="op">%&gt;%</span>
+<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">example_isolates</span> <span class="op">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op">%&gt;%</span>
  <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"linear"</span><span class="op">)</span> <span class="op">%&gt;%</span> 
-  <span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span></pre></div>
+  <span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span>
+<span class="co"># ℹ Using column 'date' as input for `col_date`.</span></code></pre></div>
 <p><img src="resistance_predict_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
 <p>This seems more likely, doesn’t it?</p>
 <p>The model itself is also available from the object, as an <code>attribute</code>:</p>
-<div class="sourceCode" id="cb10"><pre class="downlit">
-<span class="va">model</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/attributes.html">attributes</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span><span class="op">$</span><span class="va">model</span>
+<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">model</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/attributes.html">attributes</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span><span class="op">$</span><span class="va">model</span>

 <span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">$</span><span class="va">family</span>
 <span class="co"># </span>
@ -350,7 +351,7 @@
 <span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">$</span><span class="va">coefficients</span>
 <span class="co">#                  Estimate  Std. Error   z value     Pr(&gt;|z|)</span>
 <span class="co"># (Intercept) -200.67944891 46.17315349 -4.346237 1.384932e-05</span>
-<span class="co"># year           0.09883005  0.02295317  4.305725 1.664395e-05</span></pre></div>
+<span class="co"># year           0.09883005  0.02295317  4.305725 1.664395e-05</span></code></pre></div>
 </div>
 </div>
  </div>
--- a/docs/articles/resistance_predict_files/figure-html/unnamed-chunk-4-1.png
+++ b/docs/articles/resistance_predict_files/figure-html/unnamed-chunk-4-1.png
--- a/docs/articles/resistance_predict_files/figure-html/unnamed-chunk-5-1.png
+++ b/docs/articles/resistance_predict_files/figure-html/unnamed-chunk-5-1.png
--- a/docs/articles/resistance_predict_files/figure-html/unnamed-chunk-5-2.png
+++ b/docs/articles/resistance_predict_files/figure-html/unnamed-chunk-5-2.png
--- a/docs/articles/resistance_predict_files/figure-html/unnamed-chunk-6-1.png
+++ b/docs/articles/resistance_predict_files/figure-html/unnamed-chunk-6-1.png
--- a/docs/articles/resistance_predict_files/figure-html/unnamed-chunk-7-1.png
+++ b/docs/articles/resistance_predict_files/figure-html/unnamed-chunk-7-1.png
--- a/docs/articles/resistance_predict_files/header-attrs-2.8/header-attrs.js
+++ b/docs/articles/resistance_predict_files/header-attrs-2.8/header-attrs.js
@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
--- a/docs/articles/welcome_to_AMR.html
+++ b/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">1.6.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -47,14 +47,14 @@
      <ul class="nav navbar-nav">
 <li>
  <a href="../index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -63,77 +63,77 @@
  <ul class="dropdown-menu" role="menu">
 <li>
      <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="../articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="../articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="../articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="../reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="../articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -142,21 +142,21 @@
 </li>
 <li>
  <a href="../reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="../authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="../news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -165,14 +165,14 @@
 <ul class="nav navbar-nav navbar-right">
 <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
@ -187,8 +187,7 @@

      

-      </header><link href="welcome_to_AMR_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
-<script src="welcome_to_AMR_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
+      </header><script src="welcome_to_AMR_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
  <div class="col-md-9 contents">
    <div class="page-header toc-ignore">
      <h1 data-toc-skip>Welcome to the AMR package</h1>
--- a/docs/articles/welcome_to_AMR_files/header-attrs-2.8/header-attrs.js
+++ b/docs/articles/welcome_to_AMR_files/header-attrs-2.8/header-attrs.js
@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
--- a/docs/authors.html
+++ b/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">1.6.0.9060</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -241,7 +241,7 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
    <pre>@Article{,
  title = {AMR - An R Package for Working with Antimicrobial Resistance Data},
  author = {M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner},
-  doi = {1.24720276528394e-05},
+  doi = {10.1101/810622},
  journal = {Journal of Statistical Software},
  pages = {Accepted for publication},
  year = {2021},
--- a/docs/extra.css
+++ b/docs/extra.css
@ -222,6 +222,9 @@ table a:not(.btn) {
 table a:not(.btn):hover {
  text-decoration: underline;
 }
+.template-article thead th {
+  text-align: inherit;
+}

 /* text below header in manual overview */
 .template-reference-index h2 ~ p {
--- a/docs/index.html
+++ b/docs/index.html
@ -42,7 +42,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9060</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -376,11 +376,11 @@
 <div id="latest-released-version" class="section level4">
 <h4 class="hasAnchor">
 <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>
+<p>This package is available on the <a href="https://ropensci.org/r-universe/">rOpenSci R-universe platform</a>, as CRAN does not allow frequent updates of large packages. With CRAN, we cannot update this package frequently enough to implement the latest EUCAST/CLSI guidelines or the latest microbial taxonomy.</p>
+<p>Install this package in R by using the command:</p>
 <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>
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span>, repos <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span></code></pre></div>
+<p>It will be downloaded and installed automatically.</p>
 <p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
 </div>
 <div id="latest-development-version" class="section level4">
@ -411,7 +411,7 @@
 <div id="antimicrobial-reference-data" class="section level4">
 <h4 class="hasAnchor">
 <a href="#antimicrobial-reference-data" class="anchor"></a>Antimicrobial reference data</h4>
-<p>This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="uri">https://www.whocc.no</a>) and the <a href="http://ec.europa.eu/health/documents/community-register/html/atc.htm">Pharmaceuticals Community Register of the European Commission</a>.</p>
+<p>This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="uri">https://www.whocc.no</a>) and the <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm">Pharmaceuticals Community Register of the European Commission</a>.</p>
 <p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href="https://www.whocc.no/copyright_disclaimer/" class="uri">https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
 <p>Read more about the data from WHOCC <a href="./reference/WHOCC.html">in our manual</a>.</p>
 </div>
--- a/docs/news/index.html
+++ b/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">1.6.0.9060</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -236,13 +236,9 @@
      <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
    </div>

-    <div id="amr-1609060" class="section level1">
-<h1 class="page-header" data-toc-text="1.6.0.9060">
-<a href="#amr-1609060" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9060</h1>
-<div id="last-updated-22-may-2021" class="section level2">
-<h2 class="hasAnchor">
-<a href="#last-updated-22-may-2021" class="anchor"></a><small>Last updated: 22 May 2021</small>
-</h2>
+    <div id="amr-170" class="section level1">
+<h1 class="page-header" data-toc-text="1.7.0">
+<a href="#amr-170" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.0</h1>
 <div id="breaking-change" class="section level3">
 <h3 class="hasAnchor">
 <a href="#breaking-change" class="anchor"></a>Breaking change</h3>
@ -288,7 +284,7 @@
 </ul>
 </li>
 <li>Function <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code> as additional antbiotic column selector and function <code><a href="../reference/AMR-deprecated.html">filter_betalactams()</a></code> as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.</li>
-<li>A <code>ggplot()</code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
+<li>A <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
 </li>
 </ul>
 </div>
@ -335,6 +331,9 @@
 <li>Antibiotic class selectors (such as <code><a href="../reference/antibiotic_class_selectors.html">cephalosporins()</a></code>) now maintain the column order from the original data</li>
 <li>Fix for selecting columns using <code><a href="../reference/antibiotic_class_selectors.html">fluoroquinolones()</a></code>
 </li>
+<li>
+<code><a href="../reference/age.html">age()</a></code> now vectorises over both <code>x</code> and <code>reference</code>
+</li>
 </ul>
 </div>
 <div id="other" class="section level3">
@ -344,7 +343,6 @@
 <li>All unit tests are now processed by the <code>tinytest</code> package, instead of the <code>testthat</code> package. The <code>testthat</code> package unfortunately requires tons of dependencies that are also heavy and only usable for recent R versions, disallowing developers to test a package under any R 3.* version. On the contrary, the <code>tinytest</code> package is very lightweight and dependency-free.</li>
 </ul>
 </div>
-</div>
 </div>
    <div id="amr-160" class="section level1">
 <h1 class="page-header" data-toc-text="1.6.0">
@ -384,7 +382,7 @@
 <span class="co">#&gt; Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
 </li>
 <li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
-<li><p><code>ggplot()</code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
+<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
 <li>
 <p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
@ -441,7 +439,7 @@
 <li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
 <li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
 <li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
-<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
+<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
 </ul>
 </li>
 <li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>
@ -793,7 +791,7 @@
 <p>Making this package independent of especially the tidyverse (e.g. packages <code>dplyr</code> and <code>tidyr</code>) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.</p>
 <p>Negative effects of this change are:</p>
 <ul>
-<li>Function <code>freq()</code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code>freq()</code>.</li>
+<li>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>.</li>
 <li><del>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code>&lt;ord&gt;</code>, not <code>&lt;rsi&gt;</code> anymore. This is purely a visual effect.</del></li>
 <li><del>All functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</del></li>
 <li>For developers: classes <code>mo</code> and <code>ab</code> now both also inherit class <code>character</code>, to support any data transformation. This change invalidates code that checks for class length == 1.</li>
@ -1125,7 +1123,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <span class="co">#&gt; invalid microorganism code, NA generated</span></code></pre></div>
 <p>This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</p>
 </li>
-<li><p>Function <code>freq()</code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code>freq()</code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
+<li><p>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
 <li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
 </ul>
 </div>
@ -1392,7 +1390,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>The <code><a href="../reference/age.html">age()</a></code> function gained a new argument <code>exact</code> to determine ages with decimals</li>
 <li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code><a href="../reference/as.rsi.html">rsi()</a></code>
 </li>
-<li>Frequency tables (<code>freq()</code>):
+<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>):
 <ul>
 <li><p>speed improvement for microbial IDs</p></li>
 <li><p>fixed factor level names for R Markdown</p></li>
@ -1402,12 +1400,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span> 
-  <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span> 
+  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span>
 <span class="co"># grouped boxplots:</span>
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span> 
-  <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span>
+  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span>
  <span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
 </li>
 </ul>
@ -1417,7 +1415,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
 </li>
 <li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
-<li>Fix for <code>freq()</code> for when all values are <code>NA</code>
+<li>Fix for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> for when all values are <code>NA</code>
 </li>
 <li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
 <li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
@ -1574,7 +1572,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </ul>
 </li>
 <li>Removed data sets <code>microorganisms.oldDT</code>, <code>microorganisms.prevDT</code>, <code>microorganisms.unprevDT</code> and <code>microorganismsDT</code> since they were no longer needed and only contained info already available in the <code>microorganisms</code> data set</li>
-<li>Added 65 antibiotics to the <code>antibiotics</code> data set, from the <a href="http://ec.europa.eu/health/documents/community-register/html/atc.htm">Pharmaceuticals Community Register</a> of the European Commission</li>
+<li>Added 65 antibiotics to the <code>antibiotics</code> data set, from the <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm">Pharmaceuticals Community Register</a> of the European Commission</li>
 <li>Removed columns <code>atc_group1_nl</code> and <code>atc_group2_nl</code> from the <code>antibiotics</code> data set</li>
 <li>Functions <code>atc_ddd()</code> and <code>atc_groups()</code> have been renamed <code><a href="../reference/atc_online_property.html">atc_online_ddd()</a></code> and <code><a href="../reference/atc_online_property.html">atc_online_groups()</a></code>. The old functions are deprecated and will be removed in a future version.</li>
 <li>Function <code>guess_mo()</code> is now deprecated in favour of <code><a href="../reference/as.mo.html">as.mo()</a></code> and will be removed in future versions</li>
@ -1656,7 +1654,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 </ul>
 </li>
-<li>Frequency tables (<code>freq()</code> function):
+<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function):
 <ul>
 <li>
 <p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
@ -1666,15 +1664,15 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <span class="co"># OLD WAY</span>
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
-  <span class="fu">freq</span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
+  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
 <span class="co"># NEW WAY</span>
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span> 
-  <span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
+  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>

 <span class="co"># Even supports grouping variables:</span>
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span> <span class="op">%&gt;%</span> 
-  <span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
 </li>
 <li><p>Header info is now available as a list, with the <code>header</code> function</p></li>
 <li><p>The argument <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</p></li>
@ -1756,7 +1754,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Using <code>portion_*</code> functions now throws a warning when total available isolate is below argument <code>minimum</code></p></li>
 <li><p>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</p></li>
 <li>
-<p>Frequency tables - <code>freq()</code>:</p>
+<p>Frequency tables - <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>:</p>
 <ul>
 <li>
 <p>Support for grouping variables, test with:</p>
@ -1764,14 +1762,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span> 
-  <span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
+  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
 </li>
 <li>
 <p>Support for (un)selecting columns:</p>
 <div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span> 
-  <span class="fu">freq</span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span> 
+  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">count</span>, <span class="op">-</span><span class="va">cum_count</span><span class="op">)</span> <span class="co"># only get item, percent, cum_percent</span></code></pre></div>
 </li>
 <li><p>Check for <code><a href="https://hms.tidyverse.org/reference/Deprecated.html">hms::is.hms</a></code></p></li>
@ -1789,7 +1787,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Removed diacritics from all authors (columns <code>microorganisms$ref</code> and <code>microorganisms.old$ref</code>) to comply with CRAN policy to only allow ASCII characters</p></li>
 <li><p>Fix for <code>mo_property</code> not working properly</p></li>
 <li><p>Fix for <code>eucast_rules</code> where some Streptococci would become ceftazidime R in EUCAST rule 4.5</p></li>
-<li><p>Support for named vectors of class <code>mo</code>, useful for <code>top_freq()</code></p></li>
+<li><p>Support for named vectors of class <code>mo</code>, useful for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">top_freq()</a></code></p></li>
 <li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> argument</p></li>
 <li>
 <p>AI improvements for <code>as.mo</code>:</p>
@ -1956,13 +1954,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <div class="sourceCode" id="cb49"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="va">age</span>, <span class="va">gender</span><span class="op">)</span>, ncol <span class="op">=</span> <span class="fl">2</span><span class="op">)</span><span class="op">)</span>
-<span class="fu">freq</span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
+<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
 <p>For lists, subsetting is possible:</p>
 <div class="sourceCode" id="cb50"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span>age <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">age</span>, gender <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">gender</span><span class="op">)</span>
-<span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
-<span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
+<span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
+<span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
 </li>
 </ul>
 </div>
@ -2035,13 +2033,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>A vignette to explain its usage</li>
 <li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li>
-<li>Support for <code>table</code> to use as input: <code>freq(table(x, y))</code>
+<li>Support for <code>table</code> to use as input: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(table(x, y))</a></code>
 </li>
 <li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><a href="https://rdrr.io/r/graphics/hist.html">hist(freq(df$age))</a></code>
 </li>
 <li>Support for <code>as.vector</code>, <code>as.data.frame</code>, <code>as_tibble</code> and <code>format</code>
 </li>
-<li>Support for quasiquotation: <code>freq(mydata, mycolumn)</code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
+<li>Support for quasiquotation: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
 </li>
 <li>Function <code>top_freq</code> function to return the top/below <em>n</em> items as vector</li>
 <li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li>
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@ -1,4 +1,4 @@
-pandoc: 2.11.2
+pandoc: 2.11.4
 pkgdown: 1.6.1
 pkgdown_sha: ~
 articles:
@ -12,7 +12,7 @@ articles:
  datasets: datasets.html
  resistance_predict: resistance_predict.html
  welcome_to_AMR: welcome_to_AMR.html
-last_built: 2021-05-22T07:53Z
+last_built: 2021-05-26T09:09Z
 urls:
  reference: https://msberends.github.io/AMR//reference
  article: https://msberends.github.io/AMR//articles
--- a/docs/reference/AMR-deprecated.html
+++ b/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">1.6.0.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

--- a/docs/reference/AMR.html
+++ b/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">1.6.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -90,14 +90,14 @@
      <ul class="nav navbar-nav">
        <li>
  <a href="../index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -106,77 +106,77 @@
  <ul class="dropdown-menu" role="menu">
    <li>
      <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="../articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="../articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="../articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="../reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="../articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -185,21 +185,21 @@
 </li>
 <li>
  <a href="../reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="../authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="../news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -208,14 +208,14 @@
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
--- a/docs/reference/WHOCC.html
+++ b/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">1.6.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -90,14 +90,14 @@
      <ul class="nav navbar-nav">
        <li>
  <a href="../index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -106,77 +106,77 @@
  <ul class="dropdown-menu" role="menu">
    <li>
      <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="../articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="../articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="../articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="../reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="../articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -185,21 +185,21 @@
 </li>
 <li>
  <a href="../reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="../authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="../news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -208,14 +208,14 @@
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
@ -249,7 +249,7 @@
    

 <p><img src='figures/logo_who.png' height=60px style=margin-bottom:5px /> <br />
-This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>).</p>
+This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm'>https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a>).</p>
 <p>These have become the gold standard for international drug utilisation monitoring and research.</p>
 <p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
 <p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.</strong> See <a href='https://www.whocc.no/copyright_disclaimer/.'>https://www.whocc.no/copyright_disclaimer/.</a></p>
--- a/docs/reference/WHONET.html
+++ b/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">1.6.0.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

--- a/docs/reference/ab_from_text.html
+++ b/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">1.6.0.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

--- a/docs/reference/ab_property.html
+++ b/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">1.6.0.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -332,7 +332,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s

 <p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href='https://www.whocc.no/atc_ddd_index/'>https://www.whocc.no/atc_ddd_index/</a></p>
 <p>WHONET 2019 software: <a href='http://www.whonet.org/software.html'>http://www.whonet.org/software.html</a></p>
-<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a></p>
+<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href='https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm'>https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a></p>
    <h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference Data Publicly Available</h2>

    
--- a/docs/reference/age.html
+++ b/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">1.6.0.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -249,11 +249,11 @@
    <colgroup><col class="name" /><col class="desc" /></colgroup>
    <tr>
      <th>x</th>
-      <td><p>date(s), will be coerced with <code><a href='https://rdrr.io/r/base/as.POSIXlt.html'>as.POSIXlt()</a></code></p></td>
+      <td><p>date(s), <a href='https://rdrr.io/r/base/character.html'>character</a> (vectors) will be coerced with <code><a href='https://rdrr.io/r/base/as.POSIXlt.html'>as.POSIXlt()</a></code></p></td>
    </tr>
    <tr>
      <th>reference</th>
-      <td><p>reference date(s) (defaults to today), will be coerced with <code><a href='https://rdrr.io/r/base/as.POSIXlt.html'>as.POSIXlt()</a></code></p></td>
+      <td><p>reference date(s) (defaults to today), <a href='https://rdrr.io/r/base/character.html'>character</a> (vectors) will be coerced with <code><a href='https://rdrr.io/r/base/as.POSIXlt.html'>as.POSIXlt()</a></code></p></td>
    </tr>
    <tr>
      <th>exact</th>
@ -275,6 +275,7 @@
    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>

    <p>Ages below 0 will be returned as <code>NA</code> with a warning. Ages above 120 will only give a warning.</p>
+<p>This function vectorises over both <code>x</code> and <code>reference</code>, meaning that either can have a length of 1 while the other argument has a larger length.</p>
    <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>

    
--- a/docs/reference/age_groups.html
+++ b/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">1.6.0.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

--- a/docs/reference/antibiotic_class_selectors.html
+++ b/docs/reference/antibiotic_class_selectors.html
@ -83,7 +83,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -281,7 +281,7 @@
    <colgroup><col class="name" /><col class="desc" /></colgroup>
    <tr>
      <th>ab_class</th>
-      <td><p>an antimicrobial class, like <code>"carbapenems"</code>. The columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code> of the <a href='antibiotics.html'>antibiotics</a> data set will be searched (case-insensitive) for this value.</p></td>
+      <td><p>an antimicrobial class, such as <code>"carbapenems"</code>. The columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code> of the <a href='antibiotics.html'>antibiotics</a> data set will be searched (case-insensitive) for this value.</p></td>
    </tr>
    <tr>
      <th>only_rsi_columns</th>
@ -342,7 +342,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s


 <span class='co'># dplyr -------------------------------------------------------------------</span>
-
+<span class='co'># \donttest{</span>
 <span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>

  <span class='co'># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</span>
@ -391,6 +391,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
  <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span>
  <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span>, <span class='op'>~</span><span class='va'>.x</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span><span class='op'>)</span>
 <span class='op'>}</span>
+<span class='co'># }</span>
 </pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
--- a/docs/reference/antibiotics.html
+++ b/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">1.6.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -90,14 +90,14 @@
      <ul class="nav navbar-nav">
        <li>
  <a href="../index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -106,77 +106,77 @@
  <ul class="dropdown-menu" role="menu">
    <li>
      <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="../articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="../articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="../articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="../reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="../articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -185,21 +185,21 @@
 </li>
 <li>
  <a href="../reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="../authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="../news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -208,14 +208,14 @@
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
@ -290,7 +290,7 @@

    <p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <a href='https://www.whocc.no/atc_ddd_index/'>https://www.whocc.no/atc_ddd_index/</a></p>
 <p>WHONET 2019 software: <a href='http://www.whonet.org/software.html'>http://www.whonet.org/software.html</a></p>
-<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a></p>
+<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href='https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm'>https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a></p>
    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>

    <p>Properties that are based on an ATC code are only available when an ATC is available. These properties are: <code>atc_group1</code>, <code>atc_group2</code>, <code>oral_ddd</code>, <code>oral_units</code>, <code>iv_ddd</code> and <code>iv_units</code>.</p>
@ -318,7 +318,7 @@
    

 <p><img src='figures/logo_who.png' height=60px style=margin-bottom:5px /> <br />
-This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>).</p>
+This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm'>https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a>).</p>
 <p>These have become the gold standard for international drug utilisation monitoring and research.</p>
 <p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
 <p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.</strong> See <a href='https://www.whocc.no/copyright_disclaimer/.'>https://www.whocc.no/copyright_disclaimer/.</a></p>
--- a/docs/reference/as.ab.html
+++ b/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">1.6.0.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -288,7 +288,7 @@

 <p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href='https://www.whocc.no/atc_ddd_index/'>https://www.whocc.no/atc_ddd_index/</a></p>
 <p>WHONET 2019 software: <a href='http://www.whonet.org/software.html'>http://www.whonet.org/software.html</a></p>
-<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a></p>
+<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href='https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm'>https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a></p>
    <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>

    
@ -301,7 +301,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
    

 <p><img src='figures/logo_who.png' height=60px style=margin-bottom:5px /> <br />
-This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>).</p>
+This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm'>https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a>).</p>
 <p>These have become the gold standard for international drug utilisation monitoring and research.</p>
 <p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
 <p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.</strong> See <a href='https://www.whocc.no/copyright_disclaimer/.'>https://www.whocc.no/copyright_disclaimer/.</a></p>
@ -347,7 +347,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
 <span class='co'># they use as.ab() internally:</span>
 <span class='fu'><a href='ab_property.html'>ab_name</a></span><span class='op'>(</span><span class='st'>"J01FA01"</span><span class='op'>)</span>    <span class='co'># "Erythromycin"</span>
 <span class='fu'><a href='ab_property.html'>ab_name</a></span><span class='op'>(</span><span class='st'>"eryt"</span><span class='op'>)</span>       <span class='co'># "Erythromycin"</span>
-
+<span class='co'># \donttest{</span>
 <span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>

  <span class='co'># you can quickly rename &lt;rsi&gt; columns using dplyr &gt;= 1.0.0:</span>
@ -355,6 +355,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/rename.html'>rename_with</a></span><span class='op'>(</span><span class='va'>as.ab</span>, <span class='fu'>where</span><span class='op'>(</span><span class='va'>is.rsi</span><span class='op'>)</span><span class='op'>)</span>
   
 <span class='op'>}</span>
+<span class='co'># }</span>
 </pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
--- a/docs/reference/as.disk.html
+++ b/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">1.6.0.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

--- a/docs/reference/as.mic.html
+++ b/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">1.6.0.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

--- a/docs/reference/as.mo.html
+++ b/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">1.6.0.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

--- a/docs/reference/as.rsi.html
+++ b/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">1.6.0.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -419,12 +419,12 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span> <span class='co'># see all R/SI results at a glance</span>
-
+<span class='co'># \donttest{</span>
 <span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://docs.ropensci.org/skimr/'>"skimr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
  <span class='co'># class &lt;rsi&gt; supported in skim() too:</span>
  <span class='fu'><a href='https://docs.ropensci.org/skimr/reference/skim.html'>skim</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>
 <span class='op'>}</span>
-
+<span class='co'># }</span>
 <span class='co'># For INTERPRETING disk diffusion and MIC values -----------------------</span>
       
 <span class='co'># a whole data set, even with combined MIC values and disk zones</span>
--- a/docs/reference/atc_online.html
+++ b/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">1.6.0.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -328,13 +328,15 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><span class='co'># \donttest{</span>
-<span class='co'># oral DDD (Defined Daily Dose) of amoxicillin</span>
-<span class='fu'>atc_online_property</span><span class='op'>(</span><span class='st'>"J01CA04"</span>, <span class='st'>"DDD"</span>, <span class='st'>"O"</span><span class='op'>)</span>
+<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span><span class='op'>(</span><span class='st'>"curl"</span><span class='op'>)</span> <span class='op'>&amp;&amp;</span> <span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span><span class='op'>(</span><span class='st'>"rvest"</span><span class='op'>)</span> <span class='op'>&amp;&amp;</span> <span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span><span class='op'>(</span><span class='st'>"xml2"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span> 
+  <span class='co'># oral DDD (Defined Daily Dose) of amoxicillin</span>
+  <span class='fu'>atc_online_property</span><span class='op'>(</span><span class='st'>"J01CA04"</span>, <span class='st'>"DDD"</span>, <span class='st'>"O"</span><span class='op'>)</span>

-<span class='co'># parenteral DDD (Defined Daily Dose) of amoxicillin</span>
-<span class='fu'>atc_online_property</span><span class='op'>(</span><span class='st'>"J01CA04"</span>, <span class='st'>"DDD"</span>, <span class='st'>"P"</span><span class='op'>)</span>
+  <span class='co'># parenteral DDD (Defined Daily Dose) of amoxicillin</span>
+  <span class='fu'>atc_online_property</span><span class='op'>(</span><span class='st'>"J01CA04"</span>, <span class='st'>"DDD"</span>, <span class='st'>"P"</span><span class='op'>)</span>

-<span class='fu'>atc_online_property</span><span class='op'>(</span><span class='st'>"J01CA04"</span>, property <span class='op'>=</span> <span class='st'>"groups"</span><span class='op'>)</span> <span class='co'># search hierarchical groups of amoxicillin</span>
+  <span class='fu'>atc_online_property</span><span class='op'>(</span><span class='st'>"J01CA04"</span>, property <span class='op'>=</span> <span class='st'>"groups"</span><span class='op'>)</span> <span class='co'># search hierarchical groups of amoxicillin</span>
+<span class='op'>}</span>
 <span class='co'># }</span>
 </pre>
  </div>
--- a/docs/reference/availability.html
+++ b/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">1.6.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -90,14 +90,14 @@
      <ul class="nav navbar-nav">
        <li>
  <a href="../index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -106,77 +106,77 @@
  <ul class="dropdown-menu" role="menu">
    <li>
      <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="../articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="../articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="../articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="../reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="../articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -185,21 +185,21 @@
 </li>
 <li>
  <a href="../reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="../authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="../news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -208,14 +208,14 @@
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
@ -278,13 +278,14 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><span class='fu'>availability</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>
-
+<span class='co'># \donttest{</span>
 <span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
  <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>mo</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select_all.html'>select_if</a></span><span class='op'>(</span><span class='va'>is.rsi</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
    <span class='fu'>availability</span><span class='op'>(</span><span class='op'>)</span>
 <span class='op'>}</span>
+<span class='co'># }</span>
 </pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
--- a/docs/reference/bug_drug_combinations.html
+++ b/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">1.6.0.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

--- a/docs/reference/catalogue_of_life.html
+++ b/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">1.6.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -90,14 +90,14 @@
      <ul class="nav navbar-nav">
        <li>
  <a href="../index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -106,77 +106,77 @@
  <ul class="dropdown-menu" role="menu">
    <li>
      <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="../articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="../articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="../articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="../reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="../articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -185,21 +185,21 @@
 </li>
 <li>
  <a href="../reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="../authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="../news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -208,14 +208,14 @@
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
--- a/docs/reference/catalogue_of_life_version.html
+++ b/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">1.6.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -90,14 +90,14 @@
      <ul class="nav navbar-nav">
        <li>
  <a href="../index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -106,77 +106,77 @@
  <ul class="dropdown-menu" role="menu">
    <li>
      <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="../articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="../articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="../articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="../reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="../articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -185,21 +185,21 @@
 </li>
 <li>
  <a href="../reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="../authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="../news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -208,14 +208,14 @@
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
--- a/docs/reference/count.html
+++ b/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">1.6.0.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -399,7 +399,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
 <span class='fu'>count_susceptible</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
 <span class='fu'><a href='proportion.html'>susceptibility</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span> <span class='op'>*</span> <span class='fu'>n_rsi</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>

-
+<span class='co'># \donttest{</span>
 <span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
  <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
@ -433,6 +433,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
    <span class='fu'>count_df</span><span class='op'>(</span>translate <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
 <span class='op'>}</span>
+<span class='co'># }</span>
 </pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
--- a/docs/reference/custom_eucast_rules.html
+++ b/docs/reference/custom_eucast_rules.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9017</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

--- a/docs/reference/dosage.html
+++ b/docs/reference/dosage.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">1.6.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
      </span>
    </div>

@ -90,14 +90,14 @@
      <ul class="nav navbar-nav">
        <li>
  <a href="../index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -106,77 +106,77 @@
  <ul class="dropdown-menu" role="menu">
    <li>
      <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="../articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="../articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="../articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="../reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="../articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -185,21 +185,21 @@
 </li>
 <li>
  <a href="../reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="../authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="../news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -208,14 +208,14 @@
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
dr. M.S. (Matthijs) Berends	41d279daa1	(v1.7.0) v1.7.0	2021-05-26 11:10:34 +02:00
dr. M.S. (Matthijs) Berends	a12572c752	doc update	2021-05-26 11:00:32 +02:00
dr. M.S. (Matthijs) Berends	a33c8a51a2	v1.7.0	2021-05-26 10:59:54 +02:00
dr. M.S. (Matthijs) Berends	55457d0ab6	v1.7.0	2021-05-25 10:00:11 +02:00
dr. M.S. (Matthijs) Berends	d0f38a03d5	v1.7.0	2021-05-24 15:29:31 +02:00
dr. M.S. (Matthijs) Berends	ac73a8d849	v1.7.0	2021-05-24 15:29:17 +02:00
dr. M.S. (Matthijs) Berends	e5599bc694	(v1.6.0.9065) unit tests	2021-05-24 11:01:32 +02:00
dr. M.S. (Matthijs) Berends	4fbf9e1720	(v1.6.0.9064) prepare new release	2021-05-24 09:34:08 +02:00
dr. M.S. (Matthijs) Berends	a13fd98e8b	(v1.6.0.9063) prepare new release	2021-05-24 09:00:11 +02:00
dr. M.S. (Matthijs) Berends	06302d296a	(v1.6.0.9062) code consistency	2021-05-24 00:06:28 +02:00
dr. M.S. (Matthijs) Berends	07939b1a14	(v1.6.0.9061) age() update	2021-05-23 23:11:16 +02:00