website update

v1.8.1
(v1.8.0.9010) as.mo improvement
2025-09-09 18:09:37 +02:00 · 2022-03-27 09:37:55 +02:00 · 2022-03-24 23:05:04 +01:00 · 2022-03-15 17:35:02 +01:00 · 2022-03-14 16:43:15 +01:00 · 2022-03-14 16:37:37 +01:00
208 changed files with 1678 additions and 1513 deletions
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -33,3 +33,4 @@
 ^vignettes/SPSS.Rmd$
 ^vignettes/WHONET.Rmd$
 ^logo.svg$
+^CRAN-SUBMISSION$
--- a/3
+++ b/3
@@ -0,0 +1,3 @@
+Version: 1.8.1
+Date: 2022-03-16 18:22:51 UTC
+SHA: 7b0f1596bd65fbb72681a7e3a6a7e4e469a891e8
--- a/9
+++ b/9
@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.0
-Date: 2022-01-03
+Version: 1.8.1
+Date: 2022-03-17
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
    data analysis and to work with microbial and antimicrobial properties by
@@ -9,7 +9,7 @@ Description: Functions to simplify and standardise antimicrobial resistance (AMR
 Authors@R: c(
  person(given = c("Matthijs", "S."),
         family = "Berends", 
-         email = "m.s.berends@umcg.nl",
+         email = "m.berends@certe.nl",
         role = c("aut", "cre"),
         comment = c(ORCID = "0000-0001-7620-1800")),
  person(given = c("Christian", "F."),
@@ -71,7 +71,8 @@ Depends: R (>= 3.0.0)
 Enhances:
  cleaner,
  skimr,
-  ggplot2
+  ggplot2,
+  tidyselect
 Suggests: 
  curl,
  dplyr,
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,8 +1,28 @@
+# `AMR` 1.8.1
+
+
+All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.
+
+### Changed
+* Fix for using `as.rsi()` on values containing capped values (such as `>=`), sometimes leading to `NA`
+* Support for antibiotic interpretations of the MIPS laboratory system: `"U"` for S ('susceptible urine'), `"D"` for I ('susceptible dose-dependent')
+* Improved algorithm of `as.mo()`, especially for ignoring non-taxonomic text, such as:
+  ```r
+  mo_name("methicillin-resistant S. aureus (MRSA)")
+  #> [1] "Staphylococcus aureus"
+  ```
+* More informative warning messages
+* Added 192 as valid MIC
+* Updated MIC printing in tibbles
+* Increased speed for loading the package
+
+### Other
+* Fix for unit testing on R 3.3
+* Fix for size of some image elements, as requested by CRAN
+
+
 # `AMR` 1.8.0

-
-All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.
-
 ### Breaking changes
 * Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version
 * Removed the `key_antibiotics()` and `key_antibiotics_equal()` functions, which were deprecated and superseded by `key_antimicrobials()` and `antimicrobials_equal()`
@@ -256,7 +276,7 @@ All functions in this package are now all considered to be stable. Updates to th
    filter(is_new_episode(date, episode_days = 60))
  ```
 * Functions `mo_is_gram_negative()` and `mo_is_gram_positive()` as wrappers around `mo_gramstain()`. They always return `TRUE` or `FALSE` (except when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.
-* Function `mo_is_intrinsic_resistant()` to test for intrinsic resistance, based on [EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2](https://www.eucast.org/expert_rules_and_intrinsic_resistance/) from 2020.
+* Function `mo_is_intrinsic_resistant()` to test for intrinsic resistance, based on EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2 from 2020.
 * Functions `random_mic()`, `random_disk()` and `random_rsi()` for random value generation. The functions `random_mic()` and `random_disk()` take microorganism names and antibiotic names as input to make generation more realistic.

 ### Changed
@@ -1352,7 +1372,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
 * Function `guess_atc` to **determine the ATC** of an antibiotic based on name, trade name, or known abbreviations
 * Function `freq` to create **frequency tables**, with additional info in a header
 * Function `MDRO` to **determine Multi Drug Resistant Organisms (MDRO)** with support for country-specific guidelines.
-  * [Exceptional resistances defined by EUCAST](https://www.eucast.org/expert_rules_and_intrinsic_resistance/) are also supported instead of countries alone
+  * Exceptional resistances defined by EUCAST are also supported instead of countries alone
  * Functions `BRMO` and `MRGN` are wrappers for Dutch and German guidelines, respectively
 * New algorithm to determine weighted isolates, can now be `"points"` or `"keyantibiotics"`, see `?first_isolate`
 * New print format for `tibble`s and `data.table`s
--- a/R/aa_globals.R
+++ b/R/aa_globals.R
@@ -36,15 +36,15 @@ EUCAST_VERSION_BREAKPOINTS <- list("11.0" = list(version_txt = "v11.0",
 EUCAST_VERSION_EXPERT_RULES <- list("3.1" = list(version_txt = "v3.1",
                                                 year = 2016, 
                                                 title = "'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes'",
-                                                 url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"),
+                                                 url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"),
                                    "3.2" = list(version_txt = "v3.2",
                                                 year = 2020, 
                                                 title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
-                                                 url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"),
+                                                 url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"),
                                    "3.3" = list(version_txt = "v3.3",
                                                 year = 2021, 
                                                 title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
-                                                 url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"))
+                                                 url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"))

 SNOMED_VERSION <- list(title = "Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)",
                       current_source = "US Edition of SNOMED CT from 1 September 2020",
--- a/R/aa_helper_functions.R
+++ b/R/aa_helper_functions.R
@@ -206,7 +206,7 @@ check_dataset_integrity <- function() {
               " overwritten by your global environment and prevent", plural[2], 
               " the AMR package from working correctly: ",
               vector_and(overwritten, quotes = "'"),
-               ".\nPlease rename your object", plural[3], ".", call = FALSE)
+               ".\nPlease rename your object", plural[3], ".")
    }
  }
  # check if other packages did not overwrite our data sets
@@ -492,7 +492,7 @@ message_ <- function(...,
 warning_ <- function(...,
                     add_fn = list(),
                     immediate = FALSE,
-                     call = TRUE) {
+                     call = FALSE) {
  warning(word_wrap(..., 
                    add_fn = add_fn,
                    as_note = FALSE),
@@ -559,7 +559,7 @@ stop_ifnot <- function(expr, ..., call = TRUE) {

 return_after_integrity_check <- function(value, type, check_vector) {
  if (!all(value[!is.na(value)] %in% check_vector)) {
-    warning_(paste0("invalid ", type, ", NA generated"), call = FALSE)
+    warning_(paste0("invalid ", type, ", NA generated"))
    value[!value %in% check_vector] <- NA
  }
  value
--- a/R/ab.R
+++ b/R/ab.R
@@ -455,15 +455,13 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
  x_unknown_ATCs <- x_unknown[x_unknown %like% "[A-Z][0-9][0-9][A-Z][A-Z][0-9][0-9]"]
  x_unknown <- x_unknown[!x_unknown %in% x_unknown_ATCs]
  if (length(x_unknown_ATCs) > 0 & fast_mode == FALSE) {
-    warning_("These ATC codes are not (yet) in the antibiotics data set: ",
-             vector_and(x_unknown_ATCs), ".",
-             call = FALSE)
+    warning_("in `as.ab()`: these ATC codes are not (yet) in the antibiotics data set: ",
+             vector_and(x_unknown_ATCs), ".")
  }
  
  if (length(x_unknown) > 0 & fast_mode == FALSE) {
-    warning_("These values could not be coerced to a valid antimicrobial ID: ",
-             vector_and(x_unknown), ".",
-             call = FALSE)
+    warning_("in `as.ab()`: these values could not be coerced to a valid antimicrobial ID: ",
+             vector_and(x_unknown), ".")
  }

  x_result <- x_new[match(x_bak_clean, x)]
--- a/R/ab_property.R
+++ b/R/ab_property.R
@@ -240,8 +240,8 @@ ab_ddd <- function(x, administration = "oral", ...) {
  units <- list(...)$units
  if (!is.null(units) && isTRUE(units)) {
    if (message_not_thrown_before("ab_ddd", entire_session = TRUE)) {
-      warning_("Using `ab_ddd(..., units = TRUE)` is deprecated, use `ab_ddd_units()` to retrieve units instead. ",
-               "This warning will be shown once per session.", call = FALSE)
+      warning_("in `ab_ddd()`: using `ab_ddd(..., units = TRUE)` is deprecated, use `ab_ddd_units()` to retrieve units instead.",
+               "This warning will be shown once per session.")
    }
    ddd_prop <- paste0(ddd_prop, "_units")
  } else {
@@ -250,9 +250,9 @@ ab_ddd <- function(x, administration = "oral", ...) {
  out <- ab_validate(x = x, property = ddd_prop)
  
  if (any(ab_name(x, language = NULL) %like% "/" & is.na(out))) {
-    warning_("DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package. ",
+    warning_("in `ab_ddd()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
             "Please refer to the WHOCC website:\n",
-             "www.whocc.no/ddd/list_of_ddds_combined_products/", call = FALSE)
+             "www.whocc.no/ddd/list_of_ddds_combined_products/")
  }
  out
 }
@@ -265,9 +265,9 @@ ab_ddd_units <- function(x, administration = "oral", ...) {
  
  x <- as.ab(x, ...)
  if (any(ab_name(x, language = NULL) %like% "/")) {
-    warning_("DDDs of combined products are available for different dose combinations and not (yet) part of the AMR package. ",
+    warning_("in `ab_ddd_units()`: DDDs of combined products are available for different dose combinations and not (yet) part of the AMR package.",
             "Please refer to the WHOCC website:\n",
-             "www.whocc.no/ddd/list_of_ddds_combined_products/", call = FALSE)
+             "www.whocc.no/ddd/list_of_ddds_combined_products/")
  }
  
  ddd_prop <- paste0(administration, "_units")
@@ -311,12 +311,12 @@ ab_url <- function(x, open = FALSE, ...) {
  
  NAs <- ab_name(ab, tolower = TRUE, language = NULL)[!is.na(ab) & is.na(atcs)]
  if (length(NAs) > 0) {
-    warning_("No ATC code available for ", vector_and(NAs, quotes = FALSE), ".")
+    warning_("in `ab_url()`: no ATC code available for ", vector_and(NAs, quotes = FALSE), ".")
  }
  
  if (open == TRUE) {
    if (length(u) > 1 & !is.na(u[1L])) {
-      warning_("Only the first URL will be opened, as `browseURL()` only suports one string.")
+      warning_("in `ab_url()`: only the first URL will be opened, as `browseURL()` only suports one string.")
    }
    if (!is.na(u[1L])) {
      utils::browseURL(u[1L])
@@ -385,7 +385,8 @@ set_ab_names <- function(data, ..., property = "name", language = get_AMR_locale
              },
              USE.NAMES = FALSE)
  if (any(x %in% c("", NA))) {
-    warning_("No ", property, " found for column(s): ", vector_and(vars[x %in% c("", NA)], sort = FALSE), call = FALSE)
+    warning_("in `set_ab_names()`: no ", property, " found for column(s): ",
+             vector_and(vars[x %in% c("", NA)], sort = FALSE))
    x[x %in% c("", NA)] <- vars[x %in% c("", NA)]
  }
  
--- a/R/ab_selectors.R
+++ b/R/ab_selectors.R
@@ -481,14 +481,13 @@ ab_select_exec <- function(function_name,
    untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate|macromethod|screening|/nacubactam"), "ab", drop = TRUE]
    if (any(untreatable %in% names(ab_in_data))) {
      if (message_not_thrown_before(function_name, "ab_class", "untreatable", entire_session = TRUE)) {
-        warning_("Some agents in `", function_name, "()` were ignored since they cannot be used for treating patients: ",
+        warning_("in `", function_name, "()`: some agents were ignored since they cannot be used for treating patients: ",
                 vector_and(ab_name(names(ab_in_data)[names(ab_in_data) %in% untreatable],
                                    language = NULL,
                                    tolower = TRUE),
                            quotes = FALSE,
                            sort = TRUE), ". They can be included using `", function_name, "(only_treatable = FALSE)`. ",
-                 "This warning will be shown once per session.",
-                 call = FALSE)
+                 "This warning will be shown once per session.")
      }
      ab_in_data <- ab_in_data[!names(ab_in_data) %in% untreatable]
    }
--- a/R/age.R
+++ b/R/age.R
@@ -95,10 +95,10 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
  
  if (any(ages < 0, na.rm = TRUE)) {
    ages[!is.na(ages) & ages < 0] <- NA
-    warning_("NAs introduced for ages below 0.", call = TRUE)
+    warning_("in `age()`: NAs introduced for ages below 0.")
  }
  if (any(ages > 120, na.rm = TRUE)) {
-    warning_("Some ages are above 120.", call = TRUE)
+    warning_("in `age()`: some ages are above 120.")
  }
  
  if (isTRUE(na.rm)) {
@@ -171,7 +171,7 @@ age_groups <- function(x, split_at = c(12, 25, 55, 75), na.rm = FALSE) {
  
  if (any(x < 0, na.rm = TRUE)) {
    x[x < 0] <- NA
-    warning_("NAs introduced for ages below 0.", call = TRUE)
+    warning_("in `age_groups()`: NAs introduced for ages below 0.")
  }
  if (is.character(split_at)) {
    split_at <- split_at[1L]
--- a/R/atc_online.R
+++ b/R/atc_online.R
@@ -175,7 +175,7 @@ atc_online_property <- function(atc_code,
      colnames(out) <- gsub("^atc.*", "atc", tolower(colnames(out)))
      
      if (length(out) == 0) {
-        warning_("ATC not found: ", atc_code[i], ". Please check ", atc_url, ".", call = FALSE)
+        warning_("in `atc_online_property()`: ATC not found: ", atc_code[i], ". Please check ", atc_url, ".")
        returnvalue[i] <- NA
        next
      }
--- a/R/bug_drug_combinations.R
+++ b/R/bug_drug_combinations.R
@@ -184,7 +184,7 @@ format.bug_drug_combinations <- function(x,
  
  if (inherits(x, "grouped")) {
    # bug_drug_combinations() has been run on groups, so de-group here
-    warning_("formatting the output of `bug_drug_combinations()` does not support grouped variables, they are ignored", call = FALSE)
+    warning_("in `format()`: formatting the output of `bug_drug_combinations()` does not support grouped variables, they were ignored")
    idx <- split(seq_len(nrow(x)), paste0(x$mo, "%%", x$ab))
    x <- data.frame(mo = gsub("(.*)%%(.*)", "\\1", names(idx)),
                    ab = gsub("(.*)%%(.*)", "\\2", names(idx)),
--- a/R/catalogue_of_life.R
+++ b/R/catalogue_of_life.R
@@ -43,7 +43,7 @@ format_included_data_number <- function(data) {
 #'
 #' This package contains the complete taxonomic tree (last updated: `r CATALOGUE_OF_LIFE$yearmonth_LPSN`) of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (CoL), supplemented with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN).
 #' @section Catalogue of Life:
-#' \if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
+#' \if{html}{\figure{logo_col.png}{options: height="40" style=margin-bottom:"5"} \cr}
 #' This package contains the complete taxonomic tree of almost all microorganisms (`r format_included_data_number(microorganisms)` species) from the authoritative and comprehensive Catalogue of Life (CoL, <http://www.catalogueoflife.org>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, [lpsn.dsmz.de](https://lpsn.dsmz.de)). This supplementation is needed until the [CoL+ project](https://github.com/CatalogueOfLife/general) is finished, which we await.
 #'
 #' [Click here][catalogue_of_life] for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with [catalogue_of_life_version()].
--- a/R/disk.R
+++ b/R/disk.R
@@ -100,10 +100,10 @@ as.disk <- function(x, na.rm = FALSE) {
        unique() %pm>%
        sort() %pm>%
        vector_and(quotes = TRUE)
-      warning_(na_after - na_before, " results truncated (",
+      warning_("in `as.disk()`: ", na_after - na_before, " results truncated (",
               round(((na_after - na_before) / length(x)) * 100),
               "%) that were invalid disk zones: ",
-               list_missing, call = FALSE)
+               list_missing)
    }
  }
  set_clean_class(as.integer(x),
--- a/R/eucast_rules.R
+++ b/R/eucast_rules.R
@@ -181,8 +181,7 @@ eucast_rules <- function(x,
  meet_criteria(custom_rules, allow_class = "custom_eucast_rules", allow_NULL = TRUE)
  
  if ("custom" %in% rules & is.null(custom_rules)) {
-    warning_("No custom rules were set with the `custom_rules` argument",
-             call = FALSE,
+    warning_("in `eucast_rules()`: no custom rules were set with the `custom_rules` argument",
             immediate = TRUE)
    rules <- rules[rules != "custom"]
    if (length(rules) == 0) {
@@ -915,13 +914,12 @@ eucast_rules <- function(x,
    # take order from original data set
    warn_lacking_rsi_class <- warn_lacking_rsi_class[order(colnames(x.bak))]
    warn_lacking_rsi_class <- warn_lacking_rsi_class[!is.na(warn_lacking_rsi_class)]
-    warning_("Not all columns with antimicrobial results are of class <rsi>. Transform them on beforehand, with e.g.:\n",
+    warning_("in `eucast_rules()`: not all columns with antimicrobial results are of class <rsi>. Transform them on beforehand, with e.g.:\n",
             "  - ", x_deparsed, " %>% as.rsi(", ifelse(length(warn_lacking_rsi_class) == 1, 
                                                      warn_lacking_rsi_class,
                                                      paste0(warn_lacking_rsi_class[1], ":", warn_lacking_rsi_class[length(warn_lacking_rsi_class)])), ")\n", 
             "  - ", x_deparsed, " %>% mutate_if(is.rsi.eligible, as.rsi)\n",
-             "  - ", x_deparsed, " %>% mutate(across(where(is.rsi.eligible), as.rsi))",
-             call = FALSE)
+             "  - ", x_deparsed, " %>% mutate(across(where(is.rsi.eligible), as.rsi))")
  }
  
  # Return data set ---------------------------------------------------------
@@ -986,14 +984,14 @@ edit_rsi <- function(x,
            TRUE
          })
          suppressWarnings(new_edits[rows, cols] <<- to)
-          warning_("Value \"", to, "\" added to the factor levels of column", ifelse(length(cols) == 1, "", "s"), 
+          warning_("in `eucast_rules()`: value \"", to, "\" added to the factor levels of column",
+                   ifelse(length(cols) == 1, "", "s"), 
                   " ", vector_and(cols, quotes = "`", sort = FALSE), 
-                   " because this value was not an existing factor level.",
-                   call = FALSE)
+                   " because this value was not an existing factor level.")
          txt_warning()
          warned <- FALSE
        } else {
-          warning_(w$message, call = FALSE)
+          warning_("in `eucast_rules()`: ", w$message)
          txt_warning()
        }
      },
--- a/R/guess_ab_col.R
+++ b/R/guess_ab_col.R
@@ -267,7 +267,6 @@ get_column_abx <- function(x,
                        ", as it is already set for ", 
                        names(already_set_as), " (", ab_name(names(already_set_as), tolower = TRUE, language = NULL), ")"),
                 add_fn = font_red,
-                 call = FALSE, 
                 immediate = verbose)
      }
    }
@@ -338,6 +337,5 @@ generate_warning_abs_missing <- function(missing, any = FALSE) {
  }
  warning_(paste0("Introducing NAs since", any_txt[1], " these antimicrobials ", any_txt[2], " required: ",
                  vector_and(missing, quotes = FALSE)),
-           immediate = TRUE,
-           call = FALSE)
+           immediate = TRUE)
 }
--- a/R/join_microorganisms.R
+++ b/R/join_microorganisms.R
@@ -170,7 +170,7 @@ join_microorganisms <- function(type, x, by, suffix, ...) {
  }
  
  if (type %like% "full|left|right|inner" && NROW(joined) > NROW(x)) {
-    warning_("The newly joined data set contains ", nrow(joined) - nrow(x), " rows more than the number of rows of `x`.", call = FALSE)
+    warning_("in `", type, "_join()`: the newly joined data set contains ", nrow(joined) - nrow(x), " rows more than the number of rows of `x`.")
  }
  
  joined
--- a/R/key_antimicrobials.R
+++ b/R/key_antimicrobials.R
@@ -150,7 +150,7 @@ key_antimicrobials <- function(x = NULL,
    col_mo <- search_type_in_df(x = x, type = "mo", info = FALSE)
  }
  if (is.null(col_mo)) {
-    warning_("No column found for `col_mo`, ignoring antibiotics set in `gram_negative` and `gram_positive`, and antimycotics set in `antifungal`", call = FALSE)
+    warning_("in `key_antimicrobials()`: no column found for `col_mo`, ignoring antibiotics set in `gram_negative` and `gram_positive`, and antimycotics set in `antifungal`")
    gramstain <- NA_character_
    kingdom <- NA_character_
  } else {
@@ -172,11 +172,11 @@ key_antimicrobials <- function(x = NULL,
    if (values_new_length < values_old_length &
        any(filter, na.rm = TRUE) &
        message_not_thrown_before("key_antimicrobials", name)) {
-      warning_(ifelse(values_new_length == 0,
+      warning_("in `key_antimicrobials()`: ",
+               ifelse(values_new_length == 0,
                      "No columns available ",
                      paste0("Only using ", values_new_length, " out of ", values_old_length, " defined columns ")),
-               "as key antimicrobials for ", name, "s. See ?key_antimicrobials.",
-               call = FALSE)
+               "as key antimicrobials for ", name, "s. See ?key_antimicrobials.")
    }
    
    generate_antimcrobials_string(x[which(filter), c(universal, values), drop = FALSE])
@@ -217,7 +217,7 @@ key_antimicrobials <- function(x = NULL,
                                             cols = cols)
  
  if (length(unique(key_ab)) == 1) {
-    warning_("No distinct key antibiotics determined.", call = FALSE)
+    warning_("in `key_antimicrobials()`: no distinct key antibiotics determined.")
  }
  
  key_ab
--- a/R/lifecycle.R
+++ b/R/lifecycle.R
@@ -32,23 +32,23 @@
 #' @rdname lifecycle
 #' @description Functions in this `AMR` package are categorised using [the lifecycle circle of the Tidyverse as found on www.tidyverse.org/lifecycle](https://lifecycle.r-lib.org/articles/stages.html).
 #' 
-#' \if{html}{\figure{lifecycle_tidyverse.svg}{options: height=200px style=margin-bottom:5px} \cr}
+#' \if{html}{\figure{lifecycle_tidyverse.svg}{options: height="200" style=margin-bottom:"5"} \cr}
 #' This page contains a section for every lifecycle (with text borrowed from the aforementioned Tidyverse website), so they can be used in the manual pages of the functions. 
 #' @section Experimental Lifecycle:
-#' \if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:5px} \cr}
+#' \if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:"5"} \cr}
 #' The [lifecycle][AMR::lifecycle] of this function is **experimental**. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this `AMR` package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
 #' @section Maturing Lifecycle:
-#' \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
+#' \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:"5"} \cr}
 #' The [lifecycle][AMR::lifecycle] of this function is **maturing**. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome [to suggest changes at our repository](https://github.com/msberends/AMR/issues) or [write us an email (see section 'Contact Us')][AMR::AMR].
 #' @section Stable Lifecycle:
-#' \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
+#' \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 #' The [lifecycle][AMR::lifecycle] of this function is **stable**. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 #' 
-#' If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+#' If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 #' @section Retired Lifecycle:
-#' \if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:5px} \cr}
+#' \if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:"5"} \cr}
 #' The [lifecycle][AMR::lifecycle] of this function is **retired**. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.
 #' @section Questioning Lifecycle:
-#' \if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
+#' \if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:"5"} \cr}
 #' The [lifecycle][AMR::lifecycle] of this function is **questioning**. This function might be no longer be optimal approach, or is it questionable whether this function should be in this `AMR` package at all.
 NULL
--- a/R/mdro.R
+++ b/R/mdro.R
@@ -65,7 +65,7 @@
 #' 
 #' * `guideline = "TB"`
 #'
-#'   The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" ([link](https://www.who.int/tb/publications/pmdt_companionhandbook/en/))
+#'   The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" ([link](https://www.who.int/publications/i/item/9789241548809))
 #' 
 #' * `guideline = "MRGN"`
 #'
@@ -240,7 +240,7 @@ mdro <- function(x = NULL,
  }
  
  if (!is.null(list(...)$country)) {
-    warning_("Using `country` is deprecated, use `guideline` instead. See ?mdro.", call = FALSE)
+    warning_("in `mdro()`: using `country` is deprecated, use `guideline` instead. See ?mdro")
    guideline <- list(...)$country
  }
  
@@ -343,7 +343,7 @@ mdro <- function(x = NULL,
    guideline$name <- "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis"
    guideline$author <- "WHO (World Health Organization)"
    guideline$version <- "WHO/HTM/TB/2014.11, 2014"
-    guideline$source_url <- "https://www.who.int/tb/publications/pmdt_companionhandbook/en/"
+    guideline$source_url <- "https://www.who.int/publications/i/item/9789241548809"
    guideline$type <- "MDR-TB's"
    
    # support per country:
@@ -1550,8 +1550,8 @@ mdro <- function(x = NULL,
  if (guideline$code == "cmi2012") {
    if (any(x$MDRO == -1, na.rm = TRUE)) {
      if (message_not_thrown_before("mdro", "availability")) {
-        warning_("NA introduced for isolates where the available percentage of antimicrobial classes was below ",
-                 percentage(pct_required_classes), " (set with `pct_required_classes`)", call = FALSE)
+        warning_("in `mdro()`: NA introduced for isolates where the available percentage of antimicrobial classes was below ",
+                 percentage(pct_required_classes), " (set with `pct_required_classes`)")
      }
      # set these -1s to NA
      x[which(x$MDRO == -1), "MDRO"] <- NA_integer_
@@ -1709,7 +1709,7 @@ run_custom_mdro_guideline <- function(df, guideline, info) {
                      return("error")
                    })
    if (identical(qry, "error")) {
-      warning_("in custom_mdro_guideline(): rule ", i, 
+      warning_("in `custom_mdro_guideline()`: rule ", i, 
               " (`", as.character(guideline[[i]]$query), "`) was ignored because of this error message: ",
               pkg_env$err_msg,
               call = FALSE, 
--- a/R/mic.R
+++ b/R/mic.R
@@ -37,8 +37,8 @@ valid_mic_levels <- c(c(t(vapply(FUN.VALUE = character(9), ops,
                                 function(x) paste0(x, sort(c(1:9, 1.5)))))),
                      c(t(vapply(FUN.VALUE = character(45), ops,
                                 function(x) paste0(x, c(10:98)[9:98 %% 2 == TRUE])))),
-                      c(t(vapply(FUN.VALUE = character(16), ops,
-                                 function(x) paste0(x, sort(c(2 ^ c(7:11), 80 * c(2:12))))))))
+                      c(t(vapply(FUN.VALUE = character(17), ops,
+                                 function(x) paste0(x, sort(c(2 ^ c(7:11), 192, 80 * c(2:12))))))))

 #' Transform Input to Minimum Inhibitory Concentrations (MIC)
 #'
@@ -175,7 +175,7 @@ as.mic <- function(x, na.rm = FALSE) {
        unique() %pm>%
        sort() %pm>%
        vector_and(quotes = TRUE)
-      warning_(na_after - na_before, " results truncated (",
+      warning_("in `as.mic()`: ", na_after - na_before, " results truncated (",
               round(((na_after - na_before) / length(x)) * 100),
               "%) that were invalid MICs: ",
               list_missing, call = FALSE)
@@ -243,12 +243,12 @@ droplevels.mic <- function(x, exclude = if (any(is.na(levels(x)))) NULL else NA,
 pillar_shaft.mic <- function(x, ...) {
  crude_numbers <- as.double(x)
  operators <- gsub("[^<=>]+", "", as.character(x))
-  pasted <- trimws(paste0(operators, trimws(format(crude_numbers))))
-  out <- pasted
+  operators[!is.na(operators) & operators != ""] <- font_silver(operators[!is.na(operators) & operators != ""], collapse = NULL)
+  out <- trimws(paste0(operators, trimws(format(crude_numbers))))
  out[is.na(x)] <- font_na(NA)
-  out <- gsub("(<|=|>)", font_silver("\\1"), out)
-  out <- gsub("([.]?0+)$", font_white("\\1"), out)
-  create_pillar_column(out, align = "right", width = max(nchar(pasted)))
+  # maketrailing zeroes almost invisible
+  out[out %like% "[.]"] <- gsub("([.]?0+)$", font_white("\\1"), out[out %like% "[.]"], perl = TRUE)
+  create_pillar_column(out, align = "right", width = max(nchar(font_stripstyle(out))))
 }

 # will be exported using s3_register() in R/zzz.R
@@ -358,7 +358,7 @@ sort.mic <- function(x, decreasing = FALSE, ...) {
 #' @export
 #' @noRd
 hist.mic <- function(x, ...) {
-  warning_("Use `plot()` or ggplot2's `autoplot()` for optimal plotting of MIC values", call = FALSE)
+  warning_("in `hist()`: use `plot()` or ggplot2's `autoplot()` for optimal plotting of MIC values")
  hist(log2(x))
 }

--- a/R/mo.R
+++ b/R/mo.R
@@ -31,9 +31,9 @@
 #' @param Becker a [logical] to indicate whether staphylococci should be categorised into coagulase-negative staphylococci ("CoNS") and coagulase-positive staphylococci ("CoPS") instead of their own species, according to Karsten Becker *et al.* (1,2,3).
 #'
 #' This excludes *Staphylococcus aureus* at default, use `Becker = "all"` to also categorise *S. aureus* as "CoPS".
-#' @param Lancefield a [logical] to indicate whether beta-haemolytic *Streptococci* should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (4). These *Streptococci* will be categorised in their first group, e.g. *Streptococcus dysgalactiae* will be group C, although officially it was also categorised into groups G and L.
+#' @param Lancefield a [logical] to indicate whether a beta-haemolytic *Streptococcus* should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (4). These streptococci will be categorised in their first group, e.g. *Streptococcus dysgalactiae* will be group C, although officially it was also categorised into groups G and L.
 #'
-#' This excludes *Enterococci* at default (who are in group D), use `Lancefield = "all"` to also categorise all *Enterococci* as group D.
+#' This excludes enterococci at default (who are in group D), use `Lancefield = "all"` to also categorise all enterococci as group D.
 #' @param allow_uncertain a number between `0` (or `"none"`) and `3` (or `"all"`), or `TRUE` (= `2`) or `FALSE` (= `0`) to indicate whether the input should be checked for less probable results, see *Details*
 #' @param reference_df a [data.frame] to be used for extra reference when translating `x` to a valid [`mo`]. See [set_mo_source()] and [get_mo_source()] to automate the usage of your own codes (e.g. used in your analysis or organisation).
 #' @param ignore_pattern a regular expression (case-insensitive) of which all matches in `x` must return `NA`. This can be convenient to exclude known non-relevant input and can also be set with the option `AMR_ignore_pattern`, e.g. `options(AMR_ignore_pattern = "(not reported|contaminated flora)")`.
@@ -1003,6 +1003,35 @@ exec_as.mo <- function(x,
            }
          }
          
+          # try splitting of characters in the middle and then find ID based on old names ----
+          # only when text length is 6 or lower
+          # like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus, staaur = S. aureus
+          if (nchar(g.x_backup_without_spp) <= 6) {
+            x_length <- nchar(g.x_backup_without_spp)
+            x_split <- paste0("^",
+                              g.x_backup_without_spp %pm>% substr(1, x_length / 2),
+                              ".* ",
+                              g.x_backup_without_spp %pm>% substr((x_length / 2) + 1, x_length))
+            found <- lookup(fullname_lower %like_case% x_split,
+                            haystack = MO.old_lookup,
+                            column = NULL)
+            if (!all(is.na(found))) {
+              # it's an old name, so return it
+              if (property == "ref") {
+                x[i] <- found["ref"]
+              } else {
+                x[i] <- lookup(fullname == found["fullname_new"], haystack = MO_lookup)
+              }
+              pkg_env$mo_renamed_last_run <- found["fullname"]
+              was_renamed(name_old = found["fullname"],
+                          name_new = lookup(fullname == found["fullname_new"], "fullname", haystack = MO_lookup),
+                          ref_old = found["ref"],
+                          ref_new = lookup(fullname == found["fullname_new"], "ref", haystack = MO_lookup),
+                          mo = lookup(fullname == found["fullname_new"], "mo", haystack = MO_lookup))
+              return(x[i])
+            }
+          }
+          
          # try fullname without start and without nchar limit of >= 6 ----
          # like "K. pneu rhino" >> "Klebsiella pneumoniae (rhinoscleromatis)" = KLEPNERH
          found <- lookup(fullname_lower %like_case% e.x_withspaces_start_only,
@@ -1188,9 +1217,38 @@ exec_as.mo <- function(x,
                return(found)
              }
              
-              # (6) try to strip off half an element from end and check the remains ----
+              # (6) remove non-taxonomic prefix and suffix ----
              if (isTRUE(debug)) {
-                cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (6) try to strip off half an element from end and check the remains\n"))
+                cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (6) remove non-taxonomic prefix and suffix\n"))
+              }
+              x_without_nontax <- gsub("(^[a-zA-Z]+[./-]+[a-zA-Z]+[^a-zA-Z]* )([a-zA-Z.]+ [a-zA-Z]+.*)",
+                                              "\\2", a.x_backup, perl = TRUE)
+              x_without_nontax <- gsub("( *[(].*[)] *)[^a-zA-Z]*$", "", x_without_nontax, perl = TRUE)
+              if (isTRUE(debug)) {
+                message("Running '", x_without_nontax, "'")
+              }
+              
+              # first try without dyslexia mode
+              found <- suppressMessages(suppressWarnings(exec_as.mo(x_without_nontax, initial_search = FALSE, dyslexia_mode = FALSE, allow_uncertain = FALSE, debug = debug, reference_data_to_use = uncertain.reference_data_to_use, actual_uncertainty = 2, actual_input = x_without_nontax)))
+              if (empty_result(found)) {
+                # then with dyslexia mode
+                found <- suppressMessages(suppressWarnings(exec_as.mo(x_without_nontax, initial_search = FALSE, dyslexia_mode = TRUE, allow_uncertain = FALSE, debug = debug, reference_data_to_use = uncertain.reference_data_to_use, actual_uncertainty = 2, actual_input = x_without_nontax)))
+              }
+              if (!empty_result(found) & nchar(g.x_backup_without_spp) >= 6) {
+                # we ran with actual_input = x_without_nontax, so now correct for a.x_backup:
+                uncertain_df <- attr(found, which = "uncertainties", exact = TRUE)
+                uncertain_df$input <- a.x_backup
+                found_result <- found
+                uncertainties <<- rbind(uncertainties,
+                                        uncertain_df,
+                                        stringsAsFactors = FALSE)
+                found <- lookup(mo == found)
+                return(found)
+              }
+              
+              # (7) try to strip off half an element from end and check the remains ----
+              if (isTRUE(debug)) {
+                cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (7) try to strip off half an element from end and check the remains\n"))
              }
              x_strip <- a.x_backup %pm>% strsplit("[ .]") %pm>% unlist()
              if (length(x_strip) > 1) {
@@ -1220,9 +1278,9 @@ exec_as.mo <- function(x,
                  }
                }
              }
-              # (7) try to strip off one element from end and check the remains ----
+              # (8) try to strip off one element from end and check the remains ----
              if (isTRUE(debug)) {
-                cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (7) try to strip off one element from end and check the remains\n"))
+                cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (8) try to strip off one element from end and check the remains\n"))
              }
              if (length(x_strip) > 1) {
                for (i in seq_len(length(x_strip) - 1)) {
@@ -1249,9 +1307,9 @@ exec_as.mo <- function(x,
                  }
                }
              }
-              # (8) check for unknown yeasts/fungi ----
+              # (9) check for unknown yeasts/fungi ----
              if (isTRUE(debug)) {
-                cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (8) check for unknown yeasts/fungi\n"))
+                cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (9) check for unknown yeasts/fungi\n"))
              }
              if (b.x_trimmed %like_case% "yeast") {
                found <- "F_YEAST"
@@ -1275,9 +1333,9 @@ exec_as.mo <- function(x,
                                        stringsAsFactors = FALSE)
                return(found)
              }
-              # (9) try to strip off one element from start and check the remains (only allow >= 2-part name outcome) ----
+              # (10) try to strip off one element from start and check the remains (only allow >= 2-part name outcome) ----
              if (isTRUE(debug)) {
-                cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (9) try to strip off one element from start and check the remains (only allow >= 2-part name outcome)\n"))
+                cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (10) try to strip off one element from start and check the remains (only allow >= 2-part name outcome)\n"))
              }
              x_strip <- a.x_backup %pm>% strsplit("[ .]") %pm>% unlist()
              if (length(x_strip) > 1 & nchar(g.x_backup_without_spp) >= 6) {
@@ -1311,9 +1369,9 @@ exec_as.mo <- function(x,
            if (uncertainty_level >= 3) {
              now_checks_for_uncertainty_level <- 3
              
-              # (10) try to strip off one element from start and check the remains (any text size) ----
+              # (11) try to strip off one element from start and check the remains (any text size) ----
              if (isTRUE(debug)) {
-                cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (10) try to strip off one element from start and check the remains (any text size)\n"))
+                cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (11) try to strip off one element from start and check the remains (any text size)\n"))
              }
              x_strip <- a.x_backup %pm>% strsplit("[ .]") %pm>% unlist()
              if (length(x_strip) > 1 & nchar(g.x_backup_without_spp) >= 6) {
@@ -1338,10 +1396,10 @@ exec_as.mo <- function(x,
                  }
                }
              }
-              # (11) try to strip off one element from end and check the remains (any text size) ----
+              # (12) try to strip off one element from end and check the remains (any text size) ----
              # (this is in fact 7 but without nchar limit of >=6)
              if (isTRUE(debug)) {
-                cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (11) try to strip off one element from end and check the remains (any text size)\n"))
+                cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (12) try to strip off one element from end and check the remains (any text size)\n"))
              }
              if (length(x_strip) > 1) {
                for (i in seq_len(length(x_strip) - 1)) {
@@ -1366,9 +1424,9 @@ exec_as.mo <- function(x,
                }
              }
              
-              # (12) part of a name (very unlikely match) ----
+              # (13) part of a name (very unlikely match) ----
              if (isTRUE(debug)) {
-                cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (12) part of a name (very unlikely match)\n"))
+                cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (13) part of a name (very unlikely match)\n"))
              }
              if (isTRUE(debug)) {
                message("Running '", f.x_withspaces_end_only, "'")
@@ -1460,9 +1518,8 @@ exec_as.mo <- function(x,
                      "You can also use your own reference data with set_mo_source() or directly, e.g.:\n",
                      '  as.mo("mycode", reference_df = data.frame(own = "mycode", mo = "', MO_lookup$mo[match("Escherichia coli", MO_lookup$fullname)], '"))\n',
                      '  mo_name("mycode", reference_df = data.frame(own = "mycode", mo = "', MO_lookup$mo[match("Escherichia coli", MO_lookup$fullname)], '"))\n')
-        warning_(paste0("\n", msg),
+        warning_(paste0("\nin `as.mo()`: ", msg),
                 add_fn = font_red,
-                 call = FALSE,
                 immediate = TRUE) # thus will always be shown, even if >= warnings
      }
      # handling uncertainties ----
@@ -1502,12 +1559,11 @@ exec_as.mo <- function(x,
    # comment below code if all staphylococcal species are categorised as CoNS/CoPS
    if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) {
      if (message_not_thrown_before("as.mo", "becker")) {
-        warning_("Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
+        warning_("in `as.mo()`: Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
                 font_italic(paste("S.",
                                   sort(mo_species(unique(x[x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property]]))),
                                   collapse = ", ")),
                 ". Categorisation to CoNS/CoPS was taken from the original scientific publication(s).",
-                 call = FALSE,
                 immediate = TRUE)
      }
    }
@@ -1680,8 +1736,7 @@ pillar_shaft.mo <- function(x, ...) {
      col <- "The data"
    }
    warning_(col, " contains old MO codes (from a previous AMR package version). ",
-             "Please update your MO codes with `as.mo()`.",
-             call = FALSE)
+             "Please update your MO codes with `as.mo()`.")
  }
  
  # make it always fit exactly
@@ -1755,8 +1810,7 @@ print.mo <- function(x, print.shortnames = FALSE, ...) {
  names(x) <- x_names
  if (!all(x[!is.na(x)] %in% MO_lookup$mo)) {
    warning_("Some MO codes are from a previous AMR package version. ",
-             "Please update these MO codes with `as.mo()`.",
-             call = FALSE)
+             "Please update the MO codes with `as.mo()`.")
  }
  print.default(x, quote = FALSE)
 }
@@ -1785,8 +1839,7 @@ summary.mo <- function(object, ...) {
 as.data.frame.mo <- function(x, ...) {
  if (!all(x[!is.na(x)] %in% MO_lookup$mo)) {
    warning_("The data contains old MO codes (from a previous AMR package version). ",
-             "Please update your MO codes with `as.mo()`.",
-             call = FALSE)
+             "Please update your MO codes with `as.mo()`.")
  }
  nm <- deparse1(substitute(x))
  if (!"nm" %in% names(list(...))) {
@@ -1882,7 +1935,7 @@ print.mo_uncertainties <- function(x, ...) {
  if (NROW(x) == 0) {
    return(NULL)
  }
-  cat(word_wrap("Matching scores", ifelse(has_colour(), " (in blue)", ""), " are based on human pathogenic prevalence and the resemblance between the input and the full taxonomic name. See `?mo_matching_score`.\n\n", add_fn = font_blue))
+  cat(word_wrap("Matching scores", ifelse(has_colour(), " (in blue)", ""), " are based on pathogenicity in humans and the resemblance between the input and the full taxonomic name. See `?mo_matching_score`.\n\n", add_fn = font_blue))
  
  txt <- ""
  for (i in seq_len(nrow(x))) {
@@ -2090,24 +2143,22 @@ replace_old_mo_codes <- function(x, property) {
      n_unique <- ""
    }
    if (property != "mo") {
-      warning_(paste0("The input contained ", n_matched,
-                      " old MO code", ifelse(n_matched == 1, "", "s"),
-                      " (", n_unique, "from a previous AMR package version). ",
-                      "Please update your MO codes with `as.mo()` to increase speed."),
-               call = FALSE)
+      warning_("in `mo_", property, "()`: the input contained ", n_matched,
+               " old MO code", ifelse(n_matched == 1, "", "s"),
+               " (", n_unique, "from a previous AMR package version). ",
+               "Please update your MO codes with `as.mo()` to increase speed.")
    } else {
-      warning_(paste0("The input contained ", n_matched,
-                      " old MO code", ifelse(n_matched == 1, "", "s"),
-                      " (", n_unique, "from a previous AMR package version). ",
-                      n_solved, " old MO code", ifelse(n_solved == 1, "", "s"), 
-                      ifelse(n_solved == 1, " was", " were"), 
-                      ifelse(all_direct_matches, " updated ", font_bold(" guessed ")),
-                      "to ", ifelse(n_solved == 1, "a ", ""), 
-                      "currently used MO code", ifelse(n_solved == 1, "", "s"),
-                      ifelse(n_unsolved > 0,
-                             paste0(" and ", n_unsolved, " old MO code", ifelse(n_unsolved == 1, "", "s"), " could not be updated."),
-                             ".")),
-               call = FALSE)
+      warning_("in `as.mo()`: the input contained ", n_matched,
+               " old MO code", ifelse(n_matched == 1, "", "s"),
+               " (", n_unique, "from a previous AMR package version). ",
+               n_solved, " old MO code", ifelse(n_solved == 1, "", "s"), 
+               ifelse(n_solved == 1, " was", " were"), 
+               ifelse(all_direct_matches, " updated ", font_bold(" guessed ")),
+               "to ", ifelse(n_solved == 1, "a ", ""), 
+               "currently used MO code", ifelse(n_solved == 1, "", "s"),
+               ifelse(n_unsolved > 0,
+                      paste0(" and ", n_unsolved, " old MO code", ifelse(n_unsolved == 1, "", "s"), " could not be updated."),
+                      "."))
    }
  }
  x
--- a/R/mo_matching_score.R
+++ b/R/mo_matching_score.R
@@ -27,13 +27,13 @@
 #' 
 #' This algorithm is used by [as.mo()] and all the [`mo_*`][mo_property()] functions to determine the most probable match of taxonomic records based on user input. 
 #' @inheritSection lifecycle Stable Lifecycle
-#' @author Dr. Matthijs Berends
+#' @author Dr Matthijs Berends
 #' @param x Any user input value(s)
 #' @param n A full taxonomic name, that exists in [`microorganisms$fullname`][microorganisms]
 #' @section Matching Score for Microorganisms:
 #' With ambiguous user input in [as.mo()] and all the [`mo_*`][mo_property()] functions, the returned results are chosen based on their matching score using [mo_matching_score()]. This matching score \eqn{m}, is calculated as:
 #' 
-#' \ifelse{latex}{\deqn{m_{(x, n)} = \frac{l_{n} - 0.5 \cdot \min \begin{cases}l_{n} \\ \textrm{lev}(x, n)\end{cases}}{l_{n} \cdot p_{n} \cdot k_{n}}}}{\ifelse{html}{\figure{mo_matching_score.png}{options: width="300px" alt="mo matching score"}}{m(x, n) = ( l_n * min(l_n, lev(x, n) ) ) / ( l_n * p_n * k_n )}}
+#' \ifelse{latex}{\deqn{m_{(x, n)} = \frac{l_{n} - 0.5 \cdot \min \begin{cases}l_{n} \\ \textrm{lev}(x, n)\end{cases}}{l_{n} \cdot p_{n} \cdot k_{n}}}}{\ifelse{html}{\figure{mo_matching_score.png}{options: width="300" alt="mo matching score"}}{m(x, n) = ( l_n * min(l_n, lev(x, n) ) ) / ( l_n * p_n * k_n )}}
 #' 
 #' where:
 #' 
@@ -49,6 +49,8 @@
 #' All characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
 #' 
 #' All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., `"E. coli"` will return the microbial ID of *Escherichia coli* (\eqn{m = `r round(mo_matching_score("E. coli", "Escherichia coli"), 3)`}, a highly prevalent microorganism found in humans) and not *Entamoeba coli* (\eqn{m = `r round(mo_matching_score("E. coli", "Entamoeba coli"), 3)`}, a less prevalent microorganism in humans), although the latter would alphabetically come first. 
+#' 
+#' Since `AMR` version 1.8.1, common microorganism abbreviations are ignored in determining the matching score. These abbreviations are currently: `r vector_and(pkg_env$mo_field_abbreviations, quotes = FALSE)`.
 #' @export
 #' @inheritSection AMR Reference Data Publicly Available
 #' @inheritSection AMR Read more on Our Website!
@@ -65,9 +67,16 @@ mo_matching_score <- function(x, n) {
  x <- parse_and_convert(x)
  # no dots and other non-whitespace characters
  x <- gsub("[^a-zA-Z0-9 \\(\\)]+", "", x)
+  
+  # remove abbreviations known to the field
+  x <- gsub(paste0("(^|[^a-z0-9]+)(",
+                   paste0(pkg_env$mo_field_abbreviations, collapse = "|"),
+                   ")([^a-z0-9]+|$)"),
+            "", x, perl = TRUE, ignore.case = TRUE)
+  
  # only keep one space
  x <- gsub(" +", " ", x)
-
+  
  # n is always a taxonomically valid full name
  if (length(n) == 1) {
    n <- rep(n, length(x))
@@ -82,7 +91,7 @@ mo_matching_score <- function(x, n) {
  l_n.lev <- double(length = length(x))
  for (i in seq_len(length(x))) {
    # determine Levenshtein distance, but maximise to nchar of n
-    lev[i] <- utils::adist(x[i], n[i], ignore.case = FALSE, fixed = TRUE)
+    lev[i] <- utils::adist(x[i], n[i], ignore.case = FALSE, fixed = TRUE, costs = c(ins = 1, del = 1, sub = 1))
    # minimum of (l_n, Levenshtein distance)
    l_n.lev[i] <- min(l_n[i], as.double(lev[i]))
  }
--- a/R/mo_property.R
+++ b/R/mo_property.R
@@ -684,7 +684,7 @@ mo_url <- function(x, open = FALSE, language = get_AMR_locale(), ...) {
  
  if (isTRUE(open)) {
    if (length(u) > 1) {
-      warning_("Only the first URL will be opened, as `browseURL()` only suports one string.")
+      warning_("in `mo_url()`: only the first URL will be opened, as `browseURL()` only suports one string.")
    }
    utils::browseURL(u[1L])
  }
--- a/R/pca.R
+++ b/R/pca.R
@@ -98,7 +98,7 @@ pca <- function(x,
    
    x <- as.data.frame(new_list, stringsAsFactors = FALSE)
    if (any(vapply(FUN.VALUE = logical(1), x, function(y) !is.numeric(y)))) {
-      warning_("Be sure to first calculate the resistance (or susceptibility) of variables with antimicrobial test results, since PCA works with [numeric] variables only. See Examples in ?pca.", call = FALSE)
+      warning_("in `pca()`: be sure to first calculate the resistance (or susceptibility) of variables with antimicrobial test results, since PCA works with numeric variables only. See Examples in ?pca.", call = FALSE)
    }
    
    # set column names
--- a/R/random.R
+++ b/R/random.R
@@ -106,7 +106,7 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
    if (nrow(df_new) > 0) {
      df <- df_new
    } else {
-      warning_("No rows found that match mo '", mo, "', ignoring argument `mo`", call = FALSE)
+      warning_("in `random_", tolower(type), "()`: no rows found that match mo '", mo, "', ignoring argument `mo`")
    }
  }
  
@@ -117,7 +117,7 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
    if (nrow(df_new) > 0) {
      df <- df_new
    } else {
-      warning_("No rows found that match ab '", ab, "', ignoring argument `ab`", call = FALSE)
+      warning_("in `random_", tolower(type), "()`: no rows found that match ab '", ab, "', ignoring argument `ab`")
    }
  }
 
--- a/R/resistance_predict.R
+++ b/R/resistance_predict.R
@@ -153,7 +153,7 @@ resistance_predict <- function(x,
      x <- dots[which(dots.names == "tbl")]
    }
    if ("I_as_R" %in% dots.names) {
-      warning_("`I_as_R is deprecated - use I_as_S instead.", call = FALSE)
+      warning_("in `resistance_predict()`: I_as_R is deprecated - use I_as_S instead.")
    }
  }
  
--- a/R/rsi.R
+++ b/R/rsi.R
@@ -67,7 +67,7 @@
 #' 
 #' For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`). 
 #' 
-#' Thus, the `guideline` argument must be set to e.g., ``r paste0('"', subset(rsi_translation, guideline %like% "EUCAST")$guideline[1], '"')`` or ``r paste0('"', subset(rsi_translation, guideline %like% "CLSI")$guideline[1], '"')``. By simply using `"EUCAST"` (the default) or `"CLSI"` as input, the latest version of that guideline will automatically be selected. You can set your own data set using the `reference_data` argument. The `guideline` argument will then be ignored.
+#' Thus, the `guideline` argument must be set to e.g., ``r paste0('"', subset(rsi_translation, guideline %like% "EUCAST")$guideline[1], '"')`` or ``r paste0('"', subset(rsi_translation, guideline %like% "CLSI")$guideline[1], '"')``. By simply using `"EUCAST"` (the default) or `"CLSI"` as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the `reference_data` argument. The `guideline` argument will then be ignored.
 #' 
 #' ## After Interpretation
 #' 
@@ -233,9 +233,9 @@ is.rsi.eligible <- function(x, threshold = 0.05) {
  } else if (!any(c("R", "S", "I") %in% x, na.rm = TRUE) & !all(is.na(x))) {
    return(FALSE)
  } else {
-    x <- x[!is.na(x) & !is.null(x) & x != ""]
+    x <- x[!is.na(x) & !is.null(x) & !x %in% c("", "-", "NULL")]
    if (length(x) == 0) {
-      # no other values than NA or ""
+      # no other values than empty
      cur_col <- get_current_column()
      if (!is.null(cur_col)) {
        ab <- suppressWarnings(as.ab(cur_col, fast_mode = TRUE, info = FALSE))
@@ -257,7 +257,7 @@ is.rsi.eligible <- function(x, threshold = 0.05) {
 }

 #' @export
-# extra param: warn (never throw warning)
+# extra param: warn (logical, to never throw a warning)
 as.rsi.default <- function(x, ...) {
  if (is.rsi(x)) {
    return(x)
@@ -278,22 +278,23 @@ as.rsi.default <- function(x, ...) {
      x[x.bak == 2] <- "I"
      x[x.bak == 3] <- "R"  
    }
-
+    
  } else if (!all(is.na(x)) && !identical(levels(x), c("R", "S", "I")) && !all(x %in% c("R", "S", "I", NA))) {
-
+    
    if (all(x %unlike% "(R|S|I)", na.rm = TRUE)) {
      # check if they are actually MICs or disks
      if (all_valid_mics(x)) {
-        warning_("The input seems to contain MIC values. You can transform them with `as.mic()` before running `as.rsi()` to interpret them.", call = FALSE)
+        warning_("in `as.rsi()`: the input seems to contain MIC values. You can transform them with `as.mic()` before running `as.rsi()` to interpret them.")
      } else if (all_valid_disks(x)) {
-        warning_("The input seems to contain disk diffusion values. You can transform them with `as.disk()` before running `as.rsi()` to interpret them.", call = FALSE)
+        warning_("in `as.rsi()`: the input seems to contain disk diffusion values. You can transform them with `as.disk()` before running `as.rsi()` to interpret them.")
      }
    }
    
    # trim leading and trailing spaces, new lines, etc.
    x <- trimws2(as.character(unlist(x)))
+    x[x %in% c(NA, "", "-", "NULL")] <- NA_character_
    x.bak <- x
-    na_before <- length(x[is.na(x) | x == ""])
+    na_before <- length(x[is.na(x)])
    
    # correct for translations
    trans_R <- unlist(TRANSLATIONS[which(TRANSLATIONS$pattern == "Resistant"),
@@ -310,11 +311,15 @@ as.rsi.default <- function(x, ...) {
    x[x %like% "([^a-z]|^)sus(cep(tible)?)?"] <- "S"
    x[x %like% "([^a-z]|^)int(er(mediate)?)?|incr.*exp"] <- "I"
    # remove other invalid characters
-    x <- gsub("[^rsiRSIHi]+", "", x, perl = TRUE)
-    # some labs now report "H" instead of "I" to not interfere with EUCAST prior to 2019
-    x <- gsub("H", "I", x, ignore.case = TRUE)
    # set to capitals
    x <- toupper(x)
+    x <- gsub("[^RSIHDU]+", "", x, perl = TRUE)
+    # some labs now report "H" instead of "I" to not interfere with EUCAST prior to 2019
+    x <- gsub("^H$", "I", x, perl = TRUE)
+    # and MIPS uses D for Dose-dependent (which is I, but it will throw a note)
+    x <- gsub("^D$", "I", x, perl = TRUE)
+    # and MIPS uses U for "susceptible urine"
+    x <- gsub("^U$", "S", x, perl = TRUE)
    # in cases of "S;S" keep S, but in case of "S;I" make it NA
    x <- gsub("^S+$", "S", x)
    x <- gsub("^I+$", "I", x)
@@ -328,11 +333,20 @@ as.rsi.default <- function(x, ...) {
          unique() %pm>%
          sort() %pm>%
          vector_and(quotes = TRUE)
-        warning_(na_after - na_before, " results truncated (",
+        warning_("in `as.rsi()`: ", na_after - na_before, " results truncated (",
                 round(((na_after - na_before) / length(x)) * 100),
                 "%) that were invalid antimicrobial interpretations: ",
                 list_missing, call = FALSE)
      }
+      if (any(toupper(x.bak[!is.na(x.bak)]) == "U") && message_not_thrown_before("as.rsi", "U")) {
+        warning_("in `as.rsi()`: 'U' was interpreted as 'S', following some laboratory systems")
+      }
+      if (any(toupper(x.bak[!is.na(x.bak)]) == "D") && message_not_thrown_before("as.rsi", "D")) {
+        warning_("in `as.rsi()`: 'D' (dose-dependent) was interpreted as 'I', following some laboratory systems")
+      }
+      if (any(toupper(x.bak[!is.na(x.bak)]) == "H") && message_not_thrown_before("as.rsi", "H")) {
+        warning_("in `as.rsi()`: 'H' was interpreted as 'I', following some laboratory systems")
+      }
    }
  }
  
@@ -351,89 +365,17 @@ as.rsi.mic <- function(x,
                       add_intrinsic_resistance = FALSE,
                       reference_data = AMR::rsi_translation,
                       ...) {
-  meet_criteria(x)
-  meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
-  meet_criteria(ab, allow_class = c("ab", "character"))
-  meet_criteria(guideline, allow_class = "character", has_length = 1)
-  meet_criteria(uti, allow_class = "logical", has_length = c(1, length(x)))
-  meet_criteria(conserve_capped_values, allow_class = "logical", has_length = 1)
-  meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1)
-  meet_criteria(reference_data, allow_class = "data.frame")
-  check_reference_data(reference_data)
-  
-  # for dplyr's across()
-  cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
-  if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", call = 0)), error = function(e) FALSE)) {
-    # try to get current column, which will only be available when in across()
-    ab <- tryCatch(cur_column_dplyr(),
-                   error = function(e) ab)
-  }
-  
-  # for auto-determining mo
-  mo_var_found <- ""
-  if (is.null(mo)) {
-    tryCatch({
-      df <- get_current_data(arg_name = "mo", call = -3) # will return an error if not found
-      mo <- NULL
-      try({
-        mo <- suppressMessages(search_type_in_df(df, "mo"))
-      }, silent = TRUE)
-      if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
-        mo_var_found <- paste0(" based on column '", font_bold(mo), "'")
-        mo <- df[, mo, drop = TRUE]
-      }
-    }, error = function(e) 
-      stop_('No information was supplied about the microorganisms (missing argument `mo`). See ?as.rsi.\n\n',
-            "To transform certain columns with e.g. mutate_at(), use `data %>% mutate_at(vars(...), as.rsi, mo = .$x)`, where x is your column with microorganisms.\n",
-            "To tranform all disk diffusion zones in a data set, use `data %>% as.rsi()` or data %>% mutate_if(is.disk, as.rsi).", call = FALSE)
-    )
-  }
-  if (length(ab) == 1 && ab %like% "as.mic") {
-    stop_('No unambiguous name was supplied about the antibiotic (argument `ab`). See ?as.rsi.', call = FALSE)
-  }
-  
-  ab_coerced <- suppressWarnings(as.ab(ab))
-  mo_coerced <- suppressWarnings(as.mo(mo))
-  guideline_coerced <- get_guideline(guideline, reference_data)
-  if (is.na(ab_coerced)) {
-    message_("Returning NAs for unknown drug: '", font_bold(ab),
-             "'. Rename this column to a drug name or code, and check the output with `as.ab()`.", 
-             add_fn = font_red, 
-             as_note = FALSE)
-    return(as.rsi(rep(NA, length(x))))
-  }
-  if (length(mo_coerced) == 1) {
-    mo_coerced <- rep(mo_coerced, length(x))
-  }
-  if (length(uti) == 1) {
-    uti <- rep(uti, length(x))
-  }
-  
-  agent_formatted <- paste0("'", font_bold(ab), "'")
-  agent_name <- ab_name(ab_coerced, tolower = TRUE, language = NULL)
-  if (generalise_antibiotic_name(ab) != generalise_antibiotic_name(agent_name)) {
-    agent_formatted <- paste0(agent_formatted, " (", ab_coerced, ", ", agent_name, ")")
-  }
-  message_("=> Interpreting MIC values of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
-           agent_formatted,
-           mo_var_found, 
-           " according to ", ifelse(identical(reference_data, AMR::rsi_translation),
-                                    font_bold(guideline_coerced),
-                                    "manually defined 'reference_data'"),
-           "... ",
-           appendLF = FALSE,
-           as_note = FALSE)
-  
-  result <- exec_as.rsi(method = "mic",
-                        x = x,
-                        mo = mo_coerced,
-                        ab = ab_coerced,
-                        guideline = guideline_coerced,
-                        uti = uti,
-                        conserve_capped_values = conserve_capped_values,
-                        add_intrinsic_resistance = add_intrinsic_resistance,
-                        reference_data = reference_data) # exec_as.rsi will return message 'OK'
-  result
+  as_rsi_method(method_short = "mic",
+                method_long = "MIC values",
+                x = x,
+                mo = mo, 
+                ab = ab, 
+                guideline = guideline, 
+                uti = uti,
+                conserve_capped_values = conserve_capped_values, 
+                add_intrinsic_resistance = add_intrinsic_resistance,
+                reference_data = reference_data,
+                ...)
 }

 #' @rdname as.rsi
@@ -446,88 +388,17 @@ as.rsi.disk <- function(x,
                        add_intrinsic_resistance = FALSE,
                        reference_data = AMR::rsi_translation,
                        ...) {
-  meet_criteria(x)
-  meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
-  meet_criteria(ab, allow_class = c("ab", "character"))
-  meet_criteria(guideline, allow_class = "character", has_length = 1)
-  meet_criteria(uti, allow_class = "logical", has_length = c(1, length(x)))
-  meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1)
-  meet_criteria(reference_data, allow_class = "data.frame")
-  check_reference_data(reference_data)
-  
-  # for dplyr's across()
-  cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
-  if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", call = 0)), error = function(e) FALSE)) {
-    # try to get current column, which will only be available when in across()
-    ab <- tryCatch(cur_column_dplyr(),
-                   error = function(e) ab)
-  }
-  
-  # for auto-determining mo
-  mo_var_found <- ""
-  if (is.null(mo)) {
-    tryCatch({
-      df <- get_current_data(arg_name = "mo", call = -3) # will return an error if not found
-      mo <- NULL
-      try({
-        mo <- suppressMessages(search_type_in_df(df, "mo"))
-      }, silent = TRUE)
-      if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
-        mo_var_found <- paste0(" based on column '", font_bold(mo), "'")
-        mo <- df[, mo, drop = TRUE]
-      }
-    }, error = function(e) 
-      stop_('No information was supplied about the microorganisms (missing argument `mo`). See ?as.rsi.\n\n',
-            "To transform certain columns with e.g. mutate_at(), use `data %>% mutate_at(vars(...), as.rsi, mo = .$x)`, where x is your column with microorganisms.\n",
-            "To tranform all disk diffusion zones in a data set, use `data %>% as.rsi()` or data %>% mutate_if(is.disk, as.rsi).", call = FALSE)
-    )
-  }
-  if (length(ab) == 1 && ab %like% "as.disk") {
-    stop_('No unambiguous name was supplied about the antibiotic (argument `ab`). See ?as.rsi.', call = FALSE)
-  }
-  
-  ab_coerced <- suppressWarnings(as.ab(ab))
-  mo_coerced <- suppressWarnings(as.mo(mo))
-  guideline_coerced <- get_guideline(guideline, reference_data)
-  if (is.na(ab_coerced)) {
-    message_("Returning NAs for unknown drug: '", font_bold(ab),
-             "'. Rename this column to a drug name or code, and check the output with `as.ab()`.", 
-             add_fn = font_red, 
-             as_note = FALSE)
-    return(as.rsi(rep(NA, length(x))))
-  }
-  if (length(mo_coerced) == 1) {
-    mo_coerced <- rep(mo_coerced, length(x))
-  }
-  if (length(uti) == 1) {
-    uti <- rep(uti, length(x))
-  }
-  
-  agent_formatted <- paste0("'", font_bold(ab), "'")
-  agent_name <- ab_name(ab_coerced, tolower = TRUE, language = NULL)
-  if (generalise_antibiotic_name(ab) != generalise_antibiotic_name(agent_name)) {
-    agent_formatted <- paste0(agent_formatted, " (", ab_coerced, ", ", agent_name, ")")
-  }
-  message_("=> Interpreting disk zones of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
-           agent_formatted,
-           mo_var_found, 
-           " according to ", ifelse(identical(reference_data, AMR::rsi_translation),
-                                    font_bold(guideline_coerced),
-                                    "manually defined 'reference_data'"),
-           "... ",
-           appendLF = FALSE,
-           as_note = FALSE)
-  
-  result <- exec_as.rsi(method = "disk",
-                        x = x,
-                        mo = mo_coerced,
-                        ab = ab_coerced,
-                        guideline = guideline_coerced,
-                        uti = uti,
-                        conserve_capped_values = FALSE,
-                        add_intrinsic_resistance = add_intrinsic_resistance,
-                        reference_data = reference_data) # exec_as.rsi will return message 'OK'
-  result
+  as_rsi_method(method_short = "disk",
+                method_long = "disk diffusion zones",
+                x = x,
+                mo = mo, 
+                ab = ab, 
+                guideline = guideline, 
+                uti = uti,
+                conserve_capped_values = FALSE, 
+                add_intrinsic_resistance = add_intrinsic_resistance,
+                reference_data = reference_data,
+                ...)
 }

 #' @rdname as.rsi
@@ -547,7 +418,7 @@ as.rsi.data.frame <- function(x,
  meet_criteria(conserve_capped_values, allow_class = "logical", has_length = 1)
  meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1)
  meet_criteria(reference_data, allow_class = "data.frame")
-
+  
  x.bak <- x
  for (i in seq_len(ncol(x))) {
    # don't keep factors, overwriting them is hard
@@ -561,7 +432,7 @@ as.rsi.data.frame <- function(x,
  if (is.null(col_mo)) {
    col_mo <- search_type_in_df(x = x, type = "mo", info = FALSE)
  }
-
+  
  # -- UTIs
  col_uti <- uti
  if (is.null(col_uti)) {
@@ -602,7 +473,7 @@ as.rsi.data.frame <- function(x,
      uti <- FALSE
    }
  }
-
+  
  i <- 0
  if (tryCatch(length(list(...)) > 0, error = function(e) TRUE)) {
    sel <- colnames(pm_select(x, ...))
@@ -612,7 +483,7 @@ as.rsi.data.frame <- function(x,
  if (!is.null(col_mo)) {
    sel <- sel[sel != col_mo]
  }
-
+  
  ab_cols <- colnames(x)[vapply(FUN.VALUE = logical(1), x, function(y) {
    i <<- i + 1
    check <- is.mic(y) | is.disk(y)
@@ -635,7 +506,7 @@ as.rsi.data.frame <- function(x,
      return(FALSE)
    }
  })]
-
+  
  stop_if(length(ab_cols) == 0,
          "no columns with MIC values, disk zones or antibiotic column names found in this data set. Use as.mic() or as.disk() to transform antimicrobial columns.")
  # set type per column
@@ -654,7 +525,7 @@ as.rsi.data.frame <- function(x,
    }
    x_mo <- as.mo(x[, col_mo, drop = TRUE])
  }
-
+  
  for (i in seq_len(length(ab_cols))) {
    if (types[i] == "mic") {
      x[, ab_cols[i]] <- as.rsi(x = x %pm>% 
@@ -732,6 +603,105 @@ get_guideline <- function(guideline, reference_data) {
  guideline_param
 }

+as_rsi_method <- function(method_short = "mic",
+                          method_long = "MIC values",
+                          x = x,
+                          mo = NULL, 
+                          ab = deparse(substitute(x)), 
+                          guideline = "EUCAST", 
+                          uti = FALSE,
+                          conserve_capped_values = FALSE,
+                          add_intrinsic_resistance = FALSE,
+                          reference_data = AMR::rsi_translation,
+                          ...) {
+  meet_criteria(x)
+  meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
+  meet_criteria(ab, allow_class = c("ab", "character"))
+  meet_criteria(guideline, allow_class = "character", has_length = 1)
+  meet_criteria(uti, allow_class = "logical", has_length = c(1, length(x)))
+  meet_criteria(conserve_capped_values, allow_class = "logical", has_length = 1)
+  meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1)
+  meet_criteria(reference_data, allow_class = "data.frame")
+  check_reference_data(reference_data)
+  
+  # for dplyr's across()
+  cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
+  if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", call = 0)), error = function(e) FALSE)) {
+    # try to get current column, which will only be available when in across()
+    ab <- tryCatch(cur_column_dplyr(),
+                   error = function(e) ab)
+  }
+  
+  # for auto-determining mo
+  mo_var_found <- ""
+  if (is.null(mo)) {
+    tryCatch({
+      df <- get_current_data(arg_name = "mo", call = -3) # will return an error if not found
+      mo <- NULL
+      try({
+        mo <- suppressMessages(search_type_in_df(df, "mo"))
+      }, silent = TRUE)
+      if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
+        mo_var_found <- paste0(" based on column '", font_bold(mo), "'")
+        mo <- df[, mo, drop = TRUE]
+      }
+    }, error = function(e) {
+      mo <- NULL
+    })
+  }
+  if (is.null(mo)) {
+    stop_("No information was supplied about the microorganisms (missing argument `mo` and no column of class <mo> found). See ?as.rsi.\n\n",
+          "To transform certain columns with e.g. mutate(), use `data %>% mutate(across(..., as.rsi, mo = x))`, where x is your column with microorganisms.\n",
+          "To tranform all ", method_long, " in a data set, use `data %>% as.rsi()` or `data %>% mutate(across(where(is.", method_short, "), as.rsi))`.", call = FALSE)
+  }
+  
+  if (length(ab) == 1 && ab %like% paste0("as.", method_short)) {
+    stop_('No unambiguous name was supplied about the antibiotic (argument `ab`). See ?as.rsi.', call = FALSE)
+  }
+  
+  ab_coerced <- suppressWarnings(as.ab(ab))
+  mo_coerced <- suppressWarnings(as.mo(mo))
+  guideline_coerced <- get_guideline(guideline, reference_data)
+  if (is.na(ab_coerced)) {
+    message_("Returning NAs for unknown drug: '", font_bold(ab),
+             "'. Rename this column to a drug name or code, and check the output with `as.ab()`.", 
+             add_fn = font_red, 
+             as_note = FALSE)
+    return(as.rsi(rep(NA, length(x))))
+  }
+  if (length(mo_coerced) == 1) {
+    mo_coerced <- rep(mo_coerced, length(x))
+  }
+  if (length(uti) == 1) {
+    uti <- rep(uti, length(x))
+  }
+  
+  agent_formatted <- paste0("'", font_bold(ab), "'")
+  agent_name <- ab_name(ab_coerced, tolower = TRUE, language = NULL)
+  if (generalise_antibiotic_name(ab) != generalise_antibiotic_name(agent_name)) {
+    agent_formatted <- paste0(agent_formatted, " (", ab_coerced, ", ", agent_name, ")")
+  }
+  message_("=> Interpreting ", method_long, " of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
+           agent_formatted,
+           mo_var_found, 
+           " according to ", ifelse(identical(reference_data, AMR::rsi_translation),
+                                    font_bold(guideline_coerced),
+                                    "manually defined 'reference_data'"),
+           "... ",
+           appendLF = FALSE,
+           as_note = FALSE)
+  result <- exec_as.rsi(method = method_short,
+                        x = x,
+                        mo = mo_coerced,
+                        ab = ab_coerced,
+                        guideline = guideline_coerced,
+                        uti = uti,
+                        conserve_capped_values = conserve_capped_values,
+                        add_intrinsic_resistance = add_intrinsic_resistance,
+                        reference_data = reference_data) # exec_as.rsi will return message 'OK'
+  result
+}
+
 exec_as.rsi <- function(method,
                        x,
                        mo,
@@ -744,7 +714,7 @@ exec_as.rsi <- function(method,
  metadata_mo <- get_mo_failures_uncertainties_renamed()
  
  x_bak <- data.frame(x_mo = paste0(x, mo), stringsAsFactors = FALSE)
-  df <- unique(data.frame(x, mo), stringsAsFactors = FALSE)
+  df <- unique(data.frame(x, mo, x_mo = paste0(x, mo), stringsAsFactors = FALSE))
  x <- df$x
  mo <- df$mo
  
@@ -754,7 +724,7 @@ exec_as.rsi <- function(method,
    x <- as.disk(x) # when as.rsi.disk is called directly
  }
  
-  warned <- FALSE
+  rise_warning <- FALSE
  method_param <- toupper(method)
  
  genera <- mo_genus(mo, language = NULL)
@@ -799,13 +769,6 @@ exec_as.rsi <- function(method,
  lookup_lancefield <- paste(mo_lancefield, ab)
  lookup_other <- paste(mo_other, ab)
  
-  if (length(unique(paste(trans$mo, trans$ab))) == length(unique(paste(trans$mo, trans$ab, trans$uti))) &&
-      any(trans$uti == TRUE, na.rm = TRUE) && all(uti == FALSE)) {
-    message_("WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
-    warning_("Introducing NA: interpretation of ", font_bold(ab_name(ab, tolower = TRUE)), " for some microorganisms is only available for (uncomplicated) urinary tract infections (UTI). Use argument `uti` to set which isolates are from urine. See ?as.rsi.", call = FALSE)
-    warned <- TRUE
-  }
-  
  any_is_intrinsic_resistant <- FALSE
  
  for (i in seq_len(length(x))) {
@@ -815,7 +778,7 @@ exec_as.rsi <- function(method,
    if (isTRUE(add_intrinsic_resistance) & is_intrinsic_r) {
      if (guideline_coerced %unlike% "EUCAST") {
        if (message_not_thrown_before("as.rsi", "msg2")) {
-          warning_("Using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.", call = FALSE)
+          warning_("in `as.rsi()`: using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.")
        }
      } else {
        new_rsi[i] <- "R"
@@ -824,7 +787,7 @@ exec_as.rsi <- function(method,
    }
    
    get_record <- trans %pm>%
-      # no subsetting to UTI for now
+      # no subsetting to UTI here
      subset(lookup %in% c(lookup_mo[i],
                           lookup_genus[i],
                           lookup_family[i],
@@ -833,6 +796,11 @@ exec_as.rsi <- function(method,
                           lookup_lancefield[i],
                           lookup_other[i]))
    
+    if (any(get_record$uti == TRUE, na.rm = TRUE) && message_not_thrown_before("as.rsi", "msg3", ab)) {
+      warning_("in `as.rsi()`: interpretation of ", font_bold(ab_name(ab, tolower = TRUE)), " is only available for (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use argument `uti` to set which isolates are from urine. See ?as.rsi.")
+      rise_warning <- TRUE
+    }
+    
    if (isTRUE(uti[i])) {
      get_record <- get_record %pm>% 
        # be as specific as possible (i.e. prefer species over genus):
@@ -843,7 +811,7 @@ exec_as.rsi <- function(method,
        pm_filter(uti == FALSE) %pm>% # 'uti' is a column in rsi_translation
        pm_arrange(rank_index)
    }
-    
+  
    get_record <- get_record[1L, , drop = FALSE]
    
    if (NROW(get_record) > 0) {
@@ -872,20 +840,21 @@ exec_as.rsi <- function(method,
  
  if (any_is_intrinsic_resistant & guideline_coerced %like% "EUCAST" & !isTRUE(add_intrinsic_resistance)) {
    # found some intrinsic resistance, but was not applied
-    message_("WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
-    if (message_not_thrown_before("as.rsi", "msg3")) {
-      warning_("Found intrinsic resistance in some bug/drug combinations, although it was not applied.\nUse `as.rsi(..., add_intrinsic_resistance = TRUE)` to apply it.", call = FALSE)
+    if (message_not_thrown_before("as.rsi", "msg4")) {
+      warning_("in `as.rsi()`: found intrinsic resistance in some bug/drug combinations, although it was not applied.\nUse `as.rsi(..., add_intrinsic_resistance = TRUE)` to apply it.")
    }
-    warned <- TRUE
+    rise_warning <- TRUE
  }
  
  new_rsi <- x_bak %pm>%
-    pm_left_join(data.frame(x_mo = paste0(df$x, df$mo), new_rsi,
+    pm_left_join(data.frame(x_mo = paste0(x, mo), new_rsi,
                            stringsAsFactors = FALSE),
                 by = "x_mo") %pm>%
    pm_pull(new_rsi)
  
-  if (warned == FALSE) {
+  if (isTRUE(rise_warning)) {
+    message_("WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
+  } else {
    message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
  }
  
@@ -937,13 +906,13 @@ freq.rsi <- function(x, ...) {
                          .add_header = list(
                            Drug = paste0(ab_name(ab, language = NULL), " (", ab, ", ", paste(ab_atc(ab), collapse = "/"), ")"),
                            `Drug group` = ab_group(ab, language = NULL),
-                            `%SI` = percentage(susceptibility(x, minimum = 0, as_percent = FALSE),
-                                               digits = digits)))
+                            `%SI` = trimws(percentage(susceptibility(x, minimum = 0, as_percent = FALSE),
+                                                      digits = digits))))
  } else {
    cleaner::freq.default(x = x, ...,
                          .add_header = list(
-                            `%SI` = percentage(susceptibility(x, minimum = 0, as_percent = FALSE),
-                                               digits = digits)))
+                            `%SI` = trimws(percentage(susceptibility(x, minimum = 0, as_percent = FALSE),
+                                                      digits = digits))))
  }
 }

--- a/R/rsi_calc.R
+++ b/R/rsi_calc.R
@@ -95,7 +95,7 @@ rsi_calc <- function(...,
  }
  
  if (is.null(x)) {
-    warning_("argument is NULL (check if columns exist): returning NA", call = FALSE)
+    warning_("argument is NULL (check if columns exist): returning NA")
    if (as_percent == TRUE) {
      return(NA_character_)
    } else {
--- a/R/sysdata.rda
+++ b/R/sysdata.rda
--- a/R/translate.R
+++ b/R/translate.R
@@ -193,7 +193,7 @@ translate_AMR <- function(from,
  any_form_in_patterns <- tryCatch(
    any(from_unique %like% paste0("(", paste(gsub(" +\\(.*", "", df_trans$pattern), collapse = "|"), ")")),
    error = function(e) {
-      warning_("Translation not possible. Please open an issue on GitHub (https://github.com/msberends/AMR/issues).", call = FALSE)
+      warning_("Translation not possible. Please open an issue on GitHub (https://github.com/msberends/AMR/issues).")
      return(FALSE)
    })
  
--- a/R/whocc.R
+++ b/R/whocc.R
@@ -27,7 +27,7 @@
 #'
 #' 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}
+#' \if{html}{\figure{logo_who.png}{options: height="60" style=margin-bottom:"5"} \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 (<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/R/zzz.R
+++ b/R/zzz.R
@@ -26,6 +26,11 @@
 # set up package environment, used by numerous AMR functions
 pkg_env <- new.env(hash = FALSE)
 pkg_env$mo_failed <- character(0)
+pkg_env$mo_field_abbreviations <- c("AIEC", "ATEC", "BORSA", "CRSM", "DAEC", "EAEC",
+                                    "EHEC", "EIEC", "EPEC", "ETEC", "GISA", "MRPA",
+                                    "MRSA", "MRSE", "MSSA", "MSSE", "NMEC", "PISP",
+                                    "PRSP", "STEC", "UPEC", "VISA", "VISP", "VRE",
+                                    "VRSA", "VRSP")

 # determine info icon for messages
 utf8_supported <- isTRUE(base::l10n_info()$`UTF-8`)
@@ -111,21 +116,7 @@ if (utf8_supported && !is_latex) {
 # Helper functions --------------------------------------------------------

 create_AB_lookup <- function() {
-  AB_lookup <- AMR::antibiotics
-  AB_lookup$generalised_name <- generalise_antibiotic_name(AB_lookup$name)
-  AB_lookup$generalised_synonyms <- lapply(AB_lookup$synonyms, generalise_antibiotic_name)
-  AB_lookup$generalised_abbreviations <- lapply(AB_lookup$abbreviations, generalise_antibiotic_name)
-  AB_lookup$generalised_loinc <- lapply(AB_lookup$loinc, generalise_antibiotic_name)
-  AB_lookup$generalised_all <- unname(lapply(as.list(as.data.frame(t(AB_lookup[, 
-                                                                               c("ab", "atc", "cid", "name",
-                                                                                 colnames(AB_lookup)[colnames(AB_lookup) %like% "generalised"]),
-                                                                               drop = FALSE]),
-                                                                   stringsAsFactors = FALSE)),
-                                             function(x) {
-                                               x <- generalise_antibiotic_name(unname(unlist(x)))
-                                               x[x != ""]
-                                             }))
-  AB_lookup
+  cbind(AMR::antibiotics, AB_LOOKUP)
 }

 create_MO_lookup <- function() {
@@ -140,12 +131,7 @@ create_MO_lookup <- function() {
  MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5
  
  # use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
-  MO_lookup$fullname_lower <- tolower(trimws(paste(MO_lookup$genus, 
-                                                   MO_lookup$species,
-                                                   MO_lookup$subspecies)))
-  ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname, perl = TRUE)
-  MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname"])
-  MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
+  MO_lookup$fullname_lower <- MO_FULLNAME_LOWER
  
  # add a column with only "e coli" like combinations
  MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower, perl = TRUE)
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1 +1,2 @@
-* This package has a data folder size of ~1.7 MB, which might return a NOTE on some R CMD CHECKs. This package size is needed to provide users reference data for the complete taxonomy of microorganisms - one of the most important features of this package, as it has been in the 16 previous releases of this package. All data sets were compressed using `compression = "xz"` to make them as small as possible.
+Extra release for fixing image options, as requested by CRAN team on 17 February 2022 (Kurt Hornik).
+
--- a/data-raw/AMR_latest.tar.gz
+++ b/data-raw/AMR_latest.tar.gz
--- a/data-raw/_internals.R
+++ b/data-raw/_internals.R
@@ -122,9 +122,21 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
             "mo", drop = TRUE]
  }
 }
+create_MO_fullname_lower <- function() {
+  MO_lookup <- AMR::microorganisms
+  # use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
+  MO_lookup$fullname_lower <- tolower(trimws(paste(MO_lookup$genus, 
+                                                   MO_lookup$species,
+                                                   MO_lookup$subspecies)))
+  ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname, perl = TRUE)
+  MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname"])
+  MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
+  MO_lookup$fullname_lower
+}
 MO_CONS <- create_species_cons_cops("CoNS")
 MO_COPS <- create_species_cons_cops("CoPS")
 MO_STREP_ABCG <- as.mo(MO_lookup[which(MO_lookup$genus == "Streptococcus"), "mo", drop = TRUE], Lancefield = TRUE) %in% c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_GRPC", "B_STRPT_GRPG")
+MO_FULLNAME_LOWER <- create_MO_fullname_lower()

 # antibiotic groups
 # (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv)
@@ -160,6 +172,24 @@ AB_BETALACTAMS <- c(AB_PENICILLINS, AB_CEPHALOSPORINS, AB_CARBAPENEMS)
 # this will be used for documentation:
 DEFINED_AB_GROUPS <- ls(envir = globalenv())
 DEFINED_AB_GROUPS <- DEFINED_AB_GROUPS[!DEFINED_AB_GROUPS %in% globalenv_before_ab]
+create_AB_lookup <- function() {
+  AB_lookup <- AMR::antibiotics
+  AB_lookup$generalised_name <- generalise_antibiotic_name(AB_lookup$name)
+  AB_lookup$generalised_synonyms <- lapply(AB_lookup$synonyms, generalise_antibiotic_name)
+  AB_lookup$generalised_abbreviations <- lapply(AB_lookup$abbreviations, generalise_antibiotic_name)
+  AB_lookup$generalised_loinc <- lapply(AB_lookup$loinc, generalise_antibiotic_name)
+  AB_lookup$generalised_all <- unname(lapply(as.list(as.data.frame(t(AB_lookup[, 
+                                                                               c("ab", "atc", "cid", "name",
+                                                                                 colnames(AB_lookup)[colnames(AB_lookup) %like% "generalised"]),
+                                                                               drop = FALSE]),
+                                                                   stringsAsFactors = FALSE)),
+                                             function(x) {
+                                               x <- generalise_antibiotic_name(unname(unlist(x)))
+                                               x[x != ""]
+                                             }))
+  AB_lookup[, colnames(AB_lookup)[colnames(AB_lookup) %like% "^generalised"]]
+}
+AB_LOOKUP <- create_AB_lookup()

 # Export to package as internal data ----
 usethis::use_data(EUCAST_RULES_DF, 
@@ -169,6 +199,8 @@ usethis::use_data(EUCAST_RULES_DF,
                  MO_CONS,
                  MO_COPS,
                  MO_STREP_ABCG,
+                  MO_FULLNAME_LOWER,
+                  AB_LOOKUP,
                  AB_AMINOGLYCOSIDES,
                  AB_AMINOPENICILLINS,
                  AB_ANTIFUNGALS,
--- a/data-raw/reproduction_of_microorganisms.R
+++ b/data-raw/reproduction_of_microorganisms.R
@@ -26,8 +26,8 @@
 # Reproduction of the `microorganisms` data set

 # Data retrieved from the Catalogue of Life (CoL):
-# https://download.catalogueoflife.org/col/monthly/life/
-# (download latest dwca, such as https://download.catalogueoflife.org/col/monthly/2020-12-01_dwca.zip)
+# https://download.catalogueoflife.org/col/monthly/
+# (download latest dwca, such as https://download.catalogueoflife.org/col/monthly/2022-01-14_dwca.zip)
 # Data retrieved from the Global Biodiversity Information Facility (GBIF): 
 # https://doi.org/10.15468/rffz4x
 #
--- a/docs/404.html
+++ b/docs/404.html
@@ -43,7 +43,7 @@
      </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="Released version">1.8.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
      </span>
    </div>

@@ -210,7 +210,7 @@ Content not found. Please use links in the navbar.

 <div class="pkgdown">
  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>

      </footer>
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -17,7 +17,7 @@
      </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="Released version">1.8.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
      </span>
    </div>

@@ -420,7 +420,7 @@ END OF TERMS AND CONDITIONS
 </div>

 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>

      </footer></div>
--- a/docs/articles/AMR.html
+++ b/docs/articles/AMR.html
--- a/docs/articles/AMR_files/accessible-code-block-0.0.1/empty-anchor.js
+++ b/docs/articles/AMR_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});
--- 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-2.11/header-attrs.js
+++ b/docs/articles/AMR_files/header-attrs-2.11/header-attrs.js
@@ -1,12 +0,0 @@
-// 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]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
-    a = h.attributes;
-    while (a.length > 0) h.removeAttribute(a[0].name);
-  }
-});
--- a/docs/articles/AMR_files/header-attrs-2.9/header-attrs.js
+++ b/docs/articles/AMR_files/header-attrs-2.9/header-attrs.js
@@ -1,12 +0,0 @@
-// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
-// be compatible with the behavior of Pandoc < 2.8).
-document.addEventListener('DOMContentLoaded', function(e) {
-  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
-  var i, h, a;
-  for (i = 0; i < hs.length; i++) {
-    h = hs[i];
-    if (!/^h[1-6]$/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
@@ -44,7 +44,7 @@
      </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="Released version">1.8.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
      </span>
    </div>

@@ -185,7 +185,7 @@

      

-      </header><div class="row">
+      </header><script src="EUCAST_files/accessible-code-block-0.0.1/empty-anchor.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>
@@ -402,7 +402,7 @@

 <div class="pkgdown">
  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>

      </footer>
--- a/docs/articles/EUCAST_files/accessible-code-block-0.0.1/empty-anchor.js
+++ b/docs/articles/EUCAST_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});
--- a/docs/articles/EUCAST_files/header-attrs-2.9/header-attrs.js
+++ b/docs/articles/EUCAST_files/header-attrs-2.9/header-attrs.js
@@ -1,12 +0,0 @@
-// 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
@@ -44,7 +44,7 @@
      </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="Released version">1.8.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
      </span>
    </div>

@@ -185,7 +185,7 @@

      

-      </header><div class="row">
+      </header><script src="MDR_files/accessible-code-block-0.0.1/empty-anchor.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>
@@ -295,8 +295,8 @@
 <span class="co"># Table 3 - Enterobacteriaceae... OK.</span>
 <span class="co"># Table 4 - Pseudomonas aeruginosa... OK.</span>
 <span class="co"># Table 5 - Acinetobacter spp.... OK.</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></code></pre></div>
+<span class="co"># Warning: in `mdro()`: NA introduced for isolates where the available percentage of</span>
+<span class="co"># antimicrobial classes was below 50% (set with `pct_required_classes`)</span></code></pre></div>
 <p>Only results with ‘R’ are considered as resistance. Use <code>combine_SI = FALSE</code> to also consider ‘I’ as resistance.</p>
 <p>Determining multidrug-resistant organisms (MDRO), according to: Guideline: Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Author(s): Magiorakos AP, Srinivasan A, Carey RB, …, Vatopoulos A, Weber JT, Monnet DL Source: Clinical Microbiology and Infection 18:3, 2012; doi: 10.1111/j.1469-0691.2011.03570.x</p>
 <p>(16 isolates had no test results)</p>
@@ -320,17 +320,17 @@ Unique: 2</p>
 <td align="left">1</td>
 <td align="left">Negative</td>
 <td align="right">1601</td>
-<td align="right">92.60%</td>
+<td align="right">92.6%</td>
 <td align="right">1601</td>
-<td align="right">92.60%</td>
+<td align="right">92.6%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Multi-drug-resistant (MDR)</td>
 <td align="right">128</td>
-<td align="right">7.40%</td>
+<td align="right">7.4%</td>
 <td align="right">1729</td>
-<td align="right">100.00%</td>
+<td align="right">100.0%</td>
 </tr>
 </tbody>
 </table>
@@ -358,19 +358,19 @@ Unique: 2</p>
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
 <span class="co">#   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
-<span class="co"># 1          I         R            I          S            R            S</span>
-<span class="co"># 2          I         S            R          R            S            R</span>
-<span class="co"># 3          R         I            S          I            R            S</span>
-<span class="co"># 4          S         S            I          R            I            S</span>
-<span class="co"># 5          S         R            S          S            S            I</span>
-<span class="co"># 6          S         R            R          S            R            I</span>
+<span class="co"># 1          S         R            S          I            R            S</span>
+<span class="co"># 2          I         I            S          S            I            I</span>
+<span class="co"># 3          I         S            R          R            R            S</span>
+<span class="co"># 4          S         S            I          S            R            S</span>
+<span class="co"># 5          R         R            S          I            R            I</span>
+<span class="co"># 6          R         S            R          S            S            I</span>
 <span class="co">#   kanamycin</span>
-<span class="co"># 1         S</span>
-<span class="co"># 2         I</span>
-<span class="co"># 3         R</span>
-<span class="co"># 4         R</span>
+<span class="co"># 1         I</span>
+<span class="co"># 2         S</span>
+<span class="co"># 3         S</span>
+<span class="co"># 4         I</span>
 <span class="co"># 5         I</span>
-<span class="co"># 6         R</span></code></pre></div>
+<span class="co"># 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 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>
@@ -390,7 +390,7 @@ Unique: 2</p>
 <span class="co">#            management of drug-resistant tuberculosis</span>
 <span class="co"># Author(s): WHO (World Health Organization)</span>
 <span class="co"># Version:   WHO/HTM/TB/2014.11, 2014</span>
-<span class="co"># Source:    https://www.who.int/tb/publications/pmdt_companionhandbook/en/</span></code></pre></div>
+<span class="co"># Source:    https://www.who.int/publications/i/item/9789241548809</span></code></pre></div>
 <p>Create a frequency table of the results:</p>
 <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" class="external-link">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>
@@ -398,7 +398,7 @@ Unique: 2</p>
 <p>Class: factor &gt; ordered (numeric)<br>
 Length: 5,000<br>
 Levels: 5: Negative &lt; Mono-resistant &lt; Poly-resistant &lt; Multi-drug-resistant &lt;…<br>
-Available: 5,000 (100.0%, NA: 0 = 0.0%)<br>
+Available: 5,000 (100%, NA: 0 = 0%)<br>
 Unique: 5</p>
 <table class="table">
 <thead><tr class="header">
@@ -413,40 +413,40 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistant</td>
-<td align="right">3250</td>
-<td align="right">65.00%</td>
-<td align="right">3250</td>
-<td align="right">65.00%</td>
+<td align="right">3244</td>
+<td align="right">64.88%</td>
+<td align="right">3244</td>
+<td align="right">64.88%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">975</td>
-<td align="right">19.50%</td>
-<td align="right">4225</td>
-<td align="right">84.50%</td>
+<td align="right">990</td>
+<td align="right">19.80%</td>
+<td align="right">4234</td>
+<td align="right">84.68%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Multi-drug-resistant</td>
-<td align="right">474</td>
-<td align="right">9.48%</td>
-<td align="right">4699</td>
-<td align="right">93.98%</td>
+<td align="right">417</td>
+<td align="right">8.34%</td>
+<td align="right">4651</td>
+<td align="right">93.02%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistant</td>
-<td align="right">203</td>
-<td align="right">4.06%</td>
-<td align="right">4902</td>
-<td align="right">98.04%</td>
+<td align="right">248</td>
+<td align="right">4.96%</td>
+<td align="right">4899</td>
+<td align="right">97.98%</td>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
 <td align="left">Extensively drug-resistant</td>
-<td align="right">98</td>
-<td align="right">1.96%</td>
+<td align="right">101</td>
+<td align="right">2.02%</td>
 <td align="right">5000</td>
 <td align="right">100.00%</td>
 </tr>
@@ -470,7 +470,7 @@ Unique: 5</p>

 <div class="pkgdown">
  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>

      </footer>
--- a/docs/articles/MDR_files/accessible-code-block-0.0.1/empty-anchor.js
+++ b/docs/articles/MDR_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});
--- a/docs/articles/MDR_files/header-attrs-2.11/header-attrs.js
+++ b/docs/articles/MDR_files/header-attrs-2.11/header-attrs.js
@@ -1,12 +0,0 @@
-// 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]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
-    a = h.attributes;
-    while (a.length > 0) h.removeAttribute(a[0].name);
-  }
-});
--- a/docs/articles/MDR_files/header-attrs-2.9/header-attrs.js
+++ b/docs/articles/MDR_files/header-attrs-2.9/header-attrs.js
@@ -1,12 +0,0 @@
-// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
-// be compatible with the behavior of Pandoc < 2.8).
-document.addEventListener('DOMContentLoaded', function(e) {
-  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
-  var i, h, a;
-  for (i = 0; i < hs.length; i++) {
-    h = hs[i];
-    if (!/^h[1-6]$/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
@@ -44,7 +44,7 @@
      </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="Released version">1.8.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
      </span>
    </div>

@@ -185,7 +185,7 @@

      

-      </header><div class="row">
+      </header><script src="PCA_files/accessible-code-block-0.0.1/empty-anchor.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>
@@ -199,18 +199,18 @@
    
    
 <p><strong>NOTE: This page will be updated soon, as the pca() function is currently being developed.</strong></p>
-<div class="section level1">
-<h1 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-</h1>
+<div class="section level2">
+<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
+</h2>
 </div>
-<div class="section level1">
-<h1 id="transforming">Transforming<a class="anchor" aria-label="anchor" href="#transforming"></a>
-</h1>
+<div class="section level2">
+<h2 id="transforming">Transforming<a class="anchor" aria-label="anchor" href="#transforming"></a>
+</h2>
 <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 sourceCode r">
-<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR">AMR</a></span><span class="op">)</span>
+<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">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" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
-<span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
+<span class="fu"><a href="https://dplyr.tidyverse.org/reference/glimpse.html" class="external-link">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            <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-…</span>
@@ -283,9 +283,9 @@
 <span class="co"># <span style="color: #BCBCBC;">5</span> Caryophanales     Gemella         <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span></span>
 <span class="co"># <span style="color: #BCBCBC;">6</span> Caryophanales     Listeria        <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span></span></code></pre></div>
 </div>
-<div class="section level1">
-<h1 id="perform-principal-component-analysis">Perform principal component analysis<a class="anchor" aria-label="anchor" href="#perform-principal-component-analysis"></a>
-</h1>
+<div class="section level2">
+<h2 id="perform-principal-component-analysis">Perform principal component analysis<a class="anchor" aria-label="anchor" href="#perform-principal-component-analysis"></a>
+</h2>
 <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 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>
@@ -305,9 +305,9 @@
 <span class="co"># [1] "Caryophanales"    "Enterobacterales" "Lactobacillales"  "Pseudomonadales"</span></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" class="external-link">biplot()</a></code> function, to see which antimicrobial resistance per drug explain the difference per microorganism.</p>
 </div>
-<div class="section level1">
-<h1 id="plotting-the-results">Plotting the results<a class="anchor" aria-label="anchor" href="#plotting-the-results"></a>
-</h1>
+<div class="section level2">
+<h2 id="plotting-the-results">Plotting the results<a class="anchor" aria-label="anchor" href="#plotting-the-results"></a>
+</h2>
 <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" class="external-link">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>
@@ -340,7 +340,7 @@

 <div class="pkgdown">
  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>

      </footer>
--- a/docs/articles/PCA_files/accessible-code-block-0.0.1/empty-anchor.js
+++ b/docs/articles/PCA_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});
--- 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-2.9/header-attrs.js
+++ b/docs/articles/PCA_files/header-attrs-2.9/header-attrs.js
@@ -1,12 +0,0 @@
-// 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
@@ -44,7 +44,7 @@
      </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="Released version">1.8.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
      </span>
    </div>

@@ -185,13 +185,13 @@

      

-      </header><div class="row">
+      </header><script src="SPSS_files/accessible-code-block-0.0.1/empty-anchor.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 data-toc-skip class="author">Dr. Matthijs Berends</h4>
            
-            <h4 data-toc-skip class="date">23 December 2021</h4>
+            <h4 data-toc-skip class="date">27 March 2022</h4>
      
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
      <div class="hidden name"><code>SPSS.Rmd</code></div>
@@ -226,7 +226,7 @@
 </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" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">430,288 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" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">440,893 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>
@@ -241,7 +241,7 @@
 <li>
 <p><strong>R is (nowadays) the preferred analysis software in academic papers.</strong></p>
 <p>At present, R is among the world most powerful statistical languages, and it is generally very popular in science (Bollmann <em>et al.</em>, 2017). For all the above reasons, the number of references to R as an analysis method in academic papers <a href="https://r4stats.com/2014/08/20/r-passes-spss-in-scholarly-use-stata-growing-rapidly/" class="external-link">is rising continuously</a> and has even surpassed SPSS for academic use (Muenchen, 2014).</p>
-<p>I believe that the thing with SPSS is, that it has always had a great user interface which is very easy to learn and use. Back when they developed it, they had very little competition, let alone from R. R didn’t even had a professional user interface until the last decade (called RStudio, see below). How people used R between the nineties and 2010 is almost completely incomparable to how R is being used now. The language itself <a href="https://www.tidyverse.org/packages/" class="external-link">has been restyled completely</a> by volunteers who are dedicated professionals in the field of data science. SPSS was great when there was nothing else that could compete. But now in 2021, I don’t see any reason why SPSS would be of any better use than R.</p>
+<p>I believe that the thing with SPSS is, that it has always had a great user interface which is very easy to learn and use. Back when they developed it, they had very little competition, let alone from R. R didn’t even had a professional user interface until the last decade (called RStudio, see below). How people used R between the nineties and 2010 is almost completely incomparable to how R is being used now. The language itself <a href="https://www.tidyverse.org/packages/" class="external-link">has been restyled completely</a> by volunteers who are dedicated professionals in the field of data science. SPSS was great when there was nothing else that could compete. But now in 2022, I don’t see any reason why SPSS would be of any better use than R.</p>
 </li>
 </ul>
 <p>To demonstrate the first point:</p>
@@ -414,7 +414,7 @@

 <div class="pkgdown">
  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>

      </footer>
--- a/docs/articles/SPSS_files/accessible-code-block-0.0.1/empty-anchor.js
+++ b/docs/articles/SPSS_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});
--- a/docs/articles/SPSS_files/header-attrs-2.11/header-attrs.js
+++ b/docs/articles/SPSS_files/header-attrs-2.11/header-attrs.js
@@ -1,12 +0,0 @@
-// 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]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
-    a = h.attributes;
-    while (a.length > 0) h.removeAttribute(a[0].name);
-  }
-});
--- a/docs/articles/SPSS_files/header-attrs-2.9/header-attrs.js
+++ b/docs/articles/SPSS_files/header-attrs-2.9/header-attrs.js
@@ -1,12 +0,0 @@
-// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
-// be compatible with the behavior of Pandoc < 2.8).
-document.addEventListener('DOMContentLoaded', function(e) {
-  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
-  var i, h, a;
-  for (i = 0; i < hs.length; i++) {
-    h = hs[i];
-    if (!/^h[1-6]$/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
@@ -44,7 +44,7 @@
      </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="Released version">1.8.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
      </span>
    </div>

@@ -185,7 +185,7 @@

      

-      </header><div class="row">
+      </header><script src="WHONET_files/accessible-code-block-0.0.1/empty-anchor.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>
@@ -215,7 +215,7 @@
 <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" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">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" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">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" class="external-link">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" class="external-link">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" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/cleaner" class="external-link">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>
@@ -238,7 +238,7 @@
 <p><strong>Frequency table</strong></p>
 <p>Class: character<br>
 Length: 500<br>
-Available: 500 (100.0%, NA: 0 = 0.0%)<br>
+Available: 500 (100%, NA: 0 = 0%)<br>
 Unique: 37</p>
 <p>Shortest: 11<br>
 Longest: 40</p>
@@ -334,7 +334,7 @@ Longest: 40</p>
 </tr>
 </tbody>
 </table>
-<p>(omitted 27 entries, n = 56 [11.20%])</p>
+<p>(omitted 27 entries, n = 56 [11.2%])</p>
 <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>
@@ -413,7 +413,7 @@ Drug group: Beta-lactams/penicillins<br>

 <div class="pkgdown">
  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>

      </footer>
--- a/docs/articles/WHONET_files/accessible-code-block-0.0.1/empty-anchor.js
+++ b/docs/articles/WHONET_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});
--- 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-2.9/header-attrs.js
+++ b/docs/articles/WHONET_files/header-attrs-2.9/header-attrs.js
@@ -1,12 +0,0 @@
-// 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
@@ -44,7 +44,7 @@
      </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="Released version">1.8.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
      </span>
    </div>

@@ -185,7 +185,7 @@

      

-      </header><div class="row">
+      </header><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
  <div class="col-md-9 contents">
    <div class="page-header toc-ignore">
      <h1 data-toc-skip>Benchmarks</h1>
@@ -202,7 +202,7 @@
 <p>Using the <code>microbenchmark</code> package, we can review the calculation performance of this function. Its function <code><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark()</a></code> runs different input expressions independently of each other and measures their time-to-result.</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/joshuaulrich/microbenchmark/" class="external-link">microbenchmark</a></span><span class="op">)</span>
-<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">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" class="external-link">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" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></code></pre></div>
 <p>In the next test, we try to ‘coerce’ different input values into the microbial code of <em>Staphylococcus aureus</em>. Coercion is a computational process of forcing output based on an input. For microorganism names, coercing user input to taxonomically valid microorganism names is crucial to ensure correct interpretation and to enable grouping based on taxonomic properties.</p>
 <p>The actual result is the same every time: it returns its microorganism code <code>B_STPHY_AURS</code> (<em>B</em> stands for <em>Bacteria</em>, its taxonomic kingdom).</p>
@@ -222,23 +222,23 @@
  <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://docs.ropensci.org/skimr/reference/print.html" class="external-link">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://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
 <span class="co">#                                   expr   min    lq  mean median    uq max neval</span>
-<span class="co">#                           as.mo("sau")  10.0  12.0  20.0   12.0  15.0  53    25</span>
-<span class="co">#                          as.mo("stau")  49.0  54.0  72.0   58.0  91.0  97    25</span>
-<span class="co">#                          as.mo("STAU")  50.0  54.0  71.0   57.0  90.0 110    25</span>
-<span class="co">#                        as.mo("staaur")  10.0  12.0  17.0   12.0  14.0  51    25</span>
-<span class="co">#                        as.mo("STAAUR")  10.0  12.0  17.0   12.0  14.0  54    25</span>
-<span class="co">#                     as.mo("S. aureus")  26.0  27.0  40.0   31.0  56.0  74    25</span>
-<span class="co">#                      as.mo("S aureus")  26.0  27.0  39.0   29.0  58.0  68    25</span>
-<span class="co">#         as.mo("Staphylococcus aureus")   3.5   3.9   6.6    4.1   4.8  38    25</span>
-<span class="co">#  as.mo("Staphylococcus aureus (MRSA)") 230.0 240.0 250.0  240.0 250.0 280    25</span>
-<span class="co">#       as.mo("Sthafilokkockus aaureuz") 180.0 190.0 200.0  190.0 200.0 290    25</span>
-<span class="co">#                          as.mo("MRSA")  11.0  12.0  19.0   13.0  14.0  50    25</span>
-<span class="co">#                          as.mo("VISA")  21.0  22.0  32.0   25.0  50.0  60    25</span></code></pre></div>
+<span class="co">#                           as.mo("sau")  19.0  20.0  25.0   20.0  26.0  55    25</span>
+<span class="co">#                          as.mo("stau")  94.0  95.0 110.0  100.0 130.0 140    25</span>
+<span class="co">#                          as.mo("STAU")  92.0  97.0 110.0  110.0 120.0 140    25</span>
+<span class="co">#                        as.mo("staaur")  19.0  19.0  24.0   20.0  21.0  56    25</span>
+<span class="co">#                        as.mo("STAAUR")  19.0  20.0  21.0   20.0  20.0  49    25</span>
+<span class="co">#                     as.mo("S. aureus")  54.0  57.0  72.0   64.0  86.0  96    25</span>
+<span class="co">#                      as.mo("S aureus")  55.0  55.0  72.0   57.0  90.0 100    25</span>
+<span class="co">#         as.mo("Staphylococcus aureus")   5.6   5.7   8.5    5.8   6.2  40    25</span>
+<span class="co">#  as.mo("Staphylococcus aureus (MRSA)") 360.0 370.0 400.0  400.0 420.0 550    25</span>
+<span class="co">#       as.mo("Sthafilokkockus aaureuz") 280.0 290.0 300.0  300.0 320.0 350    25</span>
+<span class="co">#                          as.mo("MRSA")  19.0  20.0  24.0   20.0  21.0  51    25</span>
+<span class="co">#                          as.mo("VISA")  34.0  34.0  48.0   36.0  65.0  73    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 47 times slower to determine.</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 69 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>
 <div class="section level3">
 <h3 id="repetitive-results">Repetitive results<a class="anchor" aria-label="anchor" href="#repetitive-results"></a>
@@ -258,8 +258,8 @@
 <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" class="external-link">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
 <span class="co"># Class &lt;mo&gt;</span>
-<span class="co"># [1] B_STPHY_AURS B_STRPT_EQNS B_KLBSL_PNMN B_STPHY_EPDR B_STPHY_AURS</span>
-<span class="co"># [6] B_CRYNB_STRT</span>
+<span class="co"># [1] B_ENTRBC_CLOC B_ESCHR_COLI  B_STRPT_PYGN  B_STPHY_AURS  B_ESCHR_COLI </span>
+<span class="co"># [6] B_STRPT_PNMN</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" class="external-link">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
@@ -272,11 +272,11 @@
 <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" class="external-link">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://docs.ropensci.org/skimr/reference/print.html" class="external-link">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://rdrr.io/r/base/print.html" class="external-link">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) 196 209  274    223 364 388    10</span></code></pre></div>
-<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.223 seconds. That is 112 nanoseconds on average. You only lose time on your unique input values.</p>
+<span class="co">#  mo_name(x) 259 264  357    299 451 509    10</span></code></pre></div>
+<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.299 seconds. That is 149 nanoseconds on average. You only lose time on your unique input values.</p>
 </div>
 <div class="section level3">
 <h3 id="precalculated-results">Precalculated results<a class="anchor" aria-label="anchor" href="#precalculated-results"></a>
@@ -287,13 +287,13 @@
                         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://docs.ropensci.org/skimr/reference/print.html" class="external-link">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://rdrr.io/r/base/print.html" class="external-link">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  8.00  9.16  9.19   9.28  9.46  9.73    10</span>
-<span class="co">#     B 23.40 27.20 32.60  27.90 28.10 80.20    10</span>
-<span class="co">#     C  1.85  2.25  2.40   2.47  2.62  2.90    10</span></code></pre></div>
-<p>So going from <code>mo_name("Staphylococcus aureus")</code> to <code>"Staphylococcus aureus"</code> takes 0.0025 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
+<span class="co">#  expr   min    lq mean median    uq   max neval</span>
+<span class="co">#     A 11.90 12.10 13.0  13.50 13.70 13.80    10</span>
+<span class="co">#     B 60.90 61.20 67.7  66.20 66.90 99.70    10</span>
+<span class="co">#     C  2.91  2.94  3.2   3.32  3.38  3.46    10</span></code></pre></div>
+<p>So going from <code>mo_name("Staphylococcus aureus")</code> to <code>"Staphylococcus aureus"</code> takes 0.0033 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" class="external-link">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>,
@@ -304,17 +304,17 @@
                         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://docs.ropensci.org/skimr/reference/print.html" class="external-link">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://rdrr.io/r/base/print.html" class="external-link">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 1.76 1.80 2.07   1.95 2.26 2.90    10</span>
-<span class="co">#     B 1.69 1.73 1.90   1.81 2.03 2.48    10</span>
-<span class="co">#     C 1.71 1.77 1.92   1.91 2.05 2.17    10</span>
-<span class="co">#     D 1.68 1.71 1.76   1.76 1.82 1.88    10</span>
-<span class="co">#     E 1.68 1.70 1.89   1.89 2.04 2.26    10</span>
-<span class="co">#     F 1.67 1.75 1.93   1.89 2.11 2.35    10</span>
-<span class="co">#     G 1.70 1.76 1.97   1.88 2.12 2.43    10</span>
-<span class="co">#     H 1.67 1.71 1.83   1.75 1.98 2.14    10</span></code></pre></div>
+<span class="co">#     A 2.92 2.93 3.02   2.94 3.02 3.40    10</span>
+<span class="co">#     B 2.87 2.90 3.14   3.09 3.32 3.71    10</span>
+<span class="co">#     C 2.91 2.94 3.15   3.12 3.33 3.46    10</span>
+<span class="co">#     D 2.86 2.90 3.05   2.96 3.27 3.30    10</span>
+<span class="co">#     E 2.87 2.88 3.03   2.96 3.16 3.29    10</span>
+<span class="co">#     F 2.92 2.95 3.08   2.98 3.29 3.35    10</span>
+<span class="co">#     G 2.89 2.96 3.04   2.99 3.11 3.29    10</span>
+<span class="co">#     H 2.85 2.95 3.11   3.08 3.31 3.38    10</span></code></pre></div>
 <p>Of course, when running <code>mo_phylum("Firmicutes")</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 class="section level3">
@@ -347,19 +347,19 @@
                         ru <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"ru"</span><span class="op">)</span>,
                         sv <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"sv"</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://docs.ropensci.org/skimr/reference/print.html" class="external-link">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://rdrr.io/r/base/print.html" class="external-link">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">#    da 1.9470 2.0220 2.190 2.0720 2.358  3.234   100</span>
-<span class="co">#    de 1.9560 2.0330 3.649 2.1610 2.401 50.670   100</span>
-<span class="co">#    en 0.8937 0.9124 1.022 0.9776 1.120  1.748   100</span>
-<span class="co">#    es 1.9710 2.0290 2.216 2.1000 2.391  3.109   100</span>
-<span class="co">#    fr 1.8280 1.8960 3.214 1.9420 2.237 71.550   100</span>
-<span class="co">#    it 1.9370 1.9970 2.163 2.0610 2.339  3.210   100</span>
-<span class="co">#    nl 1.9710 2.0280 2.698 2.1110 2.421 49.340   100</span>
-<span class="co">#    pt 1.8920 1.9600 2.119 2.0200 2.261  3.265   100</span>
-<span class="co">#    ru 1.8630 1.9420 2.779 2.0270 2.335 66.660   100</span>
-<span class="co">#    sv 1.8680 1.9190 4.062 1.9890 2.263 78.870   100</span></code></pre></div>
+<span class="co">#  expr   min    lq  mean median    uq    max neval</span>
+<span class="co">#    da 3.546 3.643 4.072  3.704 3.832 35.930   100</span>
+<span class="co">#    de 3.597 3.659 4.422  3.734 3.839 36.400   100</span>
+<span class="co">#    en 1.672 1.726 1.804  1.767 1.794  2.259   100</span>
+<span class="co">#    es 3.609 3.685 4.496  3.760 3.843 36.540   100</span>
+<span class="co">#    fr 3.484 3.567 3.725  3.654 3.713  6.281   100</span>
+<span class="co">#    it 3.523 3.615 4.419  3.720 3.787 36.720   100</span>
+<span class="co">#    nl 3.614 3.676 3.805  3.732 3.838  4.703   100</span>
+<span class="co">#    pt 3.512 3.595 4.077  3.659 3.789 37.310   100</span>
+<span class="co">#    ru 3.556 3.647 4.057  3.680 3.812 35.230   100</span>
+<span class="co">#    sv 3.540 3.642 4.093  3.732 3.803 36.340   100</span></code></pre></div>
 <p>Currently supported languages are Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish.</p>
 </div>
  </div>
@@ -379,7 +379,7 @@

 <div class="pkgdown">
  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>

      </footer>
--- a/docs/articles/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js
+++ b/docs/articles/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});
--- 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-2.9/header-attrs.js
+++ b/docs/articles/benchmarks_files/header-attrs-2.9/header-attrs.js
@@ -1,12 +0,0 @@
-// 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
@@ -44,7 +44,7 @@
      </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="Released version">1.8.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
      </span>
    </div>

@@ -185,12 +185,12 @@

      

-      </header><div class="row">
+      </header><script src="datasets_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
  <div class="col-md-9 contents">
    <div class="page-header toc-ignore">
      <h1 data-toc-skip>Data sets for download / own use</h1>
            
-            <h4 data-toc-skip class="date">23 December 2021</h4>
+            <h4 data-toc-skip class="date">27 March 2022</h4>
      
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
      <div class="hidden name"><code>datasets.Rmd</code></div>
@@ -209,7 +209,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 </h2>
 <p>A data set with 70,760 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
 <p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 29 November 2021 11:38:23 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
+<p>It was last updated on 1 February 2022 22:08:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">R file</a> (1.3 MB)<br>
@@ -430,7 +430,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <p>A data set with 14,338 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>prevalence</em>.</p>
 <p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
 <p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 6 October 2021 14:38:29 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
+<p>It was last updated on 1 February 2022 22:08:19 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">R file</a> (0.2 MB)<br>
@@ -495,7 +495,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 </h2>
 <p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
 <p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
+<p>It was last updated on 1 February 2022 22:08:19 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">R file</a> (33 kB)<br>
@@ -663,7 +663,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 </h2>
 <p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
 <p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 29 August 2020 19:53:07 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
+<p>It was last updated on 23 July 2021 20:35:47 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">R file</a> (5 kB)<br>
@@ -790,7 +790,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 </h2>
 <p>A data set with 134,956 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
 <p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
+<p>It was last updated on 1 February 2022 22:08:19 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">R file</a> (78 kB)<br>
@@ -808,7 +808,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <div class="section level3">
 <h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
 </h3>
-<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">‘EUCAST Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ v3.3</a> (2021).</p>
+<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes/" class="external-link">‘EUCAST Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ v3.3</a> (2021).</p>
 </div>
 <div class="section level3">
 <h3 id="example-content-4">Example content<a class="anchor" aria-label="anchor" href="#example-content-4"></a>
@@ -1057,7 +1057,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 </h2>
 <p>A data set with 20,318 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
 <p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
+<p>It was last updated on 1 February 2022 22:08:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R file</a> (39 kB)<br>
@@ -1195,7 +1195,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 </h2>
 <p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
 <p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 25 January 2021 20:58:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
+<p>It was last updated on 23 July 2021 20:35:47 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">R file</a> (3 kB)<br>
@@ -1321,7 +1321,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi

 <div class="pkgdown">
  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>

      </footer>
--- a/docs/articles/datasets_files/accessible-code-block-0.0.1/empty-anchor.js
+++ b/docs/articles/datasets_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});
--- a/docs/articles/datasets_files/header-attrs-2.11/header-attrs.js
+++ b/docs/articles/datasets_files/header-attrs-2.11/header-attrs.js
@@ -1,12 +0,0 @@
-// 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]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
-    a = h.attributes;
-    while (a.length > 0) h.removeAttribute(a[0].name);
-  }
-});
--- a/docs/articles/datasets_files/header-attrs-2.9/header-attrs.js
+++ b/docs/articles/datasets_files/header-attrs-2.9/header-attrs.js
@@ -1,12 +0,0 @@
-// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
-// be compatible with the behavior of Pandoc < 2.8).
-document.addEventListener('DOMContentLoaded', function(e) {
-  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
-  var i, h, a;
-  for (i = 0; i < hs.length; i++) {
-    h = hs[i];
-    if (!/^h[1-6]$/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/index.html
+++ b/docs/articles/index.html
@@ -17,7 +17,7 @@
      </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="Released version">1.8.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
      </span>
    </div>

@@ -189,7 +189,7 @@
 </div>

 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>

      </footer></div>
--- a/docs/articles/resistance_predict.html
+++ b/docs/articles/resistance_predict.html
@@ -44,7 +44,7 @@
      </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="Released version">1.8.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
      </span>
    </div>

@@ -185,7 +185,7 @@

      

-      </header><div class="row">
+      </header><script src="resistance_predict_files/accessible-code-block-0.0.1/empty-anchor.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>
@@ -206,7 +206,7 @@
 <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" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span>
-<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">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" class="external-link">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></code></pre></div>
@@ -216,18 +216,18 @@
 </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"><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>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true"></a><span class="co"># resistance prediction of piperacillin/tazobactam (TZP):</span></span>
+<span id="cb2-2"><a href="#cb2-2" aria-hidden="true"></a><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>)</span>
+<span id="cb2-3"><a href="#cb2-3" aria-hidden="true"></a></span>
+<span id="cb2-4"><a href="#cb2-4" aria-hidden="true"></a><span class="co"># or:</span></span>
+<span id="cb2-5"><a href="#cb2-5" aria-hidden="true"></a>example_isolates <span class="op">%&gt;%</span><span class="st"> </span></span>
+<span id="cb2-6"><a href="#cb2-6" aria-hidden="true"></a><span class="st">  </span><span class="kw">resistance_predict</span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>,</span>
+<span id="cb2-7"><a href="#cb2-7" aria-hidden="true"></a>                     model  <span class="st">"binomial"</span>)</span>
+<span id="cb2-8"><a href="#cb2-8" aria-hidden="true"></a></span>
+<span id="cb2-9"><a href="#cb2-9" aria-hidden="true"></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"></a>predict_TZP &lt;-<span class="st"> </span>example_isolates <span class="op">%&gt;%</span><span class="st"> </span></span>
+<span id="cb2-11"><a href="#cb2-11" aria-hidden="true"></a><span class="st">  </span><span class="kw">resistance_predict</span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>,</span>
+<span id="cb2-12"><a href="#cb2-12" aria-hidden="true"></a>                     <span class="dt">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>resistance_predict(..., info = FALSE)</code>.</p>
 <pre><code><span class="co"># ℹ Using column 'date' as input for `col_date`.</span></code></pre>
@@ -264,7 +264,8 @@
 <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></code></pre></div>
+<span class="co"># 30 2031 0.51109592 0.3973697 0.6248221           NA         NA 0.51109592</span>
+<span class="co"># 31 2032 0.53574417 0.4169574 0.6545309           NA         NA 0.53574417</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 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>
@@ -371,7 +372,7 @@

 <div class="pkgdown">
  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>

      </footer>
--- a/docs/articles/resistance_predict_files/accessible-code-block-0.0.1/empty-anchor.js
+++ b/docs/articles/resistance_predict_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});
--- 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-2.9/header-attrs.js
+++ b/docs/articles/resistance_predict_files/header-attrs-2.9/header-attrs.js
@@ -1,12 +0,0 @@
-// 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
@@ -44,7 +44,7 @@
      </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="Released version">1.8.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
      </span>
    </div>

@@ -185,7 +185,7 @@

      

-      </header><div class="row">
+      </header><script src="welcome_to_AMR_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
  <div class="col-md-9 contents">
    <div class="page-header toc-ignore">
      <h1 data-toc-skip>Welcome to the <code>AMR</code> package</h1>
@@ -242,7 +242,7 @@

 <div class="pkgdown">
  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>

      </footer>
--- a/docs/articles/welcome_to_AMR_files/accessible-code-block-0.0.1/empty-anchor.js
+++ b/docs/articles/welcome_to_AMR_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});
--- a/docs/articles/welcome_to_AMR_files/header-attrs-2.11/header-attrs.js
+++ b/docs/articles/welcome_to_AMR_files/header-attrs-2.11/header-attrs.js
@@ -1,12 +0,0 @@
-// 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]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
-    a = h.attributes;
-    while (a.length > 0) h.removeAttribute(a[0].name);
-  }
-});
--- a/docs/articles/welcome_to_AMR_files/header-attrs-2.9/header-attrs.js
+++ b/docs/articles/welcome_to_AMR_files/header-attrs-2.9/header-attrs.js
@@ -1,12 +0,0 @@
-// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
-// be compatible with the behavior of Pandoc < 2.8).
-document.addEventListener('DOMContentLoaded', function(e) {
-  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
-  var i, h, a;
-  for (i = 0; i < hs.length; i++) {
-    h = hs[i];
-    if (!/^h[1-6]$/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
@@ -17,7 +17,7 @@
      </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="Released version">1.8.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
      </span>
    </div>

@@ -218,7 +218,7 @@
          </p>
        </li>
        <li>
-          <p><strong>Anthony Underwood</strong>. Contributor. <a href="https://orcid.org/0000-0002-8547-427" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
+          <p><strong>Anthony Underwood</strong>. Contributor. <a href="https://orcid.org/0000-0002-8547-4277" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
          </p>
        </li>
      </ul></div>
@@ -273,7 +273,7 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
 </div>

 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>

      </footer></div>
--- a/docs/index.html
+++ b/docs/index.html
@@ -47,7 +47,7 @@
      </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="Released version">1.8.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
      </span>
    </div>

@@ -214,7 +214,7 @@
 </h5>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span>
-<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">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" class="external-link">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" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>

 <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
@@ -340,7 +340,7 @@
 </h4>
 <p>The development of this package is part of, related to, or made possible by:</p>
 <div align="center">
-<p><a href="https://www.rug.nl" title="University of Groningen" class="external-link"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen" class="external-link"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation" class="external-link"><img src="./logo_certe.png" class="partner_logo"></a> <a href="http://www.eurhealth-1health.eu" title="EurHealth-1-Health" class="external-link"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG" class="external-link"><img src="./logo_interreg.png" class="partner_logo"></a></p>
+<p><a href="https://www.rug.nl" title="University of Groningen" class="external-link"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen" class="external-link"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation" class="external-link"><img src="./logo_certe.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="EurHealth-1-Health" class="external-link"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG" class="external-link"><img src="./logo_interreg.png" class="partner_logo"></a></p>
 </div>
 </div>
 </div>
@@ -414,13 +414,13 @@
 <div class="section level4">
 <h4 id="microbial-taxonomic-reference-data">Microbial (taxonomic) reference data<a class="anchor" aria-label="anchor" href="#microbial-taxonomic-reference-data"></a>
 </h4>
-<p>This package contains the complete taxonomic tree of almost all ~70,000 microorganisms from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">www.catalogueoflife.org</a>), supplemented by data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/Sp2000/colplus" class="external-link">CoL+ project</a> is finished, which we await. With <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be checked which version of the CoL is included in this package.</p>
+<p>This package contains the complete taxonomic tree of almost all ~71,000 microorganisms from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">www.catalogueoflife.org</a>), supplemented by data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/Sp2000/colplus" class="external-link">CoL+ project</a> is finished, which we await. With <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be checked which version of the CoL is included in this package.</p>
 <p>Read more about which data from the Catalogue of Life <a href="./reference/catalogue_of_life.html">in our manual</a>.</p>
 </div>
 <div class="section level4">
 <h4 id="antimicrobial-reference-data">Antimicrobial reference data<a class="anchor" aria-label="anchor" href="#antimicrobial-reference-data"></a>
 </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="external-link uri">https://www.whocc.no</a>) and the <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">Pharmaceuticals Community Register of the European Commission</a>.</p>
+<p>This package contains <strong>all ~570 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="external-link uri">https://www.whocc.no</a>) and the <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">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="external-link 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>
@@ -561,7 +561,7 @@

 <div class="pkgdown">
  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>

      </footer>
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -17,7 +17,7 @@
      </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="Released version">1.8.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
      </span>
    </div>

@@ -156,10 +156,35 @@
      <small>Source: <a href="https://github.com/msberends/AMR/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
    </div>

+    <div class="section level2">
+<h2 class="page-header" data-toc-text="1.8.1" id="amr-181">
+<code>AMR</code> 1.8.1<small>2022-03-24</small><a class="anchor" aria-label="anchor" href="#amr-181"></a></h2>
+<p>All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.</p>
+<div class="section level4">
+<h4 id="changed-1-8-1">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1"></a></h4>
+<ul><li><p>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on values containing capped values (such as <code>&gt;=</code>), sometimes leading to <code>NA</code></p></li>
+<li><p>Support for antibiotic interpretations of the MIPS laboratory system: <code>"U"</code> for S (‘susceptible urine’), <code>"D"</code> for I (‘susceptible dose-dependent’)</p></li>
+<li>
+<p>Improved algorithm of <code><a href="../reference/as.mo.html">as.mo()</a></code>, especially for ignoring non-taxonomic text, such as:</p>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R">
+<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"methicillin-resistant S. aureus (MRSA)"</span><span class="op">)</span>
+<span class="co">#&gt; [1] "Staphylococcus aureus"</span></code></pre></div>
+</li>
+<li><p>More informative warning messages</p></li>
+<li><p>Added 192 as valid MIC</p></li>
+<li><p>Updated MIC printing in tibbles</p></li>
+<li><p>Increased speed for loading the package</p></li>
+</ul></div>
+<div class="section level4">
+<h4 id="other-1-8-1">Other<a class="anchor" aria-label="anchor" href="#other-1-8-1"></a></h4>
+<ul><li>Fix for unit testing on R 3.3</li>
+<li>Fix for size of some image elements, as requested by CRAN</li>
+</ul></div>
+</div>
    <div class="section level2">
 <h2 class="page-header" data-toc-text="1.8.0" id="amr-180">
-<code>AMR</code> 1.8.0<a class="anchor" aria-label="anchor" href="#amr-180"></a></h2>
-<p>All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.</p>
+<code>AMR</code> 1.8.0<small>2022-01-07</small><a class="anchor" aria-label="anchor" href="#amr-180"></a></h2>
 <div class="section level4">
 <h4 id="breaking-changes-1-8-0">Breaking changes<a class="anchor" aria-label="anchor" href="#breaking-changes-1-8-0"></a></h4>
 <ul><li>Removed <code>p_symbol()</code> and all <code>filter_*()</code> functions (except for <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>), which were all deprecated in a previous package version</li>
@@ -175,7 +200,7 @@
 <li><p>Support for all antimicrobial drug (group) names and colloquial microorganism names in Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish</p></li>
 <li>
 <p>Function <code><a href="../reference/ab_property.html">set_ab_names()</a></code> to rename data set columns that resemble antimicrobial drugs. This allows for quickly renaming columns to official names, ATC codes, etc. Its second argument can be a tidyverse way of selecting:</p>
-<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/ab_property.html">set_ab_names</a></span><span class="op">(</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="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="va">AMC</span><span class="op">:</span><span class="va">GEN</span>, property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></code></pre></div>
@@ -201,14 +226,14 @@
 <li><p>Added more selectors for antibiotic classes: <code><a href="../reference/antibiotic_class_selectors.html">aminopenicillins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">antifungals()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">antimycobacterials()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">lincosamides()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">lipoglycopeptides()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">polymyxins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">quinolones()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">streptogramins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">trimethoprims()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">ureidopenicillins()</a></code></p></li>
 <li>
 <p>Added specific selectors for certain types for treatment: <code><a href="../reference/antibiotic_class_selectors.html">administrable_per_os()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">administrable_iv()</a></code>, which are based on available Defined Daily Doses (DDDs), as defined by the WHOCC. These are ideal for e.g. analysing pathogens in primary care where IV treatment is not an option. They can be combined with other AB selectors, e.g. to select penicillins that are only administrable per os (i.e., orally):</p>
-<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">example_isolates</span><span class="op">[</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">penicillins</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu"><a href="../reference/antibiotic_class_selectors.html">administrable_per_os</a></span><span class="op">(</span><span class="op">)</span><span class="op">]</span>          <span class="co"># base R</span>
 <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">penicillins</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu"><a href="../reference/antibiotic_class_selectors.html">administrable_per_os</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="co"># dplyr</span></code></pre></div>
 </li>
 <li>
 <p>Added the selector <code><a href="../reference/antibiotic_class_selectors.html">ab_selector()</a></code>, which accepts a filter to be used internally on the <code>antibiotics</code> data set, yielding great flexibility on drug properties, such as selecting antibiotic columns with an oral DDD of at least 1 gram:</p>
-<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">example_isolates</span><span class="op">[</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">ab_selector</a></span><span class="op">(</span><span class="va">oral_ddd</span> <span class="op">&gt;</span> <span class="fl">1</span> <span class="op">&amp;</span> <span class="va">oral_units</span> <span class="op">==</span> <span class="st">"g"</span><span class="op">)</span><span class="op">]</span>          <span class="co"># base R</span>
 <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">ab_selector</a></span><span class="op">(</span><span class="va">oral_ddd</span> <span class="op">&gt;</span> <span class="fl">1</span> <span class="op">&amp;</span> <span class="va">oral_units</span> <span class="op">==</span> <span class="st">"g"</span><span class="op">)</span><span class="op">)</span> <span class="co"># dplyr</span></code></pre></div>
@@ -266,7 +291,7 @@
 <h4 id="breaking-change-1-7-1">Breaking change<a class="anchor" aria-label="anchor" href="#breaking-change-1-7-1"></a></h4>
 <ul><li>
 <p>All antibiotic class selectors (such as <code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>) can now be used for filtering as well, making all their accompanying <code>filter_*()</code> functions redundant (such as <code>filter_carbapenems()</code>, <code>filter_aminoglycosides()</code>). These functions are now deprecated and will be removed in a next release. Examples of how the selectors can be used for filtering:</p>
-<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># select columns with results for carbapenems</span>
 <span class="va">example_isolates</span><span class="op">[</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">]</span>           <span class="co"># base R</span>
@@ -321,7 +346,7 @@
 <ul><li><p>Now checks if <code>pattern</code> is a <em>valid</em> regular expression</p></li>
 <li>
 <p>Added <code>%unlike%</code> and <code>%unlike_case%</code> (as negations of the existing <code>%like%</code> and <code>%like_case%</code>). This greatly improves readability:</p>
-<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">grepl</a></span><span class="op">(</span><span class="st">"EUCAST"</span>, <span class="va">guideline</span><span class="op">)</span><span class="op">)</span> <span class="va">...</span>
 <span class="co"># same:</span>
@@ -336,8 +361,8 @@
 <li>Colour fix for using <code><a href="https://rdrr.io/r/graphics/barplot.html" class="external-link">barplot()</a></code> on an RSI class</li>
 <li>Added 25 common system codes for bacteria to the <code>microorganisms.codes</code> data set</li>
 <li>Added 16 common system codes for antimicrobial agents to the <code>antibiotics</code> data set</li>
-<li>Fix for using <code><a href="https://docs.ropensci.org/skimr/reference/skim.html" class="external-link">skimr::skim()</a></code> on classes <code>mo</code>, <code>mic</code> and <code>disk</code> when using the just released <code>dplyr</code> v1.0.6</li>
-<li>Updated <code><a href="https://docs.ropensci.org/skimr/reference/skim.html" class="external-link">skimr::skim()</a></code> usage for MIC values to also include 25th and 75th percentiles</li>
+<li>Fix for using <code>skimr::skim()</code> on classes <code>mo</code>, <code>mic</code> and <code>disk</code> when using the just released <code>dplyr</code> v1.0.6</li>
+<li>Updated <code>skimr::skim()</code> usage for MIC values to also include 25th and 75th percentiles</li>
 <li>Fix for plotting missing MIC/disk diffusion values</li>
 <li>Updated join functions to always use <code>dplyr</code> join functions if the <code>dplyr</code> package is installed - now also preserving grouped variables</li>
 <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>
@@ -374,7 +399,7 @@
 </ul></li>
 <li>
 <p>Functions <code><a href="../reference/antibiotic_class_selectors.html">oxazolidinones()</a></code> (an antibiotic selector function) and <code>filter_oxazolidinones()</code> (an antibiotic filter function) to select/filter on e.g. linezolid and tedizolid</p>
-<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
 <span class="va">x</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">date</span>, <span class="va">hospital_id</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">oxazolidinones</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
@@ -387,7 +412,7 @@
 <li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">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="cb7"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Aspergillus"</span>, <span class="st">"Candida"</span><span class="op">)</span><span class="op">)</span>
 <span class="co">#&gt; [1] "Fungi" "Fungi"</span>
@@ -399,7 +424,7 @@
 <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_is_yeast</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span>   <span class="co"># base R</span>
 <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_is_yeast</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="co"># dplyr</span></code></pre></div>
 <p>The <code><a href="../reference/mo_property.html">mo_type()</a></code> function has also been updated to reflect this change:</p>
-<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/mo_property.html">mo_type</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Aspergillus"</span>, <span class="st">"Candida"</span><span class="op">)</span><span class="op">)</span>
 <span class="co"># [1] "Fungi"  "Yeasts"</span>
@@ -409,7 +434,7 @@
 <li><p>Added Pretomanid (PMD, J04AK08) to the <code>antibiotics</code> data set</p></li>
 <li>
 <p>MIC values (see <code><a href="../reference/as.mic.html">as.mic()</a></code>) can now be used in any mathematical processing, such as usage inside functions <code><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">min()</a></code>, <code><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max()</a></code>, <code><a href="https://rdrr.io/r/base/range.html" class="external-link">range()</a></code>, and with binary operators (<code>+</code>, <code>-</code>, etc.). This allows for easy distribution analysis and fast filtering on MIC values:</p>
-<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span>
 <span class="va">x</span>
@@ -451,7 +476,7 @@
 <code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> now detects if the column name resembles an antibiotic name or code and now returns <code>TRUE</code> immediately if the input contains any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.</li>
 <li>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> now support less than a day as value for argument <code>episode_days</code> (e.g., to include one patient/test per hour)</li>
 <li>Argument <code>ampc_cephalosporin_resistance</code> in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> now also applies to value “I” (not only “S”)</li>
-<li>Functions <code><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">dplyr::group_by()</a></code>
+<li>Functions <code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">dplyr::group_by()</a></code>
 </li>
 <li>Improved speed and reliability of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>. As this also internally improves the reliability of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>, this might have a slight impact on the results of those functions.</li>
 <li>Fix for <code><a href="../reference/mo_property.html">mo_name()</a></code> when used in other languages than English</li>
@@ -469,7 +494,7 @@
 <div class="section level4">
 <h4 id="other-1-6-0">Other<a class="anchor" aria-label="anchor" href="#other-1-6-0"></a></h4>
 <ul><li>Big documentation updates</li>
-<li>Loading the package (i.e., <code><a href="https://msberends.github.io/AMR">library(AMR)</a></code>) now is ~50 times faster than before, in costs of package size (which increased by ~3 MB)</li>
+<li>Loading the package (i.e., <code><a href="https://msberends.github.io/AMR/">library(AMR)</a></code>) now is ~50 times faster than before, in costs of package size (which increased by ~3 MB)</li>
 </ul></div>
 </div>
    <div class="section level2">
@@ -478,7 +503,7 @@
 <h4 id="new-1-5-0">New<a class="anchor" aria-label="anchor" href="#new-1-5-0"></a></h4>
 <ul><li>
 <p>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> to determine (patient) episodes which are not necessarily based on microorganisms. The <code><a href="../reference/get_episode.html">get_episode()</a></code> function returns the index number of the episode per group, while the <code><a href="../reference/get_episode.html">is_new_episode()</a></code> function returns values <code>TRUE</code>/<code>FALSE</code> to indicate whether an item in a vector is the start of a new episode. They also support <code>dplyr</code>s grouping (i.e. using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code>):</p>
-<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
 <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
@@ -486,7 +511,7 @@
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/get_episode.html">is_new_episode</a></span><span class="op">(</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span><span class="op">)</span></code></pre></div>
 </li>
 <li><p>Functions <code><a href="../reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="../reference/mo_property.html">mo_is_gram_positive()</a></code> as wrappers around <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>. They always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p></li>
-<li><p>Function <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> to test for intrinsic resistance, based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2</a> from 2020.</p></li>
+<li><p>Function <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> to test for intrinsic resistance, based on EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2 from 2020.</p></li>
 <li><p>Functions <code><a href="../reference/random.html">random_mic()</a></code>, <code><a href="../reference/random.html">random_disk()</a></code> and <code><a href="../reference/random.html">random_rsi()</a></code> for random value generation. The functions <code><a href="../reference/random.html">random_mic()</a></code> and <code><a href="../reference/random.html">random_disk()</a></code> take microorganism names and antibiotic names as input to make generation more realistic.</p></li>
 </ul></div>
 <div class="section level4">
@@ -523,7 +548,7 @@
 <li>
 <code><a href="../reference/mdro.html">mdr_cmi2012()</a></code>,</li>
 <li><code><a href="../reference/mdro.html">eucast_exceptional_phenotypes()</a></code></li>
-</ul><div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
+</ul><div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># to select first isolates that are Gram-negative </span>
 <span class="co"># and view results of cephalosporins and aminoglycosides:</span>
@@ -535,7 +560,7 @@
 </li>
 <li>
 <p>For antibiotic selection functions (such as <code><a href="../reference/antibiotic_class_selectors.html">cephalosporins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>) to select columns based on a certain antibiotic group, the dependency on the <code>tidyselect</code> package was removed, meaning that they can now also be used without the need to have this package installed and now also work in base R function calls (they rely on R 3.2 or later):</p>
-<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># above example in base R:</span>
 <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu"><a href="../reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,
@@ -578,9 +603,9 @@
 <li>
 <p>Data set <code>intrinsic_resistant</code>. This data set contains all bug-drug combinations where the ‘bug’ is intrinsic resistant to the ‘drug’ according to the latest EUCAST insights. It contains just two columns: <code>microorganism</code> and <code>antibiotic</code>.</p>
 <p>Curious about which enterococci are actually intrinsic resistant to vancomycin?</p>
-<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
-<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">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" class="external-link">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" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
 <span class="va">intrinsic_resistant</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">antibiotic</span> <span class="op">==</span> <span class="st">"Vancomycin"</span>, <span class="va">microorganism</span> <span class="op"><a href="../reference/like.html">%like%</a></span> <span class="st">"Enterococcus"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
@@ -597,7 +622,7 @@
 <p>Improvements for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>:</p>
 <ul><li>
 <p>Support for using <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across()</a></code> to interpret MIC values or disk zone diameters, which also automatically determines the column with microorganism names or codes.</p>
-<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># until dplyr 1.0.0</span>
 <span class="va">your_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.rsi</span><span class="op">)</span>
@@ -614,7 +639,7 @@
 </ul></li>
 <li>
 <p>Added intelligent data cleaning to <code><a href="../reference/as.disk.html">as.disk()</a></code>, so numbers can also be extracted from text and decimal numbers will always be rounded up:</p>
-<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/as.disk.html">as.disk</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"disk zone: 23.4 mm"</span>, <span class="fl">23.4</span><span class="op">)</span><span class="op">)</span>
 <span class="co">#&gt; Class &lt;disk&gt;</span>
@@ -663,7 +688,7 @@
 <ul><li><p>Function <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code> to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses <code><a href="../reference/as.ab.html">as.ab()</a></code> internally</p></li>
 <li>
 <p><a href="https://tidyselect.r-lib.org/reference/language.html" class="external-link">Tidyverse selection helpers</a> for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like <code><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">dplyr::select()</a></code> and <code><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html" class="external-link">tidyr::pivot_longer()</a></code>:</p>
-<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>

@@ -804,7 +829,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul><li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li>
 <li>
 <p>Interpretation from MIC values (and disk zones) to R/SI can now be used with <code><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at()</a></code> of the <code>dplyr</code> package:</p>
-<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">yourdata</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">antibiotic1</span><span class="op">:</span><span class="va">antibiotic25</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span><span class="op">)</span>
@@ -827,7 +852,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>Support for LOINC and SNOMED codes
 <ul><li>
 <p>Support for LOINC codes in the <code>antibiotics</code> data set. Use <code><a href="../reference/ab_property.html">ab_loinc()</a></code> to retrieve LOINC codes, or use a LOINC code for input in any <code>ab_*</code> function:</p>
-<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/ab_property.html">ab_loinc</a></span><span class="op">(</span><span class="st">"ampicillin"</span><span class="op">)</span>
 <span class="co">#&gt; [1] "21066-6" "3355-5"  "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"</span>
@@ -838,7 +863,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 <li>
 <p>Support for SNOMED CT codes in the <code>microorganisms</code> data set. Use <code><a href="../reference/mo_property.html">mo_snomed()</a></code> to retrieve SNOMED codes, or use a SNOMED code for input in any <code>mo_*</code> function:</p>
-<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/mo_property.html">mo_snomed</a></span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>
 <span class="co">#&gt; [1] 115329001   3092008 113961008</span>
@@ -886,11 +911,11 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul><li>Adopted Adeolu <em>et al.</em> (2016), <a href="https:/pubmed.ncbi.nlm.nih.gov/27620848/">PMID 27620848</a> for the <code>microorganisms</code> data set, which means that the new order Enterobacterales now consists of a part of the existing family Enterobacteriaceae, but that this family has been split into other families as well (like <em>Morganellaceae</em> and <em>Yersiniaceae</em>). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations with <code><a href="../reference/mdro.html">mdro()</a></code> will now use the Enterobacterales order for all guidelines before 2016 that were dependent on the Enterobacteriaceae family.
 <ul><li>
 <p>If you were dependent on the old Enterobacteriaceae family e.g. by using in your code:</p>
-<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_family</a></span><span class="op">(</span><span class="va">somebugs</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Enterobacteriaceae"</span><span class="op">)</span> <span class="va">...</span></code></pre></div>
 <p>then please adjust this to:</p>
-<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_order</a></span><span class="op">(</span><span class="va">somebugs</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Enterobacterales"</span><span class="op">)</span> <span class="va">...</span></code></pre></div>
 </li>
@@ -900,7 +925,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <h4 id="new-0-9-0">New<a class="anchor" aria-label="anchor" href="#new-0-9-0"></a></h4>
 <ul><li>
 <p>Functions <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> as aliases of <code><a href="../reference/proportion.html">proportion_SI()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code>, respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.</p>
-<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
 <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
@@ -923,7 +948,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>More intelligent way of coping with some consonants like “l” and “r”</p></li>
 <li>
 <p>Added a score (a certainty percentage) to <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code>, that is calculated using the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance" class="external-link">Levenshtein distance</a>:</p>
-<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Stafylococcus aureus"</span>,
        <span class="st">"staphylokok aureuz"</span><span class="op">)</span><span class="op">)</span>
@@ -971,14 +996,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <h4 id="breaking-0-8-0">Breaking<a class="anchor" aria-label="anchor" href="#breaking-0-8-0"></a></h4>
 <ul><li>
 <p>Determination of first isolates now <strong>excludes</strong> all ‘unknown’ microorganisms at default, i.e. microbial code <code>"UNKNOWN"</code>. They can be included with the new argument <code>include_unknown</code>:</p>
-<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="va">...</span>, include_unknown <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
 <p>For WHONET users, this means that all records/isolates with organism code <code>"con"</code> (<em>contamination</em>) will be excluded at default, since <code>as.mo("con") = "UNKNOWN"</code>. The function always shows a note with the number of ‘unknown’ microorganisms that were included or excluded.</p>
 </li>
 <li>
 <p>For code consistency, classes <code>ab</code> and <code>mo</code> will now be preserved in any subsetting or assignment. For the sake of data integrity, this means that invalid assignments will now result in <code>NA</code>:</p>
-<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># how it works in base R:</span>
 <span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="st">"A"</span><span class="op">)</span>
@@ -1000,7 +1025,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <h4 id="new-0-8-0">New<a class="anchor" aria-label="anchor" href="#new-0-8-0"></a></h4>
 <ul><li>
 <p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with <code><a href="../reference/mo_property.html">mo_shortname()</a></code> at default:</p>
-<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
 <span class="co">#&gt; NOTE: Using column `mo` as input for `col_mo`.</span>
@@ -1023,13 +1048,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <span class="co">#&gt; 4 Gram-negative AMX 227  0 405   632</span>
 <span class="co">#&gt; NOTE: Use 'format()' on this result to get a publicable/printable format.</span></code></pre></div>
 <p>You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R <code><a href="https://rdrr.io/r/base/format.html" class="external-link">format()</a></code> function:</p>
-<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span><span class="va">x</span>, combine_IR <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
 </li>
 <li>
 <p>Additional way to calculate co-resistance, i.e. when using multiple antimicrobials as input for <code>portion_*</code> functions or <code>count_*</code> functions. This can be used to determine the empiric susceptibility of a combination therapy. A new argument <code>only_all_tested</code> (<strong>which defaults to <code>FALSE</code></strong>) replaces the old <code>also_single_tested</code> and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the <code>portion</code> and <code>count</code> help pages), where the %SI is being determined:</p>
-<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># --------------------------------------------------------------------</span>
 <span class="co">#                     only_all_tested = FALSE  only_all_tested = TRUE</span>
@@ -1051,7 +1076,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 <li>
 <p><code>tibble</code> printing support for classes <code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code> <code>mo</code>. When using <code>tibble</code>s containing antimicrobial columns, values <code>S</code> will print in green, values <code>I</code> will print in yellow and values <code>R</code> will print in red. Microbial IDs (class <code>mo</code>) will emphasise on the genus and species, not on the kingdom.</p>
-<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># (run this on your own console, as this page does not support colour printing)</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
@@ -1119,7 +1144,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <h5 id="new-0-7-1">New<a class="anchor" aria-label="anchor" href="#new-0-7-1"></a></h5>
 <ul><li>
 <p>Function <code><a href="../reference/proportion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code>portion_df()</code> to immediately show resistance percentages and number of available isolates:</p>
-<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">AMX</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
@@ -1144,7 +1169,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>STEC (Shiga-toxin producing <em>E. coli</em>)</li>
 <li>UPEC (Uropathogenic <em>E. coli</em>)</li>
 </ul><p>All these lead to the microbial ID of <em>E. coli</em>:</p>
-<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"UPEC"</span><span class="op">)</span>
 <span class="co"># B_ESCHR_COL</span>
@@ -1228,7 +1253,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>when all values are unique it now shows a message instead of a warning</p></li>
 <li>
 <p>support for boxplots:</p>
-<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
@@ -1303,7 +1328,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </ul></li>
 <li>
 <p>New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:</p>
-<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu">filter_aminoglycosides</span><span class="op">(</span><span class="op">)</span>
 <span class="fu">filter_carbapenems</span><span class="op">(</span><span class="op">)</span>
@@ -1317,7 +1342,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <span class="fu">filter_macrolides</span><span class="op">(</span><span class="op">)</span>
 <span class="fu">filter_tetracyclines</span><span class="op">(</span><span class="op">)</span></code></pre></div>
 <p>The <code>antibiotics</code> data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set. For example:</p>
-<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu">filter_glycopeptides</span><span class="op">(</span>result <span class="op">=</span> <span class="st">"R"</span><span class="op">)</span>
 <span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span>
@@ -1326,7 +1351,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 <li>
 <p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
-<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">ab_property</span> <span class="op">-&gt;</span> <span class="fu">atc_property</span><span class="op">(</span><span class="op">)</span>
 <span class="va">ab_name</span> <span class="op">-&gt;</span> <span class="fu">atc_name</span><span class="op">(</span><span class="op">)</span>
@@ -1347,7 +1372,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic AMR data analysis per age group.</p></li>
 <li>
 <p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="../reference/plot.html">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
-<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span><span class="va">septic_patients</span>, col_ab <span class="op">=</span> <span class="st">"amox"</span><span class="op">)</span>
 <span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
@@ -1355,13 +1380,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 <li>
 <p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code>filter_first_weighted_isolate()</code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
-<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="va">...</span><span class="op">)</span>
 <span class="co"># or</span>
 <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="va">...</span><span class="op">)</span></code></pre></div>
 <p>is equal to:</p>
-<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>only_firsts <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="va">...</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
@@ -1388,7 +1413,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>Improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code>:
 <ul><li>
 <p>Now handles incorrect spelling, like <code>i</code> instead of <code>y</code> and <code>f</code> instead of <code>ph</code>:</p>
-<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># mo_fullname() uses as.mo() internally</span>

@@ -1400,7 +1425,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 <li>
 <p>Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default <code>allow_uncertain = TRUE</code> is equal to uncertainty level 2. Run <code><a href="../reference/as.mo.html">?as.mo</a></code> for more info about these levels.</p>
-<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># equal:</span>
 <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">...</span>, allow_uncertain <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
@@ -1451,7 +1476,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> function):
 <ul><li>
 <p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
-<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span>
 <span class="co"># OLD WAY</span>
@@ -1521,7 +1546,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Fewer than 3 characters as input for <code>as.mo</code> will return NA</p></li>
 <li>
 <p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
-<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. species"</span><span class="op">)</span>        <span class="co"># B_ESCHR</span>
 <span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"E. spp."</span><span class="op">)</span>     <span class="co"># "Escherichia species"</span>
@@ -1537,7 +1562,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <p>Frequency tables - <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code>:</p>
 <ul><li>
 <p>Support for grouping variables, test with:</p>
-<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
@@ -1545,7 +1570,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 <li>
 <p>Support for (un)selecting columns:</p>
-<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
@@ -1612,7 +1637,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>Author and year: <code>mo_ref</code>
 </li>
 </ul><p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
-<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
 <span class="co"># [1] "Gram negative"</span>
@@ -1623,7 +1648,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"S. group A"</span>, language <span class="op">=</span> <span class="st">"pt"</span><span class="op">)</span> <span class="co"># Portuguese</span>
 <span class="co"># [1] "Streptococcus grupo A"</span></code></pre></div>
 <p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
-<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"Esc blattae"</span><span class="op">)</span>
 <span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span>
@@ -1636,7 +1661,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Function <code>is.rsi.eligible</code> to check for columns that have valid antimicrobial results, but do not have the <code>rsi</code> class yet. Transform the columns of your raw data with: <code>data %&gt;% mutate_if(is.rsi.eligible, as.rsi)</code></p></li>
 <li>
 <p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using intelligent rules:</p>
-<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb48"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
 <span class="co"># [1] B_ESCHR_COL</span>
@@ -1645,7 +1670,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"S group A"</span><span class="op">)</span>
 <span class="co"># [1] B_STRPTC_GRA</span></code></pre></div>
 <p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p>
-<div class="sourceCode" id="cb48"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb49"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">thousands_of_E_colis</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"E. coli"</span>, <span class="fl">25000</span><span class="op">)</span>
 <span class="fu">microbenchmark</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">thousands_of_E_colis</span><span class="op">)</span>, unit <span class="op">=</span> <span class="st">"s"</span><span class="op">)</span>
@@ -1674,7 +1699,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul><li><p>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</p></li>
 <li>
 <p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
-<div class="sourceCode" id="cb49"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu">ab_official</span><span class="op">(</span><span class="st">"Bactroban"</span><span class="op">)</span>
 <span class="co"># [1] "Mupirocin"</span>
@@ -1691,7 +1716,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Added arguments <code>minimum</code> and <code>as_percent</code> to <code>portion_df</code></p></li>
 <li>
 <p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
-<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb51"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">amox</span>, <span class="va">cipr</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/count.html">count_IR</a></span><span class="op">(</span><span class="op">)</span>
 <span class="co"># which is the same as:</span>
@@ -1711,12 +1736,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Added longest en shortest character length in the frequency table (<code>freq</code>) header of class <code>character</code></p></li>
 <li>
 <p>Support for types (classes) list and matrix for <code>freq</code></p>
-<div class="sourceCode" id="cb51"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb52"><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" class="external-link">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" class="external-link">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">age</span>, <span class="va">gender</span><span class="op">)</span>, ncol <span class="op">=</span> <span class="fl">2</span><span class="op">)</span><span class="op">)</span>
 <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">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="cb52"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb53"><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" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
@@ -1845,8 +1870,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>Function <code>guess_atc</code> to <strong>determine the ATC</strong> of an antibiotic based on name, trade name, or known abbreviations</li>
 <li>Function <code>freq</code> to create <strong>frequency tables</strong>, with additional info in a header</li>
 <li>Function <code>MDRO</code> to <strong>determine Multi Drug Resistant Organisms (MDRO)</strong> with support for country-specific guidelines.
-<ul><li>
-<a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">Exceptional resistances defined by EUCAST</a> are also supported instead of countries alone</li>
+<ul><li>Exceptional resistances defined by EUCAST are also supported instead of countries alone</li>
 <li>Functions <code>BRMO</code> and <code>MRGN</code> are wrappers for Dutch and German guidelines, respectively</li>
 </ul></li>
 <li>New algorithm to determine weighted isolates, can now be <code>"points"</code> or <code>"keyantibiotics"</code>, see <code><a href="../reference/first_isolate.html">?first_isolate</a></code>
@@ -1906,7 +1930,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </div>

 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>

      </footer></div>
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,5 +1,5 @@
-pandoc: 2.14.0.3
-pkgdown: 2.0.0
+pandoc: 2.9.2.1
+pkgdown: 2.0.2
 pkgdown_sha: ~
 articles:
  AMR: AMR.html
@@ -12,7 +12,7 @@ articles:
  datasets: datasets.html
  resistance_predict: resistance_predict.html
  welcome_to_AMR: welcome_to_AMR.html
-last_built: 2021-12-23T17:53Z
+last_built: 2022-03-27T07:33Z
 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
@@ -17,7 +17,7 @@
      </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="Released version">1.8.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
      </span>
    </div>

@@ -161,13 +161,12 @@
    <p>These functions are so-called '<a href="https://rdrr.io/r/base/Deprecated.html" class="external-link">Deprecated</a>'. <strong>They will be removed in a future release.</strong> Using the functions will give a warning with the name of the function it has been replaced by (if there is one).</p>
    </div>

-    <div id="ref-usage">Usage,NULL</div>

    <div id="retired-lifecycle">
    <h2>Retired Lifecycle</h2>
    

-<p><img src="figures/lifecycle_retired.svg" style="margin-bottom:5px"><br>
+<p><img src="figures/lifecycle_retired.svg" style='margin-bottom:"5"'><br>
 The <a href="lifecycle.html">lifecycle</a> of this function is <strong>retired</strong>. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.</p>
    </div>
    <div id="read-more-on-our-website-">
@@ -189,7 +188,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>retired</
 </div>

 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>

      </footer></div>
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
dr. M.S. (Matthijs) Berends	641b88c814	website update	2022-03-27 09:37:55 +02:00
dr. M.S. (Matthijs) Berends	ccb09706e4	v1.8.1	2022-03-24 23:05:04 +01:00
dr. M.S. (Matthijs) Berends	7b0f1596bd	(v1.8.0.9010) as.mo improvement	2022-03-15 17:35:02 +01:00
dr. M.S. (Matthijs) Berends	0fb9a1b194	prerelease 1.8.1	2022-03-14 16:43:15 +01:00
dr. M.S. (Matthijs) Berends	45e9546538	prerelease 1.8.1 Merge branch 'development' of https://github.com/msberends/AMR into development # Conflicts: # docs/articles/AMR.html # docs/articles/AMR_files/figure-html/disk_plots-1.png # docs/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png # docs/articles/AMR_files/figure-html/mic_plots-1.png # docs/articles/AMR_files/figure-html/mic_plots-2.png # docs/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png # docs/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png # docs/articles/AMR_files/figure-html/plot 1-1.png # docs/articles/AMR_files/figure-html/plot 3-1.png # docs/articles/AMR_files/figure-html/plot 4-1.png # docs/articles/AMR_files/figure-html/plot 5-1.png # docs/articles/EUCAST.html # docs/articles/MDR.html # docs/articles/PCA.html # docs/articles/PCA_files/figure-html/unnamed-chunk-6-1.png # docs/articles/PCA_files/figure-html/unnamed-chunk-7-1.png # docs/articles/SPSS.html # docs/articles/WHONET.html # docs/articles/WHONET_files/figure-html/unnamed-chunk-7-1.png # docs/articles/benchmarks.html # docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png # docs/articles/datasets.html # docs/articles/resistance_predict.html # docs/articles/resistance_predict_files/figure-html/unnamed-chunk-4-1.png # docs/articles/resistance_predict_files/figure-html/unnamed-chunk-5-1.png # docs/articles/resistance_predict_files/figure-html/unnamed-chunk-5-2.png # docs/articles/resistance_predict_files/figure-html/unnamed-chunk-6-1.png # docs/articles/resistance_predict_files/figure-html/unnamed-chunk-7-1.png # docs/articles/welcome_to_AMR.html # docs/news/index.html # docs/pkgdown.yml # docs/reference/AMR-deprecated.html # docs/reference/AMR.html # docs/reference/WHOCC.html # docs/reference/WHONET.html # docs/reference/antibiotics.html # docs/reference/catalogue_of_life.html # docs/reference/catalogue_of_life_version.html # docs/reference/dosage.html # docs/reference/example_isolates.html # docs/reference/example_isolates_unclean.html # docs/reference/g.test.html # docs/reference/intrinsic_resistant.html # docs/reference/microorganisms.codes.html # docs/reference/microorganisms.html # docs/reference/microorganisms.old.html # docs/reference/rsi_translation.html	2022-03-14 16:37:37 +01:00
dr. M.S. (Matthijs) Berends	1b0983e382	(v1.8.1) prerelease 1.8.1	2022-03-14 16:36:10 +01:00
dr. M.S. (Matthijs) Berends	8c9feea087	website update	2022-03-12 19:53:29 +01:00
dr. M.S. (Matthijs) Berends	08d387b5ce	(v1.8.0.9005) as.rsi() fix	2022-03-10 19:33:25 +01:00
dr. M.S. (Matthijs) Berends	ad82bb4ce0	(v1.8.0.9004) MIC printing in tibbles	2022-03-03 21:11:02 +01:00
dr. M.S. (Matthijs) Berends	dedbe92322	(v1.8.0.9003) deps update	2022-03-02 23:16:37 +01:00
dr. M.S. (Matthijs) Berends	3b2b2be5f8	(v1.8.0.9002) as.rsi() cleanup, more informative warnings	2022-03-02 15:38:55 +01:00
dr. M.S. (Matthijs) Berends	18e8525d10	(v1.8.0.9001) as.mo improvement, fixes #52	2022-02-26 21:58:23 +01:00
dr. M.S. (Matthijs) Berends	be792cc9eb	(v1.8.0.9000) unit tests for R 3.3	2022-02-01 17:08:10 +01:00