(v1.6.0.9009) key_antibiotics update

(v1.6.0.9008) unlike, bugfix for col_mo naming
(v1.6.0.9007) documentation custom eucast rules, progress bar as.mo
2025-01-27 22:24:47 +01:00 · 2021-04-23 16:13:26 +02:00 · 2021-04-23 09:59:36 +02:00 · 2021-04-20 10:46:17 +02:00
57 changed files with 649 additions and 305 deletions
--- a/4
+++ b/4
@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.6.0.9006
-Date: 2021-04-16
+Version: 1.6.0.9009
+Date: 2021-04-23
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(
    person(role = c("aut", "cre"), 
--- a/2
+++ b/2
@ -142,6 +142,8 @@ S3method(unique,mo)
 S3method(unique,rsi)
 export("%like%")
 export("%like_case%")
+export("%unlike%")
+export("%unlike_case%")
 export(ab_atc)
 export(ab_atc_group1)
 export(ab_atc_group2)
--- a/NEWS.md
+++ b/NEWS.md
@ -1,5 +1,5 @@
-# AMR 1.6.0.9006
-## <small>Last updated: 16 April 2021</small>
+# AMR 1.6.0.9009
+## <small>Last updated: 23 April 2021</small>

 ### New
 * Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()`
@ -13,8 +13,22 @@
 * Fix for minor translation errors
 * Printing of microbial codes in a `data.frame` or `tibble` now gives a warning if the data contains old microbial codes (from a previous AMR package version)
 * `first_isolate()` can now take a vector of values for `col_keyantibiotics` and can have an episode length of `Inf`
-* `like()` (and `%like%`) now checks if `pattern` is a *valid* regular expression
+* Extended the `like()` functions:
+  * Now checks if `pattern` is a *valid* regular expression
+  * Added `%unlike%` and `%unlike_case%` (as negations of the existing `%like%` and `%like_case%`). This greatly improves readability:
+    ```r
+    if (!grepl("EUCAST", guideline)) ...
+    # same:
+    if (guideline %unlike% "EUCAST") ...
+    ```
+  * Altered the RStudio addin, so it now iterates over `%like%` -> `%unlike%` -> `%like_case%` -> `%unlike_case%` if you keep pressing your keyboard shortcut
 * Fixed an installation error on R-3.0
+* Added `info` argument to `as.mo()` to turn on/off the progress bar
+* Fixed a bug that `col_mo` for some functions (esp. `eucast_rules()` and `mdro()`) could not be column names of the `microorganisms` data set as it would throw an error
+* Using `first_isolate()` with key antibiotics:
+  * Fixed a bug in the algorithm when using `type == "points"`, that now leads to inclusion of slightly more isolates
+  * Big speed improvement for `key_antibiotics_equal()` when using `type == "points"`
+

 # AMR 1.6.0

--- a/R/aa_helper_functions.R
+++ b/R/aa_helper_functions.R
@ -71,7 +71,49 @@ addin_insert_in <- function() {

 # No export, no Rd
 addin_insert_like <- function() {
-  import_fn("insertText", "rstudioapi")(" %like% ")
+  # we want Shift + Ctrl/Cmd + L to iterate over %like%, %unlike%, %like_case%, and %unlike_case%
+  
+  getActiveDocumentContext <- import_fn("getActiveDocumentContext", "rstudioapi")
+  insertText <- import_fn("insertText", "rstudioapi")
+  modifyRange <- import_fn("modifyRange", "rstudioapi")
+  document_range <- import_fn("document_range", "rstudioapi")
+  document_position <- import_fn("document_position", "rstudioapi")
+  
+  context <- getActiveDocumentContext()
+  current_row <- context$selection[[1]]$range$end[1]
+  current_col <- context$selection[[1]]$range$end[2]
+  current_row_txt <- context$contents[current_row]
+  if (is.null(current_row) || current_row_txt %unlike% "%(un)?like") {
+    insertText(" %like% ")
+    return(invisible())
+  }
+  
+  pos_preceded_by <- function(txt) {
+    if (tryCatch(substr(current_row_txt, current_col - nchar(trimws(txt, which = "right")), current_col) == trimws(txt, which = "right"),
+                 error = function(e) FALSE)) {
+      return(TRUE)
+    }
+    tryCatch(substr(current_row_txt, current_col - nchar(txt), current_col) %like% paste0("^", txt),
+             error = function(e) FALSE)
+  }
+  replace_pos <- function(old, with) {
+    modifyRange(document_range(document_position(current_row, current_col - nchar(old)),
+                               document_position(current_row, current_col)),
+                text = with,
+                id = context$id)
+  }
+  
+  if (pos_preceded_by(" %like% ")) {
+    replace_pos(" %like% ", with = " %unlike% ")
+  } else if (pos_preceded_by(" %unlike% ")) {
+    replace_pos(" %unlike% ", with = " %like_case% ")
+  } else if (pos_preceded_by(" %like_case% ")) {
+    replace_pos(" %like_case% ", with = " %unlike_case% ")
+  } else if (pos_preceded_by(" %unlike_case% ")) {
+    replace_pos(" %unlike_case% ", with = " %like% ")
+  } else {
+    insertText(" %like% ")
+  }
 }

 check_dataset_integrity <- function() {
@ -234,8 +276,8 @@ stop_ifnot_installed <- function(package) {
  vapply(FUN.VALUE = character(1), package, function(pkg)
    tryCatch(get(".packageName", envir = asNamespace(pkg)),
             error = function(e) {
-               if (package == "rstudioapi") {
-                 stop("This function only works in RStudio.", call. = FALSE)
+               if (pkg == "rstudioapi") {
+                 stop("This function only works in RStudio when using R >= 3.2.", call. = FALSE)
               } else if (pkg != "base") {
                 stop("This requires the '", pkg, "' package.",
                      "\nTry to install it with: install.packages(\"", pkg, "\")",
@ -652,7 +694,7 @@ get_current_data <- function(arg_name, call) {
      return(out)
    }
  }
-  
+
  if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2) {
    # R-3.0 and R-3.1 do not have an `x` element in the call stack, rendering this function useless
    if (is.na(arg_name)) {
@ -660,6 +702,7 @@ get_current_data <- function(arg_name, call) {
      warning_("this function can only be used in R >= 3.2", call = call)
      return(data.frame())
    } else {
+      # mimic a default R error, e.g. for example_isolates[which(mo_name() %like% "^ent"), ] 
      stop_("argument `", arg_name, "` is missing with no default", call = call)
    }
  }
@ -669,12 +712,17 @@ get_current_data <- function(arg_name, call) {
  frms <- lapply(sys.frames(), function(el) {
    if (not_set == TRUE && ".Generic" %in% names(el)) {
      if (tryCatch(".data" %in% names(el) && is.data.frame(el$`.data`), error = function(e) FALSE)) {
-        # dplyr? - an element `.data` will be in the system call stack
-        # will be used in dplyr::select() (but not in dplyr::filter(), dplyr::mutate() or dplyr::summarise())
+        # - - - -
+        # dplyr
+        # - - - -
+        # an element `.data` will be in the system call stack when using dplyr::select()
+        # [but not when using dplyr::filter(), dplyr::mutate() or dplyr::summarise()]
        not_set <<- FALSE
        el$`.data`
      } else if (tryCatch(any(c("x", "xx") %in% names(el)), error = function(e) FALSE)) {
-        # otherwise try base R:
+        # - - - -
+        # base R
+        # - - - -
        # an element `x` will be in this environment for only cols, e.g. `example_isolates[, carbapenems()]`
        # an element `xx` will be in this environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
        if (tryCatch(is.data.frame(el$xx), error = function(e) FALSE)) {
@ -694,6 +742,7 @@ get_current_data <- function(arg_name, call) {
    }
  })
  
+  # lookup the matched frame and return its value: a data.frame
  vars_df <- tryCatch(frms[[which(!vapply(FUN.VALUE = logical(1), frms, is.null))]], error = function(e) NULL)
  if (is.data.frame(vars_df)) {
    return(vars_df)
@ -932,8 +981,8 @@ font_stripstyle <- function(x) {
  gsub("(?:(?:\\x{001b}\\[)|\\x{009b})(?:(?:[0-9]{1,3})?(?:(?:;[0-9]{0,3})*)?[A-M|f-m])|\\x{001b}[A-M]", "", x, perl = TRUE)
 }

-progress_ticker <- function(n = 1, n_min = 0, ...) {
-  if (!interactive() || n < n_min) {
+progress_ticker <- function(n = 1, n_min = 0, print = TRUE, ...) {
+  if (print == FALSE || n < n_min) {
    pb <- list()
    pb$tick <- function() {
      invisible()
@ -1157,6 +1206,7 @@ lengths <- function(x, use.names = TRUE) {

 if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.1) {
  # R-3.0 does not contain these functions, set them here to prevent installation failure
+  # (required for extension of the <mic> class)
  cospi <- function(...) 1
  sinpi <- function(...) 1
  tanpi <- function(...) 1
--- a/R/ab.R
+++ b/R/ab.R
@ -29,7 +29,7 @@
 #' @inheritSection lifecycle Stable Lifecycle
 #' @param x character vector to determine to antibiotic ID
 #' @param flag_multiple_results logical to indicate whether a note should be printed to the console that probably more than one antibiotic code or name can be retrieved from a single input value.
-#' @param info logical to indicate whether a progress bar should be printed
+#' @param info a [logical] to indicate whether a progress bar should be printed, defaults to `TRUE` only in interactive mode
 #' @param ... arguments passed on to internal functions
 #' @rdname as.ab
 #' @inheritSection WHOCC WHOCC
@ -90,7 +90,7 @@
 #'     rename_with(as.ab, where(is.rsi))
 #'    
 #' }
-as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
+as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
  meet_criteria(x, allow_class = c("character", "numeric", "integer", "factor"), allow_NA = TRUE)
  meet_criteria(flag_multiple_results, allow_class = "logical", has_length = 1)
  meet_criteria(info, allow_class = "logical", has_length = 1)
@ -155,8 +155,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
  }
  
  if (initial_search == TRUE) {
-    progress <- progress_ticker(n = length(x),
-                                n_min = ifelse(isTRUE(info) & isFALSE(fast_mode), 25, length(x) + 1)) # start if n >= 25
+    progress <- progress_ticker(n = length(x), n_min = 25, print = info) # start if n >= 25
    on.exit(close(progress))
  }
  
@ -390,7 +389,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
      
      # first 5 except for cephalosporins, then first 7 (those cephalosporins all start quite the same!)
      found <- suppressWarnings(as.ab(substr(x[i], 1, 5), initial_search = FALSE))
-      if (!is.na(found) && !ab_group(found, initial_search = FALSE) %like% "cephalosporins") {
+      if (!is.na(found) && ab_group(found, initial_search = FALSE) %unlike% "cephalosporins") {
        x_new[i] <- note_if_more_than_one_found(found, i, from_text)
        next
      }
--- a/R/ab_from_text.R
+++ b/R/ab_from_text.R
@ -32,6 +32,7 @@
 #' @param collapse character to pass on to `paste(, collapse = ...)` to only return one character per element of `text`, see *Examples*
 #' @param translate_ab if `type = "drug"`: a column name of the [antibiotics] data set to translate the antibiotic abbreviations to, using [ab_property()]. Defaults to `FALSE`. Using `TRUE` is equal to using "name".
 #' @param thorough_search logical to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to `TRUE` will take considerably more time than when using `FALSE`. At default, it will turn `TRUE` when all input elements contain a maximum of three words.
+#' @param info logical to indicate whether a progress bar should be printed, defaults to `TRUE` only in interactive mode
 #' @param ... arguments passed on to [as.ab()]
 #' @details This function is also internally used by [as.ab()], although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the [as.ab()] function may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems.
 #' 
@ -92,6 +93,7 @@ ab_from_text <- function(text,
                         collapse = NULL,
                         translate_ab = FALSE,
                         thorough_search = NULL,
+                         info = interactive(),
                         ...) {
  if (missing(type)) {
    type <- type[1L]
@ -102,12 +104,13 @@ ab_from_text <- function(text,
  meet_criteria(collapse, has_length = 1, allow_NULL = TRUE)
  meet_criteria(translate_ab, allow_NULL = FALSE) # get_translate_ab() will be more informative about what's allowed
  meet_criteria(thorough_search, allow_class = "logical", has_length = 1, allow_NULL = TRUE)
+  meet_criteria(info, allow_class = "logical", has_length = 1)

  type <- tolower(trimws(type))
  
  text <- tolower(as.character(text))
  text_split_all <- strsplit(text, "[ ;.,:\\|]")
-  progress <- progress_ticker(n = length(text_split_all), n_min = 5)
+  progress <- progress_ticker(n = length(text_split_all), n_min = 5, print = info)
  on.exit(close(progress))
  
  if (type %like% "(drug|ab|anti)") {
--- a/R/custom_eucast_rules.R
+++ b/R/custom_eucast_rules.R
@ -23,17 +23,76 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #

-#' Create Custom EUCAST Rules
+#' Define Custom EUCAST Rules
 #' 
-#' @inheritSection lifecycle Experimental Lifecycle
+#' Define custom EUCAST rules for your organisation or specific analysis and use the output of this function in [eucast_rules()].
+#' @inheritSection lifecycle Maturing Lifecycle
 #' @param ... rules in formula notation, see *Examples*
 #' @details
-#' This documentation page will be updated shortly. **This function is experimental.**
+#' Some organisations have their own adoption of EUCAST rules. This function can be used to define custom EUCAST rules to be used in the [eucast_rules()] function.
 #' 
 #' @section How it works:
-#' ..
 #' 
-#' It is also possible to define antibiotic groups instead of single antibiotics. The following groups are allowed (case-insensitive): `r vector_and(tolower(DEFINED_AB_GROUPS), quote = "``")`.
+#' ### Basics
+#' 
+#' If you are familiar with the [`case_when()`][dplyr::case_when()] function of the `dplyr` package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule itself is written *before* the tilde (`~`) and the consequence of the rule is written *after* the tilde:
+#' 
+#' ```
+#' x <- custom_eucast_rules(TZP == "S" ~ aminopenicillins == "S",
+#'                          TZP == "R" ~ aminopenicillins == "R")
+#' ```
+#' 
+#' These are two custom EUCAST rules: if TZP (piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must be made "R". These rules can also be printed to the console, so it is immediately clear how they work:
+#' 
+#' ```
+#' x
+#' #> A set of custom EUCAST rules:
+#' #> 
+#' #>   1. If TZP is S then set to S:
+#' #>      amoxicillin (AMX), ampicillin (AMP)
+#' #> 
+#' #>   2. If TZP is R then set to R:
+#' #>      amoxicillin (AMX), ampicillin (AMP)
+#' ```
+#' 
+#' The rules (the part *before* the tilde, in above example `TZP == "S"` and `TZP == "R"`) must be evaluable in your data set: it should be able to run as a filter in your data set without errors. This means for the above example that the column `TZP` must exist. We will create a sample data set and test the rules set:
+#' 
+#' ```
+#' df <- data.frame(mo = c("E. coli", "K. pneumoniae"),
+#'                  TZP = "R",
+#'                  amox = "",
+#'                  AMP = "")
+#' df
+#' #>              mo TZP amox AMP
+#' #> 1       E. coli   R         
+#' #> 2 K. pneumoniae   R         
+#'                  
+#' eucast_rules(df, rules = "custom", custom_rules = x)
+#' #>              mo TZP amox AMP
+#' #> 1       E. coli   R    R   R     
+#' #> 2 K. pneumoniae   R    R   R  
+#' ```
+#' 
+#' ### Using taxonomic properties in rules
+#' 
+#' There is one exception in variables used for the rules: all column names of the [microorganisms] data set can also be used, but do not have to exist in the data set. These column names are: `r vector_and(colnames(microorganisms), quote = "``", sort = FALSE)`. Thus, this next example will work as well, despite the fact that the `df` data set does not contain a column `genus`:
+#' 
+#' ```
+#' y <- custom_eucast_rules(TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",
+#'                          TZP == "R" & genus == "Klebsiella" ~ aminopenicillins == "R")
+#'
+#' eucast_rules(df, rules = "custom", custom_rules = y)
+#' #>              mo TZP amox AMP
+#' #> 1       E. coli   R         
+#' #> 2 K. pneumoniae   R    R   R
+#' ```
+#' 
+#' ### Usage of antibiotic group names
+#' 
+#' It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part *after* the tilde. In above examples, the antibiotic group `aminopenicillins` is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the antibiotic agents that will be matched when running the rule.
+#' 
+#' `r paste0("  * ", sapply(DEFINED_AB_GROUPS, function(x) paste0("``", tolower(x), "``\\cr(", paste0(sort(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE)), collapse = ", "), ")"), USE.NAMES = FALSE), "\n", collapse = "")`
+#' @returns A [list] containing the custom rules
 #' @export
 #' @examples
 #' x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
--- a/R/data.R
+++ b/R/data.R
@ -98,7 +98,7 @@
 #' @details 
 #' Please note that entries are only based on the Catalogue of Life and the LPSN (see below). Since these sources incorporate entries based on (recent) publications in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), it can happen that the year of publication is sometimes later than one might expect.
 #' 
-#' For example, *Staphylococcus pettenkoferi* was described for the first time in Diagnostic Microbiology and Infectious Disease in 2002 (\doi{10.1016/s0732-8893(02)00399-1}), but it was not before 2007 that a publication in IJSEM followed (\doi{10.1099/ijs.0.64381-0}). Consequently, the AMR package returns 2007 for `mo_year("S. pettenkoferi")`.
+#' For example, *Staphylococcus pettenkoferi* was described for the first time in Diagnostic Microbiology and Infectious Disease in 2002 (\doi{10.1016/s0732-8893(02)00399-1}), but it was not before 2007 that a publication in IJSEM followed (\doi{10.1099/ijs.0.64381-0}). Consequently, the `AMR` package returns 2007 for `mo_year("S. pettenkoferi")`.
 #' 
 #' ## Manual additions
 #' For convenience, some entries were added manually:
--- a/R/eucast_rules.R
+++ b/R/eucast_rules.R
@ -190,7 +190,7 @@ eucast_rules <- function(x,
  }
  
  x_deparsed <- deparse(substitute(x))
-  if (length(x_deparsed) > 1 || !all(x_deparsed %like% "[a-z]+")) {
+  if (length(x_deparsed) > 1 || any(x_deparsed %unlike% "[a-z]+")) {
    x_deparsed <- "your_data"
  }
  
@ -225,8 +225,6 @@ eucast_rules <- function(x,
  if (is.null(col_mo)) {
    col_mo <- search_type_in_df(x = x, type = "mo", info = info)
    stop_if(is.null(col_mo), "`col_mo` must be set")
-  } else {
-    stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found")
  }
  
  decimal.mark <- getOption("OutDec")
@ -420,8 +418,11 @@ eucast_rules <- function(x,
    pm_distinct(`.rowid`, .keep_all = TRUE) %pm>% 
    as.data.frame(stringsAsFactors = FALSE)
  x[, col_mo] <- as.mo(as.character(x[, col_mo, drop = TRUE]))
-  x <- x %pm>%
-    left_join_microorganisms(by = col_mo, suffix = c("_oldcols", ""))
+  # rename col_mo to prevent interference with joined columns
+  colnames(x)[colnames(x) == col_mo] <- ".col_mo"
+  col_mo <- ".col_mo"
+  # join to microorganisms data set
+  x <- left_join_microorganisms(x, by = col_mo, suffix = c("_oldcols", ""))
  x$gramstain <- mo_gramstain(x[, col_mo, drop = TRUE], language = NULL)
  x$genus_species <- paste(x$genus, x$species)
  if (info == TRUE & NROW(x) > 10000) {
@ -480,7 +481,6 @@ eucast_rules <- function(x,
                        extra_indent = 6))
        }
        run_changes <- edit_rsi(x = x,
-                                col_mo = col_mo,
                                to = "R",
                                rule = c(rule_current, "Other rules", "",
                                         paste0("Non-EUCAST: AMR package v", utils::packageDescription("AMR")$Version)),
@ -515,7 +515,6 @@ eucast_rules <- function(x,
                        extra_indent = 6))
        }
        run_changes <- edit_rsi(x = x,
-                                col_mo = col_mo,
                                to = "S",
                                rule = c(rule_current, "Other rules", "", 
                                         paste0("Non-EUCAST: AMR package v", utils::packageDescription("AMR")$Version)),
@ -569,19 +568,19 @@ eucast_rules <- function(x,
  # filter on user-set guideline versions ----
  if (any(c("all", "breakpoints") %in% rules)) {
    eucast_rules_df <- subset(eucast_rules_df,
-                              !reference.rule_group %like% "breakpoint" |
+                              reference.rule_group %unlike% "breakpoint" |
                                (reference.rule_group %like% "breakpoint" & reference.version == version_breakpoints))
  }
  if (any(c("all", "expert") %in% rules)) {
    eucast_rules_df <- subset(eucast_rules_df,
-                              !reference.rule_group %like% "expert" |
+                              reference.rule_group %unlike% "expert" |
                                (reference.rule_group %like% "expert" & reference.version == version_expertrules))
  }
  # filter out AmpC de-repressed cephalosporin-resistant mutants ----
  # cefotaxime, ceftriaxone, ceftazidime
  if (is.null(ampc_cephalosporin_resistance) || isFALSE(ampc_cephalosporin_resistance)) {
    eucast_rules_df <- subset(eucast_rules_df,
-                              !reference.rule %like% "ampc")
+                              reference.rule %unlike% "ampc")
  } else {
    if (isTRUE(ampc_cephalosporin_resistance)) {
      ampc_cephalosporin_resistance <- "R"
@ -627,7 +626,7 @@ eucast_rules <- function(x,
    
    if (info == TRUE) {
      # Print EUCAST intro ------------------------------------------------------
-      if (!rule_group_current %like% "other" & eucast_notification_shown == FALSE) {
+      if (rule_group_current %unlike% "other" & eucast_notification_shown == FALSE) {
        cat(
          paste0("\n", font_grey(strrep("-", 0.95 * options()$width)), "\n",
                 word_wrap("Rules by the ", font_bold("European Committee on Antimicrobial Susceptibility Testing (EUCAST)")), "\n", 
@ -750,7 +749,6 @@ eucast_rules <- function(x,
    # Apply rule on data ------------------------------------------------------
    # this will return the unique number of changes
    run_changes <- edit_rsi(x = x,
-                            col_mo = col_mo,
                            to = target_value,
                            rule = c(rule_text, rule_group_current, rule_current, 
                                     ifelse(rule_group_current %like% "breakpoint",
@ -803,7 +801,6 @@ eucast_rules <- function(x,
        warned <- FALSE
      }
      run_changes <- edit_rsi(x = x,
-                              col_mo = col_mo,
                              to = target_value,
                              rule = c(rule_text, 
                                       "Custom EUCAST rules",
@ -949,13 +946,12 @@ eucast_rules <- function(x,
 }

 # helper function for editing the table ----
-edit_rsi <- function(x, 
-                     col_mo,
-                     to, 
-                     rule, 
+edit_rsi <- function(x,
+                     to,
+                     rule,
                     rows,
                     cols,
-                     last_verbose_info, 
+                     last_verbose_info,
                     original_data,
                     warned,
                     info,
--- a/R/filter_ab_class.R
+++ b/R/filter_ab_class.R
@ -425,7 +425,7 @@ find_ab_group <- function(ab_class) {

 find_ab_names <- function(ab_group, n = 3) {
  ab_group <- gsub("[^a-zA-Z0-9]", ".*", ab_group)
-  drugs <- antibiotics[which(antibiotics$group %like% ab_group & !antibiotics$ab %like% "[0-9]$"), ]$name
+  drugs <- antibiotics[which(antibiotics$group %like% ab_group & antibiotics$ab %unlike% "[0-9]$"), ]$name
  paste0(sort(ab_name(sample(drugs, size = min(n, length(drugs)), replace = FALSE),
                      tolower = TRUE, language = NULL)), 
         collapse = ", ")
--- a/R/first_isolate.R
+++ b/R/first_isolate.R
@ -42,7 +42,7 @@
 #' @param type type to determine weighed isolates; can be `"keyantibiotics"` or `"points"`, see *Details*
 #' @param ignore_I logical to indicate whether antibiotic interpretations with `"I"` will be ignored when `type = "keyantibiotics"`, see *Details*
 #' @param points_threshold points until the comparison of key antibiotics will lead to inclusion of an isolate when `type = "points"`, see *Details*
-#' @param info print progress
+#' @param info a [logical] to indicate info should be printed, defaults to `TRUE` only in interactive mode
 #' @param include_unknown logical to indicate whether 'unknown' microorganisms should be included too, i.e. microbial code `"UNKNOWN"`, which defaults to `FALSE`. For WHONET users, this means that all records with organism code `"con"` (*contamination*) will be excluded at default. Isolates with a microbial ID of `NA` will always be excluded as first isolate.
 #' @param include_untested_rsi logical to indicate whether also rows without antibiotic results are still eligible for becoming a first isolate. Use `include_untested_rsi = FALSE` to always return `FALSE` for such rows. This checks the data set for columns of class `<rsi>` and consequently requires transforming columns with antibiotic results using [as.rsi()] first.
 #' @param ... arguments passed on to [first_isolate()] when using [filter_first_isolate()], or arguments passed on to [key_antibiotics()] when using [filter_first_weighted_isolate()]
@ -402,7 +402,7 @@ first_isolate <- function(x = NULL,
                                             type = type_param,
                                             ignore_I = ignore_I,
                                             points_threshold = points_threshold,
-                                             info = info)
+                                             na.rm = TRUE)
    # with key antibiotics
    x$newvar_first_isolate <- pm_if_else(x$newvar_row_index_sorted >= row.start &
                                           x$newvar_row_index_sorted <= row.end &
@ -497,10 +497,10 @@ first_isolate <- function(x = NULL,
    n_found <- sum(x$newvar_first_isolate, na.rm = TRUE)
    p_found_total <- percentage(n_found / nrow(x[which(!is.na(x$newvar_mo)), , drop = FALSE]), digits = 1)
    p_found_scope <- percentage(n_found / scope.size, digits = 1)
-    if (!p_found_total %like% "[.]") {
+    if (p_found_total %unlike% "[.]") {
      p_found_total <- gsub("%", ".0%", p_found_total, fixed = TRUE)
    }
-    if (!p_found_scope %like% "[.]") {
+    if (p_found_scope %unlike% "[.]") {
      p_found_scope <- gsub("%", ".0%", p_found_scope, fixed = TRUE)
    }
    # mark up number of found
--- a/R/join_microorganisms.R
+++ b/R/join_microorganisms.R
@ -279,7 +279,7 @@ check_groups_before_join <- function(x, fn) {
  if (is.data.frame(x) && !is.null(attributes(x)$groups)) {
    x <- pm_ungroup(x)
    attr(x, "groups") <- NULL
-    class(x) <- class(x)[!class(x) %like% "group"]
+    class(x) <- class(x)[class(x) %unlike% "group"]
    warning_("Groups are dropped, since the ", fn, "() function relies on merge() from base R.", call = FALSE)
  }
  x
--- a/R/key_antibiotics.R
+++ b/R/key_antibiotics.R
@ -136,7 +136,7 @@ key_antibiotics <- function(x = NULL,
    x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
  }
  meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
-  meet_criteria(col_mo, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
+  meet_criteria(col_mo, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE, is_in = colnames(x))
  meet_criteria(universal_1, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
  meet_criteria(universal_2, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
  meet_criteria(universal_3, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
@ -173,8 +173,6 @@ key_antibiotics <- function(x = NULL,
  # -- mo
  if (is.null(col_mo)) {
    col_mo <- search_type_in_df(x = x, type = "mo")
-  } else {
-    stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found")
  }
  if (is.null(col_mo)) {
    warning_("No column found for `col_mo`, ignoring antimicrobial agents set for Gram-negative and Gram-positive bacteria", call = FALSE)
@ -288,95 +286,75 @@ key_antibiotics <- function(x = NULL,
 }

 #' @rdname key_antibiotics
+#' @param info unused - previously used to indicate whether a progress bar should print
+#' @param na.rm a [logical] to indicate whether comparison with `NA` should return `FALSE` (defaults to `TRUE` for backwards compatibility)
 #' @export
 key_antibiotics_equal <- function(y,
                                  z,
                                  type = c("keyantibiotics", "points"),
                                  ignore_I = TRUE,
                                  points_threshold = 2,
-                                  info = FALSE) {
+                                  info = FALSE,
+                                  na.rm = TRUE,
+                                  ...) {
  meet_criteria(y, allow_class = "character")
  meet_criteria(z, allow_class = "character")
-  meet_criteria(type, allow_class = "character", has_length = c(1, 2))
+  if (length(type) == 2) {
+    type <- type[1L]
+  }
+  meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("keyantibiotics", "points"))
  meet_criteria(ignore_I, allow_class = "logical", has_length = 1)
  meet_criteria(points_threshold, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
  meet_criteria(info, allow_class = "logical", has_length = 1)
-  
+  meet_criteria(na.rm, allow_class = "logical", has_length = 1)
  stop_ifnot(length(y) == length(z), "length of `y` and `z` must be equal")
-  # y is active row, z is lag
-  x <- y
-  y <- z
-  
-  type <- type[1]
-  
-  # only show progress bar on points or when at least 5000 isolates
-  info_needed <- info == TRUE & (type == "points" | length(x) > 5000)
-  
-  result <- logical(length(x))
-  
-  if (info_needed == TRUE) {
-    p <- progress_ticker(length(x))
-    on.exit(close(p))
+
+  key2rsi <- function(val) {
+    as.double(as.rsi(gsub(".", NA_character_, unlist(strsplit(val, "")), fixed = TRUE)))
  }
+  y <- lapply(y, key2rsi)
+  z <- lapply(z, key2rsi)
  
-  for (i in seq_len(length(x))) {
-    
-    if (info_needed == TRUE) {
-      p$tick()
+  determine_equality <- function(a, b, type, points_threshold, ignore_I) {
+    if (length(a) != length(b)) {
+      # incomparable, so not equal
+      return(FALSE)
    }
+    # ignore NAs on both sides
+    NA_ind <- which(is.na(a) | is.na(b))
+    a[NA_ind] <- NA_real_
+    b[NA_ind] <- NA_real_
    
-    if (is.na(x[i])) {
-      x[i] <- ""
-    }
-    if (is.na(y[i])) {
-      y[i] <- ""
-    }
-    
-    if (x[i] == y[i]) {
-      
-      result[i] <- TRUE
-      
-    } else if (nchar(x[i]) != nchar(y[i])) {
-      
-      result[i] <- FALSE
-      
+    if (type == "points") {
+      # count points for every single character:
+      # - no change is 0 points
+      # - I <-> S|R is 0.5 point
+      # - S|R <-> R|S is 1 point
+      # use the levels of as.rsi (S = 1, I = 2, R = 3)
+      (sum(abs(a - b), na.rm = TRUE) / 2) < points_threshold
    } else {
-      
-      x_split <- strsplit(x[i], "")[[1]]
-      y_split <- strsplit(y[i], "")[[1]]
-      
-      if (type == "keyantibiotics") {
-        
-        if (ignore_I == TRUE) {
-          x_split[x_split == "I"] <- "."
-          y_split[y_split == "I"] <- "."
-        }
-        
-        y_split[x_split == "."] <- "."
-        x_split[y_split == "."] <- "."
-        
-        result[i] <- all(x_split == y_split)
-        
-      } else if (type == "points") {
-        # count points for every single character:
-        # - no change is 0 points
-        # - I <-> S|R is 0.5 point
-        # - S|R <-> R|S is 1 point
-        # use the levels of as.rsi (S = 1, I = 2, R = 3)
-        
-        suppressWarnings(x_split <- x_split %pm>% as.rsi() %pm>% as.double())
-        suppressWarnings(y_split <- y_split %pm>% as.rsi() %pm>% as.double())
-        
-        points <- (x_split - y_split) %pm>% abs() %pm>% sum(na.rm = TRUE) / 2
-        result[i] <- points >= points_threshold
-        
-      } else {
-        stop("`", type, '` is not a valid value for type, must be "points" or "keyantibiotics". See ?key_antibiotics')
+      if (ignore_I == TRUE) {
+        ind <- which(a == 2 | b == 2) # since as.double(as.rsi("I")) == 2
+        a[ind] <- NA_real_
+        b[ind] <- NA_real_
      }
+      all(a == b, na.rm = TRUE)
    }
  }
-  if (info_needed == TRUE) {
-    close(p)
+  out <- unlist(mapply(FUN = determine_equality,
+                       y,
+                       z,
+                       MoreArgs = list(type = type,
+                                       points_threshold = points_threshold,
+                                       ignore_I = ignore_I),
+                       SIMPLIFY = FALSE,
+                       USE.NAMES = FALSE))
+  if (na.rm == FALSE) {
+    out[is.na(y) | is.na(z)] <- NA
+  } else  {
+    # NA means not equal if `na.rm == TRUE`, as per the manual
+    out[is.na(y) | is.na(z)] <- FALSE
  }
-  result
+  
+  out
 }
--- a/R/like.R
+++ b/R/like.R
@ -35,18 +35,17 @@
 #' @rdname like
 #' @export
 #' @details
-#' This `%like%` function:
-#' * Is case-insensitive (use `%like_case%` for case-sensitive matching)
-#' * Supports multiple patterns
-#' * Checks if `pattern` is a valid regular expression and sets `fixed = TRUE` if not, to greatly improve speed (vectorised over `pattern`)
-#' * Always uses compatibility with Perl unless `fixed = TRUE`, to greatly improve speed
+#' These [like()] and `%like%`/`%unlike%` functions:
+#' * Are case-insensitive (use `%like_case%`/`%unlike_case%` for case-sensitive matching)
+#' * Support multiple patterns
+#' * Check if `pattern` is a valid regular expression and sets `fixed = TRUE` if not, to greatly improve speed (vectorised over `pattern`)
+#' * Always use compatibility with Perl unless `fixed = TRUE`, to greatly improve speed
 #' 
-#' Using RStudio? The text `%like%` can also be directly inserted in your code from the Addins menu and can have its own Keyboard Shortcut like `Ctrl+Shift+L` or `Cmd+Shift+L` (see `Tools` > `Modify Keyboard Shortcuts...`).
+#' Using RStudio? The `%like%`/`%unlike%` functions can also be directly inserted in your code from the Addins menu and can have its own keyboard shortcut like `Shift+Ctrl+L` or `Shift+Cmd+L` (see menu `Tools` > `Modify Keyboard Shortcuts...`). If you keep pressing your shortcut, the inserted text will be iterated over `%like%` -> `%unlike%` -> `%like_case%` -> `%unlike_case%`.
 #' @source Idea from the [`like` function from the `data.table` package](https://github.com/Rdatatable/data.table/blob/ec1259af1bf13fc0c96a1d3f9e84d55d8106a9a4/R/like.R), although altered as explained in *Details*.
 #' @seealso [grepl()]
 #' @inheritSection AMR Read more on Our Website!
 #' @examples
-#' # simple test
 #' a <- "This is a test"
 #' b <- "TEST"
 #' a %like% b
@ -59,13 +58,20 @@
 #' b <- c(     "case",           "diff",      "yet")
 #' a %like% b
 #' #> TRUE TRUE TRUE
+#' a %unlike% b
+#' #> FALSE FALSE FALSE
+#' 
 #' a[1] %like% b
 #' #> TRUE FALSE FALSE
 #' a %like% b[1]
 #' #> TRUE FALSE FALSE
 #' 
 #' # get isolates whose name start with 'Ent' or 'ent'
+#' example_isolates[which(mo_name(example_isolates$mo) %like% "^ent"), ]
 #' \donttest{
+#' # faster way, only works in R 3.2 and later:
+#' example_isolates[which(mo_name() %like% "^ent"), ]
+#' 
 #' if (require("dplyr")) {
 #'   example_isolates %>%
 #'     filter(mo_name() %like% "^ent")
@ -123,6 +129,14 @@ like <- function(x, pattern, ignore.case = TRUE) {
  like(x, pattern, ignore.case = TRUE)
 }

+#' @rdname like
+#' @export
+"%unlike%" <- function(x, pattern) {
+  meet_criteria(x, allow_NA = TRUE)
+  meet_criteria(pattern, allow_NA = FALSE)
+  !like(x, pattern, ignore.case = TRUE)
+}
+
 #' @rdname like
 #' @export
 "%like_case%" <- function(x, pattern) {
@ -130,3 +144,11 @@ like <- function(x, pattern, ignore.case = TRUE) {
  meet_criteria(pattern, allow_NA = FALSE)
  like(x, pattern, ignore.case = FALSE)
 }
+
+#' @rdname like
+#' @export
+"%unlike_case%" <- function(x, pattern) {
+  meet_criteria(x, allow_NA = TRUE)
+  meet_criteria(pattern, allow_NA = FALSE)
+  !like(x, pattern, ignore.case = FALSE)
+}
--- a/R/mdro.R
+++ b/R/mdro.R
@ -78,7 +78,7 @@
 #' 
 #' Custom guidelines can be set with the [custom_mdro_guideline()] function. This is of great importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.
 #' 
-#' If you are familiar with `case_when()` of the `dplyr` package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation':
+#' If you are familiar with the [`case_when()`][dplyr::case_when()] function of the `dplyr` package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule is written *before* the tilde (`~`) and the consequence of the rule is written *after* the tilde:
 #' 
 #' ```
 #' custom <- custom_mdro_guideline(CIP == "R" & age > 60 ~ "Elderly Type A",
@ -311,7 +311,6 @@ mdro <- function(x = NULL,
    col_mo <- "mo"
  }
  stop_if(is.null(col_mo), "`col_mo` must be set")
-  stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found")
  
  if (guideline$code == "cmi2012") {
    guideline$name <- "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance."
@ -761,7 +760,11 @@ mdro <- function(x = NULL,
      row_filter <- x[which(row_filter), "row_number", drop = TRUE]
      rows <- rows[rows %in% row_filter]
      x[rows, "MDRO"] <<- to
-      x[rows, "reason"] <<- paste0(any_all, " of the required antibiotics ", ifelse(any_all == "any", "is", "are"), " R")
+      x[rows, "reason"] <<- paste0(any_all, 
+                                   " of the required antibiotics ",
+                                   ifelse(any_all == "any", "is", "are"),
+                                   " R",
+                                   ifelse(!isTRUE(combine_SI), " or I", ""))
    }
  }
  trans_tbl2 <- function(txt, rows, lst) {
@ -814,6 +817,9 @@ mdro <- function(x = NULL,
  }
  
  x[, col_mo] <- as.mo(as.character(x[, col_mo, drop = TRUE]))
+  # rename col_mo to prevent interference with joined columns
+  colnames(x)[colnames(x) == col_mo] <- ".col_mo"
+  col_mo <- ".col_mo"
  # join to microorganisms data set
  x <- left_join_microorganisms(x, by = col_mo)
  x$MDRO <- ifelse(!is.na(x$genus), 1, NA_integer_)
@ -1027,7 +1033,10 @@ mdro <- function(x = NULL,
    # PDR (=4): all agents are R 
    x[which(x$classes_affected == 999 & x$classes_in_guideline == x$classes_available), "MDRO"] <- 4
    if (verbose == TRUE) {
-      x[which(x$MDRO == 4), "reason"] <- paste("all antibiotics in all", x$classes_in_guideline[which(x$MDRO == 4)], "classes were tested R or I")
+      x[which(x$MDRO == 4), "reason"] <- paste("all antibiotics in all",
+                                               x$classes_in_guideline[which(x$MDRO == 4)], 
+                                               "classes were tested R",
+                                               ifelse(!isTRUE(combine_SI), " or I", ""))
    }
    
    # not enough classes available
@ -1390,7 +1399,12 @@ mdro <- function(x = NULL,
  # some more info on negative results
  if (verbose == TRUE) {
    if (guideline$code == "cmi2012") {
-      x[which(x$MDRO == 1 & !is.na(x$classes_affected)), "reason"] <- paste0(x$classes_affected[which(x$MDRO == 1 & !is.na(x$classes_affected))], " of ", x$classes_available[which(x$MDRO == 1 & !is.na(x$classes_affected))], " available classes contain R or I (3 required for MDR)")
+      x[which(x$MDRO == 1 & !is.na(x$classes_affected)), "reason"] <- paste0(x$classes_affected[which(x$MDRO == 1 & !is.na(x$classes_affected))],
+                                                                             " of ",
+                                                                             x$classes_available[which(x$MDRO == 1 & !is.na(x$classes_affected))],
+                                                                             " available classes contain R",
+                                                                             ifelse(!isTRUE(combine_SI), " or I", ""),
+                                                                             " (3 required for MDR)")
    } else {
      x[which(x$MDRO == 1), "reason"] <- "too few antibiotics are R"
    }
@ -1431,8 +1445,10 @@ mdro <- function(x = NULL,
  }
  
  if (verbose == TRUE) {
+    colnames(x)[colnames(x) == col_mo] <- "microorganism"
+    x$microorganism <- mo_name(x$microorganism, language = NULL)
    x[, c("row_number",
-          col_mo,
+          "microorganism",
          "MDRO",
          "reason",
          "columns_nonsusceptible"), 
--- a/R/mic.R
+++ b/R/mic.R
@ -133,7 +133,7 @@ as.mic <- function(x, na.rm = FALSE) {
    # keep only one zero before dot
    x <- gsub("0+[.]", "0.", x, perl = TRUE)
    # starting 00 is probably 0.0 if there's no dot yet
-    x[!x %like% "[.]"] <- gsub("^00", "0.0", x[!x %like% "[.]"])
+    x[x %unlike% "[.]"] <- gsub("^00", "0.0", x[!x %like% "[.]"])
    # remove last zeroes
    x <- gsub("([.].?)0+$", "\\1", x, perl = TRUE)
    x <- gsub("(.*[.])0+$", "\\10", x, perl = TRUE)
--- a/R/mo.R
+++ b/R/mo.R
@ -38,6 +38,7 @@
 #' @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)")`.
 #' @param language language to translate text like "no growth", which defaults to the system language (see [get_locale()])
+#' @param info a [logical] to indicate if a progress bar should be printed if more than 25 items are to be coerced, defaults to `TRUE` only in interactive mode
 #' @param ... other arguments passed on to functions
 #' @rdname as.mo
 #' @aliases mo
@ -161,6 +162,7 @@ as.mo <- function(x,
                  reference_df = get_mo_source(),
                  ignore_pattern = getOption("AMR_ignore_pattern"),
                  language = get_locale(),
+                  info = interactive(),
                  ...) {
  meet_criteria(x, allow_class = c("mo", "data.frame", "list", "character", "numeric", "integer", "factor"), allow_NA = TRUE)
  meet_criteria(Becker, allow_class = c("logical", "character"), has_length = 1)
@ -169,7 +171,8 @@ as.mo <- function(x,
  meet_criteria(reference_df, allow_class = "data.frame", allow_NULL = TRUE)
  meet_criteria(ignore_pattern, allow_class = "character", has_length = 1, allow_NULL = TRUE)
  meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
-
+  meet_criteria(info, allow_class = "logical", has_length = 1)
+  
  check_dataset_integrity()

  if (tryCatch(all(x[!is.na(x)] %in% MO_lookup$mo)
@ -227,6 +230,7 @@ as.mo <- function(x,
                     reference_df = reference_df,
                     ignore_pattern = ignore_pattern,
                     language = language,
+                     info = info,
                     ...)
  }

@ -253,6 +257,7 @@ exec_as.mo <- function(x,
                       Lancefield = FALSE,
                       allow_uncertain = TRUE,
                       reference_df = get_mo_source(),
+                       info = interactive(),
                       property = "mo",
                       initial_search = TRUE,
                       dyslexia_mode = FALSE,
@ -600,7 +605,7 @@ exec_as.mo <- function(x,
      }
      
      if (initial_search == TRUE) {
-        progress <- progress_ticker(n = length(x[!already_known]), n_min = 25) # start if n >= 25
+        progress <- progress_ticker(n = length(x[!already_known]), n_min = 25, print = info) # start if n >= 25
        on.exit(close(progress))
      }
      
@ -703,7 +708,7 @@ exec_as.mo <- function(x,
        
        # check for very small input, but ignore the O antigens of E. coli
        if (nchar(gsub("[^a-zA-Z]", "", x_trimmed[i])) < 3
-            & !toupper(x_backup_without_spp[i]) %like_case% "O?(26|103|104|104|111|121|145|157)") {
+            & toupper(x_backup_without_spp[i]) %unlike_case% "O?(26|103|104|104|111|121|145|157)") {
          # fewer than 3 chars and not looked for species, add as failure
          x[i] <- lookup(mo == "UNKNOWN")
          if (initial_search == TRUE) {
@ -855,7 +860,7 @@ exec_as.mo <- function(x,
            x[i] <- lookup(genus == "Salmonella", uncertainty = -1)
            next
          } else if (x_backup[i] %like_case% "[sS]almonella [A-Z][a-z]+ ?.*" &
-                     !x_backup[i] %like% "t[iy](ph|f)[iy]") {
+                     x_backup[i] %unlike% "t[iy](ph|f)[iy]") {
            # Salmonella with capital letter species like "Salmonella Goettingen" - they're all S. enterica
            # except for S. typhi, S. paratyphi, S. typhimurium
            x[i] <- lookup(fullname == "Salmonella enterica", uncertainty = -1)
@ -911,7 +916,7 @@ exec_as.mo <- function(x,
          # FIRST TRY FULLNAMES AND CODES ----
          # if only genus is available, return only genus
          
-          if (all(!c(x[i], b.x_trimmed) %like_case% " ")) {
+          if (all(c(x[i], b.x_trimmed) %unlike_case% " ")) {
            found <- lookup(fullname_lower %in% c(h.x_species, i.x_trimmed_species),
                            haystack = data_to_check)
            if (!is.na(found)) {
@ -1118,8 +1123,8 @@ exec_as.mo <- function(x,
              if (isTRUE(debug)) {
                cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (3) look for genus only, part of name\n"))
              }
-              if (nchar(g.x_backup_without_spp) > 4 & !b.x_trimmed %like_case% " ") {
-                if (!b.x_trimmed %like_case% "^[A-Z][a-z]+") {
+              if (nchar(g.x_backup_without_spp) > 4 & b.x_trimmed %unlike_case% " ") {
+                if (b.x_trimmed %unlike_case% "^[A-Z][a-z]+") {
                  if (isTRUE(debug)) {
                    message("Running '", paste(b.x_trimmed, "species"), "'")
                  }
@ -1263,7 +1268,7 @@ exec_as.mo <- function(x,
                                        stringsAsFactors = FALSE)
                return(found)
              }
-              if (b.x_trimmed %like_case% "(fungus|fungi)" & !b.x_trimmed %like_case% "fungiphrya") {
+              if (b.x_trimmed %like_case% "(fungus|fungi)" & b.x_trimmed %unlike_case% "fungiphrya") {
                found <- "F_FUNGUS"
                found_result <- found
                found <- lookup(mo == found)
--- a/R/plot.R
+++ b/R/plot.R
@ -688,7 +688,7 @@ plot_prepare_table <- function(x, expand) {
 }

 plot_name_of_I <- function(guideline) {
-  if (!guideline %like% "CLSI" && as.double(gsub("[^0-9]+", "", guideline)) >= 2019) {
+  if (guideline %unlike% "CLSI" && as.double(gsub("[^0-9]+", "", guideline)) >= 2019) {
    # interpretation since 2019
    "Incr. exposure"
  } else {
--- a/R/rsi.R
+++ b/R/rsi.R
@ -263,9 +263,9 @@ as.rsi.default <- function(x, ...) {
    x[x == 2] <- "I"
    x[x == 3] <- "R"
    
-  } else if (!all(is.na(x)) && !identical(levels(x), c("S", "I", "R"))) {
-    
-    if (!any(x %like% "(R|S|I)", na.rm = TRUE)) {
+  } else if (!all(is.na(x)) && !identical(levels(x), c("S", "I", "R")) && !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 be MIC values. Transform them with `as.mic()` before running `as.rsi()` to interpret them.")
@ -683,7 +683,7 @@ get_guideline <- function(guideline, reference_data) {
  if (guideline_param %in% c("CLSI", "EUCAST")) {
    guideline_param <- rev(sort(subset(reference_data, guideline %like% guideline_param)$guideline))[1L]
  }
-  if (!guideline_param %like% " ") {
+  if (guideline_param %unlike% " ") {
    # like 'EUCAST2020', should be 'EUCAST 2020'
    guideline_param <- gsub("([a-z]+)([0-9]+)", "\\1 \\2", guideline_param, ignore.case = TRUE)
  }
@ -776,7 +776,7 @@ exec_as.rsi <- function(method,
    any_is_intrinsic_resistant <- any_is_intrinsic_resistant | is_intrinsic_r
    
    if (isTRUE(add_intrinsic_resistance) & is_intrinsic_r) {
-      if (!guideline_coerced %like% "EUCAST") {
+      if (guideline_coerced %unlike% "EUCAST") {
        if (message_not_thrown_before("as.rsi2")) {
          warning_("Using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.", call = FALSE)
          remember_thrown_message("as.rsi2")
--- a/R/zzz.R
+++ b/R/zzz.R
@ -61,20 +61,3 @@ pkg_env$mo_failed <- character(0)
    }
  }, silent = TRUE)
 }
-
-.onAttach <- function(...) {
-  # show notice in 10% of cases in interactive session
-  if (!interactive() || stats::runif(1) > 0.1 || isTRUE(as.logical(getOption("AMR_silentstart", FALSE)))) {
-    return()
-  }
-  packageStartupMessage(word_wrap("Thank you for using the AMR package! ",
-                                  "If you have a minute, please anonymously fill in this short questionnaire to improve the package and its functionalities: ",
-                                  font_blue("https://msberends.github.io/AMR/survey.html\n"),
-                                  "[prevent his notice with ",
-                                  font_bold("suppressPackageStartupMessages(library(AMR))"),
-                                  " or use ",
-                                  font_bold("options(AMR_silentstart = TRUE)"), "]"))
-}
-
-
-
--- a/data-raw/AMR_latest.tar.gz
+++ b/data-raw/AMR_latest.tar.gz
--- a/data-raw/read_EUCAST.R
+++ b/data-raw/read_EUCAST.R
@ -136,8 +136,8 @@ read_EUCAST <- function(sheet, file, guideline_name) {
              disk_R = ifelse(has_zone_diameters, G, NA_character_)) %>% 
    filter(!is.na(drug),
           !(is.na(MIC_S) & is.na(MIC_R) & is.na(disk_S) & is.na(disk_R)),
-           !MIC_S %like% "(MIC|S ≤|note)",
-           !MIC_S %like% "^[-]",
+           MIC_S %unlike% "(MIC|S ≤|note)",
+           MIC_S %unlike% "^[-]",
           drug != MIC_S,) %>% 
    mutate(administration = case_when(drug %like% "[( ]oral" ~ "oral",
                                      drug %like% "[( ]iv"   ~ "iv",
--- a/data-raw/reproduction_of_antibiotics.R
+++ b/data-raw/reproduction_of_antibiotics.R
@ -114,8 +114,8 @@ abx_atc2 <- ab_old %>%
  filter(!atc %in% abx_atc1$atc,
         is.na(ears_net),
         !is.na(atc_group1),
-         !atc_group1 %like% ("virus|vaccin|viral|immun"),
-         !official %like% "(combinations| with )") %>%
+         atc_group1 %unlike% ("virus|vaccin|viral|immun"),
+         official %unlike% "(combinations| with )") %>%
  mutate(ab = NA_character_) %>%
  as.data.frame(stringsAsFactors = FALSE) %>%
  select(ab, atc, name = official)
--- a/data-raw/reproduction_of_microorganisms.R
+++ b/data-raw/reproduction_of_microorganisms.R
@ -382,7 +382,7 @@ MOs <- MOs %>%

 # what characters are in the fullnames?
 table(sort(unlist(strsplit(x = paste(MOs$fullname, collapse = ""), split = ""))))
-MOs %>% filter(!fullname %like% "^[a-z ]+$") %>% arrange(fullname) %>% View()
+MOs %>% filter(fullname %unlike% "^[a-z ]+$") %>% arrange(fullname) %>% View()

 table(MOs$kingdom, MOs$rank)
 table(AMR::microorganisms$kingdom, AMR::microorganisms$rank)
--- a/data-raw/reproduction_of_poorman.R
+++ b/data-raw/reproduction_of_poorman.R
@ -9,9 +9,9 @@ files <- xml2::read_html(paste0("https://github.com/nathaneastwood/poorman/tree/
 # get full URLs of all raw R files
 files <- sort(paste0("https://raw.githubusercontent.com", gsub("blob/", "", files[files %like% "/R/.*.R$"])))
 # remove files with only pkg specific code
-files <- files[!files %like% "(zzz|init)[.]R$"]
+files <- files[files %unlike% "(zzz|init)[.]R$"]
 # also, there's a lot of functions we don't use
-files <- files[!files %like% "(slice|glimpse|recode|replace_na|coalesce)[.]R$"]
+files <- files[files %unlike% "(slice|glimpse|recode|replace_na|coalesce)[.]R$"]

 # add our prepend file, containing info about the source of the data
 intro <- readLines("data-raw/poorman_prepend.R")
--- a/docs/404.html
+++ b/docs/404.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
      </span>
    </div>

--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
      </span>
    </div>

--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
      </span>
    </div>

--- a/docs/authors.html
+++ b/docs/authors.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
      </span>
    </div>

--- a/docs/index.html
+++ b/docs/index.html
@ -42,7 +42,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
      </span>
    </div>

--- a/docs/news/index.html
+++ b/docs/news/index.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
      </span>
    </div>

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

-    <div id="amr-1609006" class="section level1">
-<h1 class="page-header" data-toc-text="1.6.0.9006">
-<a href="#amr-1609006" class="anchor"></a>AMR 1.6.0.9006<small> Unreleased </small>
+    <div id="amr-1609009" class="section level1">
+<h1 class="page-header" data-toc-text="1.6.0.9009">
+<a href="#amr-1609009" class="anchor"></a>AMR 1.6.0.9009<small> Unreleased </small>
 </h1>
-<div id="last-updated-16-april-2021" class="section level2">
+<div id="last-updated-23-april-2021" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-16-april-2021" class="anchor"></a><small>Last updated: 16 April 2021</small>
+<a href="#last-updated-23-april-2021" class="anchor"></a><small>Last updated: 23 April 2021</small>
 </h2>
 <div id="new" class="section level3">
 <h3 class="hasAnchor">
@ -270,9 +270,30 @@
 <li>
 <code><a href="../reference/first_isolate.html">first_isolate()</a></code> can now take a vector of values for <code>col_keyantibiotics</code> and can have an episode length of <code>Inf</code>
 </li>
+<li>Extended the <code><a href="../reference/like.html">like()</a></code> functions:
+<ul>
+<li><p>Now checks if <code>pattern</code> is a <em>valid</em> regular expression</p></li>
 <li>
-<code><a href="../reference/like.html">like()</a></code> (and <code><a href="../reference/like.html">%like%</a></code>) now checks if <code>pattern</code> is a <em>valid</em> regular expression</li>
+<p>Added <code><a href="../reference/like.html">%unlike%</a></code> and <code><a href="../reference/like.html">%unlike_case%</a></code> (as negations of the existing <code><a href="../reference/like.html">%like%</a></code> and <code><a href="../reference/like.html">%like_case%</a></code>). This greatly improves readability:</p>
+<div class="sourceCode" id="cb1"><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">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>
+<span class="kw">if</span> <span class="op">(</span><span class="va">guideline</span> <span class="op">%unlike%</span> <span class="st">"EUCAST"</span><span class="op">)</span> <span class="va">...</span></code></pre></div>
+</li>
+<li><p>Altered the RStudio addin, so it now iterates over <code><a href="../reference/like.html">%like%</a></code> -&gt; <code><a href="../reference/like.html">%unlike%</a></code> -&gt; <code><a href="../reference/like.html">%like_case%</a></code> -&gt; <code><a href="../reference/like.html">%unlike_case%</a></code> if you keep pressing your keyboard shortcut</p></li>
+</ul>
+</li>
 <li>Fixed an installation error on R-3.0</li>
+<li>Added <code>info</code> argument to <code><a href="../reference/as.mo.html">as.mo()</a></code> to turn on/off the progress bar</li>
+<li>Fixed a bug that <code>col_mo</code> for some functions (esp. <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>) could not be column names of the <code>microorganisms</code> data set as it would throw an error</li>
+<li>Using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> with key antibiotics:
+<ul>
+<li>Fixed a bug in the algorithm when using <code>type == "points"</code>, that now leads to inclusion of slightly more isolates</li>
+<li>Big speed improvement for <code><a href="../reference/key_antibiotics.html">key_antibiotics_equal()</a></code> when using <code>type == "points"</code>
+</li>
+</ul>
+</li>
 </ul>
 </div>
 </div>
@ -306,7 +327,7 @@
 </li>
 <li>
 <p>Functions <code><a href="../reference/antibiotic_class_selectors.html">oxazolidinones()</a></code> (an antibiotic selector function) and <code><a href="../reference/filter_ab_class.html">filter_oxazolidinones()</a></code> (an antibiotic filter function) to select/filter on e.g. linezolid and tedizolid</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="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
 <span class="va">x</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">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>
@ -319,7 +340,7 @@
 <li><p><code>ggplot()</code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
 <li>
 <p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
-<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Aspergillus"</span>, <span class="st">"Candida"</span><span class="op">)</span><span class="op">)</span>
 <span class="co">#&gt; [1] "Fungi" "Fungi"</span>
@ -331,7 +352,7 @@
 <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html">which</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_is_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">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_is_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="cb3"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/mo_property.html">mo_type</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Aspergillus"</span>, <span class="st">"Candida"</span><span class="op">)</span><span class="op">)</span>
 <span class="co"># [1] "Fungi"  "Yeasts"</span>
@ -341,7 +362,7 @@
 <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">min()</a></code>, <code><a href="https://rdrr.io/r/base/Extremes.html">max()</a></code>, <code><a href="https://rdrr.io/r/base/range.html">range()</a></code>, and with binary operators (<code><a href="https://rdrr.io/r/base/Arithmetic.html">+</a></code>, <code><a href="https://rdrr.io/r/base/Arithmetic.html">-</a></code>, etc.). This allows for easy distribution analysis and fast filtering on MIC values:</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="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>
@ -425,7 +446,7 @@
 <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">group_by()</a></code>):</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"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
 <span class="va">example_isolates</span> <span class="op">%&gt;%</span>
@ -479,7 +500,7 @@
 <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="cb6"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb7"><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>
@ -491,7 +512,7 @@
 </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="cb7"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># above example in base R:</span>
 <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html">which</a></span><span class="op">(</span><span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu"><a href="../reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,
@ -542,7 +563,7 @@
 <li>
 <p>Data set <code>intrinsic_resistant</code>. This data set contains all bug-drug combinations where the ‘bug’ is intrinsic resistant to the ‘drug’ according to the latest EUCAST insights. It contains just two columns: <code>microorganism</code> and <code>antibiotic</code>.</p>
 <p>Curious about which enterococci are actually intrinsic resistant to vancomycin?</p>
-<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
@ -565,7 +586,7 @@
 <ul>
 <li>
 <p>Support for using <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/across.html">across()</a></code> to interpret MIC values or disk zone diameters, which also automatically determines the column with microorganism names or codes.</p>
-<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># until dplyr 1.0.0</span>
 <span class="va">your_data</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.rsi</span><span class="op">)</span>
@ -583,7 +604,7 @@
 </li>
 <li>
 <p>Added intelligent data cleaning to <code><a href="../reference/as.disk.html">as.disk()</a></code>, so numbers can also be extracted from text and decimal numbers will always be rounded up:</p>
-<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/as.disk.html">as.disk</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"disk zone: 23.4 mm"</span>, <span class="fl">23.4</span><span class="op">)</span><span class="op">)</span>
 <span class="co">#&gt; Class &lt;disk&gt;</span>
@ -644,7 +665,7 @@
 <li><p>Function <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code> to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses <code><a href="../reference/as.ab.html">as.ab()</a></code> internally</p></li>
 <li>
 <p><a href="https://tidyselect.r-lib.org/reference/language.html">Tidyverse selection helpers</a> for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code> and <code><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html">tidyr::pivot_longer()</a></code>:</p>
-<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>

@ -833,7 +854,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li>
 <li>
 <p>Interpretation from MIC values (and disk zones) to R/SI can now be used with <code><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at()</a></code> of the <code>dplyr</code> package:</p>
-<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">yourdata</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span><span class="op">(</span><span class="va">antibiotic1</span><span class="op">:</span><span class="va">antibiotic25</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span><span class="op">)</span>
@ -862,7 +883,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>Support for LOINC codes in the <code>antibiotics</code> data set. Use <code><a href="../reference/ab_property.html">ab_loinc()</a></code> to retrieve LOINC codes, or use a LOINC code for input in any <code>ab_*</code> function:</p>
-<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/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>
@ -873,7 +894,7 @@ 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="cb14"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/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>
@ -938,11 +959,11 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>If you were dependent on the old Enterobacteriaceae family e.g. by using in your code:</p>
-<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb16"><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="cb16"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb17"><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>
@ -956,7 +977,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>Functions <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> as aliases of <code><a href="../reference/proportion.html">proportion_SI()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code>, respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.</p>
-<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
 <span class="va">example_isolates</span> <span class="op">%&gt;%</span>
@ -985,7 +1006,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>More intelligent way of coping with some consonants like “l” and “r”</p></li>
 <li>
 <p>Added a score (a certainty percentage) to <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code>, that is calculated using the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance">Levenshtein distance</a>:</p>
-<div class="sourceCode" id="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/as.mo.html">as.mo</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Stafylococcus aureus"</span>,
        <span class="st">"staphylokok aureuz"</span><span class="op">)</span><span class="op">)</span>
@ -1044,14 +1065,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>Determination of first isolates now <strong>excludes</strong> all ‘unknown’ microorganisms at default, i.e. microbial code <code>"UNKNOWN"</code>. They can be included with the new argument <code>include_unknown</code>:</p>
-<div class="sourceCode" id="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/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="cb20"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># how it works in base R:</span>
 <span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html">factor</a></span><span class="op">(</span><span class="st">"A"</span><span class="op">)</span>
@ -1076,7 +1097,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with <code><a href="../reference/mo_property.html">mo_shortname()</a></code> at default:</p>
-<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb22"><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>
@ -1099,13 +1120,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <span class="co">#&gt; 4 Gram-negative AMX 227  0 405   632</span>
 <span class="co">#&gt; NOTE: Use 'format()' on this result to get a publicable/printable format.</span></code></pre></div>
 <p>You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R <code><a href="https://rdrr.io/r/base/format.html">format()</a></code> function:</p>
-<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="https://rdrr.io/r/base/format.html">format</a></span><span class="op">(</span><span class="va">x</span>, combine_IR <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
 </li>
 <li>
 <p>Additional way to calculate co-resistance, i.e. when using multiple antimicrobials as input for <code>portion_*</code> functions or <code>count_*</code> functions. This can be used to determine the empiric susceptibility of a combination therapy. A new argument <code>only_all_tested</code> (<strong>which defaults to <code>FALSE</code></strong>) replaces the old <code>also_single_tested</code> and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the <code>portion</code> and <code>count</code> help pages), where the %SI is being determined:</p>
-<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb24"><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>
@ -1127,7 +1148,7 @@ 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="cb24"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># (run this on your own console, as this page does not support colour printing)</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
@ -1210,7 +1231,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>Function <code><a href="../reference/proportion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code>portion_df()</code> to immediately show resistance percentages and number of available isolates:</p>
-<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">AMX</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op">%&gt;%</span>
@ -1237,7 +1258,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>UPEC (Uropathogenic <em>E. coli</em>)</li>
 </ul>
 <p>All these lead to the microbial ID of <em>E. coli</em>:</p>
-<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb27"><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>
@ -1342,7 +1363,7 @@ 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="cb27"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span> 
  <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span> 
@ -1437,7 +1458,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 <li>
 <p>New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:</p>
-<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>
 <span class="fu"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span><span class="op">(</span><span class="op">)</span>
@ -1451,7 +1472,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <span class="fu"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span><span class="op">(</span><span class="op">)</span>
 <span class="fu"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
 <p>The <code>antibiotics</code> data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set. For example:</p>
-<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span><span class="op">(</span>result <span class="op">=</span> <span class="st">"R"</span><span class="op">)</span>
 <span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span>
@ -1460,7 +1481,7 @@ 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="cb30"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb31"><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>
@ -1481,7 +1502,7 @@ 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="cb31"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb32"><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>
@ -1489,13 +1510,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 <li>
 <p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
-<div class="sourceCode" id="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">%&gt;%</span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="va">...</span><span class="op">)</span>
 <span class="co"># or</span>
 <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="va">...</span><span class="op">)</span></code></pre></div>
 <p>is equal to:</p>
-<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>only_firsts <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="va">...</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
@ -1528,7 +1549,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>Now handles incorrect spelling, like <code>i</code> instead of <code>y</code> and <code>f</code> instead of <code>ph</code>:</p>
-<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="co"># mo_fullname() uses as.mo() internally</span>

@ -1540,7 +1561,7 @@ 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="cb35"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb36"><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>
@ -1555,7 +1576,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>All microbial IDs that found are now saved to a local file <code>~/.Rhistory_mo</code>. Use the new function <code>clean_mo_history()</code> to delete this file, which resets the algorithms.</p></li>
 <li>
 <p>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</p>
-<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"qwerty"</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span>
 <span class="co"># Warning: </span>
@ -1605,7 +1626,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
-<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb38"><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>
@ -1689,7 +1710,7 @@ 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="cb38"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. 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>
@ -1706,7 +1727,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>Support for grouping variables, test with:</p>
-<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span> 
@ -1714,7 +1735,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 <li>
 <p>Support for (un)selecting columns:</p>
-<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span> 
  <span class="fu">freq</span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span> 
@ -1794,7 +1815,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 </ul>
 <p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
-<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb42"><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>
@ -1805,7 +1826,7 @@ 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="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/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>
@ -1820,7 +1841,7 @@ 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="cb43"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb44"><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>
@ -1829,7 +1850,7 @@ 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="cb44"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">thousands_of_E_colis</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span><span class="op">(</span><span class="st">"E. coli"</span>, <span class="fl">25000</span><span class="op">)</span>
 <span class="fu">microbenchmark</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span><span class="op">(</span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">thousands_of_E_colis</span><span class="op">)</span>, unit <span class="op">=</span> <span class="st">"s"</span><span class="op">)</span>
@ -1863,7 +1884,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</p></li>
 <li>
 <p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
-<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb46"><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>
@ -1880,7 +1901,7 @@ 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="cb46"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">amox</span>, <span class="va">cipr</span><span class="op">)</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span><span class="op">(</span><span class="op">)</span>
 <span class="co"># which is the same as:</span>
@ -1900,12 +1921,12 @@ 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="cb47"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb48"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="va">age</span>, <span class="va">gender</span><span class="op">)</span>, ncol <span class="op">=</span> <span class="fl">2</span><span class="op">)</span><span class="op">)</span>
 <span class="fu">freq</span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
 <p>For lists, subsetting is possible:</p>
-<div class="sourceCode" id="cb48"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb49"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span>age <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">age</span>, gender <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">gender</span><span class="op">)</span>
 <span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@ -12,7 +12,7 @@ articles:
  datasets: datasets.html
  resistance_predict: resistance_predict.html
  welcome_to_AMR: welcome_to_AMR.html
-last_built: 2021-04-16T12:59Z
+last_built: 2021-04-23T14:13Z
 urls:
  reference: https://msberends.github.io/AMR//reference
  article: https://msberends.github.io/AMR//articles
--- a/docs/reference/ab_from_text.html
+++ b/docs/reference/ab_from_text.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9040</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9007</span>
      </span>
    </div>

@ -248,6 +248,7 @@
  collapse <span class='op'>=</span> <span class='cn'>NULL</span>,
  translate_ab <span class='op'>=</span> <span class='cn'>FALSE</span>,
  thorough_search <span class='op'>=</span> <span class='cn'>NULL</span>,
+  info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>,
  <span class='va'>...</span>
 <span class='op'>)</span></pre>

@ -274,6 +275,10 @@
      <th>thorough_search</th>
      <td><p>logical to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to <code>TRUE</code> will take considerably more time than when using <code>FALSE</code>. At default, it will turn <code>TRUE</code> when all input elements contain a maximum of three words.</p></td>
    </tr>
+    <tr>
+      <th>info</th>
+      <td><p>logical to indicate whether a progress bar should be printed, defaults to <code>TRUE</code> only in interactive mode</p></td>
+    </tr>
    <tr>
      <th>...</th>
      <td><p>arguments passed on to <code><a href='as.ab.html'>as.ab()</a></code></p></td>
--- a/docs/reference/as.ab.html
+++ b/docs/reference/as.ab.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9007</span>
      </span>
    </div>

@ -242,7 +242,7 @@
    <p>Use this function to determine the antibiotic code of one or more antibiotics. The data set <a href='antibiotics.html'>antibiotics</a> will be searched for abbreviations, official names and synonyms (brand names).</p>
    </div>

-    <pre class="usage"><span class='fu'>as.ab</span><span class='op'>(</span><span class='va'>x</span>, flag_multiple_results <span class='op'>=</span> <span class='cn'>TRUE</span>, info <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span>
+    <pre class="usage"><span class='fu'>as.ab</span><span class='op'>(</span><span class='va'>x</span>, flag_multiple_results <span class='op'>=</span> <span class='cn'>TRUE</span>, info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>

 <span class='fu'>is.ab</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></pre>

@ -259,7 +259,7 @@
    </tr>
    <tr>
      <th>info</th>
-      <td><p>logical to indicate whether a progress bar should be printed</p></td>
+      <td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether a progress bar should be printed, defaults to <code>TRUE</code> only in interactive mode</p></td>
    </tr>
    <tr>
      <th>...</th>
--- a/docs/reference/as.mo.html
+++ b/docs/reference/as.mo.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9003</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9007</span>
      </span>
    </div>

@ -250,6 +250,7 @@
  reference_df <span class='op'>=</span> <span class='fu'><a href='mo_source.html'>get_mo_source</a></span><span class='op'>(</span><span class='op'>)</span>,
  ignore_pattern <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"AMR_ignore_pattern"</span><span class='op'>)</span>,
  language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
+  info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>,
  <span class='va'>...</span>
 <span class='op'>)</span>

@ -294,6 +295,10 @@
      <th>language</th>
      <td><p>language to translate text like "no growth", which defaults to the system language (see <code><a href='translate.html'>get_locale()</a></code>)</p></td>
    </tr>
+    <tr>
+      <th>info</th>
+      <td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate if a progress bar should be printed if more than 25 items are to be coerced, defaults to <code>TRUE</code> only in interactive mode</p></td>
+    </tr>
    <tr>
      <th>...</th>
      <td><p>other arguments passed on to functions</p></td>
--- a/docs/reference/custom_eucast_rules.html
+++ b/docs/reference/custom_eucast_rules.html
@ -6,7 +6,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">

-<title>Create Custom EUCAST Rules — custom_eucast_rules • AMR (for R)</title>
+<title>Define Custom EUCAST Rules — custom_eucast_rules • AMR (for R)</title>

 <!-- favicons -->
 <link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -48,8 +48,8 @@
  <link href="../extra.css" rel="stylesheet">
  <script src="../extra.js"></script>

-<meta property="og:title" content="Create Custom EUCAST Rules — custom_eucast_rules" />
-<meta property="og:description" content="Create Custom EUCAST Rules" />
+<meta property="og:title" content="Define Custom EUCAST Rules — custom_eucast_rules" />
+<meta property="og:description" content="Define custom EUCAST rules for your organisation or specific analysis and use the output of this function in eucast_rules()." />
 <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />


@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9001</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9007</span>
      </span>
    </div>

@ -233,13 +233,13 @@
 <div class="row">
  <div class="col-md-9 contents">
    <div class="page-header">
-    <h1>Create Custom EUCAST Rules</h1>
+    <h1>Define Custom EUCAST Rules</h1>
    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/custom_eucast_rules.R'><code>R/custom_eucast_rules.R</code></a></small>
    <div class="hidden name"><code>custom_eucast_rules.Rd</code></div>
    </div>

    <div class="ref-description">
-    <p>Create Custom EUCAST Rules</p>
+    <p>Define custom EUCAST rules for your organisation or specific analysis and use the output of this function in <code><a href='eucast_rules.html'>eucast_rules()</a></code>.</p>
    </div>

    <pre class="usage"><span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>...</span><span class='op'>)</span></pre>
@ -253,21 +253,97 @@
    </tr>
    </table>

+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>A <a href='https://rdrr.io/r/base/list.html'>list</a> containing the custom rules</p>
    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>

-    <p>This documentation page will be updated shortly. <strong>This function is experimental.</strong></p>
+    <p>Some organisations have their own adoption of EUCAST rules. This function can be used to define custom EUCAST rules to be used in the <code><a href='eucast_rules.html'>eucast_rules()</a></code> function.</p>
    <h2 class="hasAnchor" id="how-it-works"><a class="anchor" href="#how-it-works"></a>How it works</h2>

    

-<p>..</p>
-<p>It is also possible to define antibiotic groups instead of single antibiotics. The following groups are allowed (case-insensitive): <code>aminoglycosides</code>, <code>aminopenicillins</code>, <code>betalactams</code>, <code>carbapenems</code>, <code>cephalosporins</code>, <code>cephalosporins_1st</code>, <code>cephalosporins_2nd</code>, <code>cephalosporins_3rd</code>, <code>cephalosporins_except_caz</code>, <code>fluoroquinolones</code>, <code>glycopeptides</code>, <code>glycopeptides_except_lipo</code>, <code>lincosamides</code>, <code>lipoglycopeptides</code>, <code>macrolides</code>, <code>oxazolidinones</code>, <code>penicillins</code>, <code>polymyxins</code>, <code>streptogramins</code>, <code>tetracyclines</code>, <code>tetracyclines_except_tgc</code> and <code>ureidopenicillins</code>.</p>
-    <h2 class="hasAnchor" id="experimental-lifecycle"><a class="anchor" href="#experimental-lifecycle"></a>Experimental Lifecycle</h2>
+<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Basics</h3>
+
+
+<p>If you are familiar with the <code><a href='https://dplyr.tidyverse.org/reference/case_when.html'>case_when()</a></code> function of the <code>dplyr</code> package, you will recognise the input method to set your own rules. Rules must be set using what <span style="R">R</span> considers to be the 'formula notation'. The rule itself is written <em>before</em> the tilde (<code><a href='https://rdrr.io/r/base/tilde.html'>~</a></code>) and the consequence of the rule is written <em>after</em> the tilde:</p><pre><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"S"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"S"</span>,
+                         <span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span>
+</pre>
+
+<p>These are two custom EUCAST rules: if TZP (piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must be made "R". These rules can also be printed to the console, so it is immediately clear how they work:</p><pre><span class='va'>x</span>
+<span class='co'>#&gt; A set of custom EUCAST rules:</span>
+<span class='co'>#&gt; </span>
+<span class='co'>#&gt;   1. If TZP is S then set to S:</span>
+<span class='co'>#&gt;      amoxicillin (AMX), ampicillin (AMP)</span>
+<span class='co'>#&gt; </span>
+<span class='co'>#&gt;   2. If TZP is R then set to R:</span>
+<span class='co'>#&gt;      amoxicillin (AMX), ampicillin (AMP)</span>
+</pre>
+
+<p>The rules (the part <em>before</em> the tilde, in above example <code>TZP == "S"</code> and <code>TZP == "R"</code>) must be evaluable in your data set: it should be able to run as a filter in your data set without errors. This means for the above example that the column <code>TZP</code> must exist. We will create a sample data set and test the rules set:</p><pre><span class='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>mo <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"E. coli"</span>, <span class='st'>"K. pneumoniae"</span><span class='op'>)</span>,
+                 TZP <span class='op'>=</span> <span class='st'>"R"</span>,
+                 amox <span class='op'>=</span> <span class='st'>""</span>,
+                 AMP <span class='op'>=</span> <span class='st'>""</span><span class='op'>)</span>
+<span class='va'>df</span>
+<span class='co'>#&gt;              mo TZP amox AMP</span>
+<span class='co'>#&gt; 1       E. coli   R         </span>
+<span class='co'>#&gt; 2 K. pneumoniae   R         </span>
+                 
+<span class='fu'><a href='eucast_rules.html'>eucast_rules</a></span><span class='op'>(</span><span class='va'>df</span>, rules <span class='op'>=</span> <span class='st'>"custom"</span>, custom_rules <span class='op'>=</span> <span class='va'>x</span><span class='op'>)</span>
+<span class='co'>#&gt;              mo TZP amox AMP</span>
+<span class='co'>#&gt; 1       E. coli   R    R   R     </span>
+<span class='co'>#&gt; 2 K. pneumoniae   R    R   R  </span>
+</pre>
+
+
+<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Using taxonomic properties in rules</h3>
+
+
+<p>There is one exception in variables used for the rules: all column names of the <a href='microorganisms.html'>microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: <code>mo</code>, <code>fullname</code>, <code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code>, <code>rank</code>, <code>ref</code>, <code>species_id</code>, <code>source</code>, <code>prevalence</code> and <code>snomed</code>. Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p><pre><span class='va'>y</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"S"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"S"</span>,
+                         <span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span>
+
+<span class='fu'><a href='eucast_rules.html'>eucast_rules</a></span><span class='op'>(</span><span class='va'>df</span>, rules <span class='op'>=</span> <span class='st'>"custom"</span>, custom_rules <span class='op'>=</span> <span class='va'>y</span><span class='op'>)</span>
+<span class='co'>#&gt;              mo TZP amox AMP</span>
+<span class='co'>#&gt; 1       E. coli   R         </span>
+<span class='co'>#&gt; 2 K. pneumoniae   R    R   R</span>
+</pre>
+
+
+<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage of antibiotic group names</h3>
+
+
+<p>It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part <em>after</em> the tilde. In above examples, the antibiotic group <code>aminopenicillins</code> is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the antibiotic agents that will be matched when running the rule.</p><ul>
+<li><p><code>aminoglycosides</code><br />(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, tobramycin-high)</p></li>
+<li><p><code>aminopenicillins</code><br />(amoxicillin, ampicillin)</p></li>
+<li><p><code>betalactams</code><br />(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, cadazolid, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol (Cefcatacol), cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam (Amdinocillin), meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid)</p></li>
+<li><p><code>carbapenems</code><br />(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, tebipenem)</p></li>
+<li><p><code>cephalosporins</code><br />(cadazolid, cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol (Cefcatacol), cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef, loracarbef)</p></li>
+<li><p><code>cephalosporins_1st</code><br />(cefacetrile, cefadroxil, cefaloridine, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, cephalexin, cephalothin, cephapirin, cephradine)</p></li>
+<li><p><code>cephalosporins_2nd</code><br />(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil, loracarbef)</p></li>
+<li><p><code>cephalosporins_3rd</code><br />(cadazolid, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, latamoxef)</p></li>
+<li><p><code>cephalosporins_except_caz</code><br />(cadazolid, cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol (Cefcatacol), cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef, loracarbef)</p></li>
+<li><p><code>fluoroquinolones</code><br />(ciprofloxacin, enoxacin, fleroxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, lomefloxacin, moxifloxacin, norfloxacin, ofloxacin, pazufloxacin, pefloxacin, prulifloxacin, rufloxacin, sparfloxacin, temafloxacin, trovafloxacin)</p></li>
+<li><p><code>glycopeptides</code><br />(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, vancomycin-macromethod)</p></li>
+<li><p><code>glycopeptides_except_lipo</code><br />(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, vancomycin-macromethod)</p></li>
+<li><p><code>lincosamides</code><br />(clindamycin, lincomycin, pirlimycin)</p></li>
+<li><p><code>lipoglycopeptides</code><br />(dalbavancin, oritavancin, telavancin)</p></li>
+<li><p><code>macrolides</code><br />(azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, josamycin, midecamycin, miocamycin, oleandomycin, rokitamycin, roxithromycin, spiramycin, telithromycin, troleandomycin)</p></li>
+<li><p><code>oxazolidinones</code><br />(cycloserine, linezolid, tedizolid, thiacetazone)</p></li>
+<li><p><code>penicillins</code><br />(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam (Amdinocillin), metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin, ticarcillin/clavulanic acid)</p></li>
+<li><p><code>polymyxins</code><br />(colistin, polymyxin B, polymyxin B/polysorbate 80)</p></li>
+<li><p><code>streptogramins</code><br />(pristinamycin, quinupristin/dalfopristin)</p></li>
+<li><p><code>tetracyclines</code><br />(chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline, tigecycline)</p></li>
+<li><p><code>tetracyclines_except_tgc</code><br />(chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline)</p></li>
+<li><p><code>ureidopenicillins</code><br />(azlocillin, mezlocillin, piperacillin, piperacillin/tazobactam)</p></li>
+</ul>
+
+
+    <h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing Lifecycle</h2>

    

-<p><img src='figures/lifecycle_experimental.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>experimental</strong>. 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 <code>AMR</code> package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.</p>
+<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. 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 <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span>,
--- a/docs/reference/eucast_rules.html
+++ b/docs/reference/eucast_rules.html
@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9007</span>
      </span>
    </div>

--- a/docs/reference/first_isolate.html
+++ b/docs/reference/first_isolate.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9003</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
      </span>
    </div>

@ -346,7 +346,7 @@
    </tr>
    <tr>
      <th>info</th>
-      <td><p>print progress</p></td>
+      <td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate info should be printed, defaults to <code>TRUE</code> only in interactive mode</p></td>
    </tr>
    <tr>
      <th>include_unknown</th>
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
      </span>
    </div>

@ -455,7 +455,7 @@
        <td>
          <p><code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code> </p>
        </td>
-        <td><p>Create Custom EUCAST Rules</p></td>
+        <td><p>Define Custom EUCAST Rules</p></td>
      </tr>
    </tbody><tbody>
      <tr>
@ -599,7 +599,7 @@
      </tr><tr>
        
        <td>
-          <p><code><a href="like.html">like()</a></code> <code><a href="like.html">`%like%`</a></code> <code><a href="like.html">`%like_case%`</a></code> </p>
+          <p><code><a href="like.html">like()</a></code> <code><a href="like.html">`%like%`</a></code> <code><a href="like.html">`%unlike%`</a></code> <code><a href="like.html">`%like_case%`</a></code> <code><a href="like.html">`%unlike_case%`</a></code> </p>
        </td>
        <td><p>Vectorised Pattern Matching with Keyboard Shortcut</p></td>
      </tr><tr>
--- a/docs/reference/key_antibiotics.html
+++ b/docs/reference/key_antibiotics.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9040</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
      </span>
    </div>

@ -273,7 +273,9 @@
  type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span><span class='op'>)</span>,
  ignore_I <span class='op'>=</span> <span class='cn'>TRUE</span>,
  points_threshold <span class='op'>=</span> <span class='fl'>2</span>,
-  info <span class='op'>=</span> <span class='cn'>FALSE</span>
+  info <span class='op'>=</span> <span class='cn'>FALSE</span>,
+  na.rm <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  <span class='va'>...</span>
 <span class='op'>)</span></pre>

    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@ -325,7 +327,11 @@
    </tr>
    <tr>
      <th>info</th>
-      <td><p>print progress</p></td>
+      <td><p>unused - previously used to indicate whether a progress bar should print</p></td>
+    </tr>
+    <tr>
+      <th>na.rm</th>
+      <td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether comparison with <code>NA</code> should return <code>FALSE</code> (defaults to <code>TRUE</code> for backwards compatibility)</p></td>
    </tr>
    </table>

--- a/docs/reference/like.html
+++ b/docs/reference/like.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9003</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9008</span>
      </span>
    </div>

@ -246,7 +246,11 @@

 <span class='va'>x</span> <span class='op'>%like%</span> <span class='va'>pattern</span>

-<span class='va'>x</span> <span class='op'>%like_case%</span> <span class='va'>pattern</span></pre>
+<span class='va'>x</span> <span class='op'>%unlike%</span> <span class='va'>pattern</span>
+
+<span class='va'>x</span> <span class='op'>%like_case%</span> <span class='va'>pattern</span>
+
+<span class='va'>x</span> <span class='op'>%unlike_case%</span> <span class='va'>pattern</span></pre>

    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
    <table class="ref-arguments">
@ -273,14 +277,14 @@
    <p>A <a href='https://rdrr.io/r/base/logical.html'>logical</a> vector</p>
    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>

-    <p>This <code>%like%</code> function:</p><ul>
-<li><p>Is case-insensitive (use <code>%like_case%</code> for case-sensitive matching)</p></li>
-<li><p>Supports multiple patterns</p></li>
-<li><p>Checks if <code>pattern</code> is a valid regular expression and sets <code>fixed = TRUE</code> if not, to greatly improve speed (vectorised over <code>pattern</code>)</p></li>
-<li><p>Always uses compatibility with Perl unless <code>fixed = TRUE</code>, to greatly improve speed</p></li>
+    <p>These <code>like()</code> and <code>%like%</code>/<code>%unlike%</code> functions:</p><ul>
+<li><p>Are case-insensitive (use <code>%like_case%</code>/<code>%unlike_case%</code> for case-sensitive matching)</p></li>
+<li><p>Support multiple patterns</p></li>
+<li><p>Check if <code>pattern</code> is a valid regular expression and sets <code>fixed = TRUE</code> if not, to greatly improve speed (vectorised over <code>pattern</code>)</p></li>
+<li><p>Always use compatibility with Perl unless <code>fixed = TRUE</code>, to greatly improve speed</p></li>
 </ul>

-<p>Using RStudio? The text <code>%like%</code> can also be directly inserted in your code from the Addins menu and can have its own Keyboard Shortcut like <code>Ctrl+Shift+L</code> or <code>Cmd+Shift+L</code> (see <code>Tools</code> &gt; <code>Modify Keyboard Shortcuts...</code>).</p>
+<p>Using RStudio? The <code>%like%</code>/<code>%unlike%</code> functions can also be directly inserted in your code from the Addins menu and can have its own keyboard shortcut like <code>Shift+Ctrl+L</code> or <code>Shift+Cmd+L</code> (see menu <code>Tools</code> &gt; <code>Modify Keyboard Shortcuts...</code>). If you keep pressing your shortcut, the inserted text will be iterated over <code>%like%</code> -&gt; <code>%unlike%</code> -&gt; <code>%like_case%</code> -&gt; <code>%unlike_case%</code>.</p>
    <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>

    
@ -298,8 +302,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
    <div class='dont-index'><p><code><a href='https://rdrr.io/r/base/grep.html'>grepl()</a></code></p></div>

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># simple test</span>
-<span class='va'>a</span> <span class='op'>&lt;-</span> <span class='st'>"This is a test"</span>
+    <pre class="examples"><span class='va'>a</span> <span class='op'>&lt;-</span> <span class='st'>"This is a test"</span>
 <span class='va'>b</span> <span class='op'>&lt;-</span> <span class='st'>"TEST"</span>
 <span class='va'>a</span> <span class='op'>%like%</span> <span class='va'>b</span>
 <span class='co'>#&gt; TRUE</span>
@ -311,13 +314,20 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 <span class='va'>b</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>     <span class='st'>"case"</span>,           <span class='st'>"diff"</span>,      <span class='st'>"yet"</span><span class='op'>)</span>
 <span class='va'>a</span> <span class='op'>%like%</span> <span class='va'>b</span>
 <span class='co'>#&gt; TRUE TRUE TRUE</span>
+<span class='va'>a</span> <span class='op'>%unlike%</span> <span class='va'>b</span>
+<span class='co'>#&gt; FALSE FALSE FALSE</span>
+
 <span class='va'>a</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>]</span> <span class='op'>%like%</span> <span class='va'>b</span>
 <span class='co'>#&gt; TRUE FALSE FALSE</span>
 <span class='va'>a</span> <span class='op'>%like%</span> <span class='va'>b</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>]</span>
 <span class='co'>#&gt; TRUE FALSE FALSE</span>

 <span class='co'># get isolates whose name start with 'Ent' or 'ent'</span>
+<span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/which.html'>which</a></span><span class='op'>(</span><span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>mo</span><span class='op'>)</span> <span class='op'>%like%</span> <span class='st'>"^ent"</span><span class='op'>)</span>, <span class='op'>]</span>
 <span class='co'># \donttest{</span>
+<span class='co'># faster way, only works in R 3.2 and later:</span>
+<span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/which.html'>which</a></span><span class='op'>(</span><span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%like%</span> <span class='st'>"^ent"</span><span class='op'>)</span>, <span class='op'>]</span>
+
 <span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
  <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%like%</span> <span class='st'>"^ent"</span><span class='op'>)</span>
--- a/docs/reference/mdro.html
+++ b/docs/reference/mdro.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9001</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9007</span>
      </span>
    </div>

@ -360,7 +360,7 @@ Ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with levels <cod


 <p>Custom guidelines can be set with the <code>custom_mdro_guideline()</code> function. This is of great importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.</p>
-<p>If you are familiar with <code><a href='https://dplyr.tidyverse.org/reference/case_when.html'>case_when()</a></code> of the <code>dplyr</code> package, you will recognise the input method to set your own rules. Rules must be set using what <span style="R">R</span> considers to be the 'formula notation':</p><pre><span class='va'>custom</span> <span class='op'>&lt;-</span> <span class='fu'>custom_mdro_guideline</span><span class='op'>(</span><span class='va'>CIP</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>age</span> <span class='op'>&gt;</span> <span class='fl'>60</span> <span class='op'>~</span> <span class='st'>"Elderly Type A"</span>,
+<p>If you are familiar with the <code><a href='https://dplyr.tidyverse.org/reference/case_when.html'>case_when()</a></code> function of the <code>dplyr</code> package, you will recognise the input method to set your own rules. Rules must be set using what <span style="R">R</span> considers to be the 'formula notation'. The rule is written <em>before</em> the tilde (<code><a href='https://rdrr.io/r/base/tilde.html'>~</a></code>) and the consequence of the rule is written <em>after</em> the tilde:</p><pre><span class='va'>custom</span> <span class='op'>&lt;-</span> <span class='fu'>custom_mdro_guideline</span><span class='op'>(</span><span class='va'>CIP</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>age</span> <span class='op'>&gt;</span> <span class='fl'>60</span> <span class='op'>~</span> <span class='st'>"Elderly Type A"</span>,
                                <span class='va'>ERY</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>age</span> <span class='op'>&gt;</span> <span class='fl'>60</span> <span class='op'>~</span> <span class='st'>"Elderly Type B"</span><span class='op'>)</span>
 </pre>

--- a/docs/reference/microorganisms.html
+++ b/docs/reference/microorganisms.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9007</span>
      </span>
    </div>

@ -281,7 +281,7 @@
    <p>Please note that entries are only based on the Catalogue of Life and the LPSN (see below). Since these sources incorporate entries based on (recent) publications in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), it can happen that the year of publication is sometimes later than one might expect.</p>
 <p>For example, <em>Staphylococcus pettenkoferi</em> was described for the first time in Diagnostic Microbiology and Infectious Disease in 2002 (doi: <a href='https://doi.org/10.1016/s0732-8893(02)00399-1'>10.1016/s0732-8893(02)00399-1</a>
 ), but it was not before 2007 that a publication in IJSEM followed (doi: <a href='https://doi.org/10.1099/ijs.0.64381-0'>10.1099/ijs.0.64381-0</a>
-). Consequently, the AMR package returns 2007 for <code><a href='mo_property.html'>mo_year("S. pettenkoferi")</a></code>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Manual additions</h3>
+). Consequently, the <code>AMR</code> package returns 2007 for <code><a href='mo_property.html'>mo_year("S. pettenkoferi")</a></code>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Manual additions</h3>


 <p>For convenience, some entries were added manually:</p><ul>
--- a/docs/reference/mo_matching_score.html
+++ b/docs/reference/mo_matching_score.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9003</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9007</span>
      </span>
    </div>

--- a/docs/reference/mo_property.html
+++ b/docs/reference/mo_property.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9003</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9007</span>
      </span>
    </div>

--- a/docs/survey.html
+++ b/docs/survey.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
      </span>
    </div>

--- a/inst/rstudio/addins.dcf
+++ b/inst/rstudio/addins.dcf
@ -2,6 +2,6 @@ Name: Insert %in%
 Binding: addin_insert_in
 Interactive: false

-Name: Insert %like%
+Name: Insert %like% or %unlike% 
 Binding: addin_insert_like
 Interactive: false
--- a/man/ab_from_text.Rd
+++ b/man/ab_from_text.Rd
@ -10,6 +10,7 @@ ab_from_text(
  collapse = NULL,
  translate_ab = FALSE,
  thorough_search = NULL,
+  info = interactive(),
  ...
 )
 }
@ -24,6 +25,8 @@ ab_from_text(

 \item{thorough_search}{logical to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to \code{TRUE} will take considerably more time than when using \code{FALSE}. At default, it will turn \code{TRUE} when all input elements contain a maximum of three words.}

+\item{info}{logical to indicate whether a progress bar should be printed, defaults to \code{TRUE} only in interactive mode}
+
 \item{...}{arguments passed on to \code{\link[=as.ab]{as.ab()}}}
 }
 \value{
--- a/man/as.ab.Rd
+++ b/man/as.ab.Rd
@ -6,7 +6,7 @@
 \alias{is.ab}
 \title{Transform Input to an Antibiotic ID}
 \usage{
-as.ab(x, flag_multiple_results = TRUE, info = TRUE, ...)
+as.ab(x, flag_multiple_results = TRUE, info = interactive(), ...)

 is.ab(x)
 }
@ -15,7 +15,7 @@ is.ab(x)

 \item{flag_multiple_results}{logical to indicate whether a note should be printed to the console that probably more than one antibiotic code or name can be retrieved from a single input value.}

-\item{info}{logical to indicate whether a progress bar should be printed}
+\item{info}{a \link{logical} to indicate whether a progress bar should be printed, defaults to \code{TRUE} only in interactive mode}

 \item{...}{arguments passed on to internal functions}
 }
--- a/man/as.mo.Rd
+++ b/man/as.mo.Rd
@ -17,6 +17,7 @@ as.mo(
  reference_df = get_mo_source(),
  ignore_pattern = getOption("AMR_ignore_pattern"),
  language = get_locale(),
+  info = interactive(),
  ...
 )

@ -47,6 +48,8 @@ This excludes \emph{Enterococci} at default (who are in group D), use \code{Lanc

 \item{language}{language to translate text like "no growth", which defaults to the system language (see \code{\link[=get_locale]{get_locale()}})}

+\item{info}{a \link{logical} to indicate if a progress bar should be printed if more than 25 items are to be coerced, defaults to \code{TRUE} only in interactive mode}
+
 \item{...}{other arguments passed on to functions}
 }
 \value{
--- a/man/custom_eucast_rules.Rd
+++ b/man/custom_eucast_rules.Rd
@ -2,30 +2,102 @@
 % Please edit documentation in R/custom_eucast_rules.R
 \name{custom_eucast_rules}
 \alias{custom_eucast_rules}
-\title{Create Custom EUCAST Rules}
+\title{Define Custom EUCAST Rules}
 \usage{
 custom_eucast_rules(...)
 }
 \arguments{
 \item{...}{rules in formula notation, see \emph{Examples}}
 }
+\value{
+A \link{list} containing the custom rules
+}
 \description{
-Create Custom EUCAST Rules
+Define custom EUCAST rules for your organisation or specific analysis and use the output of this function in \code{\link[=eucast_rules]{eucast_rules()}}.
 }
 \details{
-This documentation page will be updated shortly. \strong{This function is experimental.}
+Some organisations have their own adoption of EUCAST rules. This function can be used to define custom EUCAST rules to be used in the \code{\link[=eucast_rules]{eucast_rules()}} function.
 }
 \section{How it works}{

-..
+\subsection{Basics}{

-It is also possible to define antibiotic groups instead of single antibiotics. The following groups are allowed (case-insensitive): \code{aminoglycosides}, \code{aminopenicillins}, \code{betalactams}, \code{carbapenems}, \code{cephalosporins}, \code{cephalosporins_1st}, \code{cephalosporins_2nd}, \code{cephalosporins_3rd}, \code{cephalosporins_except_caz}, \code{fluoroquinolones}, \code{glycopeptides}, \code{glycopeptides_except_lipo}, \code{lincosamides}, \code{lipoglycopeptides}, \code{macrolides}, \code{oxazolidinones}, \code{penicillins}, \code{polymyxins}, \code{streptogramins}, \code{tetracyclines}, \code{tetracyclines_except_tgc} and \code{ureidopenicillins}.
+If you are familiar with the \code{\link[dplyr:case_when]{case_when()}} function of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule itself is written \emph{before} the tilde (\code{~}) and the consequence of the rule is written \emph{after} the tilde:\preformatted{x <- custom_eucast_rules(TZP == "S" ~ aminopenicillins == "S",
+                         TZP == "R" ~ aminopenicillins == "R")
 }

-\section{Experimental Lifecycle}{
+These are two custom EUCAST rules: if TZP (piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must be made "R". These rules can also be printed to the console, so it is immediately clear how they work:\preformatted{x
+#> A set of custom EUCAST rules:
+#> 
+#>   1. If TZP is S then set to S:
+#>      amoxicillin (AMX), ampicillin (AMP)
+#> 
+#>   2. If TZP is R then set to R:
+#>      amoxicillin (AMX), ampicillin (AMP)
+}

-\if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:5px} \cr}
-The \link[=lifecycle]{lifecycle} of this function is \strong{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 \code{AMR} package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
+The rules (the part \emph{before} the tilde, in above example \code{TZP == "S"} and \code{TZP == "R"}) must be evaluable in your data set: it should be able to run as a filter in your data set without errors. This means for the above example that the column \code{TZP} must exist. We will create a sample data set and test the rules set:\preformatted{df <- data.frame(mo = c("E. coli", "K. pneumoniae"),
+                 TZP = "R",
+                 amox = "",
+                 AMP = "")
+df
+#>              mo TZP amox AMP
+#> 1       E. coli   R         
+#> 2 K. pneumoniae   R         
+                 
+eucast_rules(df, rules = "custom", custom_rules = x)
+#>              mo TZP amox AMP
+#> 1       E. coli   R    R   R     
+#> 2 K. pneumoniae   R    R   R  
+}
+}
+
+\subsection{Using taxonomic properties in rules}{
+
+There is one exception in variables used for the rules: all column names of the \link{microorganisms} data set can also be used, but do not have to exist in the data set. These column names are: \code{mo}, \code{fullname}, \code{kingdom}, \code{phylum}, \code{class}, \code{order}, \code{family}, \code{genus}, \code{species}, \code{subspecies}, \code{rank}, \code{ref}, \code{species_id}, \code{source}, \code{prevalence} and \code{snomed}. Thus, this next example will work as well, despite the fact that the \code{df} data set does not contain a column \code{genus}:\preformatted{y <- custom_eucast_rules(TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",
+                         TZP == "R" & genus == "Klebsiella" ~ aminopenicillins == "R")
+
+eucast_rules(df, rules = "custom", custom_rules = y)
+#>              mo TZP amox AMP
+#> 1       E. coli   R         
+#> 2 K. pneumoniae   R    R   R
+}
+}
+
+\subsection{Usage of antibiotic group names}{
+
+It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part \emph{after} the tilde. In above examples, the antibiotic group \code{aminopenicillins} is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the antibiotic agents that will be matched when running the rule.
+\itemize{
+\item \code{aminoglycosides}\cr(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, tobramycin-high)
+\item \code{aminopenicillins}\cr(amoxicillin, ampicillin)
+\item \code{betalactams}\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, cadazolid, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol (Cefcatacol), cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam (Amdinocillin), meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid)
+\item \code{carbapenems}\cr(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, tebipenem)
+\item \code{cephalosporins}\cr(cadazolid, cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol (Cefcatacol), cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef, loracarbef)
+\item \code{cephalosporins_1st}\cr(cefacetrile, cefadroxil, cefaloridine, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, cephalexin, cephalothin, cephapirin, cephradine)
+\item \code{cephalosporins_2nd}\cr(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil, loracarbef)
+\item \code{cephalosporins_3rd}\cr(cadazolid, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, latamoxef)
+\item \code{cephalosporins_except_caz}\cr(cadazolid, cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol (Cefcatacol), cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef, loracarbef)
+\item \code{fluoroquinolones}\cr(ciprofloxacin, enoxacin, fleroxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, lomefloxacin, moxifloxacin, norfloxacin, ofloxacin, pazufloxacin, pefloxacin, prulifloxacin, rufloxacin, sparfloxacin, temafloxacin, trovafloxacin)
+\item \code{glycopeptides}\cr(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, vancomycin-macromethod)
+\item \code{glycopeptides_except_lipo}\cr(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, vancomycin-macromethod)
+\item \code{lincosamides}\cr(clindamycin, lincomycin, pirlimycin)
+\item \code{lipoglycopeptides}\cr(dalbavancin, oritavancin, telavancin)
+\item \code{macrolides}\cr(azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, josamycin, midecamycin, miocamycin, oleandomycin, rokitamycin, roxithromycin, spiramycin, telithromycin, troleandomycin)
+\item \code{oxazolidinones}\cr(cycloserine, linezolid, tedizolid, thiacetazone)
+\item \code{penicillins}\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam (Amdinocillin), metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin, ticarcillin/clavulanic acid)
+\item \code{polymyxins}\cr(colistin, polymyxin B, polymyxin B/polysorbate 80)
+\item \code{streptogramins}\cr(pristinamycin, quinupristin/dalfopristin)
+\item \code{tetracyclines}\cr(chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline, tigecycline)
+\item \code{tetracyclines_except_tgc}\cr(chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline)
+\item \code{ureidopenicillins}\cr(azlocillin, mezlocillin, piperacillin, piperacillin/tazobactam)
+}
+}
+}
+
+\section{Maturing Lifecycle}{
+
+\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
+The \link[=lifecycle]{lifecycle} of this function is \strong{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 \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
 }

 \examples{
--- a/man/first_isolate.Rd
+++ b/man/first_isolate.Rd
@ -81,7 +81,7 @@ filter_first_weighted_isolate(

 \item{points_threshold}{points until the comparison of key antibiotics will lead to inclusion of an isolate when \code{type = "points"}, see \emph{Details}}

-\item{info}{print progress}
+\item{info}{a \link{logical} to indicate info should be printed, defaults to \code{TRUE} only in interactive mode}

 \item{include_unknown}{logical to indicate whether 'unknown' microorganisms should be included too, i.e. microbial code \code{"UNKNOWN"}, which defaults to \code{FALSE}. For WHONET users, this means that all records with organism code \code{"con"} (\emph{contamination}) will be excluded at default. Isolates with a microbial ID of \code{NA} will always be excluded as first isolate.}

--- a/man/key_antibiotics.Rd
+++ b/man/key_antibiotics.Rd
@ -36,7 +36,9 @@ key_antibiotics_equal(
  type = c("keyantibiotics", "points"),
  ignore_I = TRUE,
  points_threshold = 2,
-  info = FALSE
+  info = FALSE,
+  na.rm = TRUE,
+  ...
 )
 }
 \arguments{
@ -62,7 +64,9 @@ key_antibiotics_equal(

 \item{points_threshold}{points until the comparison of key antibiotics will lead to inclusion of an isolate when \code{type = "points"}, see \emph{Details}}

-\item{info}{print progress}
+\item{info}{unused - previously used to indicate whether a progress bar should print}
+
+\item{na.rm}{a \link{logical} to indicate whether comparison with \code{NA} should return \code{FALSE} (defaults to \code{TRUE} for backwards compatibility)}
 }
 \description{
 These function can be used to determine first isolates (see \code{\link[=first_isolate]{first_isolate()}}). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates can then be called first 'weighted' isolates.
--- a/man/like.Rd
+++ b/man/like.Rd
@ -3,7 +3,9 @@
 \name{like}
 \alias{like}
 \alias{\%like\%}
+\alias{\%unlike\%}
 \alias{\%like_case\%}
+\alias{\%unlike_case\%}
 \title{Vectorised Pattern Matching with Keyboard Shortcut}
 \source{
 Idea from the \href{https://github.com/Rdatatable/data.table/blob/ec1259af1bf13fc0c96a1d3f9e84d55d8106a9a4/R/like.R}{\code{like} function from the \code{data.table} package}, although altered as explained in \emph{Details}.
@ -13,7 +15,11 @@ like(x, pattern, ignore.case = TRUE)

 x \%like\% pattern

+x \%unlike\% pattern
+
 x \%like_case\% pattern
+
+x \%unlike_case\% pattern
 }
 \arguments{
 \item{x}{a character vector where matches are sought, or an object which can be coerced by \code{\link[=as.character]{as.character()}} to a character vector.}
@ -29,15 +35,15 @@ A \link{logical} vector
 Convenient wrapper around \code{\link[=grepl]{grepl()}} to match a pattern: \code{x \%like\% pattern}. It always returns a \code{\link{logical}} vector and is always case-insensitive (use \code{x \%like_case\% pattern} for case-sensitive matching). Also, \code{pattern} can be as long as \code{x} to compare items of each index in both vectors, or they both can have the same length to iterate over all cases.
 }
 \details{
-This \verb{\%like\%} function:
+These \code{\link[=like]{like()}} and \verb{\%like\%}/\verb{\%unlike\%} functions:
 \itemize{
-\item Is case-insensitive (use \verb{\%like_case\%} for case-sensitive matching)
-\item Supports multiple patterns
-\item Checks if \code{pattern} is a valid regular expression and sets \code{fixed = TRUE} if not, to greatly improve speed (vectorised over \code{pattern})
-\item Always uses compatibility with Perl unless \code{fixed = TRUE}, to greatly improve speed
+\item Are case-insensitive (use \verb{\%like_case\%}/\verb{\%unlike_case\%} for case-sensitive matching)
+\item Support multiple patterns
+\item Check if \code{pattern} is a valid regular expression and sets \code{fixed = TRUE} if not, to greatly improve speed (vectorised over \code{pattern})
+\item Always use compatibility with Perl unless \code{fixed = TRUE}, to greatly improve speed
 }

-Using RStudio? The text \verb{\%like\%} can also be directly inserted in your code from the Addins menu and can have its own Keyboard Shortcut like \code{Ctrl+Shift+L} or \code{Cmd+Shift+L} (see \code{Tools} > \verb{Modify Keyboard Shortcuts...}).
+Using RStudio? The \verb{\%like\%}/\verb{\%unlike\%} functions can also be directly inserted in your code from the Addins menu and can have its own keyboard shortcut like \code{Shift+Ctrl+L} or \code{Shift+Cmd+L} (see menu \code{Tools} > \verb{Modify Keyboard Shortcuts...}). If you keep pressing your shortcut, the inserted text will be iterated over \verb{\%like\%} -> \verb{\%unlike\%} -> \verb{\%like_case\%} -> \verb{\%unlike_case\%}.
 }
 \section{Stable Lifecycle}{

@ -53,7 +59,6 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
 }

 \examples{
-# simple test
 a <- "This is a test"
 b <- "TEST"
 a \%like\% b
@ -66,13 +71,20 @@ a <- c("Test case", "Something different", "Yet another thing")
 b <- c(     "case",           "diff",      "yet")
 a \%like\% b
 #> TRUE TRUE TRUE
+a \%unlike\% b
+#> FALSE FALSE FALSE
+
 a[1] \%like\% b
 #> TRUE FALSE FALSE
 a \%like\% b[1]
 #> TRUE FALSE FALSE

 # get isolates whose name start with 'Ent' or 'ent'
+example_isolates[which(mo_name(example_isolates$mo) \%like\% "^ent"), ]
 \donttest{
+# faster way, only works in R 3.2 and later:
+example_isolates[which(mo_name() \%like\% "^ent"), ]
+
 if (require("dplyr")) {
  example_isolates \%>\%
    filter(mo_name() \%like\% "^ent")
--- a/man/mdro.Rd
+++ b/man/mdro.Rd
@ -119,7 +119,7 @@ Please suggest your own (country-specific) guidelines by letting us know: \url{h

 Custom guidelines can be set with the \code{\link[=custom_mdro_guideline]{custom_mdro_guideline()}} function. This is of great importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.

-If you are familiar with \code{case_when()} of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation':\preformatted{custom <- custom_mdro_guideline(CIP == "R" & age > 60 ~ "Elderly Type A",
+If you are familiar with the \code{\link[dplyr:case_when]{case_when()}} function of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule is written \emph{before} the tilde (\code{~}) and the consequence of the rule is written \emph{after} the tilde:\preformatted{custom <- custom_mdro_guideline(CIP == "R" & age > 60 ~ "Elderly Type A",
                                ERY == "R" & age > 60 ~ "Elderly Type B")
 }

--- a/man/microorganisms.Rd
+++ b/man/microorganisms.Rd
@ -46,7 +46,7 @@ A data set containing the microbial taxonomy, last updated in March 2021, of six
 \details{
 Please note that entries are only based on the Catalogue of Life and the LPSN (see below). Since these sources incorporate entries based on (recent) publications in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), it can happen that the year of publication is sometimes later than one might expect.

-For example, \emph{Staphylococcus pettenkoferi} was described for the first time in Diagnostic Microbiology and Infectious Disease in 2002 (\doi{10.1016/s0732-8893(02)00399-1}), but it was not before 2007 that a publication in IJSEM followed (\doi{10.1099/ijs.0.64381-0}). Consequently, the AMR package returns 2007 for \code{mo_year("S. pettenkoferi")}.
+For example, \emph{Staphylococcus pettenkoferi} was described for the first time in Diagnostic Microbiology and Infectious Disease in 2002 (\doi{10.1016/s0732-8893(02)00399-1}), but it was not before 2007 that a publication in IJSEM followed (\doi{10.1099/ijs.0.64381-0}). Consequently, the \code{AMR} package returns 2007 for \code{mo_year("S. pettenkoferi")}.
 \subsection{Manual additions}{

 For convenience, some entries were added manually:
--- a/tests/testthat/test-first_isolate.R
+++ b/tests/testthat/test-first_isolate.R
@ -50,7 +50,7 @@ test_that("first isolates work", {
                      type = "keyantibiotics",
                      info = TRUE),
        na.rm = TRUE)),
-    1395)
+    1398)

  # when not ignoring I
  expect_equal(
@ -65,7 +65,7 @@ test_that("first isolates work", {
                      type = "keyantibiotics",
                      info = TRUE),
        na.rm = TRUE)),
-    1418)
+    1421)
  # when using points
  expect_equal(
    suppressWarnings(
@ -78,7 +78,7 @@ test_that("first isolates work", {
                      type = "points",
                      info = TRUE),
        na.rm = TRUE)),
-    1398)
+    1348)

  # first non-ICU isolates
  expect_equal(
Author	SHA1	Message	Date
dr. M.S. (Matthijs) Berends	5f9e7bd3ee	(v1.6.0.9009) key_antibiotics update	2021-04-23 16:13:26 +02:00
dr. M.S. (Matthijs) Berends	70b803dbb6	(v1.6.0.9008) unlike, bugfix for col_mo naming	2021-04-23 09:59:36 +02:00
dr. M.S. (Matthijs) Berends	c6289c3fc3	(v1.6.0.9007) documentation custom eucast rules, progress bar as.mo	2021-04-20 10:46:17 +02:00