(v1.8.1.9014) add Toxoplasma

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.1.9010
-Date: 2022-05-16
+Version: 1.8.1.9014
+Date: 2022-08-12
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
     data analysis and to work with microbial and antimicrobial properties by
@@ -90,5 +90,5 @@ BugReports: https://github.com/msberends/AMR/issues
 License: GPL-2 | file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1
 Roxygen: list(markdown = TRUE)

NEWS.md

@@ -1,5 +1,5 @@
-# `AMR` 1.8.1.9010
-## <small>Last updated: 16 May 2022</small>
+# `AMR` 1.8.1.9014
+## <small>Last updated: 12 August 2022</small>
 
 ### New
 * EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.
@@ -11,7 +11,8 @@
 * Small fix for using `ab_from_text()`
 * Fixes for reading in text files using `set_mo_source()`, which now also allows the source file to contain valid taxonomic names instead of only valid microorganism ID of this package
 * Using any `random_*()` function (such as `random_mic()`) is now possible by directly calling the package without loading it first: `AMR::random_mic(10)`
-
+* Added *Toxoplasma gondii* (`P_TXPL_GOND`) to the `microorganisms` data set, together with its genus, family, and order
+* Changed value in column `prevalence` of the `microorganisms` data set from 3 to 2 for these genera: *Acholeplasma*, *Alistipes*, *Alloprevotella*, *Bergeyella*, *Borrelia*, *Brachyspira*, *Butyricimonas*, *Cetobacterium*, *Chlamydia*, *Chlamydophila*, *Deinococcus*, *Dysgonomonas*, *Elizabethkingia*, *Empedobacter*, *Haloarcula*, *Halobacterium*, *Halococcus*, *Myroides*, *Odoribacter*, *Ornithobacterium*, *Parabacteroides*, *Pedobacter*, *Phocaeicola*, *Porphyromonas*, *Riemerella*, *Sphingobacterium*, *Streptobacillus*, *Tenacibaculum*, *Terrimonas*, *Victivallis*, *Wautersiella*, *Weeksella*
 
 # `AMR` 1.8.1
 

R/atc_online.R

@@ -51,7 +51,7 @@
 #' 
 #' - `"g"` = gram
 #' - `"mg"` = milligram
-#' - `"mcg"`` = microgram
+#' - `"mcg"` = microgram
 #' - `"U"` = unit
 #' - `"TU"` = thousand units
 #' - `"MU"` = million units

R/custom_eucast_rules.R

@@ -27,7 +27,7 @@
 #' 
 #' Define custom EUCAST rules for your organisation or specific analysis and use the output of this function in [eucast_rules()].
 #' @inheritSection lifecycle Stable Lifecycle
-#' @param ... rules in formula notation, see *Examples*
+#' @param ... rules in [formula][`~`()] notation, see *Examples*
 #' @details
 #' 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.
 #' 
@@ -75,7 +75,7 @@
 #' 
 #' ### 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`:
+#' 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 = "\u0096", 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",
@@ -91,7 +91,7 @@
 #' 
 #' 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 agents that will be matched when running the rule.
 #' 
-#' `r paste0("  * ", sapply(DEFINED_AB_GROUPS, function(x) paste0("``", tolower(gsub("^AB_", "", x)), "``\\cr(", vector_and(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), quotes = FALSE), ")"), USE.NAMES = FALSE), "\n", collapse = "")`
+#' `r paste0("  * ", sapply(DEFINED_AB_GROUPS, function(x) paste0("\u0096", tolower(gsub("^AB_", "", x)), "\u0096\\cr(", vector_and(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), quotes = FALSE), ")"), USE.NAMES = FALSE), "\n", collapse = "")`
 #' @returns A [list] containing the custom rules
 #' @inheritSection AMR Read more on Our Website!
 #' @export

R/data.R

@@ -104,6 +104,7 @@
 #' - 11 entries of *Streptococcus* (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)
 #' - 2 entries of *Staphylococcus* (coagulase-negative (CoNS) and coagulase-positive (CoPS))
 #' - 3 entries of *Trichomonas* (*T. vaginalis*, and its family and genus)
+#' - 4 entries of *Toxoplasma* (*T. gondii*, and its order, family and genus)
 #' - 1 entry of *Candida* (*C.  krusei*), that is not (yet) in the Catalogue of Life
 #' - 1 entry of *Blastocystis* (*B.  hominis*), although it officially does not exist (Noel *et al.* 2005, PMID 15634993)
 #' - 1 entry of *Moraxella* (*M. catarrhalis*), which was formally named *Branhamella catarrhalis* (Catlin, 1970) though this change was never accepted within the field of clinical microbiology
@@ -111,13 +112,10 @@
 #' - 6 families under the Enterobacterales order, according to Adeolu *et al.* (2016, PMID 27620848), that are not (yet) in the Catalogue of Life
 #' 
 #' ## Direct download
-#' This data set is available as 'flat file' for use even without \R - you can find the file here:
+#' This data set is available as 'flat file' for use even without \R - you can find the file here: <https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt>. 
 #' 
-#' * <https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt>
+#' The file in \R format (with preserved data structure) can be found here: <https://github.com/msberends/AMR/raw/main/data/microorganisms.rda>.
 #' 
-#' The file in \R format (with preserved data structure) can be found here:
-#' 
-#' * <https://github.com/msberends/AMR/raw/main/data/microorganisms.rda>
 #' @section About the Records from LPSN (see *Source*):
 #' The List of Prokaryotic names with Standing in Nomenclature (LPSN) provides comprehensive information on the nomenclature of prokaryotes. LPSN is a free to use service founded by Jean P. Euzeby in 1997 and later on maintained by Aidan C. Parte.
 #' 

R/mo.R

@@ -2208,3 +2208,282 @@ strip_words <- function(text, n, side = "right") {
   })
   vapply(FUN.VALUE = character(1), out, paste, collapse = " ")
 }
+
+
+as.mo2 <- function(x,
+                   Becker = FALSE,
+                   Lancefield = FALSE,
+                   allow_uncertain = TRUE,
+                   reference_df = get_mo_source(),
+                   info = interactive(),
+                   property = "mo",
+                   initial_search = TRUE,
+                   dyslexia_mode = FALSE,
+                   debug = FALSE,
+                   ignore_pattern = getOption("AMR_ignore_pattern"),
+                   reference_data_to_use = MO_lookup,
+                   actual_uncertainty = 1,
+                   actual_input = NULL,
+                   language = get_AMR_locale()) {
+  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)
+  meet_criteria(Lancefield, allow_class = c("logical", "character"), has_length = 1)
+  meet_criteria(allow_uncertain, allow_class = c("logical", "numeric", "integer"), has_length = 1)
+  meet_criteria(reference_df, allow_class = "data.frame", allow_NULL = TRUE)
+  meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(microorganisms))
+  meet_criteria(initial_search, allow_class = "logical", has_length = 1)
+  meet_criteria(dyslexia_mode, allow_class = "logical", has_length = 1)
+  meet_criteria(debug, allow_class = "logical", has_length = 1)
+  meet_criteria(ignore_pattern, allow_class = "character", has_length = 1, allow_NULL = TRUE)
+  meet_criteria(reference_data_to_use, allow_class = "data.frame")
+  meet_criteria(actual_uncertainty, allow_class = "numeric", has_length = 1)
+  meet_criteria(actual_input, allow_class = "character", allow_NULL = TRUE)
+  meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
+  
+  check_dataset_integrity()
+  
+  if (isTRUE(debug) && initial_search == TRUE) {
+    time_start_tracking()
+  }
+  
+  lookup <- function(needle,
+                     column = property,
+                     haystack = reference_data_to_use,
+                     n = 1,
+                     debug_mode = debug,
+                     initial = initial_search,
+                     uncertainty = actual_uncertainty,
+                     input_actual = actual_input) {
+    
+    if (!is.null(input_actual)) {
+      input <- input_actual
+    } else {
+      input <- tryCatch(x_backup[i], error = function(e) "")
+    }
+    
+    # `column` can be NULL for all columns, or a selection
+    # returns a [character] (vector) - if `column` > length 1 then with columns as names
+    if (isTRUE(debug_mode)) {
+      cat(font_silver("Looking up: ", substitute(needle), collapse = ""), 
+          "\n           ", time_track())
+    }
+    if (length(column) == 1) {
+      res_df <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
+      if (NROW(res_df) > 1 & uncertainty != -1) {
+        # sort the findings on matching score
+        scores <- mo_matching_score(x = input,
+                                    n = res_df[, "fullname", drop = TRUE])
+        res_df <- res_df[order(scores, decreasing = TRUE), , drop = FALSE]
+      }
+      res <- as.character(res_df[, column, drop = TRUE])
+      if (length(res) == 0) {
+        if (isTRUE(debug_mode)) {
+          cat(font_red(" (no match)\n"))
+        }
+        NA_character_
+      } else {
+        if (isTRUE(debug_mode)) {
+          cat(font_green(paste0(" MATCH (", NROW(res_df), " results)\n")))
+        }
+        if ((length(res) > n | uncertainty > 1) & uncertainty != -1) {
+          # save the other possible results as well, but not for forced certain results (then uncertainty == -1)
+          uncertainties <<- rbind(uncertainties,
+                                  format_uncertainty_as_df(uncertainty_level = uncertainty,
+                                                           input = input,
+                                                           result_mo = res_df[1, "mo", drop = TRUE],
+                                                           candidates = as.character(res_df[, "fullname", drop = TRUE])),
+                                  stringsAsFactors = FALSE)
+        }
+        res[seq_len(min(n, length(res)))]
+      }
+    } else {
+      if (is.null(column)) {
+        column <- names(haystack)
+      }
+      res <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
+      res <- res[seq_len(min(n, nrow(res))), column, drop = TRUE]
+      if (NROW(res) == 0) {
+        if (isTRUE(debug_mode)) {
+          cat(font_red(" (no rows)\n"))
+        }
+        res <- rep(NA_character_, length(column))
+      } else {
+        if (isTRUE(debug_mode)) {
+          cat(font_green(paste0(" MATCH (", NROW(res), " rows)\n")))
+        }
+      }
+      res <- as.character(res)
+      names(res) <- column
+      res
+    }
+  }
+  
+  # start off with replaced language-specific non-ASCII characters with ASCII characters
+  x <- parse_and_convert(x)
+  # replace mo codes used in older package versions
+  x <- replace_old_mo_codes(x, property)
+  # ignore cases that match the ignore pattern
+  x <- replace_ignore_pattern(x, ignore_pattern)
+  
+  # WHONET: xxx = no growth
+  x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_
+  # Laboratory systems: remove (translated) entries like "no growth", etc.
+  x[trimws2(x) %like% translate_AMR("no .*growth", language = language)] <- NA_character_
+  x[trimws2(x) %like% paste0("^(", translate_AMR("no|not", language = language), ") [a-z]+")] <- "UNKNOWN"
+  
+  if (initial_search == TRUE) {
+    # keep track of time - give some hints to improve speed if it takes a long time
+    start_time <- Sys.time()
+    
+    pkg_env$mo_failures <- NULL
+    pkg_env$mo_uncertainties <- NULL
+    pkg_env$mo_renamed <- NULL
+  }
+  pkg_env$mo_renamed_last_run <- NULL
+  
+  failures <- character(0)
+  uncertainty_level <- translate_allow_uncertain(allow_uncertain)
+  uncertainties <- data.frame(uncertainty = integer(0),
+                              input = character(0),
+                              fullname = character(0),
+                              renamed_to = character(0),
+                              mo = character(0),
+                              candidates = character(0),
+                              stringsAsFactors = FALSE)
+  
+  x_input <- x
+  # already strip leading and trailing spaces
+  x <- trimws(x)
+  # only check the uniques, which is way faster
+  x <- unique(x)
+  # remove empty values (to later fill them in again with NAs)
+  # ("xxx" is WHONET code for 'no growth')
+  x <- x[!is.na(x)
+         & !is.null(x)
+         & !identical(x, "")
+         & !identical(x, "xxx")]
+  
+  # defined df to check for
+  if (!is.null(reference_df)) {
+    check_validity_mo_source(reference_df)
+    reference_df <- repair_reference_df(reference_df)
+  }
+  
+  # all empty
+  if (all(identical(trimws(x_input), "") | is.na(x_input) | length(x) == 0)) {
+    if (property == "mo") {
+      return(set_clean_class(rep(NA_character_, length(x_input)),
+                             new_class = c("mo", "character")))
+    } else {
+      return(rep(NA_character_, length(x_input)))
+    }
+    
+  } else if (all(x %in% reference_df[, 1][[1]])) {
+    # all in reference df
+    colnames(reference_df)[1] <- "x"
+    suppressWarnings(
+      x <- MO_lookup[match(reference_df[match(x, reference_df$x), "mo", drop = TRUE], MO_lookup$mo), property, drop = TRUE]
+    )
+    
+  } else if (all(x %in% reference_data_to_use$mo)) {
+    x <- MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE]
+    
+  } else if (all(tolower(x) %in% reference_data_to_use$fullname_lower)) {
+    # we need special treatment for very prevalent full names, they are likely!
+    # e.g. as.mo("Staphylococcus aureus")
+    x <- MO_lookup[match(tolower(x), MO_lookup$fullname_lower), property, drop = TRUE]
+    
+  } else if (all(x %in% reference_data_to_use$fullname)) {
+    # we need special treatment for very prevalent full names, they are likely!
+    # e.g. as.mo("Staphylococcus aureus")
+    x <- MO_lookup[match(x, MO_lookup$fullname), property, drop = TRUE]
+    
+  } else if (all(toupper(x) %in% microorganisms.codes$code)) {
+    # commonly used MO codes
+    x <- MO_lookup[match(microorganisms.codes[match(toupper(x),
+                                                    microorganisms.codes$code),
+                                              "mo",
+                                              drop = TRUE],
+                         MO_lookup$mo),
+                   property,
+                   drop = TRUE]
+    
+  } else if (!all(x %in% microorganisms[, property])) {
+    
+    strip_whitespace <- function(x, dyslexia_mode) {
+      # all whitespaces (tab, new lines, etc.) should be one space
+      # and spaces before and after should be left blank
+      trimmed <- trimws2(x)
+      # also, make sure the trailing and leading characters are a-z or 0-9
+      # in case of non-regex
+      if (dyslexia_mode == FALSE) {
+        trimmed <- gsub("^[^a-zA-Z0-9)(]+", "", trimmed, perl = TRUE)
+        trimmed <- gsub("[^a-zA-Z0-9)(]+$", "", trimmed, perl = TRUE)
+      }
+      trimmed
+    }
+    
+    x_backup_untouched <- x
+    x <- strip_whitespace(x, dyslexia_mode)
+    # translate 'unknown' names back to English
+    if (any(tolower(x) %like_case% "unbekannt|onbekend|desconocid|sconosciut|iconnu|desconhecid", na.rm = TRUE)) {
+      trns <- subset(TRANSLATIONS, pattern %like% "unknown")
+      langs <- LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED != "en"]
+      for (l in langs) {
+        for (i in seq_len(nrow(trns))) {
+          if (!is.na(trns[i, l, drop = TRUE])) {
+            x <- gsub(pattern = trns[i, l, drop = TRUE],
+                      replacement = trns$pattern[i],
+                      x = x,
+                      ignore.case = TRUE,
+                      perl = TRUE)
+          }
+        }
+      }
+    }
+    
+    # remove spp and species
+    x <- gsub("(^| )[ .]*(spp|ssp|ss|sp|subsp|subspecies|biovar|biotype|serovar|species)[ .]*( |$)", "", x, ignore.case = TRUE, perl = TRUE)
+    x <- strip_whitespace(x, dyslexia_mode)
+    
+    x_backup <- x
+    
+    # from here on case-insensitive
+    x <- tolower(x)
+    
+    x_backup[x %like_case% "^(fungus|fungi)$"] <- "(unknown fungus)" # will otherwise become the kingdom
+    x_backup[x_backup_untouched == "Fungi"] <- "Fungi" # is literally the kingdom
+    
+    # Fill in fullnames and MO codes directly
+    known_names <- tolower(x_backup) %in% MO_lookup$fullname_lower
+    x[known_names] <- MO_lookup[match(tolower(x_backup)[known_names], MO_lookup$fullname_lower), property, drop = TRUE]
+    known_codes_mo <- toupper(x_backup) %in% MO_lookup$mo
+    x[known_codes_mo] <- MO_lookup[match(toupper(x_backup)[known_codes_mo], MO_lookup$mo), property, drop = TRUE]
+    known_codes_lis <- toupper(x_backup) %in% microorganisms.codes$code
+    x[known_codes_lis] <- MO_lookup[match(microorganisms.codes[match(toupper(x_backup)[known_codes_lis],
+                                                                     microorganisms.codes$code), "mo", drop = TRUE],
+                                          MO_lookup$mo), property, drop = TRUE]
+    already_known <- known_names | known_codes_mo | known_codes_lis
+    
+    # now only continue where the right taxonomic output is not already known
+    if (any(!already_known)) {
+      x_unknown <- x[!already_known]
+      x_unknown <- gsub(" ?[(].*[)] ?", "", x_unknown, perl = TRUE)
+      x_unknown <- gsub("[^a-z ]", " ", x_unknown, perl = TRUE)
+      x_unknown <- gsub(" +", " ", x_unknown, perl = TRUE)
+      print(x_unknown)
+      x_search <- gsub("([a-z])[a-z]*( ([a-z])[a-z]*)?( ([a-z])[a-z]*)?", "^\\1.* \\3.* \\5.*", x_unknown, perl = TRUE)
+      x_search <- gsub("( [.][*])+$", "", x_search, perl = TRUE)
+      print(x_search)
+      for (i in seq_len(length(x_unknown))) {
+        # search first, second and third part
+        mos_to_search <- MO_lookup[which(MO_lookup$fullname_lower %like_case% x_search[i]), "fullname", drop = TRUE]
+        score <- mo_matching_score(x_unknown[i], mos_to_search)
+        out <- mos_to_search[order(score, decreasing = TRUE)][1:25] # keep first 25
+        print(score[order(score, decreasing = TRUE)][1])
+        x[!already_known][i] <- MO_lookup$mo[match(out[1], MO_lookup$fullname)]
+      }
+    }
+  }
+  x
+}

R/resistance_predict.R

@@ -34,7 +34,7 @@
 #' @param year_max highest year to use in the prediction model, defaults to 10 years after today
 #' @param year_every unit of sequence between lowest year found in the data and `year_max`
 #' @param minimum minimal amount of available isolates per year to include. Years containing less observations will be estimated by the model.
-#' @param model the statistical model of choice. This could be a generalised linear regression model with binomial distribution (i.e. using `glm(..., family = binomial)``, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See *Details* for all valid options.
+#' @param model the statistical model of choice. This could be a generalised linear regression model with binomial distribution (i.e. using `glm(..., family = binomial)`, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See *Details* for all valid options.
 #' @param I_as_S a [logical] to indicate whether values `"I"` should be treated as `"S"` (will otherwise be treated as `"R"`). The default, `TRUE`, follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section *Interpretation of S, I and R* below. 
 #' @param preserve_measurements a [logical] to indicate whether predictions of years that are actually available in the data should be overwritten by the original data. The standard errors of those years will be `NA`.
 #' @param info a [logical] to indicate whether textual analysis should be printed with the name and [summary()] of the statistical model.

R/zzz.R

@@ -131,7 +131,12 @@ create_MO_lookup <- function() {
   MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5
   
   # use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
-  MO_lookup$fullname_lower <- MO_FULLNAME_LOWER
+  if (length(MO_FULLNAME_LOWER) == nrow(MO_lookup)) {
+    MO_lookup$fullname_lower <- MO_FULLNAME_LOWER
+  } else {
+    MO_lookup$fullname_lower <- ""
+    warning("MO table updated - Run: source(\"data-raw/_internals.R\")", call. = FALSE)
+  }
   
   # add a column with only "e coli" like combinations
   MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower, perl = TRUE)

data-raw/_internals.R

@@ -137,6 +137,29 @@ MO_CONS <- create_species_cons_cops("CoNS")
 MO_COPS <- create_species_cons_cops("CoPS")
 MO_STREP_ABCG <- as.mo(MO_lookup[which(MO_lookup$genus == "Streptococcus"), "mo", drop = TRUE], Lancefield = TRUE) %in% c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_GRPC", "B_STRPT_GRPG")
 MO_FULLNAME_LOWER <- create_MO_fullname_lower()
+MO_PREVALENT_GENERA <- c("Absidia", "Acholeplasma", "Acremonium", "Actinotignum", "Aedes", "Alistipes", "Alloprevotella",
+                         "Alternaria", "Anaerosalibacter", "Ancylostoma", "Angiostrongylus", "Anisakis", "Anopheles",
+                         "Apophysomyces", "Arachnia", "Aspergillus", "Aureobasidium", "Bacteroides", "Basidiobolus",
+                         "Beauveria", "Bergeyella", "Blastocystis", "Blastomyces", "Borrelia", "Brachyspira", "Branhamella",
+                         "Butyricimonas", "Candida", "Capillaria", "Capnocytophaga", "Catabacter", "Cetobacterium", "Chaetomium",
+                         "Chlamydia", "Chlamydophila", "Chryseobacterium", "Chrysonilia", "Cladophialophora", "Cladosporium",
+                         "Conidiobolus", "Contracaecum", "Cordylobia", "Cryptococcus", "Curvularia", "Deinococcus", "Demodex",
+                         "Dermatobia", "Diphyllobothrium", "Dirofilaria", "Dysgonomonas", "Echinostoma", "Elizabethkingia",
+                         "Empedobacter", "Enterobius", "Exophiala", "Exserohilum", "Fasciola", "Flavobacterium", "Fonsecaea",
+                         "Fusarium", "Fusobacterium", "Giardia", "Haloarcula", "Halobacterium", "Halococcus", "Hendersonula",
+                         "Heterophyes", "Histoplasma", "Hymenolepis", "Hypomyces", "Hysterothylacium", "Lelliottia",
+                         "Leptosphaeria", "Leptotrichia", "Lucilia", "Lumbricus", "Malassezia", "Malbranchea", "Metagonimus",
+                         "Microsporum", "Mortierella", "Mucor", "Mycocentrospora", "Mycoplasma", "Myroides", "Necator",
+                         "Nectria", "Ochroconis", "Odoribacter", "Oesophagostomum", "Oidiodendron", "Opisthorchis",
+                         "Ornithobacterium", "Parabacteroides", "Pediculus", "Pedobacter", "Phlebotomus", "Phocaeicola",
+                         "Phocanema", "Phoma", "Piedraia", "Pithomyces", "Pityrosporum", "Porphyromonas", "Prevotella",
+                         "Pseudallescheria", "Pseudoterranova", "Pulex", "Rhizomucor", "Rhizopus", "Rhodotorula", "Riemerella",
+                         "Saccharomyces", "Sarcoptes", "Scolecobasidium", "Scopulariopsis", "Scytalidium", "Sphingobacterium",
+                         "Spirometra", "Spiroplasma", "Sporobolomyces", "Stachybotrys", "Streptobacillus", "Strongyloides",
+                         "Syngamus", "Taenia", "Tannerella", "Tenacibaculum", "Terrimonas", "Toxocara", "Treponema", "Trichinella",
+                         "Trichobilharzia", "Trichoderma", "Trichomonas", "Trichophyton", "Trichosporon", "Trichostrongylus",
+                         "Trichuris", "Tritirachium", "Trombicula", "Tunga", "Ureaplasma", "Victivallis", "Wautersiella",
+                         "Weeksella", "Wuchereria")
 
 # antibiotic groups
 # (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv)
@@ -200,6 +223,7 @@ usethis::use_data(EUCAST_RULES_DF,
                   MO_COPS,
                   MO_STREP_ABCG,
                   MO_FULLNAME_LOWER,
+                  MO_PREVALENT_GENERA,
                   AB_LOOKUP,
                   AB_AMINOGLYCOSIDES,
                   AB_AMINOPENICILLINS,
@@ -275,7 +299,7 @@ if (changed_md5(mo)) {
   try(haven::write_sas(dplyr::select(mo, -snomed), "data-raw/microorganisms.sas"), silent = TRUE)
   try(haven::write_sav(dplyr::select(mo, -snomed), "data-raw/microorganisms.sav"), silent = TRUE)
   try(haven::write_dta(dplyr::select(mo, -snomed), "data-raw/microorganisms.dta"), silent = TRUE)
-  try(openxlsx::write.xlsx(mo, "data-raw/microorganisms.xlsx"), silent = TRUE)
+  try(openxlsx::write.xlsx(dplyr::select(mo, -snomed), "data-raw/microorganisms.xlsx"), silent = TRUE)
 }
 
 if (changed_md5(microorganisms.old)) {

data-raw/microorganisms.old.md5

@@ -1 +1 @@
-ee4434541c7b6529b391d2684748e28b
+19af89838b60bc8549d4474609629e8d

data-raw/microorganisms.old.txt

@@ -278,9 +278,9 @@
 "Adelosina duthiersi"	"Quinqueloculina duthiersi"	"Schlumberger, 1886"	3
 "Adelosina linneiana"	"Pseudotriloculina linneiana"	"DOrbigny, 1839"	3
 "Aecidium ipomoeae-panduratae"	"Albugo ipomoeae-panduratae"	"Schwein, 1822"	3
-"Aedimorphus alboannulatus"	"Aedes alboannulatus"	"Theobald, 1905"	3
-"Aedimorphus albotaeniatus"	"Aedes albotaeniatus"	"Theobald, 1903"	3
-"Aedimorphus australis"	"Aedes australis"	"Taylor, 1914"	3
+"Aedimorphus alboannulatus"	"Aedes alboannulatus"	"Theobald, 1905"	2
+"Aedimorphus albotaeniatus"	"Aedes albotaeniatus"	"Theobald, 1903"	2
+"Aedimorphus australis"	"Aedes australis"	"Taylor, 1914"	2
 "Aegyria angustata"	"Dysteria angustata"	"Claparede et al., 1859"	3
 "Aegyria astyla"	"Dysteria astyla"	"Maskell, 1887"	3
 "Aegyria distyla"	"Dysteria distyla"	"Maskell, 1887"	3
@@ -880,7 +880,7 @@
 "Astacolus subaculeata"	"Vaginulinopsis subaculeata"	"Cushman, 1923"	3
 "Astacolus sublegumen"	"Vaginulinopsis sublegumen"	"Parr, 1950"	3
 "Asterellina pulchella"	"Eoeponidella pulchella"	"Parker, 1952"	3
-"Asterias ocellifera"	"Nectria ocellifera"	"Lamarck, 1816"	3
+"Asterias ocellifera"	"Nectria ocellifera"	"Lamarck, 1816"	2
 "Asterigerinata pulchella"	"Eoeponidella pulchella"	"Parker, 1952"	3
 "Asteromella anthemidis"	"Phoma anthemidis"	"Ruppr, 1958"	2
 "Asteromella longissima"	"Phoma longissima"	"Petr"	2
@@ -1324,8 +1324,8 @@
 "Bacteriovorax marinus"	"Halobacteriovorax marinus"	"Baer et al., 2004"	2
 "Bacteriovorax starrii"	"Peredibacter starrii"	"Baer et al., 2000"	2
 "Bacteroides amylophilus"	"Ruminobacter amylophilus"	"Hamlin et al., 1956"	1
-"Bacteroides asaccharolyticus"	"Porphyromonas asaccharolytica"	"Finegold et al., 1977"	3
-"Bacteroides barnesiae"	"Phocaeicola barnesiae"	"Lan et al., 2006"	3
+"Bacteroides asaccharolyticus"	"Porphyromonas asaccharolytica"	"Finegold et al., 1977"	2
+"Bacteroides barnesiae"	"Phocaeicola barnesiae"	"Lan et al., 2006"	2
 "Bacteroides bivius"	"Prevotella bivia"	"Holdeman et al., 1977"	2
 "Bacteroides buccae"	"Prevotella buccae"	"Holdeman et al., 1982"	2
 "Bacteroides buccalis"	"Prevotella buccalis"	"Shah et al., 1982"	2
@@ -1333,32 +1333,32 @@
 "Bacteroides capillus"	"Prevotella buccae"	"Kornman et al., 1982"	2
 "Bacteroides cellulosolvens"	"Pseudobacteroides cellulosolvens"	"Murray et al., 1984"	2
 "Bacteroides chinchillae"	"Bacteroides sartorii"	"Kitahara et al., 2011"	
-"Bacteroides chinchillae"	"Phocaeicola sartorii"	"Kitahara et al., 2011"	3
+"Bacteroides chinchillae"	"Phocaeicola sartorii"	"Kitahara et al., 2011"	2
 "Bacteroides coagulans"	"Ezakiella coagulans"	"Eggerth et al., 1933"	2
-"Bacteroides coprocola"	"Phocaeicola coprocola"	"Kitahara et al., 2005"	3
-"Bacteroides coprophilus"	"Phocaeicola coprophilus"	"Hayashi et al., 2016"	3
+"Bacteroides coprocola"	"Phocaeicola coprocola"	"Kitahara et al., 2005"	2
+"Bacteroides coprophilus"	"Phocaeicola coprophilus"	"Hayashi et al., 2016"	2
 "Bacteroides corporis"	"Prevotella corporis"	"Johnson et al., 1983"	2
 "Bacteroides denticola"	"Prevotella denticola"	"Shah et al., 1982"	2
 "Bacteroides disiens"	"Prevotella disiens"	"Holdeman et al., 1977"	2
-"Bacteroides distasonis"	"Parabacteroides distasonis"	"Eggerth et al., 1933"	3
-"Bacteroides dorei"	"Phocaeicola dorei"	"Bakir et al., 2016"	3
-"Bacteroides endodontalis"	"Porphyromonas endodontalis"	"Van Steenbergen et al., 1984"	3
+"Bacteroides distasonis"	"Parabacteroides distasonis"	"Eggerth et al., 1933"	2
+"Bacteroides dorei"	"Phocaeicola dorei"	"Bakir et al., 2016"	2
+"Bacteroides endodontalis"	"Porphyromonas endodontalis"	"Van Steenbergen et al., 1984"	2
 "Bacteroides forsythus"	"Tannerella forsythia"	"Tanner et al., 1986"	3
 "Bacteroides furcosus"	"Anaerorhabdus furcosa"	"Hauduroy et al., 1937"	2
-"Bacteroides gingivalis"	"Porphyromonas gingivalis"	"Coykendall et al., 1980"	3
-"Bacteroides goldsteinii"	"Parabacteroides goldsteinii"	"Song et al., 2006"	3
+"Bacteroides gingivalis"	"Porphyromonas gingivalis"	"Coykendall et al., 1980"	2
+"Bacteroides goldsteinii"	"Parabacteroides goldsteinii"	"Song et al., 2006"	2
 "Bacteroides gracilis"	"Campylobacter gracilis"	"Tanner et al., 1981"	2
 "Bacteroides heparinolyticus"	"Prevotella heparinolytica"	"Okuda et al., 1985"	2
 "Bacteroides hypermegas"	"Megamonas hypermegale"	"Harrison et al., 1963"	2
 "Bacteroides intermedius"	"Prevotella intermedia"	"Johnson et al., 1983"	2
-"Bacteroides levii"	"Porphyromonas levii"	"Johnson et al., 1983"	3
+"Bacteroides levii"	"Porphyromonas levii"	"Johnson et al., 1983"	2
 "Bacteroides loescheii"	"Prevotella loescheii"	"Holdeman et al., 1982"	2
-"Bacteroides macacae"	"Porphyromonas macacae"	"Coykendall et al., 1980"	3
-"Bacteroides massiliensis"	"Phocaeicola massiliensis"	"Fenner et al., 2016"	3
+"Bacteroides macacae"	"Porphyromonas macacae"	"Coykendall et al., 1980"	2
+"Bacteroides massiliensis"	"Phocaeicola massiliensis"	"Fenner et al., 2016"	2
 "Bacteroides melaninogenicus"	"Prevotella melaninogenica"	"Roy et al., 1982"	2
 "Bacteroides melaninogenicus intermedius"	"Prevotella intermedia"	"Holdeman et al., 1970"	2
-"Bacteroides melaninogenicus macacae"	"Porphyromonas macacae"	"Slots et al., 1980"	3
-"Bacteroides merdae"	"Parabacteroides merdae"	"Johnson et al., 1986"	3
+"Bacteroides melaninogenicus macacae"	"Porphyromonas macacae"	"Slots et al., 1980"	2
+"Bacteroides merdae"	"Parabacteroides merdae"	"Johnson et al., 1986"	2
 "Bacteroides microfusus"	"Rikenella microfusus"	"Kaneuchi et al., 1978"	3
 "Bacteroides multiacidus"	"Mitsuokella multacida"	"Mitsuoka et al., 1974"	2
 "Bacteroides nodosus"	"Dichelobacter nodosus"	"Mraz, 1963"	1
@@ -1366,19 +1366,19 @@
 "Bacteroides oralis"	"Prevotella oralis"	"Loesche et al., 1964"	2
 "Bacteroides oris"	"Prevotella oris"	"Holdeman et al., 1982"	2
 "Bacteroides oulorum"	"Prevotella oulorum"	"Shah et al., 1985"	2
-"Bacteroides paurosaccharolyticus"	"Phocaeicola paurosaccharolyticus"	"Ueki et al., 2011"	3
+"Bacteroides paurosaccharolyticus"	"Phocaeicola paurosaccharolyticus"	"Ueki et al., 2011"	2
 "Bacteroides pentosaceus"	"Prevotella buccae"	"Shah et al., 1982"	2
-"Bacteroides plebeius"	"Phocaeicola plebeius"	"Kitahara et al., 2005"	3
+"Bacteroides plebeius"	"Phocaeicola plebeius"	"Kitahara et al., 2005"	2
 "Bacteroides pneumosintes"	"Dialister pneumosintes"	"Holdeman et al., 1970"	2
 "Bacteroides praeacutus"	"Tissierella praeacuta"	"Holdeman et al., 1970"	2
-"Bacteroides putredinis"	"Alistipes putredinis"	"Kelly, 1957"	3
+"Bacteroides putredinis"	"Alistipes putredinis"	"Kelly, 1957"	2
 "Bacteroides ruminicola"	"Prevotella ruminicola"	"Bryant et al., 1958"	2
 "Bacteroides ruminicola brevis"	"Prevotella brevis"	"Bryant et al., 1958"	2
-"Bacteroides salanitronis"	"Phocaeicola salanitronis"	"Lan et al., 2006"	3
-"Bacteroides salivosus"	"Porphyromonas macacae"	"Love et al., 1987"	3
+"Bacteroides salanitronis"	"Phocaeicola salanitronis"	"Lan et al., 2006"	2
+"Bacteroides salivosus"	"Porphyromonas macacae"	"Love et al., 1987"	2
 "Bacteroides salyersae"	"Bacteroides salyersiae"	"Song et al., 2005"	2
-"Bacteroides sartorii"	"Phocaeicola sartorii"	"Clavel et al., 2012"	3
-"Bacteroides splanchnicus"	"Odoribacter splanchnicus"	"Werner et al., 1975"	3
+"Bacteroides sartorii"	"Phocaeicola sartorii"	"Clavel et al., 2012"	2
+"Bacteroides splanchnicus"	"Odoribacter splanchnicus"	"Werner et al., 1975"	2
 "Bacteroides succinogenes"	"Fibrobacter succinogenes"	"Hungate, 1950"	3
 "Bacteroides suis"	"Bacteroides pyogenes"	"Benno et al., 1983"	2
 "Bacteroides tectum"	"Bacteroides pyogenes"	"Love et al., 2019"	2
@@ -1386,7 +1386,7 @@
 "Bacteroides termitidis"	"Sebaldella termitidis"	"Holdeman et al., 1970"	3
 "Bacteroides ureolyticus"	"Campylobacter ureolyticus"	"Jackson et al., 1978"	2
 "Bacteroides veroralis"	"Prevotella veroralis"	"Watabe et al., 1983"	2
-"Bacteroides vulgatus"	"Phocaeicola vulgatus"	"Hahnke et al., 2016"	3
+"Bacteroides vulgatus"	"Phocaeicola vulgatus"	"Hahnke et al., 2016"	2
 "Bacteroides xylanolyticus"	"Hungatella xylanolytica"	"Scholten-Koerselman et al., 1988"	2
 "Bacteroides zoogleoformans"	"Prevotella zoogleoformans"	"Cato et al., 1982"	
 "Bacteroides zoogleoformans"	"Capsularis zoogleoformans"	"Cato et al., 1982"	3
@@ -1650,27 +1650,27 @@
 "Bolivinita subangularis"	"Saidovina subangularis"	"Brady, 1881"	3
 "Bolivinita subangularis lineata"	"Saidovina subangularis lineata"	"Cushman, 1933"	3
 "Borelis (Fasciolites) pygmaea"	"Neoalveolina pygmaea"	"Hanzawa, 1930"	3
-"Borrelia baltazardi"	"Borrelia baltazardii"	"Karimi et al., 1983"	3
-"Borrelia bavariensis"	"Borrelia garinii bavariensis"	"Margos et al., 2020"	3
-"Borrelia turdae"	"Borrelia turdi"	"Fukunaga et al., 1997"	3
-"Borreliella"	"Borrelia"	"Adeolu et al., 2015"	3
-"Borreliella afzelii"	"Borrelia afzelii"	"Adeolu et al., 2018"	3
-"Borreliella americana"	"Borrelia americana"	"Adeolu et al., 2018"	3
+"Borrelia baltazardi"	"Borrelia baltazardii"	"Karimi et al., 1983"	2
+"Borrelia bavariensis"	"Borrelia garinii bavariensis"	"Margos et al., 2020"	2
+"Borrelia turdae"	"Borrelia turdi"	"Fukunaga et al., 1997"	2
+"Borreliella"	"Borrelia"	"Adeolu et al., 2015"	2
+"Borreliella afzelii"	"Borrelia afzelii"	"Adeolu et al., 2018"	2
+"Borreliella americana"	"Borrelia americana"	"Adeolu et al., 2018"	2
 "Borreliella bavariensis"	"Borrelia bavariensis"	"Adeolu et al., 2015"	
-"Borreliella bavariensis"	"Borrelia garinii bavariensis"	"Adeolu et al., 2015"	3
-"Borreliella bissettiae"	"Borrelia bissettiae"	"Gupta, 2020"	3
-"Borreliella burgdorferi"	"Borrelia burgdorferi"	"Adeolu et al., 2015"	3
-"Borreliella californiensis"	"Borrelia californiensis"	"Gupta, 2020"	3
-"Borreliella carolinensis"	"Borrelia carolinensis"	"Adeolu et al., 2015"	3
-"Borreliella garinii"	"Borrelia garinii"	"Adeolu et al., 2015"	3
-"Borreliella japonica"	"Borrelia japonica"	"Adeolu et al., 2015"	3
-"Borreliella kurtenbachii"	"Borrelia kurtenbachii"	"Adeolu et al., 2015"	3
-"Borreliella lanei"	"Borrelia lanei"	"Gupta, 2020"	3
-"Borreliella mayonii"	"Borrelia mayonii"	"Gupta, 2020"	3
-"Borreliella sinica"	"Borrelia sinica"	"Adeolu et al., 2015"	3
-"Borreliella spielmanii"	"Borrelia spielmanii"	"Adeolu et al., 2015"	3
-"Borreliella valaisiana"	"Borrelia valaisiana"	"Adeolu et al., 2018"	3
-"Borreliella yangtzensis"	"Borrelia yangtzensis"	"Gupta, 2020"	3
+"Borreliella bavariensis"	"Borrelia garinii bavariensis"	"Adeolu et al., 2015"	2
+"Borreliella bissettiae"	"Borrelia bissettiae"	"Gupta, 2020"	2
+"Borreliella burgdorferi"	"Borrelia burgdorferi"	"Adeolu et al., 2015"	2
+"Borreliella californiensis"	"Borrelia californiensis"	"Gupta, 2020"	2
+"Borreliella carolinensis"	"Borrelia carolinensis"	"Adeolu et al., 2015"	2
+"Borreliella garinii"	"Borrelia garinii"	"Adeolu et al., 2015"	2
+"Borreliella japonica"	"Borrelia japonica"	"Adeolu et al., 2015"	2
+"Borreliella kurtenbachii"	"Borrelia kurtenbachii"	"Adeolu et al., 2015"	2
+"Borreliella lanei"	"Borrelia lanei"	"Gupta, 2020"	2
+"Borreliella mayonii"	"Borrelia mayonii"	"Gupta, 2020"	2
+"Borreliella sinica"	"Borrelia sinica"	"Adeolu et al., 2015"	2
+"Borreliella spielmanii"	"Borrelia spielmanii"	"Adeolu et al., 2015"	2
+"Borreliella valaisiana"	"Borrelia valaisiana"	"Adeolu et al., 2018"	2
+"Borreliella yangtzensis"	"Borrelia yangtzensis"	"Gupta, 2020"	2
 "Botryonipha aurantiaca"	"Nectria aurantiaca"	"Kuntze, 1891"	2
 "Botryonipha flavipes"	"Trichoderma flavipes"	"Kuntze, 1891"	2
 "Botryopyle setosa"	"Amphimelissa setosa"	"Cleve, 1899"	3
@@ -1857,9 +1857,9 @@
 "Buliminoides curta"	"Seiglieina curta"	"Seiglie, 1965"	3
 "Buliminoides laevigata"	"Fredsmithia laevigata"	"Seiglie, 1964"	3
 "Buliminoides milletti"	"Floresina milletti"	"Cushman, 1933"	3
-"Buliminus mantongensis"	"Giardia mantongensis"	"Kobelt, 1899"	3
-"Buliminus pharangensis"	"Giardia pharangensis"	"Dautzenberg et al., 1905"	3
-"Bulimus siamensis"	"Giardia siamensis"	"Redfield, 1853"	3
+"Buliminus mantongensis"	"Giardia mantongensis"	"Kobelt, 1899"	2
+"Buliminus pharangensis"	"Giardia pharangensis"	"Dautzenberg et al., 1905"	2
+"Bulimus siamensis"	"Giardia siamensis"	"Redfield, 1853"	2
 "Bulla ovum"	"Ovum ovum"	"Linnaeus, 1758"	3
 "Bullera aurantiaca"	"Dioszegia aurantiaca"	"Johri et al., 1984"	3
 "Bullera begoniae"	"Bulleribasidium begoniae"	"Nakase et al., 2004"	3
@@ -2009,7 +2009,7 @@
 "Caliciopsis calicioides"	"Exophiala calicioides"	"Fitzp, 1920"	2
 "Calidifontibacillus azotoformans"	"Schinkia azotoformans"	"Adiguzel et al., 2020"	2
 "Calidifontibacillus oryziterrae"	"Schinkia oryziterrae"	"Adiguzel et al., 2020"	2
-"Calliphora bicolor"	"Lucilia bicolor"	"Macquart, 1843"	3
+"Calliphora bicolor"	"Lucilia bicolor"	"Macquart, 1843"	2
 "Calomyxa longifila"	"Minakatella longifila"	"LGKrieglst, 1990"	3
 "Calonectria calami"	"Nectria calami"	"Henn et al., 1900"	2
 "Calonectria citrinoaurantia"	"Nectria citrinoaurantia"	"Sacc, 1883"	2
@@ -2302,7 +2302,7 @@
 "Cavostelium bisporum"	"Echinostelium bisporum"	"LSOlive et al., 1966"	3
 "Celeribacter manganoxidans"	"Pacificitalea manganoxidans"	"Wang et al., 2015"	2
 "Cellanthus biperforatus"	"Elphidium biperforatus"	"Whittaker et al., 1979"	3
-"Cellia pretoriensis"	"Anopheles pretoriensis"	"Gough, 1910"	3
+"Cellia pretoriensis"	"Anopheles pretoriensis"	"Gough, 1910"	2
 "Cellulomonas cartae"	"Cellulosimicrobium cellulans"	"Stackebrandt et al., 1980"	2
 "Cellulomonas cellulans"	"Cellulosimicrobium cellulans"	"Stackebrandt et al., 1988"	2
 "Cellulomonas fermentans"	"Actinotalea fermentans"	"Bagnara et al., 1985"	2
@@ -2522,11 +2522,11 @@
 "Chlamydonella distyla"	"Wilbertella distyla"	"Jankowski, 2007"	3
 "Chlamydonella polonica"	"Chlamydonellopsis polonica"	"Foissner et al., 1981"	3
 "Chlamydonella stricta"	"Wilbertiella stricta"	"Deroux, 1976"	3
-"Chlamydophila abortus"	"Chlamydia abortus"	"Everett et al., 1999"	3
-"Chlamydophila felis"	"Chlamydia felis"	"Everett et al., 1999"	3
-"Chlamydophila pecorum"	"Chlamydia pecorum"	"Everett et al., 1999"	3
-"Chlamydophila pneumoniae"	"Chlamydia pneumoniae"	"Everett et al., 1999"	3
-"Chlamydophila psittaci"	"Chlamydia psittaci"	"Everett et al., 1999"	3
+"Chlamydophila abortus"	"Chlamydia abortus"	"Everett et al., 1999"	2
+"Chlamydophila felis"	"Chlamydia felis"	"Everett et al., 1999"	2
+"Chlamydophila pecorum"	"Chlamydia pecorum"	"Everett et al., 1999"	2
+"Chlamydophila pneumoniae"	"Chlamydia pneumoniae"	"Everett et al., 1999"	2
+"Chlamydophila psittaci"	"Chlamydia psittaci"	"Everett et al., 1999"	2
 "Chlamydotomus beigelii"	"Geotrichum beigelii"	"Trevis, 1879"	3
 "Chlamydozyma pulcherrima"	"Metschnikowia pulcherrima"	"Wick, 1964"	3
 "Chlamydozyma reukaufii"	"Metschnikowia reukaufii"	"Wick, 1964"	3
@@ -2599,8 +2599,8 @@
 "Chrysalogonium piramidale"	"Acostina piramidale"	"Acosta, 1940"	3
 "Chryseobacterium arothri"	"Chryseobacterium hominis"	"Campbell et al., 2008"	2
 "Chryseobacterium greenlandense"	"Chryseobacterium aquaticum greenlandense"	"Loveland-Curtze et al., 2016"	2
-"Chryseobacterium meningosepticum"	"Elizabethkingia meningoseptica"	"Vandamme et al., 1994"	3
-"Chryseobacterium miricola"	"Elizabethkingia miricola"	"Li et al., 2004"	3
+"Chryseobacterium meningosepticum"	"Elizabethkingia meningoseptica"	"Vandamme et al., 1994"	2
+"Chryseobacterium miricola"	"Elizabethkingia miricola"	"Li et al., 2004"	2
 "Chryseomonas"	"Pseudomonas"	"Holmes et al., 1987"	1
 "Chryseomonas luteola"	"Pseudomonas luteola"	"Holmes et al., 1987"	1
 "Chryseomonas polytricha"	"Pseudomonas luteola"	"Holmes et al., 1986"	1
@@ -3331,11 +3331,11 @@
 "Cucurbitaria urceolus"	"Nectria urceolus"	"Kuntze, 1898"	2
 "Cucurbitaria uredinicola"	"Nectria uredinicola"	"Kuntze, 1898"	2
 "Cucurbitaria verrucosa"	"Nectria verrucosa"	"Kuntze, 1898"	2
-"Culex auratus"	"Aedes auratus"	"Leicester, 1908"	3
-"Culex sticticus"	"Aedes sticticus"	"Meigen, 1838"	3
-"Culex sudanensis"	"Aedes sudanensis"	"Theobald, 1911"	3
-"Culex sylvaticus"	"Aedes sylvaticus"	"Meigen, 1818"	3
-"Culicada annulipes"	"Aedes annulipes"	"Taylor, 1914"	3
+"Culex auratus"	"Aedes auratus"	"Leicester, 1908"	2
+"Culex sticticus"	"Aedes sticticus"	"Meigen, 1838"	2
+"Culex sudanensis"	"Aedes sudanensis"	"Theobald, 1911"	2
+"Culex sylvaticus"	"Aedes sylvaticus"	"Meigen, 1818"	2
+"Culicada annulipes"	"Aedes annulipes"	"Taylor, 1914"	2
 "Cuneolina angusta"	"Textulariella angusta"	"Cushman, 1919"	3
 "Cunninghamia infundibulifera"	"Choanephora infundibulifera"	"Curr, 1873"	3
 "Cupravidus yeoncheonense"	"Cupriavidus yeoncheonensis"	"Singh et al., 2015"	2
@@ -3456,11 +3456,11 @@
 "Cytophaga diffluens"	"Persicobacter diffluens"	"Reichenbach, 1989"	3
 "Cytophaga fermentans"	"Saccharicrinis fermentans"	"Bachmann, 1955"	3
 "Cytophaga flevensis"	"Flavobacterium flevense"	"Van der Meulen et al., 1974"	2
-"Cytophaga heparina"	"Pedobacter heparinus"	"Christensen, 1980"	3
+"Cytophaga heparina"	"Pedobacter heparinus"	"Christensen, 1980"	2
 "Cytophaga johnsonae"	"Flavobacterium johnsoniae"	"Stanier, 1947"	2
 "Cytophaga latercula"	"Aquimarina latercula"	"Lewin, 1969"	3
 "Cytophaga lytica"	"Cellulophaga lytica"	"Lewin, 1969"	3
-"Cytophaga marina"	"Tenacibaculum maritimum"	"Reichenbach, 1989"	3
+"Cytophaga marina"	"Tenacibaculum maritimum"	"Reichenbach, 1989"	2
 "Cytophaga marinoflava"	"Leeuwenhoekiella marinoflava"	"Reichenbach, 1989"	3
 "Cytophaga pectinovora"	"Flavobacterium pectinovorum"	"Reichenbach, 1989"	2
 "Cytophaga psychrophila"	"Flavobacterium psychrophilum"	"Reichenbach, 1989"	2
@@ -3514,11 +3514,11 @@
 "Defluviimonas pyrenivorans"	"Acidimangrovimonas pyrenivorans"	"Zhang et al., 2018"	2
 "Dehalospirillum"	"Sulfurospirillum"	"Scholz-Muramatsu et al., 2002"	2
 "Dehalospirillum multivorans"	"Sulfurospirillum multivorans"	"Scholz-Muramatsu et al., 2002"	2
-"Deinobacter"	"Deinococcus"	"Oyaizu et al., 1987"	3
-"Deinobacter grandis"	"Deinococcus grandis"	"Oyaizu et al., 1987"	3
+"Deinobacter"	"Deinococcus"	"Oyaizu et al., 1987"	2
+"Deinobacter grandis"	"Deinococcus grandis"	"Oyaizu et al., 1987"	2
 "Deinococcus erythromyxa"	"Kocuria rosea"	"Brooks et al., 1981"	2
-"Deinococcus mumbaiensis"	"Deinococcus ficus"	"Shashidhar et al., 2006"	3
-"Deinococcus xibeiensis"	"Deinococcus wulumuqiensis"	"Wang et al., 2010"	3
+"Deinococcus mumbaiensis"	"Deinococcus ficus"	"Shashidhar et al., 2006"	2
+"Deinococcus xibeiensis"	"Deinococcus wulumuqiensis"	"Wang et al., 2010"	2
 "Dekkeromyces aestuarii"	"Kluyveromyces aestuarii"	"Kock-Krat, 1982"	3
 "Dekkeromyces delphensis"	"Nakaseomyces delphensis"	"Novak et al., 1961"	3
 "Dekkeromyces dobzhanskii"	"Kluyveromyces dobzhanskii"	"Santa Maria et al., 1970"	3
@@ -3745,7 +3745,7 @@
 "Deuterammina williamsoni"	"Lepidodeuterammina williamsoni"	"Bronnimann et al., 1988"	3
 "Devosia nitraria"	"Devosia nitrariae"	"Xu et al., 2018"	2
 "Devosia subaequoris"	"Devosia soli"	"Lee, 2007"	2
-"Dexiogonimus ciureanus"	"Metagonimus ciureanus"	"Witenberg, 1929"	3
+"Dexiogonimus ciureanus"	"Metagonimus ciureanus"	"Witenberg, 1929"	2
 "Dexiotricha centralis"	"Dexiotrichides centralis"	"Stokes, 1885"	3
 "Diacanthocapsa brevithorax"	"Theocapsomma brevithorax"	"Dumitrica, 1970"	3
 "Diachaeella bulbillosa"	"Diachea bulbillosa"	"Hohn, 1909"	3
@@ -3772,11 +3772,11 @@
 "Diaphorobacter polyhydroxybutyrativorans"	"Diaphorobacter nitroreducens"	"Qiu et al., 2015"	2
 "Diatoma anceps"	"Meridion anceps"	"Kirchn"	3
 "Diatoma hyalina"	"Fragilaria hyalina"	"Kutzing"	3
-"Dibothriocephalus archeri"	"Diphyllobothrium archeri"	"Leiper et al., 1914"	3
-"Dibothriocephalus hians"	"Diphyllobothrium hians"	"Luhe, 1899"	3
-"Dibothriocephalus lashleyi"	"Diphyllobothrium lashleyi"	"Leiper et al., 1914"	3
-"Dibothriocephalus pygoscelis"	"Diphyllobothrium pygoscelis"	"Rennie et al., 1912"	3
-"Dibothriocephalus schistochilus"	"Diphyllobothrium schistochilus"	"Germanos, 1895"	3
+"Dibothriocephalus archeri"	"Diphyllobothrium archeri"	"Leiper et al., 1914"	2
+"Dibothriocephalus hians"	"Diphyllobothrium hians"	"Luhe, 1899"	2
+"Dibothriocephalus lashleyi"	"Diphyllobothrium lashleyi"	"Leiper et al., 1914"	2
+"Dibothriocephalus pygoscelis"	"Diphyllobothrium pygoscelis"	"Rennie et al., 1912"	2
+"Dibothriocephalus schistochilus"	"Diphyllobothrium schistochilus"	"Germanos, 1895"	2
 "Dicaeoma brassicae"	"Alternaria brassicae"	"Kuntze, 1898"	2
 "Dichotomomyces cejpii"	"Aspergillus cejpii"	"Scott, 1970"	2
 "Dickeya dieffenbachiae"	"Dickeya dadantii dieffenbachiae"	"Samson et al., 2005"	1
@@ -3938,7 +3938,7 @@
 "Diplodina pedicularis"	"Leptosphaeria pedicularis"	"Lind, 1924"	2
 "Diplodinium lunula"	"Gymnodinium lunula"	"Klebs, 1912"	3
 "Diplodinium uncinata"	"Blepharocorys uncinata"	"Fiorentini, 1890"	3
-"Diplogonoporus balaenopterae"	"Diphyllobothrium balaenopterae"	"Lonnberg, 1892"	3
+"Diplogonoporus balaenopterae"	"Diphyllobothrium balaenopterae"	"Lonnberg, 1892"	2
 "Diplophrys stercorea"	"Sorodiplophrys stercorea"	"Cienk, 1876"	3
 "Diplophysa saprolegniae"	"Olpidiopsis saprolegniae"	"Schrot, 1886"	3
 "Diploplenodomus piskorzii"	"Phoma piskorzii"	"Petr, 1923"	2
@@ -4105,7 +4105,7 @@
 "Drechslera spicifera"	"Curvularia spicifera"	"Arx, 1975"	2
 "Drechslera subpapendorfii"	"Curvularia subpapendorfii"	"Mouch, 1975"	2
 "Drechslera tripogonis"	"Curvularia tripogonis"	"Patil et al., 1972"	2
-"Drepanidotaenia dusmeti"	"Hymenolepis dusmeti"	"Lopez-Neyra, 1942"	3
+"Drepanidotaenia dusmeti"	"Hymenolepis dusmeti"	"Lopez-Neyra, 1942"	2
 "Drepanomonas simulans"	"Microthorax simulans"	"Kahl, 1926"	3
 "Drulanta edenshawi"	"Parahsuum edenshawi"	"Carter, 1988"	3
 "Drulanta mostleri"	"Parahsuum mostleri"	"Yeh, 1987"	3
@@ -4174,8 +4174,8 @@
 "Eidamia viridescens"	"Trichoderma viridescens"	"Horne et al., 1923"	2
 "Eilohedra weddellensis"	"Alabaminella weddellensis"	"Earland, 1936"	3
 "Electothigma acuminatus"	"Metopus acuminatus"	"Jankowski, 1967"	3
-"Elizabethkingia anophelis endophytica"	"Elizabethkingia anophelis"	"Garcia-Lopez et al., 2020"	3
-"Elizabethkingia endophytica"	"Elizabethkingia anophelis"	"Kampfer et al., 2015"	3
+"Elizabethkingia anophelis endophytica"	"Elizabethkingia anophelis"	"Garcia-Lopez et al., 2020"	2
+"Elizabethkingia endophytica"	"Elizabethkingia anophelis"	"Kampfer et al., 2015"	2
 "Elkelangia"	"Novosphingopyxis"	"Hordt et al., 2020"	2
 "Elkelangia baekryungensis"	"Novosphingopyxis baekryungensis"	"Hordt et al., 2020"	2
 "Ellipsolagena bidens"	"Parafissurina bidens"	"Cushman, 1930"	3
@@ -4255,7 +4255,7 @@
 "Emericella spectabilis"	"Aspergillus spectabilis"	"Chr, 1978"	2
 "Emericella unguis"	"Aspergillus unguis"	"Malloch et al., 1972"	2
 "Emmonsia crescens"	"Ajellomyces crescens"	"Emmons et al., 1960"	3
-"Empedobacter falsenii"	"Wautersiella falsenii"	"Zhang et al., 2014"	3
+"Empedobacter falsenii"	"Wautersiella falsenii"	"Zhang et al., 2014"	2
 "Enantiocristellaria navicula"	"Saracenaria navicula"	"DOrbigny, 1840"	3
 "Encephalitozoon cuniculi"	"Nosema cuniculi"	"Levaditi et al., 1923"	3
 "Encephalitozoon ixodis"	"Unikaryon ixodis"	"Weiser et al., 1975"	3
@@ -4341,7 +4341,7 @@
 "Enteridium splendens"	"Reticularia splendens"	"TMacbr, 1899"	3
 "Enterobacter aerogenes"	"Klebsiella aerogenes"	"Hormaeche et al., 1960"	1
 "Enterobacter agglomerans"	"Pantoea agglomerans"	"Ewing et al., 1972"	1
-"Enterobacter amnigenus"	"Lelliottia amnigena"	"Izard et al., 1981"	1
+"Enterobacter amnigenus"	"Lelliottia amnigena"	"Izard et al., 1981"	2
 "Enterobacter arachidis"	"Kosakonia arachidis"	"Madhaiyan et al., 2010"	1
 "Enterobacter cowanii"	"Kosakonia cowanii"	"Inoue et al., 2001"	1
 "Enterobacter dissolvens"	"Enterobacter cloacae dissolvens"	"Brenner et al., 1988"	1
@@ -4352,7 +4352,7 @@
 "Enterobacter massiliensis"	"Metakosakonia massiliensis"	"Lagier et al., 2014"	
 "Enterobacter massiliensis"	"Phytobacter massiliensis"	"Lagier et al., 2014"	1
 "Enterobacter muelleri"	"Enterobacter asburiae"	"Kampfer et al., 2015"	1
-"Enterobacter nimipressuralis"	"Lelliottia nimipressuralis"	"Brenner et al., 1988"	1
+"Enterobacter nimipressuralis"	"Lelliottia nimipressuralis"	"Brenner et al., 1988"	2
 "Enterobacter oligotrophica"	"Enterobacter oligotrophicus"	"Akita et al., 2020"	1
 "Enterobacter oryzae"	"Kosakonia oryzae"	"Peng et al., 2009"	1
 "Enterobacter oryzendophyticus"	"Kosakonia oryzendophytica"	"Hardoim et al., 2015"	1
@@ -4527,7 +4527,7 @@
 "Erwinia herbicola"	"Pantoea agglomerans"	"Dye, 1964"	1
 "Erwinia milletiae"	"Pantoea agglomerans"	"Magrou, 1937"	1
 "Erwinia nigrifluens"	"Brenneria nigrifluens"	"Wilson et al., 1957"	1
-"Erwinia nimipressuralis"	"Lelliottia nimipressuralis"	"Dye, 1969"	1
+"Erwinia nimipressuralis"	"Lelliottia nimipressuralis"	"Dye, 1969"	2
 "Erwinia paradisiaca"	"Dickeya paradisiaca"	"Fernandez-Borrero et al., 1970"	1
 "Erwinia persicinus"	"Erwinia persicina"	"Hao et al., 1990"	1
 "Erwinia quercina"	"Lonsdalea quercina"	"Hildebrand et al., 1967"	1
@@ -4844,33 +4844,33 @@
 "Flaviramulus ichthyoenteri"	"Wocania ichthyoenteri"	"Zhang et al., 2013"	3
 "Flavirhabdus"	"Lacinutrix"	"Shakeela et al., 2015"	3
 "Flavirhabdus iliipiscaria"	"Lacinutrix iliipiscaria"	"Shakeela et al., 2015"	3
-"Flavobacterium anatoliense"	"Myroides anatoliensis"	"Kacagan et al., 2013"	3
+"Flavobacterium anatoliense"	"Myroides anatoliensis"	"Kacagan et al., 2013"	2
 "Flavobacterium balustinum"	"Chryseobacterium balustinum"	"Harrison, 1929"	2
 "Flavobacterium bomensis"	"Flavobacterium bomense"	"Liu et al., 2019"	2
 "Flavobacterium branchiophila"	"Flavobacterium branchiophilum"	"Wakabayashi et al., 1989"	2
-"Flavobacterium breve"	"Empedobacter brevis"	"Holmes et al., 1982"	3
+"Flavobacterium breve"	"Empedobacter brevis"	"Holmes et al., 1982"	2
 "Flavobacterium capsulatum"	"Novosphingobium capsulatum"	"Leifson, 1962"	2
-"Flavobacterium ceti"	"Myroides ceti"	"Vela et al., 2013"	3
-"Flavobacterium cloacae"	"Myroides cloacae"	"Liu et al., 2017"	3
+"Flavobacterium ceti"	"Myroides ceti"	"Vela et al., 2013"	2
+"Flavobacterium cloacae"	"Myroides cloacae"	"Liu et al., 2017"	2
 "Flavobacterium daemonensis"	"Flavobacterium daemonense"	"Ngo et al., 2015"	2
 "Flavobacterium esteraromaticum"	"Microbacterium esteraromaticum"	"Bergey et al., 1930"	2
-"Flavobacterium ferrugineum"	"Terrimonas ferruginea"	"Sickles et al., 1934"	3
+"Flavobacterium ferrugineum"	"Terrimonas ferruginea"	"Sickles et al., 1934"	2
 "Flavobacterium gleum"	"Chryseobacterium gleum"	"Holmes et al., 1984"	2
 "Flavobacterium gondwanense"	"Psychroflexus gondwanensis"	"Dobson et al., 1993"	3
 "Flavobacterium halmephilium"	"Halomonas halmophila"	"Elazari-Volcani, 1940"	1
 "Flavobacterium halmophilum"	"Halomonas halmophila"	"Corrig Elazari-Volcani, 1940"	1
-"Flavobacterium heparinum"	"Pedobacter heparinus"	"Payza et al., 1956"	3
+"Flavobacterium heparinum"	"Pedobacter heparinus"	"Payza et al., 1956"	2
 "Flavobacterium indologenes"	"Chryseobacterium indologenes"	"Yabuuchi et al., 1983"	2
 "Flavobacterium indoltheticum"	"Chryseobacterium indoltheticum"	"Campbell et al., 1951"	2
 "Flavobacterium jejuensis"	"Flavobacterium jejuense"	"Park et al., 2016"	2
 "Flavobacterium johnsonae"	"Flavobacterium johnsoniae"	"Bernardet et al., 1996"	2
 "Flavobacterium kyungheensis"	"Flavobacterium kyungheense"	"Son et al., 2014"	2
 "Flavobacterium marinotypicum"	"Microbacterium maritypicum"	"ZoBell et al., 1944"	2
-"Flavobacterium marinum"	"Myroides aquimaris"	"Song et al., 2013"	3
-"Flavobacterium meningosepticum"	"Elizabethkingia meningoseptica"	"King, 1959"	3
-"Flavobacterium mizutaii"	"Sphingobacterium mizutaii"	"Holmes et al., 1988"	3
-"Flavobacterium multivorum"	"Sphingobacterium multivorum"	"Holmes et al., 1981"	3
-"Flavobacterium odoratum"	"Myroides odoratus"	"Stutzer, 1929"	3
+"Flavobacterium marinum"	"Myroides aquimaris"	"Song et al., 2013"	2
+"Flavobacterium meningosepticum"	"Elizabethkingia meningoseptica"	"King, 1959"	2
+"Flavobacterium mizutaii"	"Sphingobacterium mizutaii"	"Holmes et al., 1988"	2
+"Flavobacterium multivorum"	"Sphingobacterium multivorum"	"Holmes et al., 1981"	2
+"Flavobacterium odoratum"	"Myroides odoratus"	"Stutzer, 1929"	2
 "Flavobacterium okeanokoites"	"Planomicrobium okeanokoites"	"ZoBell et al., 1944"	
 "Flavobacterium okeanokoites"	"Planococcus okeanokoites"	"ZoBell et al., 1944"	2
 "Flavobacterium qiangtangensis"	"Flavobacterium qiangtangense"	"Huang et al., 2015"	2
@@ -4878,12 +4878,12 @@
 "Flavobacterium salegens"	"Salegentibacter salegens"	"Dobson et al., 1993"	3
 "Flavobacterium scophthalmum"	"Chryseobacterium scophthalmum"	"Mudarris et al., 1994"	2
 "Flavobacterium spartansii"	"Flavobacterium tructae"	"Loch et al., 2019"	2
-"Flavobacterium spiritivorum"	"Sphingobacterium spiritivorum"	"Holmes et al., 1982"	3
+"Flavobacterium spiritivorum"	"Sphingobacterium spiritivorum"	"Holmes et al., 1982"	2
 "Flavobacterium tangerina"	"Flavobacterium tangerinum"	"Li et al., 2020"	2
-"Flavobacterium thalpophilum"	"Sphingobacterium thalpophilum"	"Holmes et al., 1983"	3
+"Flavobacterium thalpophilum"	"Sphingobacterium thalpophilum"	"Holmes et al., 1983"	2
 "Flavobacterium uliginosum"	"Zobellia uliginosa"	"ZoBell et al., 1944"	3
 "Flavobacterium viscosus"	"Flavobacterium viscosum"	"Li et al., 2020"	2
-"Flavobacterium yabuuchiae"	"Sphingobacterium spiritivorum"	"Holmes et al., 1988"	3
+"Flavobacterium yabuuchiae"	"Sphingobacterium spiritivorum"	"Holmes et al., 1988"	2
 "Flavobacterium zhairuonensis"	"Flavobacterium zhairuonense"	"Debnath et al., 2020"	2
 "Flectobacillus glomeratus"	"Polaribacter glomeratus"	"McGuire et al., 1988"	3
 "Flectobacillus marinus"	"Cyclobacterium marinum"	"Borrall et al., 1978"	3
@@ -4895,8 +4895,8 @@
 "Flexibacter filiformis"	"Chitinophaga filiformis"	"Reichenbach, 1989"	3
 "Flexibacter japonensis"	"Chitinophaga japonensis"	"Fujita et al., 1997"	3
 "Flexibacter litoralis"	"Bernardetia litoralis"	"Lewin, 1969"	3
-"Flexibacter maritimus"	"Tenacibaculum maritimum"	"Wakabayashi et al., 1989"	3
-"Flexibacter ovolyticus"	"Tenacibaculum ovolyticum"	"Hansen et al., 1992"	3
+"Flexibacter maritimus"	"Tenacibaculum maritimum"	"Wakabayashi et al., 1989"	2
+"Flexibacter ovolyticus"	"Tenacibaculum ovolyticum"	"Hansen et al., 1992"	2
 "Flexibacter polymorphus"	"Garritya polymorpha"	"Lewin, 1974"	3
 "Flexibacter psychrophilus"	"Flavobacterium psychrophilum"	"Bernardet et al., 1989"	2
 "Flexibacter roseolus"	"Hugenholtzia roseola"	"Lewin et al., 2016"	3
@@ -5338,7 +5338,7 @@
 "Gordonia rubropertinctus"	"Gordonia rubripertincta"	"Stackebrandt et al., 1989"	2
 "Gordonibacter faecihominis"	"Gordonibacter urolithinfaciens"	"Jin et al., 2015"	2
 "Gottfriedia acidiceler"	"Gottfriedia acidiceleris"	"Gupta et al., 2020"	2
-"Grabhamia australis"	"Aedes australis"	"Strickland, 1911"	3
+"Grabhamia australis"	"Aedes australis"	"Strickland, 1911"	2
 "Grahamella"	"Bartonella"	"Ristic et al., 1984"	2
 "Grahamella peromysci"	"Bartonella peromysci"	"Ristic et al., 1984"	2
 "Grahamella talpae"	"Bartonella talpae"	"Ristic et al., 1984"	2
@@ -5486,20 +5486,20 @@
 "Haloarcobacter ebronensis"	"Halarcobacter ebronensis"	"Perez-Cataluna et al., 2019"	
 "Haloarcobacter ebronensis"	"Arcobacter ebronensis"	"Perez-Cataluna et al., 2019"	2
 "Haloarcula mukohataei"	"Halomicrobium mukohataei"	"Ihara et al., 1997"	3
-"Halobacterium cutirubrum"	"Halobacterium salinarum"	"Elazari-Volcani, 1957"	3
+"Halobacterium cutirubrum"	"Halobacterium salinarum"	"Elazari-Volcani, 1957"	2
 "Halobacterium denitrificans"	"Haloferax denitrificans"	"Tomlinson et al., 1986"	3
 "Halobacterium distributum"	"Halorubrum distributum"	"Zvyagintseva et al., 1989"	3
 "Halobacterium distributus"	"Halorubrum distributum"	"Zvyagintseva et al., 1989"	3
-"Halobacterium halobium"	"Halobacterium salinarum"	"Elazari-Volcani, 1957"	3
+"Halobacterium halobium"	"Halobacterium salinarum"	"Elazari-Volcani, 1957"	2
 "Halobacterium lacusprofundi"	"Halorubrum lacusprofundi"	"Franzmann et al., 1989"	3
 "Halobacterium mediterranei"	"Haloferax mediterranei"	"Rodriguez-Valera et al., 1983"	3
 "Halobacterium pharaonis"	"Natronomonas pharaonis"	"Soliman et al., 1983"	3
-"Halobacterium piscisalsi"	"Halobacterium salinarum"	"Yachai et al., 2008"	3
+"Halobacterium piscisalsi"	"Halobacterium salinarum"	"Yachai et al., 2008"	2
 "Halobacterium saccharovorum"	"Halorubrum saccharovorum"	"Tomlinson et al., 1977"	3
-"Halobacterium salinarium"	"Halobacterium salinarum"	"Elazari-Volcani, 1957"	3
+"Halobacterium salinarium"	"Halobacterium salinarum"	"Elazari-Volcani, 1957"	2
 "Halobacterium sodomense"	"Halorubrum sodomense"	"Oren, 1983"	3
 "Halobacterium trapanicum"	"Halorubrum trapanicum"	"Elazari-Volcani, 1957"	3
-"Halobacterium vallismortis"	"Haloarcula vallismortis"	"Gonzalez et al., 1979"	3
+"Halobacterium vallismortis"	"Haloarcula vallismortis"	"Gonzalez et al., 1979"	2
 "Halobacterium volcanii"	"Haloferax volcanii"	"Mullakhanbhai et al., 1975"	3
 "Halobacteroides acetoethylicus"	"Halanaerobium acetethylicum"	"Rengpipat et al., 1989"	2
 "Halobacteroides lacunaris"	"Halanaerobacter lacunarum"	"Zhilina et al., 1992"	2
@@ -5780,7 +5780,7 @@
 "Hendersonia pinicola"	"Hendersonula pinicola"	"Trotter, 1972"	2
 "Hendersonia symploci"	"Hendersonula symploci"	"Berk et al., 1873"	2
 "Hennebertia ovalis"	"Wardomyces ovalis"	"Morelet, 1969"	3
-"Hepatiarius longissimus"	"Opisthorchis longissimus"	"Feizullaev, 1961"	3
+"Hepatiarius longissimus"	"Opisthorchis longissimus"	"Feizullaev, 1961"	2
 "Heptameria acuta"	"Leptosphaeria acuta"	"Cooke, 1889"	2
 "Heptameria albopunctata"	"Leptosphaeria albopunctata"	"Cooke, 1889"	2
 "Heptameria artemisiae"	"Leptosphaeria artemisiae"	"Cooke, 1889"	2
@@ -5853,7 +5853,7 @@
 "Heteroconium chaetospira"	"Cladophialophora chaetospira"	"Ellis, 1976"	2
 "Heterolepa haidingeri"	"Cibicides haidingeri"	"DOrbigny, 1846"	3
 "Heteropatellina frustratiformis"	"Ungulatelloides frustratiformis"	"McCulloch, 1977"	3
-"Heterophyes yokogawai"	"Metagonimus yokogawai"	"Katsurada, 1912"	3
+"Heterophyes yokogawai"	"Metagonimus yokogawai"	"Katsurada, 1912"	2
 "Heterospiroloculina bikiniensis"	"Inaequalina bikiniensis"	"McCulloch, 1977"	3
 "Heterospiroloculina culebraensis"	"Inaequalina culebraensis"	"McCulloch, 1977"	3
 "Heterosporium algarum"	"Cladosporium algarum"	"Cooke et al., 1890"	2
@@ -5972,8 +5972,8 @@
 "Huaishuia"	"Celeribacter"	"Wang et al., 2012"	2
 "Huaishuia halophila"	"Celeribacter halophilus"	"Wang et al., 2012"	2
 "Hughesiella euricoi"	"Ceratocystis euricoi"	"Bat et al., 1956"	3
-"Hulecoeteomyia fluviatilis"	"Aedes fluviatilis"	"Leicester, 1908"	3
-"Hulecoeteomyia milsoni"	"Aedes milsoni"	"Taylor, 1916"	3
+"Hulecoeteomyia fluviatilis"	"Aedes fluviatilis"	"Leicester, 1908"	2
+"Hulecoeteomyia milsoni"	"Aedes milsoni"	"Taylor, 1916"	2
 "Humicoccus"	"Nakamurella"	"Yoon et al., 2007"	2
 "Humicoccus flavidus"	"Nakamurella flavida"	"Yoon et al., 2007"	2
 "Humicola minima"	"Ochroconis minima"	"Fassat, 1967"	2
@@ -6942,7 +6942,7 @@
 "Leifsonia pindariensis"	"Microterricola pindariensis"	"Reddy et al., 2008"	2
 "Leiotrocha serpularum"	"Cyclochaeta serpularum"	"Fabre-Domergue, 1888"	3
 "Leisingera nanhaiensis"	"Sedimentitalea nanhaiensis"	"Sun et al., 2014"	2
-"Lelliottia aquatilis"	"Lelliottia jeotgali"	"Kampfer et al., 2018"	1
+"Lelliottia aquatilis"	"Lelliottia jeotgali"	"Kampfer et al., 2018"	2
 "Lembus armatus"	"Philasterides armatus"	"Kahl, 1926"	3
 "Lembus kenti"	"Cohnilembus kenti"	"Kahl, 1931"	3
 "Lembus pusillus"	"Pseudocohnilembus pusillus"	"Quennerstedt, 1869"	3
@@ -7208,7 +7208,7 @@
 "Lonsdalea quercina iberica"	"Lonsdalea iberica"	"Brady et al., 2012"	1
 "Lonsdalea quercina populi"	"Lonsdalea populi"	"Toth et al., 2013"	1
 "Lonsdalea quercina quercina"	"Lonsdalea quercina"	"Brady et al., 2012"	1
-"Loossia dobrogiensis"	"Metagonimus dobrogiensis"	"Ciurea, 1915"	3
+"Loossia dobrogiensis"	"Metagonimus dobrogiensis"	"Ciurea, 1915"	2
 "Lophocorys neatum"	"Lophocyrtis neatum"	"Sanfilippo, 1990"	3
 "Lophophyton gallinae"	"Microsporum gallinae"	"Matr et al., 1899"	3
 "Loxocephalus colpidiopsis"	"Dexiotricha colpidiopsis"	"Kahl, 1926"	3
@@ -7490,7 +7490,7 @@
 "Mesoflavibacter sabulilitoris"	"Mesoflavibacter zeaxanthinifaciens sabulilitoris"	"Park et al., 2014"	3
 "Mesomycoplasma molaris"	"Mesomycoplasma molare"	"Gupta et al., 2018"	3
 "Mesonia maritimus"	"Mesonia maritima"	"Sung et al., 2017"	3
-"Mesoplasma pleciae"	"Acholeplasma pleciae"	"Tully et al., 1994"	3
+"Mesoplasma pleciae"	"Acholeplasma pleciae"	"Tully et al., 1994"	2
 "Metacarinina charlesensis"	"Laticarinina charlesensis"	"McCulloch, 1977"	3
 "Metacarinina chathamensis"	"Laticarinina chathamensis"	"McCulloch, 1977"	3
 "Metacarinina hoodensis"	"Laticarinina hoodensis"	"McCulloch, 1977"	3
@@ -7882,7 +7882,7 @@
 "Monosporium sclerotiale"	"Scedosporium sclerotiale"	"Pepere, 1914"	3
 "Monosporium sepedonioides"	"Chrysosporium sepedonioides"	"Harz, 1872"	3
 "Moorella thermoautotrophica"	"Moorella thermoacetica"	"Collins et al., 1994"	2
-"Moraxella anatipestifer"	"Riemerella anatipestifer"	"Bruner et al., 1954"	3
+"Moraxella anatipestifer"	"Riemerella anatipestifer"	"Bruner et al., 1954"	2
 "Moraxella phenylpyruvica"	"Psychrobacter phenylpyruvicus"	"Bovre et al., 1967"	1
 "Moraxella urethralis"	"Oligella urethralis"	"Lautrop et al., 1970"	2
 "Morella entamoebae"	"Sphaerita entamoebae"	"Perez Reyes, 1964"	3
@@ -7898,7 +7898,7 @@
 "Mrazekia niphargi"	"Microsporidium niphargi"	"Poisson, 1924"	3
 "Mrazekia piscicola"	"Jirovecia piscicola"	"Cepede, 1924"	3
 "Mrazekia tetraspora"	"Scipionospora tetraspora"	"Leger et al., 1922"	3
-"Mucidus africanus"	"Aedes africanus"	"Theobald, 1901"	3
+"Mucidus africanus"	"Aedes africanus"	"Theobald, 1901"	2
 "Mucor angarensis"	"Circinella angarensis"	"Schostak, 1897"	3
 "Mucor arrhizus"	"Rhizopus arrhizus"	"Hagem, 1908"	2
 "Mucor assamensis"	"Hyphomucor assamensis"	"Mehrotra et al., 1970"	3
@@ -7926,7 +7926,7 @@
 "Muricauda antarctica"	"Muricauda taeanensis"	"Wu et al., 2013"	3
 "Muricauda lutea"	"Croceivirga lutea"	"Wang et al., 2017"	3
 "Muriicola lacisalsi"	"Maritimibacter lacisalsi"	"Wang et al., 2021"	2
-"Musca azurea"	"Lucilia azurea"	"Doleschall, 1858"	3
+"Musca azurea"	"Lucilia azurea"	"Doleschall, 1858"	2
 "Mya nitens"	"Ervilia nitens"	"Montagu, 1808"	3
 "Myceloblastanon albicans"	"Candida albicans"	"Ota, 1927"	2
 "Myceloblastanon guilliermondii"	"Meyerozyma guilliermondii"	"Ota, 1927"	3
@@ -8221,7 +8221,7 @@
 "Mycterotrix ovata"	"Maryna ovata"	"Gelei, 1950"	3
 "Myllocercion rhodanon"	"Schadelfusslerus rhodanon"	"Foreman, 1968"	3
 "Myrionecta rubrum"	"Mesodinium rubrum"	"Jankowski, 1976"	3
-"Myroides xuanwuensis"	"Myroides odoratimimus xuanwuensis"	"Zhang et al., 2014"	3
+"Myroides xuanwuensis"	"Myroides odoratimimus xuanwuensis"	"Zhang et al., 2014"	2
 "Myxococcus coralloides"	"Corallococcus coralloides"	"Thaxter, 1892"	2
 "Myxococcus disciformis"	"Archangium disciforme"	"Thaxter, 1904"	2
 "Myxococcus flavescens"	"Myxococcus virescens"	"Yamanaka et al., 1990"	2
@@ -8231,8 +8231,8 @@
 "Myxotrichum johnstonii"	"Gymnoascus johnstonii"	"Massee et al., 1902"	3
 "Myzocytium humicola"	"Myzocytiopsis humicola"	"Barron et al., 1975"	3
 "Myzocytium vermicola"	"Myzocytiopsis vermicola"	"Fisch, 1892"	3
-"Myzorhynchus minutus"	"Anopheles minutus"	"Theobald, 1903"	3
-"Myzorhynchus pallidus"	"Anopheles pallidus"	"Swellengrebel, 1919"	3
+"Myzorhynchus minutus"	"Anopheles minutus"	"Theobald, 1903"	2
+"Myzorhynchus pallidus"	"Anopheles pallidus"	"Swellengrebel, 1919"	2
 "Mzabimyces"	"Halopolyspora"	"Saker et al., 2015"	2
 "Mzabimyces algeriensis"	"Halopolyspora algeriensis"	"Saker et al., 2015"	2
 "Naematelia aurantia"	"Tremella aurantia"	"Burt, 1921"	3
@@ -9265,8 +9265,8 @@
 "Orcadella operculata"	"Licea operculata"	"Wingate, 1889"	3
 "Orcadella parasitica"	"Licea parasitica"	"Hagelst, 1942"	3
 "Orcadella pusilla"	"Licea pusilla"	"Hagelst, 1942"	3
-"Oribaculum"	"Porphyromonas"	"Moore et al., 1994"	3
-"Oribaculum catoniae"	"Porphyromonas catoniae"	"Moore et al., 1994"	3
+"Oribaculum"	"Porphyromonas"	"Moore et al., 1994"	2
+"Oribaculum catoniae"	"Porphyromonas catoniae"	"Moore et al., 1994"	2
 "Ornatispora frondicola"	"Stachybotrys frondicola"	"Hyde et al., 1999"	2
 "Ornatispora gamsii"	"Stachybotrys gamsii"	"Hyde et al., 1999"	2
 "Ornatispora nepalensis"	"Stachybotrys nepalensis"	"Whitton et al., 2012"	2
@@ -9602,7 +9602,7 @@
 "Pedobacter huanghensis"	"Daejeonella huanghensis"	"Qiu et al., 2014"	3
 "Pedobacter luteus"	"Daejeonella lutea"	"Oh et al., 2013"	3
 "Pedobacter oryzae"	"Daejeonella oryzae"	"Jeon et al., 2009"	3
-"Pedobacter piscium"	"Pedobacter antarcticus"	"Steyn et al., 2014"	3
+"Pedobacter piscium"	"Pedobacter antarcticus"	"Steyn et al., 2014"	2
 "Pedobacter ruber"	"Daejeonella rubra"	"Margesin et al., 2013"	3
 "Pedobacter saltans"	"Pseudopedobacter saltans"	"Steyn et al., 1998"	3
 "Pedobacter tournemirensis"	"Arcticibacter tournemirensis"	"Urios et al., 2013"	3
@@ -9828,7 +9828,7 @@
 "Petersenia andreei"	"Sirolpidium andreei"	"Sparrow, 1936"	3
 "Petersenia catenophlyctidis"	"Cornumyces catenophlyctidis"	"Sundaram, 1968"	3
 "Petersenia irregularis"	"Cornumyces irregularis"	"Sparrow, 1943"	3
-"Petraeus vignei"	"Giardia vignei"	"Rochebrune, 1882"	3
+"Petraeus vignei"	"Giardia vignei"	"Rochebrune, 1882"	2
 "Petriella boulangeri"	"Microascus boulangeri"	"Curzi, 1930"	3
 "Petriellidium boydii"	"Pseudallescheria boydii"	"Malloch, 1970"	2
 "Petriellidium desertorum"	"Scedosporium desertorum"	"Arx et al., 1973"	3
@@ -9850,8 +9850,8 @@
 "Phacellium geranii"	"Graphium geranii"	"Braun, 1993"	3
 "Phacellium ligulariae"	"Graphium ligulariae"	"Braun, 1993"	3
 "Phacellium trifolii"	"Graphium trifolii"	"Braun, 1993"	3
-"Phaenicia azurea"	"Lucilia azurea"	"Robineau-Desvoidy, 1863"	3
-"Phaenicia pallescens"	"Lucilia pallescens"	"Shannon, 1924"	3
+"Phaenicia azurea"	"Lucilia azurea"	"Robineau-Desvoidy, 1863"	2
+"Phaenicia pallescens"	"Lucilia pallescens"	"Shannon, 1924"	2
 "Phaenicosphaera mammilla"	"Hegleria mammilla"	"Sheng et al., 1985"	3
 "Phaeobacter aquaemixtae"	"Leisingera aquaemixtae"	"Park et al., 2014"	2
 "Phaeobacter arcticus"	"Pseudophaeobacter arcticus"	"Zhang et al., 2008"	2
@@ -9895,7 +9895,7 @@
 "Phloeophthora syringae"	"Phytophthora syringae"	"Kleb, 1906"	3
 "Phloeospora trifolii"	"Leptosphaeria trifolii"	"Cavara, 1878"	2
 "Phlyctospora persoonii"	"Elaphomyces persoonii"	"Corda, 1854"	3
-"Phocaeicola chinchillae"	"Phocaeicola sartorii"	"Garcia-Lopez et al., 2020"	3
+"Phocaeicola chinchillae"	"Phocaeicola sartorii"	"Garcia-Lopez et al., 2020"	2
 "Phoma acuta"	"Leptosphaeria acuta"	"Fuckel, 1870"	2
 "Phoma errabunda"	"Leptosphaeria errabunda"	"Desm, 1849"	2
 "Phoma macrocapsa"	"Leptosphaeria macrocapsa"	"Trail, 1886"	2
@@ -10127,7 +10127,7 @@
 "Plagiotricha camelus"	"Trichoda camelus"	"Bory, 1824"	3
 "Plagiotricha sinuata"	"Trichoda sinuata"	"Bory, 1824"	3
 "Plagiotricha succisa"	"Psilotricha succisa"	"Bory, 1824"	3
-"Planaria punctata"	"Fasciola punctata"	"Muller, 1776"	3
+"Planaria punctata"	"Fasciola punctata"	"Muller, 1776"	2
 "Planctomyces brasiliensis"	"Rubinisphaera brasiliensis"	"Schlesner, 1990"	3
 "Planctomyces limnophilus"	"Planctopirus limnophila"	"Hirsch et al., 1986"	3
 "Planctomyces maris"	"Gimesia maris"	"Bauld et al., 1980"	3
@@ -10432,8 +10432,8 @@
 "Porphyrobacter mercurialis"	"Croceibacterium mercuriale"	"Coil et al., 2016"	2
 "Porphyrobacter neustonensis"	"Erythrobacter neustonensis"	"Fuerst et al., 2020"	2
 "Porphyrobacter sanguineus"	"Erythrobacter sanguineus"	"Hiraishi et al., 2002"	2
-"Porphyromonas cansulci"	"Porphyromonas crevioricanis"	"Collins et al., 1994"	3
-"Porphyromonas salivosa"	"Porphyromonas macacae"	"Love et al., 1992"	3
+"Porphyromonas cansulci"	"Porphyromonas crevioricanis"	"Collins et al., 1994"	2
+"Porphyromonas salivosa"	"Porphyromonas macacae"	"Love et al., 1992"	2
 "Posadasia esteriformis"	"Coccidioides esteriformis"	"Canton, 1898"	3
 "Poseidonibacter lekithochrous"	"Arcobacter lekithochrous"	"Perez-Cataluna et al., 2019"	2
 "Pottsiocles hannae"	"Manuelophrya hannae"	"Guhl, 1985"	3
@@ -10450,7 +10450,7 @@
 "Prauserella flava"	"Prauserella salsuginis"	"Li et al., 2009"	2
 "Prevotella oulora"	"Prevotella oulorum"	"Shah et al., 1990"	2
 "Prevotella ruminicola brevis"	"Prevotella brevis"	"Shah et al., 1990"	2
-"Prevotella tannerae"	"Alloprevotella tannerae"	"Moore et al., 1994"	3
+"Prevotella tannerae"	"Alloprevotella tannerae"	"Moore et al., 1994"	2
 "Prevotella zoogleoformans"	"Capsularis zoogleoformans"	"Shah et al., 1994"	3
 "Primorskyibacter insulae"	"Pseudoprimorskyibacter insulae"	"Park et al., 2015"	2
 "Procandida albicans"	"Candida albicans"	"Novak et al., 1961"	2
@@ -11111,7 +11111,7 @@
 "Rectocibicidella robertsi"	"Dyocibicides robertsi"	"McLean, 1956"	3
 "Rectoglandulina rotundata"	"Pseudonodosaria rotundata"	"Reuss, 1850"	3
 "Recurvoides trochamminiformis"	"Recurvoidatus trochamminiformis"	"Saidova, 1961"	3
-"Reedomyia sudanensis"	"Aedes sudanensis"	"Theobald, 1913"	3
+"Reedomyia sudanensis"	"Aedes sudanensis"	"Theobald, 1913"	2
 "Reichenbachia"	"Reichenbachiella"	"Nedashkovskaya et al., 2003"	3
 "Reichenbachia agariperforans"	"Reichenbachiella agariperforans"	"Nedashkovskaya et al., 2003"	3
 "Remaneica gonzalezi"	"Remaneicella gonzalezi"	"Seiglie, 1964"	3
@@ -11462,7 +11462,7 @@
 "Rotalina truncatulinoides"	"Globorotalia truncatulinoides"	"DOrbigny, 1839"	3
 "Rotamorphina minuta"	"Valvulineria minuta"	"Schubert, 1904"	3
 "Rothia dentocariosus"	"Rothia dentocariosa"	"Georg et al., 1967"	2
-"Roubaudiella caerulea"	"Lucilia caerulea"	"Seguy, 1925"	3
+"Roubaudiella caerulea"	"Lucilia caerulea"	"Seguy, 1925"	2
 "Rozella itersoniliae"	"Pleotrachelus itersoniliae"	"Barr et al., 1980"	3
 "Rozella septigena"	"Rozellopsis septigena"	"Cornu, 1872"	3
 "Rozella simulans"	"Rozellopsis simulans"	"Fisch, 1882"	3
@@ -11790,16 +11790,16 @@
 "Septotrochammina gonzalezi"	"Remaneicella gonzalezi"	"Seiglie, 1964"	3
 "Serpens"	"Pseudomonas"	"Hespell, 1977"	1
 "Serpens flexibilis"	"Pseudomonas flexibilis"	"Hespell, 1977"	1
-"Serpula"	"Brachyspira"	"Stanton et al., 1991"	3
-"Serpula hyodysenteriae"	"Brachyspira hyodysenteriae"	"Stanton et al., 1991"	3
-"Serpula innocens"	"Brachyspira innocens"	"Stanton et al., 1991"	3
-"Serpulina"	"Brachyspira"	"Stanton, 1992"	3
-"Serpulina alvinipulli"	"Brachyspira alvinipulli"	"Stanton et al., 1998"	3
-"Serpulina hyodysenteriae"	"Brachyspira hyodysenteriae"	"Stanton et al., 1992"	3
-"Serpulina innocens"	"Brachyspira innocens"	"Stanton et al., 1992"	3
-"Serpulina intermedia"	"Brachyspira intermedia"	"Stanton et al., 1997"	3
-"Serpulina murdochii"	"Brachyspira murdochii"	"Stanton et al., 1997"	3
-"Serpulina pilosicoli"	"Brachyspira pilosicoli"	"Trott et al., 1996"	3
+"Serpula"	"Brachyspira"	"Stanton et al., 1991"	2
+"Serpula hyodysenteriae"	"Brachyspira hyodysenteriae"	"Stanton et al., 1991"	2
+"Serpula innocens"	"Brachyspira innocens"	"Stanton et al., 1991"	2
+"Serpulina"	"Brachyspira"	"Stanton, 1992"	2
+"Serpulina alvinipulli"	"Brachyspira alvinipulli"	"Stanton et al., 1998"	2
+"Serpulina hyodysenteriae"	"Brachyspira hyodysenteriae"	"Stanton et al., 1992"	2
+"Serpulina innocens"	"Brachyspira innocens"	"Stanton et al., 1992"	2
+"Serpulina intermedia"	"Brachyspira intermedia"	"Stanton et al., 1997"	2
+"Serpulina murdochii"	"Brachyspira murdochii"	"Stanton et al., 1997"	2
+"Serpulina pilosicoli"	"Brachyspira pilosicoli"	"Trott et al., 1996"	2
 "Serratia glossinae"	"Serratia fonticola"	"Geiger et al., 2010"	1
 "Serratia marcescens sakuensis"	"Serratia marcescens"	"Ajithkumar et al., 2003"	1
 "Serratia marinorubra"	"Serratia rubidaea"	"ZoBell et al., 1944"	1
@@ -12111,12 +12111,12 @@
 "Sphaerulina amicta"	"Appendichordella amicta"	"Kohlm, 1962"	3
 "Sphaerulina tanaceti"	"Leptosphaeria tanaceti"	"Shoemaker, 1976"	2
 "Sphinctocystis elliptica"	"Cymatopleura elliptica"	"Kuntze"	3
-"Sphingobacterium antarcticum"	"Pedobacter antarcticus"	"Shivaji et al., 1992"	3
-"Sphingobacterium antarcticus"	"Pedobacter antarcticus"	"Shivaji et al., 1992"	3
-"Sphingobacterium heparinum"	"Pedobacter heparinus"	"Takeuchi et al., 1993"	3
-"Sphingobacterium mizutae"	"Sphingobacterium mizutaii"	"Yabuuchi et al., 1983"	3
-"Sphingobacterium pakistanensis"	"Sphingobacterium pakistanense"	"Ahmed et al., 2015"	3
-"Sphingobacterium piscium"	"Pedobacter antarcticus"	"Takeuchi et al., 1993"	3
+"Sphingobacterium antarcticum"	"Pedobacter antarcticus"	"Shivaji et al., 1992"	2
+"Sphingobacterium antarcticus"	"Pedobacter antarcticus"	"Shivaji et al., 1992"	2
+"Sphingobacterium heparinum"	"Pedobacter heparinus"	"Takeuchi et al., 1993"	2
+"Sphingobacterium mizutae"	"Sphingobacterium mizutaii"	"Yabuuchi et al., 1983"	2
+"Sphingobacterium pakistanensis"	"Sphingobacterium pakistanense"	"Ahmed et al., 2015"	2
+"Sphingobacterium piscium"	"Pedobacter antarcticus"	"Takeuchi et al., 1993"	2
 "Sphingobium algicola"	"Sphingobium limneticum"	"Lee et al., 2017"	2
 "Sphingobium barthaii"	"Sphingobium fuliginis"	"Maeda et al., 2015"	2
 "Sphingobium chinhatense"	"Sphingobium indicum"	"Dadhwal et al., 2020"	2
@@ -12415,7 +12415,7 @@
 "Staurosphaera pusilla"	"Stigmosphaerostylus pusilla"	"Hinde, 1899"	3
 "Staurosphaera sedecimporata"	"Emiluvia sedecimporata"	"Rust, 1885"	3
 "Staurosphaera trispinosa"	"Staurolonche trispinosa"	"Kozur et al., 1979"	3
-"Stegomyia wellmanii"	"Aedes wellmanii"	"Theobald, 1910"	3
+"Stegomyia wellmanii"	"Aedes wellmanii"	"Theobald, 1910"	2
 "Steinia balladynula"	"Oxytricha balladynula"	"Kahl, 1932"	3
 "Steinia candens"	"Cyrtohymena candens"	"Kahl, 1932"	3
 "Steinia citrina"	"Cyrtohymena citrina"	"Berger et al., 1987"	3
@@ -12487,7 +12487,7 @@
 "Stemphylium uredinis"	"Alternaria uredinis"	"Thirum, 1947"	2
 "Stenella gynoxidicola"	"Cladosporium gynoxidicola"	"Mulder, 1982"	2
 "Stenopterobia delicatissima"	"Surirella delicatissima"	"Van Heurck, 1896"	3
-"Stenoscutus africanus"	"Aedes africanus"	"Theobald, 1909"	3
+"Stenoscutus africanus"	"Aedes africanus"	"Theobald, 1909"	2
 "Stenothermobacter"	"Nonlabens"	"Lau et al., 2006"	3
 "Stenothermobacter spongiae"	"Nonlabens spongiae"	"Lau et al., 2006"	3
 "Stenotrophomonas africana"	"Stenotrophomonas maltophilia"	"Drancourt et al., 1997"	1
@@ -12889,7 +12889,7 @@
 "Strombidium viride"	"Limnostrombidium viride"	"Kahl, 1932"	3
 "Strombilidium tonsuratum"	"Strobilidium tonsuratum"	"Meunier, 1907"	3
 "Strongylidium wilberti"	"Hemiamphisiella wilberti"	"Foissner, 1982"	3
-"Strophalosia warwicki"	"Capillaria warwicki"	"Maxwell, 1954"	3
+"Strophalosia warwicki"	"Capillaria warwicki"	"Maxwell, 1954"	2
 "Stylocapsa catenarum"	"Plicaforacapsa catenarum"	"Matsuoka, 1982"	3
 "Stylocapsa oblongula"	"Kilinora oblongula"	"Kocher, 1981"	3
 "Stylocapsa spiralis"	"Kilinora spiralis"	"Matsuoka, 1982"	3
@@ -12986,7 +12986,7 @@
 "Tachysoma siseris"	"Oxytricha siseris"	"Stiller, 1974"	3
 "Tachysoma tricornis"	"Oxytricha tricornis"	"Milne, 1886"	3
 "Taeniolella boppii"	"Cladophialophora boppii"	"Borelli, 1983"	2
-"Taeniorhynchus africanus"	"Aedes africanus"	"Neveu-Lemaire, 1906"	3
+"Taeniorhynchus africanus"	"Aedes africanus"	"Neveu-Lemaire, 1906"	2
 "Talaromyces brevicompactus"	"Hamigera brevicompactus"	"Kong, 1999"	3
 "Talaromyces byssochlamydoides"	"Rasamsonia byssochlamydoides"	"Stolk et al., 1972"	3
 "Talaromyces cejpii"	"Aspergillus cejpii"	"Milko, 1964"	2
@@ -13539,8 +13539,8 @@
 "Tremella simplex"	"Phaeotremella simplex"	"Jacks et al., 1940"	3
 "Tremella translucens"	"Sirotrema translucens"	"Gordon, 1938"	3
 "Treponema caldaria"	"Treponema caldarium"	"Abt et al., 2013"	2
-"Treponema hyodysenteriae"	"Brachyspira hyodysenteriae"	"Harris et al., 1972"	3
-"Treponema innocens"	"Brachyspira innocens"	"Kinyon et al., 1979"	3
+"Treponema hyodysenteriae"	"Brachyspira hyodysenteriae"	"Harris et al., 1972"	2
+"Treponema innocens"	"Brachyspira innocens"	"Kinyon et al., 1979"	2
 "Treponema stenostrepta"	"Treponema stenostreptum"	"Abt et al., 2013"	2
 "Tretomphalus bermudezi"	"Cymbaloporetta bermudezi"	"Sellier de Civrieux, 1976"	3
 "Tretomphalus concinnus"	"Tretomphaloides concinnus"	"Brady, 1884"	3
@@ -14161,7 +14161,7 @@
 "Wautersia paucula"	"Cupriavidus pauculus"	"Vaneechoutte et al., 2004"	2
 "Wautersia respiraculi"	"Cupriavidus respiraculi"	"Vaneechoutte et al., 2004"	2
 "Wautersia taiwanensis"	"Cupriavidus taiwanensis"	"Vaneechoutte et al., 2004"	2
-"Weeksella zoohelcum"	"Bergeyella zoohelcum"	"Holmes et al., 1987"	3
+"Weeksella zoohelcum"	"Bergeyella zoohelcum"	"Holmes et al., 1987"	2
 "Weiseria spinosa"	"Golbergia spinosa"	"Golberg, 1971"	3
 "Weissella jogaejeotgali"	"Weissella thailandensis"	"Lee et al., 2015"	2
 "Weissella kimchii"	"Weissella cibaria"	"Choi et al., 2002"	2

data-raw/mo.md5

@@ -1 +1 @@
-638a06636d8b547c2cb9d1ec243ecb7e
+4709adde8932f9e887fbd892a27ad929

data-raw/reproduction_of_microorganisms.R

@@ -168,32 +168,6 @@ rm(ref_taxonomy)
 rm(data_col.bak)
 rm(data_dsmz.bak)
 
-mo_found_in_NL <- c("Absidia", "Acremonium", "Actinotignum", "Aedes", "Alternaria", "Anaerosalibacter", "Ancylostoma", 
-                    "Angiostrongylus", "Anisakis", "Anopheles", "Apophysomyces", "Arachnia", "Ascaris", "Aspergillus", 
-                    "Aureobacterium", "Aureobasidium", "Bacteroides", "Balantidum", "Basidiobolus", "Beauveria", 
-                    "Bilophilia", "Blastocystis", "Branhamella", "Brochontrix", "Brugia", "Calymmatobacterium", "Candida", "Capillaria",
-                    "Capnocytophaga", "Catabacter", "Cdc", "Chaetomium", "Chilomastix", "Chryseobacterium",
-                    "Chryseomonas", "Chrysonilia", "Cladophialophora", "Cladosporium", "Clonorchis", "Conidiobolus",
-                    "Contracaecum", "Cordylobia", "Cryptococcus", "Curvularia", "Demodex", "Dermatobia", "Dicrocoelium", 
-                    "Dioctophyma", "Diphyllobothrium", "Dipylidium", "Dirofilaria", "Dracunculus", "Echinococcus", 
-                    "Echinostoma", "Elisabethkingia", "Enterobius", "Enteromonas", "Euascomycetes", "Exophiala",
-                    "Exserohilum", "Fasciola", "Fasciolopsis", "Flavobacterium", "Fonsecaea", "Fusarium", "Fusobacterium",
-                    "Giardia", "Gnathostoma", "Hendersonula", "Heterophyes", "Hymenolepis", "Hypomyces", 
-                    "Hysterothylacium", "Kloeckera", "Koserella", "Larva", "Lecythophora", "Leishmania", "Lelliottia",
-                    "Leptomyxida", "Leptosphaeria", "Leptotrichia", "Loa", "Lucilia", "Lumbricus", "Malassezia", 
-                    "Malbranchea", "Mansonella", "Mesocestoides", "Metagonimus", "Metarrhizium", "Molonomonas", 
-                    "Mortierella", "Mucor", "Multiceps", "Mycocentrospora", "Mycoplasma", "Nanophetus", "Nattrassia",
-                    "Necator", "Nectria", "Novospingobium", "Ochroconis", "Oesophagostomum", "Oidiodendron", "Onchocerca",
-                    "Opisthorchis", "Opistorchis", "Paragonimus", "Paramyxovirus", "Pediculus", "Phlebotomus",
-                    "Phocanema", "Phoma", "Phthirus", "Piedraia", "Pithomyces", "Pityrosporum", "Prevotella", 
-                    "Pseudallescheria", "Pseudoterranova", "Pulex", "Retortamonas", "Rhizomucor", "Rhizopus",
-                    "Rhodotorula", "Salinococcus", "Sanguibacteroides", "Sarcophagidae", "Sarcoptes", "Schistosoma", 
-                    "Scolecobasidium", "Scopulariopsis", "Scytalidium", "Spirometra", "Sporobolomyces", "Stachybotrys",
-                    "Stenotrophomononas", "Stomatococcus", "Strongyloides", "Syncephalastraceae", "Syngamus", "Taenia",
-                    "Ternidens", "Torulopsis", "Toxocara", "Toxoplasma", "Treponema", "Trichinella", "Trichobilharzia", "Trichoderma",
-                    "Trichomonas", "Trichophyton", "Trichosporon", "Trichostrongylus", "Trichuris", "Tritirachium",
-                    "Trombicula", "Trypanosoma", "Tunga", "Ureaplasma", "Wuchereria")
-
 MOs <- data_total %>%
   filter(
     (
@@ -205,7 +179,7 @@ MOs <- data_total %>%
           & !order %in% c("Eurotiales", "Microascales", "Mucorales", "Saccharomycetales", "Schizosaccharomycetales", "Tremellales", "Onygenales", "Pneumocystales"))
     )
     # or the genus has to be one of the genera we found in our hospitals last decades (Northern Netherlands, 2002-2018)
-    | genus %in% mo_found_in_NL
+    | genus %in% MO_PREVALENT_GENERA
   ) %>%
   # really no Plantae (e.g. Dracunculus exist both as worm and as plant)
   filter(kingdom != "Plantae") %>% 
@@ -398,7 +372,7 @@ MOs <- MOs %>%
                      "Firmicutes",
                      "Actinobacteria",
                      "Sarcomastigophora")
-       | genus %in% mo_found_in_NL
+       | genus %in% MO_PREVALENT_GENERA
        | rank %in% c("kingdom", "phylum", "class", "order", "family"))
     ~ 2,
     TRUE ~ 3

data-raw/reproduction_of_microorganisms_update.R

@@ -276,18 +276,7 @@ MOs <- MOs %>%
                      "Firmicutes",
                      "Actinobacteria",
                      "Sarcomastigophora")
-       | genus %in% c("Absidia", "Acremonium", "Actinotignum", "Alternaria", "Anaerosalibacter", "Apophysomyces",
-                      "Arachnia", "Aspergillus", "Aureobacterium", "Aureobasidium", "Bacteroides", "Basidiobolus",
-                      "Beauveria", "Blastocystis", "Branhamella", "Calymmatobacterium", "Candida", "Capnocytophaga",
-                      "Catabacter", "Chaetomium", "Chryseobacterium", "Chryseomonas", "Chrysonilia", "Cladophialophora",
-                      "Cladosporium", "Conidiobolus", "Cryptococcus", "Curvularia", "Exophiala", "Exserohilum",
-                      "Flavobacterium", "Fonsecaea", "Fusarium", "Fusobacterium", "Hendersonula", "Hypomyces",
-                      "Koserella", "Lelliottia", "Leptosphaeria", "Leptotrichia", "Malassezia", "Malbranchea",
-                      "Mortierella", "Mucor", "Mycocentrospora", "Mycoplasma", "Nectria", "Ochroconis",
-                      "Oidiodendron", "Phoma", "Piedraia", "Pithomyces", "Pityrosporum", "Prevotella", "Pseudallescheria", 
-                      "Rhizomucor", "Rhizopus", "Rhodotorula", "Scolecobasidium", "Scopulariopsis", "Scytalidium", 
-                      "Sporobolomyces", "Stachybotrys", "Stomatococcus", "Treponema", "Trichoderma", "Trichophyton", 
-                      "Trichosporon", "Tritirachium", "Ureaplasma")
+       | genus %in% MO_PREVALENT_GENERA
        | rank %in% c("kingdom", "phylum", "class", "order", "family"))
     ~ 2,
     TRUE ~ 3

data-raw/toxoplasma.R

@@ -0,0 +1,68 @@
+microorganisms <- microorganisms |> bind_rows(
+  # Toxoplasma
+  data.frame(mo = "P_TXPL_GOND", # species
+             fullname = "Toxoplasma gondii",
+             kingdom = "(unknown kingdom)",
+             phylum = "Apicomplexa",
+             class = "Conoidasida",
+             order = "Eucoccidiorida",
+             family = "Sarcocystidae",
+             genus = "Toxoplasma",
+             species = "gondii",
+             subspecies = "",
+             rank = "species",
+             ref = "Nicolle et al., 1908",
+             species_id = NA_real_,
+             source = "manually added",
+             prevalence = 2,
+             stringsAsFactors = FALSE),
+  data.frame(mo = "P_TXPL", # genus
+             fullname = "Toxoplasma",
+             kingdom = "(unknown kingdom)",
+             phylum = "Apicomplexa",
+             class = "Conoidasida",
+             order = "Eucoccidiorida",
+             family = "Sarcocystidae",
+             genus = "Toxoplasma",
+             species = "",
+             subspecies = "",
+             rank = "genus",
+             ref = "Nicolle et al., 1909",
+             species_id = NA_real_,
+             source = "manually added",
+             prevalence = 2,
+             stringsAsFactors = FALSE),
+  data.frame(mo = "[FAM]_SRCCYSTD", # family
+             fullname = "Sarcocystidae",
+             kingdom = "(unknown kingdom)",
+             phylum = "Apicomplexa",
+             class = "Conoidasida",
+             order = "Eucoccidiorida",
+             family = "Sarcocystidae",
+             genus = "",
+             species = "",
+             subspecies = "",
+             rank = "family",
+             ref = "Poche, 1913",
+             species_id = NA_real_,
+             source = "manually added",
+             prevalence = 2,
+             stringsAsFactors = FALSE),
+  data.frame(mo = "[ORD]_EUCCCDRD", # order
+             fullname = "Eucoccidiorida",
+             kingdom = "(unknown kingdom)",
+             phylum = "Apicomplexa",
+             class = "Conoidasida",
+             order = "Eucoccidiorida",
+             family = "",
+             genus = "",
+             species = "",
+             subspecies = "",
+             rank = "order",
+             ref = "Leger et al., 1910",
+             species_id = NA_real_,
+             source = "manually added",
+             prevalence = 2,
+             stringsAsFactors = FALSE),
+  ) |> 
+  arrange(fullname)

docs/404.html

@@ -43,7 +43,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9010</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
       </span>
     </div>
 
@@ -210,7 +210,7 @@ Content not found. Please use links in the navbar.
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer>

docs/LICENSE-text.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9010</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
       </span>
     </div>
 
@@ -420,7 +420,7 @@ END OF TERMS AND CONDITIONS
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer></div>

docs/articles/datasets.html

@@ -44,7 +44,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9010</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
       </span>
     </div>
 
@@ -190,7 +190,7 @@
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Data sets for download / own use</h1>
             
-            <h4 data-toc-skip class="date">16 May 2022</h4>
+            <h4 data-toc-skip class="date">12 August 2022</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
       <div class="hidden name"><code>datasets.Rmd</code></div>
@@ -224,7 +224,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</e
 <em>snomed</em>.</p>
 <p>This data set is in R available as <code>microorganisms</code>, after
 you load the <code>AMR</code> package.</p>
-<p>It was last updated on 29 November 2021 11:38:23 UTC. Find more info
+<p>It was last updated on 13 June 2022 13:55:27 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
@@ -232,7 +232,7 @@ about the structure of this data set <a href="https://msberends.github.io/AMR/re
 file</a> (1.3 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Excel
-file</a> (6.4 MB)<br>
+file</a> (4.8 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">plain
 text file</a> (13.1 MB)<br>
@@ -466,8 +466,8 @@ i.e. of column <em>‘fullname_new’</em>, see the
 <code>microorganisms</code> data set.</p>
 <p>This data set is in R available as <code>microorganisms.old</code>,
 after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 6 October 2021 14:38:29 UTC. Find more info
-about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
+<p>It was last updated on 3 June 2022 11:18:30 UTC. Find more info about
+the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">R
@@ -883,7 +883,7 @@ Dipivoxil, …</td>
 <div class="section level2">
 <h2 id="interpretation-from-mic-values-disk-diameters-to-rsi">Interpretation from MIC values / disk diameters to R/SI<a class="anchor" aria-label="anchor" href="#interpretation-from-mic-values-disk-diameters-to-rsi"></a>
 </h2>
-<p>A data set with 20,318 rows and 11 columns, containing the following
+<p>A data set with 20,369 rows and 11 columns, containing the following
 column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>,
 <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>,
 <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
@@ -915,8 +915,8 @@ file</a> (3.8 MB)</li>
 <h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
 </h3>
 <p>This data set contains interpretation rules for MIC values and disk
-diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
-(2011-2021).</p>
+diffusion diameters. Included guidelines are CLSI (2011-2022) and EUCAST
+(2011-2022).</p>
 </div>
 <div class="section level3">
 <h3 id="example-content-4">Example content<a class="anchor" aria-label="anchor" href="#example-content-4"></a>
@@ -954,7 +954,7 @@ diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">EUCAST 2021</td>
+<td align="center">EUCAST 2022</td>
 <td align="center">MIC</td>
 <td align="center"></td>
 <td align="center">F_ASPRG_MGTS</td>
@@ -965,11 +965,11 @@ diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
 <td align="center">Aspergillus</td>
 <td align="center"></td>
 <td align="center">1</td>
-<td align="center">4</td>
+<td align="center">1</td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="even">
-<td align="center">EUCAST 2021</td>
+<td align="center">EUCAST 2022</td>
 <td align="center">MIC</td>
 <td align="center"></td>
 <td align="center">F_ASPRG_NIGR</td>
@@ -980,11 +980,11 @@ diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
 <td align="center">Aspergillus</td>
 <td align="center"></td>
 <td align="center">1</td>
-<td align="center">4</td>
+<td align="center">1</td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="odd">
-<td align="center">EUCAST 2021</td>
+<td align="center">EUCAST 2022</td>
 <td align="center">MIC</td>
 <td align="center"></td>
 <td align="center">F_CANDD</td>
@@ -995,11 +995,11 @@ diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
 <td align="center">Candida</td>
 <td align="center"></td>
 <td align="center">1</td>
-<td align="center">2</td>
+<td align="center">1</td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="even">
-<td align="center">EUCAST 2021</td>
+<td align="center">EUCAST 2022</td>
 <td align="center">MIC</td>
 <td align="center"></td>
 <td align="center">F_CANDD_ALBC</td>
@@ -1010,11 +1010,26 @@ diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
 <td align="center">Candida</td>
 <td align="center"></td>
 <td align="center">1</td>
-<td align="center">2</td>
+<td align="center">1</td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="odd">
-<td align="center">EUCAST 2021</td>
+<td align="center">EUCAST 2022</td>
+<td align="center">MIC</td>
+<td align="center"></td>
+<td align="center">F_CANDD_DBLN</td>
+<td align="center">Candida dubliniensis</td>
+<td align="center">2</td>
+<td align="center">AMB</td>
+<td align="center">Amphotericin B</td>
+<td align="center">Candida</td>
+<td align="center"></td>
+<td align="center">1</td>
+<td align="center">1</td>
+<td align="center">FALSE</td>
+</tr>
+<tr class="even">
+<td align="center">EUCAST 2022</td>
 <td align="center">MIC</td>
 <td align="center"></td>
 <td align="center">F_CANDD_KRUS</td>
@@ -1025,22 +1040,7 @@ diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
 <td align="center">Candida</td>
 <td align="center"></td>
 <td align="center">1</td>
-<td align="center">2</td>
-<td align="center">FALSE</td>
-</tr>
-<tr class="even">
-<td align="center">EUCAST 2021</td>
-<td align="center">MIC</td>
-<td align="center"></td>
-<td align="center">F_CANDD_PRPS</td>
-<td align="center">Candida parapsilosis</td>
-<td align="center">2</td>
-<td align="center">AMB</td>
-<td align="center">Amphotericin B</td>
-<td align="center">Candida</td>
-<td align="center"></td>
 <td align="center">1</td>
-<td align="center">2</td>
 <td align="center">FALSE</td>
 </tr>
 </tbody>
@@ -1481,7 +1481,7 @@ Breakpoint Tables’ v11.0</a> (2021).</p>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer>

docs/authors.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9010</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
       </span>
     </div>
 
@@ -273,7 +273,7 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer></div>

docs/index.html

@@ -47,7 +47,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9010</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
       </span>
     </div>
 
@@ -214,17 +214,17 @@
 <h5 id="with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side">With <code>AMR</code> (for R), there’s always a knowledgeable microbiologist by your side!<a class="anchor" aria-label="anchor" href="#with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side"></a>
 </h5>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span>
-<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
-<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
-
-<span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>bacteria <span class="op">=</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span>,
-         <span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>,
-         <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,
-         <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
+<span></span>
+<span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>bacteria <span class="op">=</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>         <span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>,</span>
+<span>         <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>         <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p>
 <table class="table">
 <thead><tr class="header">
@@ -331,10 +331,10 @@
 </table>
 <p>A base R equivalent would be, giving the exact same results:</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">example_isolates</span><span class="op">$</span><span class="va">bacteria</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">mo</span><span class="op">)</span>
-<span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</span>
-                         <span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</span><span class="op">)</span>,
-                 <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"bacteria"</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></code></pre></div>
+<code class="sourceCode R"><span><span class="va">example_isolates</span><span class="op">$</span><span class="va">bacteria</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">mo</span><span class="op">)</span></span>
+<span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</span></span>
+<span>                         <span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</span><span class="op">)</span>,</span>
+<span>                 <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"bacteria"</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span></code></pre></div>
 </div>
 <div class="section level4">
 <h4 id="partners">Partners<a class="anchor" aria-label="anchor" href="#partners"></a>
@@ -377,7 +377,7 @@
 <p><a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://www.r-pkg.org/badges/version-ago/AMR" alt="CRAN"></a> <a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt="CRANlogs"></a></p>
 <p>This package is available <a href="https://cran.r-project.org/package=AMR" class="external-link">here on the official R network (CRAN)</a>. Install this package in R from CRAN by using the command:</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></span></code></pre></div>
 <p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
 <p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
 </div>
@@ -390,14 +390,14 @@
 <li>
 <p>Manually, using:</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span>
-<span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span></span>
+<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></span></code></pre></div>
 </li>
 <li>
 <p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our R-universe address</a> to your list of repositories (‘repos’):</p>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>,
-                  msberends <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>,</span>
+<span>                  msberends <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <p>After this, you can install and update this <code>AMR</code> package like any official release (e.g., using <code>install.packages("AMR")</code> or in RStudio via <em>Tools</em> &gt; <em>Check for Package Updates…</em>).</p>
 </li>
 </ol>
@@ -562,7 +562,7 @@
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer>

docs/reference/as.mo.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
       </span>
     </div>
 
@@ -162,53 +162,76 @@
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">as.mo</span><span class="op">(</span>
-  <span class="va">x</span>,
-  Becker <span class="op">=</span> <span class="cn">FALSE</span>,
-  Lancefield <span class="op">=</span> <span class="cn">FALSE</span>,
-  allow_uncertain <span class="op">=</span> <span class="cn">TRUE</span>,
-  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" class="external-link">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_AMR_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" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,
-  <span class="va">...</span>
-<span class="op">)</span>
-
-<span class="fu">is.mo</span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
-
-<span class="fu">mo_failures</span><span class="op">(</span><span class="op">)</span>
-
-<span class="fu">mo_uncertainties</span><span class="op">(</span><span class="op">)</span>
-
-<span class="fu">mo_renamed</span><span class="op">(</span><span class="op">)</span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">as.mo</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  Becker <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  Lancefield <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  allow_uncertain <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  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>,</span>
+<span>  ignore_pattern <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_ignore_pattern"</span><span class="op">)</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">is.mo</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_failures</span><span class="op">(</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_uncertainties</span><span class="op">(</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_renamed</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
     <h2>Arguments</h2>
     <dl><dt>x</dt>
 <dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector or a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with one or two columns</p></dd>
+
+
 <dt>Becker</dt>
 <dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether staphylococci should be categorised into coagulase-negative staphylococci ("CoNS") and coagulase-positive staphylococci ("CoPS") instead of their own species, according to Karsten Becker <em>et al.</em> (1,2,3).</p>
 <p>This excludes <em>Staphylococcus aureus</em> at default, use <code>Becker = "all"</code> to also categorise <em>S. aureus</em> as "CoPS".</p></dd>
+
+
 <dt>Lancefield</dt>
 <dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a beta-haemolytic <em>Streptococcus</em> should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (4). These streptococci will be categorised in their first group, e.g. <em>Streptococcus dysgalactiae</em> will be group C, although officially it was also categorised into groups G and L.</p>
 <p>This excludes enterococci at default (who are in group D), use <code>Lancefield = "all"</code> to also categorise all enterococci as group D.</p></dd>
+
+
 <dt>allow_uncertain</dt>
 <dd><p>a number between <code>0</code> (or <code>"none"</code>) and <code>3</code> (or <code>"all"</code>), or <code>TRUE</code> (= <code>2</code>) or <code>FALSE</code> (= <code>0</code>) to indicate whether the input should be checked for less probable results, see <em>Details</em></p></dd>
+
+
 <dt>reference_df</dt>
 <dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> to be used for extra reference when translating <code>x</code> to a valid <code>mo</code>. See <code><a href="mo_source.html">set_mo_source()</a></code> and <code><a href="mo_source.html">get_mo_source()</a></code> to automate the usage of your own codes (e.g. used in your analysis or organisation).</p></dd>
+
+
 <dt>ignore_pattern</dt>
 <dd><p>a regular expression (case-insensitive) of which all matches in <code>x</code> must return <code>NA</code>. This can be convenient to exclude known non-relevant input and can also be set with the option <code>AMR_ignore_pattern</code>, e.g. <code>options(AMR_ignore_pattern = "(not reported|contaminated flora)")</code>.</p></dd>
+
+
 <dt>language</dt>
 <dd><p>language to translate text like "no growth", which defaults to the system language (see <code><a href="translate.html">get_AMR_locale()</a></code>)</p></dd>
+
+
 <dt>info</dt>
 <dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">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></dd>
+
+
 <dt>...</dt>
 <dd><p>other arguments passed on to functions</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    <p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a><a href="https://rdrr.io/r/base/vector.html" class="external-link">vector</a> with additional class <code>mo</code></p>
+    
+
+<p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a></p>
+<p></p>
+<p><a href="https://rdrr.io/r/base/vector.html" class="external-link">vector</a> with additional class <code>mo</code></p>
+
+
     </div>
     <div id="details">
     <h2>Details</h2>
@@ -217,20 +240,19 @@
 <h3 id="general-info">General Info<a class="anchor" aria-label="anchor" href="#general-info"></a></h3>
 
 
-<p>A microorganism (MO) code from this package (class: <code>mo</code>) is human readable and typically looks like these examples:</p><div class="sourceCode"><pre><code>  Code               Full name
-  ---------------    --------------------------------------
-  B_KLBSL            Klebsiella
-  B_KLBSL_PNMN       Klebsiella pneumoniae
-  B_KLBSL_PNMN_RHNS  Klebsiella pneumoniae rhinoscleromatis
-  |   |    |    |
-  |   |    |    |
-  |   |    |    \---&gt; subspecies, a 4-5 letter acronym
-  |   |    \----&gt; species, a 4-5 letter acronym
-  |   \----&gt; genus, a 5-7 letter acronym
-  \----&gt; taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
-                            C (Chromista), F (Fungi), P (Protozoa)
-</code></pre></div>
-
+<p>A microorganism (MO) code from this package (class: <code>mo</code>) is human readable and typically looks like these examples:</p>
+<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>  Code               Full name</span>
+<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>  <span class="sc">---------------</span>    <span class="sc">--------------------------------------</span></span>
+<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a>  B_KLBSL            Klebsiella</span>
+<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a>  B_KLBSL_PNMN       Klebsiella pneumoniae</span>
+<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a>  B_KLBSL_PNMN_RHNS  Klebsiella pneumoniae rhinoscleromatis</span>
+<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a>  <span class="sc">|</span>   <span class="er">|</span>    <span class="er">|</span>    <span class="er">|</span></span>
+<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a>  <span class="er">|</span>   <span class="er">|</span>    <span class="er">|</span>    <span class="er">|</span></span>
+<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a>  <span class="er">|</span>   <span class="er">|</span>    <span class="er">|</span>    \<span class="sc">--</span><span class="ot">-&gt;</span> subspecies, a <span class="dv">4-5</span> letter acronym</span>
+<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a>  <span class="sc">|</span>   <span class="er">|</span>    \<span class="sc">---</span><span class="ot">-&gt;</span> species, a <span class="dv">4-5</span> letter acronym</span>
+<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a>  <span class="sc">|</span>   \<span class="sc">---</span><span class="ot">-&gt;</span> genus, a <span class="dv">5-7</span> letter acronym</span>
+<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a>  \<span class="sc">---</span><span class="ot">-&gt;</span> taxonomic kingdom<span class="sc">:</span> <span class="fu">A</span> (Archaea), <span class="fu">AN</span> (Animalia), <span class="fu">B</span> (Bacteria),</span>
+<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a>                            <span class="fu">C</span> (Chromista), <span class="fu">F</span> (Fungi), <span class="fu">P</span> (Protozoa)</span></code></pre><p></p></div>
 <p>Values that cannot be coerced will be considered 'unknown' and will get the MO code <code>UNKNOWN</code>.</p>
 <p>Use the <code><a href="mo_property.html">mo_*</a></code> functions to get properties based on the returned code, see <em>Examples</em>.</p>
 <p>The algorithm uses data from the Catalogue of Life (see below) and from one other source (see <a href="microorganisms.html">microorganisms</a>).</p>
@@ -269,12 +291,12 @@
     <h2>Source</h2>
     
 
-<ol><li><p>Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870-926; doi: <a href="https://doi.org/10.1128/CMR.00109-13" class="external-link">10.1128/CMR.00109-13</a></p></li>
-<li><p>Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect; doi: <a href="https://doi.org/10.1016/j.cmi.2019.02.028" class="external-link">10.1016/j.cmi.2019.02.028</a></p></li>
-<li><p>Becker K <em>et al.</em> <strong>Emergence of coagulase-negative staphylococci</strong> 2020. Expert Rev Anti Infect Ther. 18(4):349-366; doi: <a href="https://doi.org/10.1080/14787210.2020.1730813" class="external-link">10.1080/14787210.2020.1730813</a></p></li>
-<li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571-95; doi: <a href="https://doi.org/10.1084/jem.57.4.571" class="external-link">10.1084/jem.57.4.571</a></p></li>
+<ol><li><p>Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870-926; <a href="https://doi.org/10.1128/CMR.00109-13" class="external-link">doi:10.1128/CMR.00109-13</a></p></li>
+<li><p>Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect; <a href="https://doi.org/10.1016/j.cmi.2019.02.028" class="external-link">doi:10.1016/j.cmi.2019.02.028</a></p></li>
+<li><p>Becker K <em>et al.</em> <strong>Emergence of coagulase-negative staphylococci</strong> 2020. Expert Rev Anti Infect Ther. 18(4):349-366; <a href="https://doi.org/10.1080/14787210.2020.1730813" class="external-link">doi:10.1080/14787210.2020.1730813</a></p></li>
+<li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571-95; <a href="https://doi.org/10.1084/jem.57.4.571" class="external-link">doi:10.1084/jem.57.4.571</a></p></li>
 <li><p>Catalogue of Life: 2019 Annual Checklist, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a></p></li>
-<li><p>List of Prokaryotic names with Standing in Nomenclature (5 October 2021), doi: <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">10.1099/ijsem.0.004332</a></p></li>
+<li><p>List of Prokaryotic names with Standing in Nomenclature (5 October 2021), <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a></p></li>
 <li><p>US Edition of SNOMED CT from 1 September 2020, retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009</a></p></li>
 </ol></div>
     <div id="stable-lifecycle">
@@ -330,44 +352,43 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
     <div id="ref-examples">
     <h2>Examples</h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># \donttest{</span>
-<span class="co"># These examples all return "B_STPHY_AURS", the ID of S. aureus:</span>
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"sau"</span><span class="op">)</span> <span class="co"># WHONET code</span>
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"stau"</span><span class="op">)</span>
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"STAU"</span><span class="op">)</span>
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"staaur"</span><span class="op">)</span>
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"S aureus"</span><span class="op">)</span>
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span>
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Staphylococcus aureus (MRSA)"</span><span class="op">)</span>
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Zthafilokkoockus oureuz"</span><span class="op">)</span> <span class="co"># handles incorrect spelling</span>
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>    <span class="co"># Methicillin Resistant S. aureus</span>
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span>    <span class="co"># Vancomycin Intermediate S. aureus</span>
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"VRSA"</span><span class="op">)</span>    <span class="co"># Vancomycin Resistant S. aureus</span>
-<span class="fu">as.mo</span><span class="op">(</span><span class="fl">115329001</span><span class="op">)</span> <span class="co"># SNOMED CT code</span>
-
-<span class="co"># Dyslexia is no problem - these all work:</span>
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplasma urealyticum"</span><span class="op">)</span>
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplasma urealyticus"</span><span class="op">)</span>
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplasmium urealytica"</span><span class="op">)</span>
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplazma urealitycium"</span><span class="op">)</span>
-
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Streptococcus group A"</span><span class="op">)</span>
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"GAS"</span><span class="op">)</span> <span class="co"># Group A Streptococci</span>
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"GBS"</span><span class="op">)</span> <span class="co"># Group B Streptococci</span>
-
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span><span class="op">)</span>                 <span class="co"># will remain species: B_STPHY_EPDR</span>
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>  <span class="co"># will not remain species: B_STPHY_CONS</span>
-
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. pyogenes"</span><span class="op">)</span>                    <span class="co"># will remain species: B_STRPT_PYGN</span>
-<span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. pyogenes"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># will not remain species: B_STRPT_GRPA</span>
-
-<span class="co"># All mo_* functions use as.mo() internally too (see ?mo_property):</span>
-<span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>                           <span class="co"># returns "Escherichia"</span>
-<span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>                       <span class="co"># returns "Gram negative"</span>
-<span class="fu"><a href="mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"E. coli"</span>, <span class="st">"vanco"</span><span class="op">)</span> <span class="co"># returns TRUE</span>
-<span class="co"># }</span>
-</code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># \donttest{</span></span>
+<span><span class="co"># These examples all return "B_STPHY_AURS", the ID of S. aureus:</span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"sau"</span><span class="op">)</span> <span class="co"># WHONET code</span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"stau"</span><span class="op">)</span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"STAU"</span><span class="op">)</span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"staaur"</span><span class="op">)</span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S aureus"</span><span class="op">)</span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Staphylococcus aureus (MRSA)"</span><span class="op">)</span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Zthafilokkoockus oureuz"</span><span class="op">)</span> <span class="co"># handles incorrect spelling</span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>    <span class="co"># Methicillin Resistant S. aureus</span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span>    <span class="co"># Vancomycin Intermediate S. aureus</span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"VRSA"</span><span class="op">)</span>    <span class="co"># Vancomycin Resistant S. aureus</span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="fl">115329001</span><span class="op">)</span> <span class="co"># SNOMED CT code</span></span>
+<span></span>
+<span><span class="co"># Dyslexia is no problem - these all work:</span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplasma urealyticum"</span><span class="op">)</span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplasma urealyticus"</span><span class="op">)</span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplasmium urealytica"</span><span class="op">)</span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplazma urealitycium"</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Streptococcus group A"</span><span class="op">)</span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"GAS"</span><span class="op">)</span> <span class="co"># Group A Streptococci</span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"GBS"</span><span class="op">)</span> <span class="co"># Group B Streptococci</span></span>
+<span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span><span class="op">)</span>                 <span class="co"># will remain species: B_STPHY_EPDR</span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>  <span class="co"># will not remain species: B_STPHY_CONS</span></span>
+<span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. pyogenes"</span><span class="op">)</span>                    <span class="co"># will remain species: B_STRPT_PYGN</span></span>
+<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. pyogenes"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># will not remain species: B_STRPT_GRPA</span></span>
+<span></span>
+<span><span class="co"># All mo_* functions use as.mo() internally too (see ?mo_property):</span></span>
+<span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>                           <span class="co"># returns "Escherichia"</span></span>
+<span><span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>                       <span class="co"># returns "Gram negative"</span></span>
+<span><span class="fu"><a href="mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"E. coli"</span>, <span class="st">"vanco"</span><span class="op">)</span> <span class="co"># returns TRUE</span></span>
+<span><span class="co"># }</span></span></code></pre></div>
     </div>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -381,7 +402,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer></div>

docs/reference/as.rsi.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9011</span>
       </span>
     </div>
 
@@ -249,12 +249,12 @@
 
 
 <p>The <code>as.rsi()</code> function works in four ways:</p><ol><li><p>For <strong>cleaning raw / untransformed data</strong>. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with R/SI interpretations and MIC values such as <code>"&lt;0.25; S"</code> will be coerced to <code>"S"</code>. Combined interpretations for multiple test methods (as seen in laboratory records) such as <code>"S; S"</code> will be coerced to <code>"S"</code>, but a value like <code>"S; I"</code> will return <code>NA</code> with a warning that the input is unclear.</p></li>
-<li><p>For <strong>interpreting minimum inhibitory concentration (MIC) values</strong> according to EUCAST or CLSI. You must clean your MIC values first using <code><a href="as.mic.html">as.mic()</a></code>, that also gives your columns the new data class <code><a href="as.mic.html">mic</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul><li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><div class="sourceCode"><pre><code><span class="va">your_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.rsi</span><span class="op">)</span>             <span class="co"># until dplyr 1.0.0</span>
-<span class="va">your_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span><span class="op">)</span> <span class="co"># since dplyr 1.0.0</span></code></pre></div></li>
+<li><p>For <strong>interpreting minimum inhibitory concentration (MIC) values</strong> according to EUCAST or CLSI. You must clean your MIC values first using <code><a href="as.mic.html">as.mic()</a></code>, that also gives your columns the new data class <code><a href="as.mic.html">mic</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul><li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div></li>
 <li><p>Operators like "&lt;=" will be stripped before interpretation. When using <code>conserve_capped_values = TRUE</code>, an MIC value of e.g. "&gt;2" will always return "R", even if the breakpoint according to the chosen guideline is "&gt;=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (<code>conserve_capped_values = FALSE</code>) considers "&gt;2" to be lower than "&gt;=4" and might in this case return "S" or "I".</p></li>
 </ul></li>
-<li><p>For <strong>interpreting disk diffusion diameters</strong> according to EUCAST or CLSI. You must clean your disk zones first using <code><a href="as.disk.html">as.disk()</a></code>, that also gives your columns the new data class <code><a href="as.disk.html">disk</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul><li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><div class="sourceCode"><pre><code><span class="va">your_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.disk</span>, <span class="va">as.rsi</span><span class="op">)</span>             <span class="co"># until dplyr 1.0.0</span>
-<span class="va">your_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.disk</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span><span class="op">)</span> <span class="co"># since dplyr 1.0.0</span></code></pre></div></li>
+<li><p>For <strong>interpreting disk diffusion diameters</strong> according to EUCAST or CLSI. You must clean your disk zones first using <code><a href="as.disk.html">as.disk()</a></code>, that also gives your columns the new data class <code><a href="as.disk.html">disk</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul><li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div></li>
 </ul></li>
 <li><p>For <strong>interpreting a complete data set</strong>, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running <code>as.rsi(your_data)</code>.</p></li>
 </ol></div>

docs/reference/atc_online.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9012</span>
       </span>
     </div>
 
@@ -210,7 +210,7 @@
 <li><p><code>"V"</code> = vaginal</p></li>
 </ul><p>Abbreviations of return values when using <code>property = "U"</code> (unit):</p><ul><li><p><code>"g"</code> = gram</p></li>
 <li><p><code>"mg"</code> = milligram</p></li>
-<li><p>`"mcg"`` = microgram</p></li>
+<li><p><code>"mcg"</code> = microgram</p></li>
 <li><p><code>"U"</code> = unit</p></li>
 <li><p><code>"TU"</code> = thousand units</p></li>
 <li><p><code>"MU"</code> = million units</p></li>

docs/reference/count.html

@@ -18,7 +18,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9011</span>
       </span>
     </div>
 
@@ -243,30 +243,12 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
     <h2>Combination Therapy</h2>
     
 
-<p>When using more than one variable for <code>...</code> (= combination therapy), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code><a href="proportion.html">susceptibility()</a></code> works to calculate the %SI:</p><div class="sourceCode"><pre><code>--------------------------------------------------------------------
-                    only_all_tested = FALSE  only_all_tested = TRUE
-                    -----------------------  -----------------------
- Drug A    Drug B   include as  include as   include as  include as
-                    numerator   denominator  numerator   denominator
---------  --------  ----------  -----------  ----------  -----------
- S or I    S or I       X            X            X            X
-   R       S or I       X            X            X            X
-  &lt;NA&gt;     S or I       X            X            -            -
- S or I      R          X            X            X            X
-   R         R          -            X            -            X
-  &lt;NA&gt;       R          -            -            -            -
- S or I     &lt;NA&gt;        X            X            -            -
-   R        &lt;NA&gt;        -            -            -            -
-  &lt;NA&gt;      &lt;NA&gt;        -            -            -            -
---------------------------------------------------------------------
-</code></pre></div>
-
-<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><div class="sourceCode"><pre><code><span class="fu"><a href="../reference/count.html">count_S</a></span><span class="op">(</span><span class="op">)</span>    <span class="op">+</span>   <span class="fu"><a href="../reference/count.html">count_I</a></span><span class="op">(</span><span class="op">)</span>    <span class="op">+</span>   <span class="fu"><a href="../reference/count.html">count_R</a></span><span class="op">(</span><span class="op">)</span>    <span class="op">=</span> <span class="fu"><a href="../reference/count.html">count_all</a></span><span class="op">(</span><span class="op">)</span>
-  <span class="fu"><a href="../reference/proportion.html">proportion_S</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="../reference/proportion.html">proportion_I</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="../reference/proportion.html">proportion_R</a></span><span class="op">(</span><span class="op">)</span> <span class="op">=</span> <span class="fl">1</span></code></pre></div>
-
-<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><div class="sourceCode"><pre><code><span class="fu"><a href="../reference/count.html">count_S</a></span><span class="op">(</span><span class="op">)</span>    <span class="op">+</span>   <span class="fu"><a href="../reference/count.html">count_I</a></span><span class="op">(</span><span class="op">)</span>    <span class="op">+</span>   <span class="fu"><a href="../reference/count.html">count_R</a></span><span class="op">(</span><span class="op">)</span>    <span class="op">&gt;=</span> <span class="fu"><a href="../reference/count.html">count_all</a></span><span class="op">(</span><span class="op">)</span>
-  <span class="fu"><a href="../reference/proportion.html">proportion_S</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="../reference/proportion.html">proportion_I</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="../reference/proportion.html">proportion_R</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&gt;=</span> <span class="fl">1</span></code></pre></div>
-
+<p>When using more than one variable for <code>...</code> (= combination therapy), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code><a href="proportion.html">susceptibility()</a></code> works to calculate the %SI:</p>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
+<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
+<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
 <p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
     </div>
     <div id="read-more-on-our-website-">

docs/reference/custom_eucast_rules.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9012</span>
       </span>
     </div>
 
@@ -186,80 +186,54 @@
 <h3 id="basics">Basics<a class="anchor" aria-label="anchor" href="#basics"></a></h3>
 
 
-<p>If you are familiar with the <code><a href="https://dplyr.tidyverse.org/reference/case_when.html" class="external-link">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>~</code>) and the consequence of the rule is written <em>after</em> the tilde:</p><div class="sourceCode"><pre><code><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_eucast_rules.html">custom_eucast_rules</a></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></code></pre></div>
-
-<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><div class="sourceCode"><pre><code><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></code></pre></div>
-
-<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><div class="sourceCode"><pre><code><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">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" class="external-link">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="../reference/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></code></pre></div>
-
+<p>If you are familiar with the <code><a href="https://dplyr.tidyverse.org/reference/case_when.html" class="external-link">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>~</code>) and the consequence of the rule is written <em>after</em> the tilde:</p>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
+<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>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
+<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>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
 </div>
 
 <div class="section">
 <h3 id="using-taxonomic-properties-in-rules">Using taxonomic properties in rules<a class="anchor" aria-label="anchor" href="#using-taxonomic-properties-in-rules"></a></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><div class="sourceCode"><pre><code><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_eucast_rules.html">custom_eucast_rules</a></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="../reference/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></code></pre></div>
-
+<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: –mo–, –fullname–, –kingdom–, –phylum–, –class–, –order–, –family–, –genus–, –species–, –subspecies–, –rank–, –ref–, –species_id–, –source–, –prevalence– and –snomed–. 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>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
 </div>
 
 <div class="section">
 <h3 id="usage-of-antibiotic-group-names">Usage of antibiotic group names<a class="anchor" aria-label="anchor" href="#usage-of-antibiotic-group-names"></a></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 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 and tobramycin-high)</p></li>
-<li><p><code>aminopenicillins</code><br>(amoxicillin and ampicillin)</p></li>
-<li><p><code>antifungals</code><br>(5-fluorocytosine, amphotericin B, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole and voriconazole)</p></li>
-<li><p><code>antimycobacterials</code><br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, morinamide, p-aminosalicylic acid, pretomanid, prothionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone/isoniazid, tiocarlide and viomycin)</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, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, 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, 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 and 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 and tebipenem)</p></li>
-<li><p><code>cephalosporins</code><br>(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, 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 and loracarbef)</p></li>
-<li><p><code>cephalosporins_1st</code><br>(cefacetrile, cefadroxil, cefaloridine, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, cephalexin, cephalothin, cephapirin and cephradine)</p></li>
-<li><p><code>cephalosporins_2nd</code><br>(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil and loracarbef)</p></li>
-<li><p><code>cephalosporins_3rd</code><br>(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 and latamoxef)</p></li>
-<li><p><code>cephalosporins_4th</code><br>(cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol, cefoselis, cefozopran, cefpirome and cefquinome)</p></li>
-<li><p><code>cephalosporins_5th</code><br>(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor and ceftolozane/tazobactam)</p></li>
-<li><p><code>cephalosporins_except_caz</code><br>(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, 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 and loracarbef)</p></li>
-<li><p><code>fluoroquinolones</code><br>(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)</p></li>
-<li><p><code>glycopeptides</code><br>(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin and vancomycin-macromethod)</p></li>
-<li><p><code>glycopeptides_except_lipo</code><br>(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin and vancomycin-macromethod)</p></li>
-<li><p><code>lincosamides</code><br>(acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin, lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin and tylvalosin)</p></li>
-<li><p><code>lipoglycopeptides</code><br>(dalbavancin, oritavancin and telavancin)</p></li>
-<li><p><code>macrolides</code><br>(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin and tylvalosin)</p></li>
-<li><p><code>oxazolidinones</code><br>(cadazolid, cycloserine, linezolid, tedizolid and 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, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, cefepime/nacubactam, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, 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 and ticarcillin/clavulanic acid)</p></li>
-<li><p><code>polymyxins</code><br>(colistin, polymyxin B and polymyxin B/polysorbate 80)</p></li>
-<li><p><code>quinolones</code><br>(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)</p></li>
-<li><p><code>streptogramins</code><br>(pristinamycin and quinupristin/dalfopristin)</p></li>
-<li><p><code>tetracyclines</code><br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline and tigecycline)</p></li>
-<li><p><code>tetracyclines_except_tgc</code><br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline and tetracycline)</p></li>
-<li><p><code>trimethoprims</code><br>(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim and trimethoprim/sulfamethoxazole)</p></li>
-<li><p><code>ureidopenicillins</code><br>(azlocillin, mezlocillin, piperacillin and piperacillin/tazobactam)</p></li>
+<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 agents that will be matched when running the rule.</p><ul><li><p>–aminoglycosides–<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 and tobramycin-high)</p></li>
+<li><p>–aminopenicillins–<br>(amoxicillin and ampicillin)</p></li>
+<li><p>–antifungals–<br>(5-fluorocytosine, amphotericin B, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole and voriconazole)</p></li>
+<li><p>–antimycobacterials–<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, morinamide, p-aminosalicylic acid, pretomanid, prothionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone/isoniazid, tiocarlide and viomycin)</p></li>
+<li><p>–betalactams–<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, 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, 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 and ticarcillin/clavulanic acid)</p></li>
+<li><p>–carbapenems–<br>(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil and tebipenem)</p></li>
+<li><p>–cephalosporins–<br>(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, 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 and loracarbef)</p></li>
+<li><p>–cephalosporins_1st–<br>(cefacetrile, cefadroxil, cefaloridine, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, cephalexin, cephalothin, cephapirin and cephradine)</p></li>
+<li><p>–cephalosporins_2nd–<br>(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil and loracarbef)</p></li>
+<li><p>–cephalosporins_3rd–<br>(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 and latamoxef)</p></li>
+<li><p>–cephalosporins_4th–<br>(cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol, cefoselis, cefozopran, cefpirome and cefquinome)</p></li>
+<li><p>–cephalosporins_5th–<br>(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor and ceftolozane/tazobactam)</p></li>
+<li><p>–cephalosporins_except_caz–<br>(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, 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 and loracarbef)</p></li>
+<li><p>–fluoroquinolones–<br>(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)</p></li>
+<li><p>–glycopeptides–<br>(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin and vancomycin-macromethod)</p></li>
+<li><p>–glycopeptides_except_lipo–<br>(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin and vancomycin-macromethod)</p></li>
+<li><p>–lincosamides–<br>(acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin, lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin and tylvalosin)</p></li>
+<li><p>–lipoglycopeptides–<br>(dalbavancin, oritavancin and telavancin)</p></li>
+<li><p>–macrolides–<br>(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin and tylvalosin)</p></li>
+<li><p>–oxazolidinones–<br>(cadazolid, cycloserine, linezolid, tedizolid and thiacetazone)</p></li>
+<li><p>–penicillins–<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, cefepime/nacubactam, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, 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 and ticarcillin/clavulanic acid)</p></li>
+<li><p>–polymyxins–<br>(colistin, polymyxin B and polymyxin B/polysorbate 80)</p></li>
+<li><p>–quinolones–<br>(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)</p></li>
+<li><p>–streptogramins–<br>(pristinamycin and quinupristin/dalfopristin)</p></li>
+<li><p>–tetracyclines–<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline and tigecycline)</p></li>
+<li><p>–tetracyclines_except_tgc–<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline and tetracycline)</p></li>
+<li><p>–trimethoprims–<br>(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim and trimethoprim/sulfamethoxazole)</p></li>
+<li><p>–ureidopenicillins–<br>(azlocillin, mezlocillin, piperacillin and piperacillin/tazobactam)</p></li>
 </ul></div>
 
     </div>

docs/reference/eucast_rules.html

@@ -18,7 +18,7 @@ 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="Released version">1.8.1.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9011</span>
       </span>
     </div>
 
@@ -185,7 +185,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
     <h2>Source</h2>
     
 <ul><li><p>EUCAST Expert Rules. Version 2.0, 2012.<br>
-Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility testing.</strong> <em>Clin Microbiol Infect.</em> 2013;19(2):141-60; doi: <a href="https://doi.org/10.1111/j.1469-0691.2011.03703.x" class="external-link">10.1111/j.1469-0691.2011.03703.x</a></p></li>
+Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility testing.</strong> <em>Clin Microbiol Infect.</em> 2013;19(2):141-60; <a href="https://doi.org/10.1111/j.1469-0691.2011.03703.x" class="external-link">doi:10.1111/j.1469-0691.2011.03703.x</a></p></li>
 <li><p>EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. <a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf" class="external-link">(link)</a></p></li>
 <li><p>EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. <a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf" class="external-link">(link)</a></p></li>
 <li><p>EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.3, 2021. <a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf" class="external-link">(link)</a></p></li>
@@ -233,11 +233,8 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
 <h3 id="custom-rules">Custom Rules<a class="anchor" aria-label="anchor" href="#custom-rules"></a></h3>
 
 
-<p>Custom rules can be created using <code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code>, e.g.:</p><div class="sourceCode"><pre><code><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_eucast_rules.html">custom_eucast_rules</a></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>,
-                         <span class="va">AMC</span> <span class="op">==</span> <span class="st">"I"</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">"I"</span><span class="op">)</span>
-
-<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">example_isolates</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></code></pre></div>
-
+<p>Custom rules can be created using <code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code>, e.g.:</p>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
 </div>
 
 <div class="section">

docs/reference/g.test.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9011</span>
       </span>
     </div>
 
@@ -249,8 +249,8 @@
 <p>Unlike the exact test of goodness-of-fit (<code><a href="https://rdrr.io/r/stats/fisher.test.html" class="external-link">fisher.test()</a></code>), the <em>G</em>-test does not directly calculate the probability of obtaining the observed results or something more extreme. Instead, like almost all statistical tests, the <em>G</em>-test has an intermediate step; it uses the data to calculate a test statistic that measures how far the observed data are from the null expectation. You then use a mathematical relationship, in this case the chi-square distribution, to estimate the probability of obtaining that value of the test statistic.</p>
 <p>The <em>G</em>-test uses the log of the ratio of two likelihoods as the test statistic, which is why it is also called a likelihood ratio test or log-likelihood ratio test. The formula to calculate a <em>G</em>-statistic is:</p>
 <p>\(G = 2 * sum(x * log(x / E))\)</p>
-<p>where <code>E</code> are the expected values. Since this is chi-square distributed, the p value can be calculated in <span style="R">R</span> with:</p><div class="sourceCode"><pre><code><span class="va">p</span> <span class="op">&lt;-</span> <span class="fu">stats</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/stats/Chisquare.html" class="external-link">pchisq</a></span><span class="op">(</span><span class="va">G</span>, <span class="va">df</span>, lower.tail <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
-
+<p>where <code>E</code> are the expected values. Since this is chi-square distributed, the p value can be calculated in <span style="R">R</span> with:</p>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
 <p>where <code>df</code> are the degrees of freedom.</p>
 <p>If there are more than two categories and you want to find out which ones are significantly different from their null expectation, you can use the same method of testing each category vs. the sum of all categories, with the Bonferroni correction. You use <em>G</em>-tests for each category, of course.</p>
 </div>

docs/reference/index.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9010</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
       </span>
     </div>
 
@@ -282,7 +282,7 @@
       </tr><tr><td>
           <p><code><a href="microorganisms.html">microorganisms</a></code> </p>
         </td>
-        <td><p>Data Set with 70,760 Microorganisms</p></td>
+        <td><p>Data Set with 70,764 Microorganisms</p></td>
       </tr><tr><td>
           <p><code><a href="microorganisms.codes.html">microorganisms.codes</a></code> </p>
         </td>
@@ -416,7 +416,7 @@
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer></div>

docs/reference/key_antimicrobials.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
       </span>
     </div>
 
@@ -162,59 +162,82 @@
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">key_antimicrobials</span><span class="op">(</span>
-  x <span class="op">=</span> <span class="cn">NULL</span>,
-  col_mo <span class="op">=</span> <span class="cn">NULL</span>,
-  universal <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"ampicillin"</span>, <span class="st">"amoxicillin/clavulanic acid"</span>, <span class="st">"cefuroxime"</span>,
-    <span class="st">"piperacillin/tazobactam"</span>, <span class="st">"ciprofloxacin"</span>, <span class="st">"trimethoprim/sulfamethoxazole"</span><span class="op">)</span>,
-  gram_negative <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"gentamicin"</span>, <span class="st">"tobramycin"</span>, <span class="st">"colistin"</span>, <span class="st">"cefotaxime"</span>,
-    <span class="st">"ceftazidime"</span>, <span class="st">"meropenem"</span><span class="op">)</span>,
-  gram_positive <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"vancomycin"</span>, <span class="st">"teicoplanin"</span>, <span class="st">"tetracycline"</span>, <span class="st">"erythromycin"</span>,
-    <span class="st">"oxacillin"</span>, <span class="st">"rifampin"</span><span class="op">)</span>,
-  antifungal <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"anidulafungin"</span>, <span class="st">"caspofungin"</span>, <span class="st">"fluconazole"</span>, <span class="st">"miconazole"</span>,
-    <span class="st">"nystatin"</span>, <span class="st">"voriconazole"</span><span class="op">)</span>,
-  only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>,
-  <span class="va">...</span>
-<span class="op">)</span>
-
-<span class="fu">all_antimicrobials</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">antimicrobials_equal</span><span class="op">(</span>
-  <span class="va">y</span>,
-  <span class="va">z</span>,
-  type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"points"</span>, <span class="st">"keyantimicrobials"</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>,
-  <span class="va">...</span>
-<span class="op">)</span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">key_antimicrobials</span><span class="op">(</span></span>
+<span>  x <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  col_mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  universal <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"ampicillin"</span>, <span class="st">"amoxicillin/clavulanic acid"</span>, <span class="st">"cefuroxime"</span>,</span>
+<span>    <span class="st">"piperacillin/tazobactam"</span>, <span class="st">"ciprofloxacin"</span>, <span class="st">"trimethoprim/sulfamethoxazole"</span><span class="op">)</span>,</span>
+<span>  gram_negative <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"gentamicin"</span>, <span class="st">"tobramycin"</span>, <span class="st">"colistin"</span>, <span class="st">"cefotaxime"</span>, <span class="st">"ceftazidime"</span>,</span>
+<span>    <span class="st">"meropenem"</span><span class="op">)</span>,</span>
+<span>  gram_positive <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"vancomycin"</span>, <span class="st">"teicoplanin"</span>, <span class="st">"tetracycline"</span>, <span class="st">"erythromycin"</span>,</span>
+<span>    <span class="st">"oxacillin"</span>, <span class="st">"rifampin"</span><span class="op">)</span>,</span>
+<span>  antifungal <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"anidulafungin"</span>, <span class="st">"caspofungin"</span>, <span class="st">"fluconazole"</span>, <span class="st">"miconazole"</span>, <span class="st">"nystatin"</span>,</span>
+<span>    <span class="st">"voriconazole"</span><span class="op">)</span>,</span>
+<span>  only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">all_antimicrobials</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">antimicrobials_equal</span><span class="op">(</span></span>
+<span>  <span class="va">y</span>,</span>
+<span>  <span class="va">z</span>,</span>
+<span>  type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"points"</span>, <span class="st">"keyantimicrobials"</span><span class="op">)</span>,</span>
+<span>  ignore_I <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  points_threshold <span class="op">=</span> <span class="fl">2</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
     <h2>Arguments</h2>
     <dl><dt>x</dt>
 <dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with antibiotics columns, like <code>AMX</code> or <code>amox</code>. Can be left blank to determine automatically</p></dd>
+
+
 <dt>col_mo</dt>
 <dd><p>column name of the IDs of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
+
+
 <dt>universal</dt>
 <dd><p>names of <strong>broad-spectrum</strong> antimicrobial agents, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default agents.</p></dd>
+
+
 <dt>gram_negative</dt>
 <dd><p>names of antibiotic agents for <strong>Gram-positives</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default agents.</p></dd>
+
+
 <dt>gram_positive</dt>
 <dd><p>names of antibiotic agents for <strong>Gram-negatives</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default agents.</p></dd>
+
+
 <dt>antifungal</dt>
 <dd><p>names of antifungal agents for <strong>fungi</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default agents.</p></dd>
+
+
 <dt>only_rsi_columns</dt>
 <dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only columns must be included that were transformed to class <code>&lt;rsi&gt;</code> (see <code><a href="as.rsi.html">as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></dd>
+
+
 <dt>...</dt>
 <dd><p>ignored, only in place to allow future extensions</p></dd>
+
+
 <dt>y, z</dt>
 <dd><p><a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vectors to compare</p></dd>
+
+
 <dt>type</dt>
 <dd><p>type to determine weighed isolates; can be <code>"keyantimicrobials"</code> or <code>"points"</code>, see <em>Details</em></p></dd>
+
+
 <dt>ignore_I</dt>
 <dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantimicrobials"</code>, see <em>Details</em></p></dd>
+
+
 <dt>points_threshold</dt>
 <dd><p>minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when <code>type = "points"</code>, see <em>Details</em></p></dd>
+
 </dl></div>
     <div id="details">
     <h2>Details</h2>
@@ -267,38 +290,37 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
     <div id="ref-examples">
     <h2>Examples</h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># `example_isolates` is a data set available in the AMR package.</span>
-<span class="co"># See ?example_isolates.</span>
-
-<span class="co"># output of the `key_antimicrobials()` function could be like this:</span>
-<span class="va">strainA</span> <span class="op">&lt;-</span> <span class="st">"SSSRR.S.R..S"</span>
-<span class="va">strainB</span> <span class="op">&lt;-</span> <span class="st">"SSSIRSSSRSSS"</span>
-
-<span class="co"># those strings can be compared with:</span>
-<span class="fu">antimicrobials_equal</span><span class="op">(</span><span class="va">strainA</span>, <span class="va">strainB</span>, type <span class="op">=</span> <span class="st">"keyantimicrobials"</span><span class="op">)</span>
-<span class="co"># TRUE, because I is ignored (as well as missing values)</span>
-
-<span class="fu">antimicrobials_equal</span><span class="op">(</span><span class="va">strainA</span>, <span class="va">strainB</span>, type <span class="op">=</span> <span class="st">"keyantimicrobials"</span>, ignore_I <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
-<span class="co"># FALSE, because I is not ignored and so the 4th [character] differs</span>
-
-<span class="co"># \donttest{</span>
-<span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span>
-  <span class="co"># set key antibiotics to a new variable</span>
-  <span class="va">my_patients</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>keyab <span class="op">=</span> <span class="fu">key_antimicrobials</span><span class="op">(</span>antifungal <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="co"># no need to define `x`</span>
-    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>
-      <span class="co"># now calculate first isolates</span>
-      first_regular <span class="op">=</span> <span class="fu"><a href="first_isolate.html">first_isolate</a></span><span class="op">(</span>col_keyantimicrobials <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-      <span class="co"># and first WEIGHTED isolates</span>
-      first_weighted <span class="op">=</span> <span class="fu"><a href="first_isolate.html">first_isolate</a></span><span class="op">(</span>col_keyantimicrobials <span class="op">=</span> <span class="st">"keyab"</span><span class="op">)</span>
-    <span class="op">)</span>
- 
-  <span class="co"># Check the difference, in this data set it results in more isolates:</span>
-  <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_regular</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
-  <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_weighted</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
-<span class="op">}</span>
-<span class="co"># }</span>
-</code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># `example_isolates` is a data set available in the AMR package.</span></span>
+<span><span class="co"># See ?example_isolates.</span></span>
+<span></span>
+<span><span class="co"># output of the `key_antimicrobials()` function could be like this:</span></span>
+<span><span class="va">strainA</span> <span class="op">&lt;-</span> <span class="st">"SSSRR.S.R..S"</span></span>
+<span><span class="va">strainB</span> <span class="op">&lt;-</span> <span class="st">"SSSIRSSSRSSS"</span></span>
+<span></span>
+<span><span class="co"># those strings can be compared with:</span></span>
+<span><span class="fu">antimicrobials_equal</span><span class="op">(</span><span class="va">strainA</span>, <span class="va">strainB</span>, type <span class="op">=</span> <span class="st">"keyantimicrobials"</span><span class="op">)</span></span>
+<span><span class="co"># TRUE, because I is ignored (as well as missing values)</span></span>
+<span></span>
+<span><span class="fu">antimicrobials_equal</span><span class="op">(</span><span class="va">strainA</span>, <span class="va">strainB</span>, type <span class="op">=</span> <span class="st">"keyantimicrobials"</span>, ignore_I <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
+<span><span class="co"># FALSE, because I is not ignored and so the 4th [character] differs</span></span>
+<span></span>
+<span><span class="co"># \donttest{</span></span>
+<span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
+<span>  <span class="co"># set key antibiotics to a new variable</span></span>
+<span>  <span class="va">my_patients</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>keyab <span class="op">=</span> <span class="fu">key_antimicrobials</span><span class="op">(</span>antifungal <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="co"># no need to define `x`</span></span>
+<span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span>
+<span>      <span class="co"># now calculate first isolates</span></span>
+<span>      first_regular <span class="op">=</span> <span class="fu"><a href="first_isolate.html">first_isolate</a></span><span class="op">(</span>col_keyantimicrobials <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>      <span class="co"># and first WEIGHTED isolates</span></span>
+<span>      first_weighted <span class="op">=</span> <span class="fu"><a href="first_isolate.html">first_isolate</a></span><span class="op">(</span>col_keyantimicrobials <span class="op">=</span> <span class="st">"keyab"</span><span class="op">)</span></span>
+<span>    <span class="op">)</span></span>
+<span> </span>
+<span>  <span class="co"># Check the difference, in this data set it results in more isolates:</span></span>
+<span>  <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_regular</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span>  <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_weighted</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span><span class="op">}</span></span>
+<span><span class="co"># }</span></span></code></pre></div>
     </div>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -312,7 +334,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer></div>

docs/reference/mdro.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9011</span>
       </span>
     </div>
 
@@ -258,31 +258,15 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
 
 
 <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 the <code><a href="https://dplyr.tidyverse.org/reference/case_when.html" class="external-link">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>~</code>) and the consequence of the rule is written <em>after</em> the tilde:</p><div class="sourceCode"><pre><code><span class="va">custom</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">custom_mdro_guideline</a></span><span class="op">(</span><span class="va">CIP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">age</span> <span class="op">&gt;</span> <span class="fl">60</span> <span class="op">~</span> <span class="st">"Elderly Type A"</span>,
-                                <span class="va">ERY</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">age</span> <span class="op">&gt;</span> <span class="fl">60</span> <span class="op">~</span> <span class="st">"Elderly Type B"</span><span class="op">)</span></code></pre></div>
-
+<p>If you are familiar with the <code><a href="https://dplyr.tidyverse.org/reference/case_when.html" class="external-link">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>~</code>) and the consequence of the rule is written <em>after</em> the tilde:</p>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
 <p>If a row/an isolate matches the first rule, the value after the first <code>~</code> (in this case <em>'Elderly Type A'</em>) will be set as MDRO value. Otherwise, the second rule will be tried and so on. The number of rules is unlimited.</p>
-<p>You can print the rules set in the console for an overview. Colours will help reading it if your console supports colours.</p><div class="sourceCode"><pre><code><span class="va">custom</span>
-<span class="co">#&gt; A set of custom MDRO rules:</span>
-<span class="co">#&gt;   1. CIP is "R" and age is higher than 60 -&gt; Elderly Type A</span>
-<span class="co">#&gt;   2. ERY is "R" and age is higher than 60 -&gt; Elderly Type B</span>
-<span class="co">#&gt;   3. Otherwise -&gt; Negative</span>
-<span class="co">#&gt; </span>
-<span class="co">#&gt; Unmatched rows will return NA.</span></code></pre></div>
-
-<p>The outcome of the function can be used for the <code>guideline</code> argument in the <code>mdro()</code> function:</p><div class="sourceCode"><pre><code><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">example_isolates</span>,
-          guideline <span class="op">=</span> <span class="va">custom</span><span class="op">)</span>
-<span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
-<span class="co">#&gt;       Negative Elderly Type A Elderly Type B</span>
-<span class="co">#&gt;           1070            198            732</span></code></pre></div>
-
-<p>Rules can also be combined with other custom rules by using <code><a href="https://rdrr.io/r/base/c.html" class="external-link">c()</a></code>:</p><div class="sourceCode"><pre><code><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">example_isolates</span>,
-          guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">custom</span>, 
-                        <span class="fu"><a href="../reference/mdro.html">custom_mdro_guideline</a></span><span class="op">(</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">50</span> <span class="op">~</span> <span class="st">"Elderly Type C"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>
-<span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
-<span class="co">#&gt;       Negative Elderly Type A Elderly Type B Elderly Type C </span>
-<span class="co">#&gt;            961            198            732            109</span></code></pre></div>
-
+<p>You can print the rules set in the console for an overview. Colours will help reading it if your console supports colours.</p>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
+<p>The outcome of the function can be used for the <code>guideline</code> argument in the <code>mdro()</code> function:</p>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
+<p>Rules can also be combined with other custom rules by using <code><a href="https://rdrr.io/r/base/c.html" class="external-link">c()</a></code>:</p>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
 <p>The rules set (the <code>custom</code> object in this case) could be exported to a shared file location using <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> if you collaborate with multiple users. The custom rules set could then be imported using <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS()</a></code>.</p>
     </div>
     <div id="stable-lifecycle">

docs/reference/microorganisms.html

@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Data Set with 70,760 Microorganisms — microorganisms • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 70,760 Microorganisms — microorganisms"><meta property="og:description" content="A data set containing the full microbial taxonomy (last updated: 5 October 2021) of six kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using as.mo()."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@univgroningen"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Data Set with 70,764 Microorganisms — microorganisms • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 70,764 Microorganisms — microorganisms"><meta property="og:description" content="A data set containing the full microbial taxonomy (last updated: 5 October 2021) of six kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using as.mo()."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@univgroningen"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9013</span>
       </span>
     </div>
 
@@ -152,7 +152,7 @@
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
-    <h1>Data Set with 70,760 Microorganisms</h1>
+    <h1>Data Set with 70,764 Microorganisms</h1>
     <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
     <div class="hidden name"><code>microorganisms.Rd</code></div>
     </div>
@@ -167,7 +167,7 @@
 
     <div id="format">
     <h2>Format</h2>
-    <p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 70,760 observations and 16 variables:</p><ul><li><p><code>mo</code><br> ID of microorganism as used by this package</p></li>
+    <p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 70,764 observations and 16 variables:</p><ul><li><p><code>mo</code><br> ID of microorganism as used by this package</p></li>
 <li><p><code>fullname</code><br> Full name, like <code>"Escherichia coli"</code></p></li>
 <li><p><code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br> Taxonomic rank of the microorganism</p></li>
 <li><p><code>rank</code><br> Text of the taxonomic rank of the microorganism, like <code>"species"</code> or <code>"genus"</code></p></li>
@@ -180,17 +180,17 @@
     <div id="source">
     <h2>Source</h2>
     <p>Catalogue of Life: 2019 Annual Checklist as currently implemented in this <code>AMR</code> package:</p><ul><li><p>Annual Checklist (public online taxonomic database), <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a></p></li>
-</ul><p>List of Prokaryotic names with Standing in Nomenclature (5 October 2021) as currently implemented in this <code>AMR</code> package:</p><ul><li><p>Parte, A.C., Sarda Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Goker, M. (2020). List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; doi: <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">10.1099/ijsem.0.004332</a></p></li>
-<li><p>Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: <a href="https://doi.org/10.1099/ijsem.0.002786" class="external-link">10.1099/ijsem.0.002786</a></p></li>
-<li><p>Parte, A.C. (2014). LPSN - List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613-D616; doi: <a href="https://doi.org/10.1093/nar/gkt1111" class="external-link">10.1093/nar/gkt1111</a></p></li>
-<li><p>Euzeby, J.P. (1997). List of Bacterial Names with Standing in Nomenclature: a Folder Available on the Internet. International Journal of Systematic Bacteriology, 47, 590-592; doi: <a href="https://doi.org/10.1099/00207713-47-2-590" class="external-link">10.1099/00207713-47-2-590</a></p></li>
+</ul><p>List of Prokaryotic names with Standing in Nomenclature (5 October 2021) as currently implemented in this <code>AMR</code> package:</p><ul><li><p>Parte, A.C., Sarda Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Goker, M. (2020). List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a></p></li>
+<li><p>Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; <a href="https://doi.org/10.1099/ijsem.0.002786" class="external-link">doi:10.1099/ijsem.0.002786</a></p></li>
+<li><p>Parte, A.C. (2014). LPSN - List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613-D616; <a href="https://doi.org/10.1093/nar/gkt1111" class="external-link">doi:10.1093/nar/gkt1111</a></p></li>
+<li><p>Euzeby, J.P. (1997). List of Bacterial Names with Standing in Nomenclature: a Folder Available on the Internet. International Journal of Systematic Bacteriology, 47, 590-592; <a href="https://doi.org/10.1099/00207713-47-2-590" class="external-link">doi:10.1099/00207713-47-2-590</a></p></li>
 </ul><p>US Edition of SNOMED CT from 1 September 2020 as currently implemented in this <code>AMR</code> package:</p><ul><li><p>Retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009</a></p></li>
 </ul></div>
     <div id="details">
     <h2>Details</h2>
     <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" class="external-link">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" class="external-link">10.1099/ijs.0.64381-0</a>
+<p>For example, <em>Staphylococcus pettenkoferi</em> was described for the first time in Diagnostic Microbiology and Infectious Disease in 2002 (<a href="https://doi.org/10.1016/s0732-8893%2802%2900399-1" class="external-link">doi:10.1016/s0732-8893(02)00399-1</a>
+), but it was not before 2007 that a publication in IJSEM followed (<a href="https://doi.org/10.1099/ijs.0.64381-0" class="external-link">doi:10.1099/ijs.0.64381-0</a>
 ). Consequently, the <code>AMR</code> package returns 2007 for <code>mo_year("S. pettenkoferi")</code>.</p><div class="section">
 <h3 id="manual-additions">Manual additions<a class="anchor" aria-label="anchor" href="#manual-additions"></a></h3>
 
@@ -198,6 +198,7 @@
 <p>For convenience, some entries were added manually:</p><ul><li><p>11 entries of <em>Streptococcus</em> (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)</p></li>
 <li><p>2 entries of <em>Staphylococcus</em> (coagulase-negative (CoNS) and coagulase-positive (CoPS))</p></li>
 <li><p>3 entries of <em>Trichomonas</em> (<em>T. vaginalis</em>, and its family and genus)</p></li>
+<li><p>4 entries of <em>Toxoplasma</em> (<em>T. gondii</em>, and its order, family and genus)</p></li>
 <li><p>1 entry of <em>Candida</em> (<em>C.  krusei</em>), that is not (yet) in the Catalogue of Life</p></li>
 <li><p>1 entry of <em>Blastocystis</em> (<em>B.  hominis</em>), although it officially does not exist (Noel <em>et al.</em> 2005, PMID 15634993)</p></li>
 <li><p>1 entry of <em>Moraxella</em> (<em>M. catarrhalis</em>), which was formally named <em>Branhamella catarrhalis</em> (Catlin, 1970) though this change was never accepted within the field of clinical microbiology</p></li>
@@ -209,9 +210,9 @@
 <h3 id="direct-download">Direct download<a class="anchor" aria-label="anchor" href="#direct-download"></a></h3>
 
 
-<p>This data set is available as 'flat file' for use even without <span style="R">R</span> - you can find the file here:</p><ul><li><p><a href="https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt" class="external-link">https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt</a></p></li>
-</ul><p>The file in <span style="R">R</span> format (with preserved data structure) can be found here:</p><ul><li><p><a href="https://github.com/msberends/AMR/raw/main/data/microorganisms.rda" class="external-link">https://github.com/msberends/AMR/raw/main/data/microorganisms.rda</a></p></li>
-</ul></div>
+<p>This data set is available as 'flat file' for use even without <span style="R">R</span> - you can find the file here: <a href="https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt" class="external-link">https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt</a>.</p>
+<p>The file in <span style="R">R</span> format (with preserved data structure) can be found here: <a href="https://github.com/msberends/AMR/raw/main/data/microorganisms.rda" class="external-link">https://github.com/msberends/AMR/raw/main/data/microorganisms.rda</a>.</p>
+</div>
 
     </div>
     <div id="about-the-records-from-lpsn-see-source-">

docs/reference/mo_matching_score.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
       </span>
     </div>
 
@@ -162,15 +162,18 @@
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mo_matching_score</span><span class="op">(</span><span class="va">x</span>, <span class="va">n</span><span class="op">)</span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mo_matching_score</span><span class="op">(</span><span class="va">x</span>, <span class="va">n</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
     <h2>Arguments</h2>
     <dl><dt>x</dt>
 <dd><p>Any user input value(s)</p></dd>
+
+
 <dt>n</dt>
 <dd><p>A full taxonomic name, that exists in <code><a href="microorganisms.html">microorganisms$fullname</a></code></p></dd>
+
 </dl></div>
     <div id="matching-score-for-microorganisms">
     <h2>Matching Score for Microorganisms</h2>
@@ -216,12 +219,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
     <div id="ref-examples">
     <h2>Examples</h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
-<span class="fu"><a href="as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span>
-
-<span class="fu">mo_matching_score</span><span class="op">(</span>x <span class="op">=</span> <span class="st">"E. coli"</span>,
-                  n <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span>, <span class="st">"Entamoeba coli"</span><span class="op">)</span><span class="op">)</span>
-</code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span>
+<span><span class="fu"><a href="as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_matching_score</span><span class="op">(</span>x <span class="op">=</span> <span class="st">"E. coli"</span>,</span>
+<span>                  n <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span>, <span class="st">"Entamoeba coli"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
     </div>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -235,7 +237,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer></div>

docs/reference/mo_property.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
       </span>
     </div>
 
@@ -162,83 +162,96 @@
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mo_name</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_fullname</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_shortname</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_subspecies</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_species</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_genus</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_family</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_order</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_class</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_phylum</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_kingdom</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_domain</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_type</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_gramstain</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_is_gram_negative</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_is_gram_positive</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_is_yeast</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_is_intrinsic_resistant</span><span class="op">(</span><span class="va">x</span>, <span class="va">ab</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_snomed</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_ref</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_authors</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_year</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_lpsn</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_rank</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_taxonomy</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_synonyms</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_info</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_url</span><span class="op">(</span><span class="va">x</span>, open <span class="op">=</span> <span class="cn">FALSE</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mo_property</span><span class="op">(</span><span class="va">x</span>, property <span class="op">=</span> <span class="st">"fullname"</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mo_name</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_fullname</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_shortname</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_subspecies</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_species</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_genus</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_family</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_order</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_class</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_phylum</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_kingdom</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_domain</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_type</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_is_gram_negative</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_is_gram_positive</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_is_yeast</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_is_intrinsic_resistant</span><span class="op">(</span><span class="va">x</span>, <span class="va">ab</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_snomed</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_ref</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_authors</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_year</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_lpsn</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_rank</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_taxonomy</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_synonyms</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_info</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_url</span><span class="op">(</span><span class="va">x</span>, open <span class="op">=</span> <span class="cn">FALSE</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_property</span><span class="op">(</span><span class="va">x</span>, property <span class="op">=</span> <span class="st">"fullname"</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
     <h2>Arguments</h2>
     <dl><dt>x</dt>
 <dd><p>any <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vector) that can be coerced to a valid microorganism code with <code><a href="as.mo.html">as.mo()</a></code>. Can be left blank for auto-guessing the column containing microorganism codes if used in a data set, see <em>Examples</em>.</p></dd>
+
+
 <dt>language</dt>
 <dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can be overwritten by setting the option <code>AMR_locale</code>, e.g. <code>options(AMR_locale = "de")</code>, see <a href="translate.html">translate</a>. Also used to translate text like "no growth". Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
+
+
 <dt>...</dt>
 <dd><p>other arguments passed on to <code><a href="as.mo.html">as.mo()</a></code>, such as 'allow_uncertain' and 'ignore_pattern'</p></dd>
+
+
 <dt>ab</dt>
 <dd><p>any (vector of) text that can be coerced to a valid antibiotic code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
+
+
 <dt>open</dt>
 <dd><p>browse the URL using <code><a href="https://rdrr.io/r/utils/browseURL.html" class="external-link">browseURL()</a></code></p></dd>
+
+
 <dt>property</dt>
 <dd><p>one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "species_id", "source", "prevalence" or "snomed", or must be <code>"shortname"</code></p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    <ul><li><p>An <a href="https://rdrr.io/r/base/integer.html" class="external-link">integer</a> in case of <code>mo_year()</code></p></li>
+    
+
+<ul><li><p>An <a href="https://rdrr.io/r/base/integer.html" class="external-link">integer</a> in case of <code>mo_year()</code></p></li>
 <li><p>A <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a> in case of <code>mo_taxonomy()</code> and <code>mo_info()</code></p></li>
 <li><p>A named <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> in case of <code>mo_url()</code></p></li>
 <li><p>A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> in case of <code>mo_snomed()</code></p></li>
@@ -322,108 +335,107 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
     <div id="ref-examples">
     <h2>Examples</h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># taxonomic tree -----------------------------------------------------------</span>
-<span class="fu">mo_kingdom</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>         <span class="co"># "Bacteria"</span>
-<span class="fu">mo_phylum</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>          <span class="co"># "Proteobacteria"</span>
-<span class="fu">mo_class</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>           <span class="co"># "Gammaproteobacteria"</span>
-<span class="fu">mo_order</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>           <span class="co"># "Enterobacterales"</span>
-<span class="fu">mo_family</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>          <span class="co"># "Enterobacteriaceae"</span>
-<span class="fu">mo_genus</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>           <span class="co"># "Escherichia"</span>
-<span class="fu">mo_species</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>         <span class="co"># "coli"</span>
-<span class="fu">mo_subspecies</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>      <span class="co"># ""</span>
-
-<span class="co"># colloquial properties ----------------------------------------------------</span>
-<span class="fu">mo_name</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>            <span class="co"># "Escherichia coli"</span>
-<span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>        <span class="co"># "Escherichia coli" - same as mo_name()</span>
-<span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>       <span class="co"># "E. coli"</span>
-
-<span class="co"># other properties ---------------------------------------------------------</span>
-<span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>       <span class="co"># "Gram-negative"</span>
-<span class="fu">mo_snomed</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>          <span class="co"># 112283007, 116395006, ... (SNOMED codes)</span>
-<span class="fu">mo_type</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>            <span class="co"># "Bacteria" (equal to kingdom, but may be translated)</span>
-<span class="fu">mo_rank</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>            <span class="co"># "species"</span>
-<span class="fu">mo_url</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>             <span class="co"># get the direct url to the online database entry</span>
-<span class="fu">mo_synonyms</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>        <span class="co"># get previously accepted taxonomic names</span>
-
-<span class="co"># scientific reference -----------------------------------------------------</span>
-<span class="fu">mo_ref</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>             <span class="co"># "Castellani et al., 1919"</span>
-<span class="fu">mo_authors</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>         <span class="co"># "Castellani et al."</span>
-<span class="fu">mo_year</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>            <span class="co"># 1919</span>
-<span class="fu">mo_lpsn</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>            <span class="co"># 776057 (LPSN record ID)</span>
-
-<span class="co"># abbreviations known in the field -----------------------------------------</span>
-<span class="fu">mo_genus</span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>              <span class="co"># "Staphylococcus"</span>
-<span class="fu">mo_species</span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>            <span class="co"># "aureus"</span>
-<span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span>          <span class="co"># "S. aureus"</span>
-<span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span>          <span class="co"># "Gram-positive"</span>
-
-<span class="fu">mo_genus</span><span class="op">(</span><span class="st">"EHEC"</span><span class="op">)</span>              <span class="co"># "Escherichia"</span>
-<span class="fu">mo_species</span><span class="op">(</span><span class="st">"EHEC"</span><span class="op">)</span>            <span class="co"># "coli"</span>
-
-<span class="co"># known subspecies ---------------------------------------------------------</span>
-<span class="fu">mo_name</span><span class="op">(</span><span class="st">"doylei"</span><span class="op">)</span>             <span class="co"># "Campylobacter jejuni doylei"</span>
-<span class="fu">mo_genus</span><span class="op">(</span><span class="st">"doylei"</span><span class="op">)</span>            <span class="co"># "Campylobacter"</span>
-<span class="fu">mo_species</span><span class="op">(</span><span class="st">"doylei"</span><span class="op">)</span>          <span class="co"># "jejuni"</span>
-<span class="fu">mo_subspecies</span><span class="op">(</span><span class="st">"doylei"</span><span class="op">)</span>       <span class="co"># "doylei"</span>
-
-<span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"K. pneu rh"</span><span class="op">)</span>     <span class="co"># "Klebsiella pneumoniae rhinoscleromatis"</span>
-<span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"K. pneu rh"</span><span class="op">)</span>    <span class="co"># "K. pneumoniae"</span>
-
-<span class="co"># \donttest{</span>
-<span class="co"># Becker classification, see ?as.mo ----------------------------------------</span>
-<span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. epi"</span><span class="op">)</span>                     <span class="co"># "Staphylococcus epidermidis"</span>
-<span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. epi"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>      <span class="co"># "Coagulase-negative Staphylococcus (CoNS)"</span>
-<span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"S. epi"</span><span class="op">)</span>                    <span class="co"># "S. epidermidis"</span>
-<span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"S. epi"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>     <span class="co"># "CoNS"</span>
-
-<span class="co"># Lancefield classification, see ?as.mo ------------------------------------</span>
-<span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyo"</span><span class="op">)</span>                     <span class="co"># "Streptococcus pyogenes"</span>
-<span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyo"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>  <span class="co"># "Streptococcus group A"</span>
-<span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"S. pyo"</span><span class="op">)</span>                    <span class="co"># "S. pyogenes"</span>
-<span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"S. pyo"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># "GAS" (='Group A Streptococci')</span>
-
-
-<span class="co"># language support  --------------------------------------------------------</span>
-<span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"E. coli"</span>, language <span class="op">=</span> <span class="st">"de"</span><span class="op">)</span>  <span class="co"># "Gramnegativ"</span>
-<span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"E. coli"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span>  <span class="co"># "Gram-negatief"</span>
-<span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"E. coli"</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span>  <span class="co"># "Gram negativo"</span>
-
-<span class="co"># mo_type is equal to mo_kingdom, but mo_kingdom will remain official</span>
-<span class="fu">mo_kingdom</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>                     <span class="co"># "Bacteria" on a German system</span>
-<span class="fu">mo_type</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>                        <span class="co"># "Bakterien" on a German system</span>
-<span class="fu">mo_type</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>                        <span class="co"># "Bacteria" on an English system</span>
-
-<span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyogenes"</span>,
-            Lancefield <span class="op">=</span> <span class="cn">TRUE</span>,
-            language <span class="op">=</span> <span class="st">"de"</span><span class="op">)</span>              <span class="co"># "Streptococcus Gruppe A"</span>
-<span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyogenes"</span>,
-            Lancefield <span class="op">=</span> <span class="cn">TRUE</span>,
-            language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span>              <span class="co"># "Streptococcus groep A"</span>
-
-
-<span class="co"># other --------------------------------------------------------------------</span>
-
-<span class="fu">mo_is_yeast</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Candida"</span>, <span class="st">"E. coli"</span><span class="op">)</span><span class="op">)</span>      <span class="co"># TRUE, FALSE</span>
-
-<span class="co"># gram stains and intrinsic resistance can also be used as a filter in dplyr verbs</span>
-<span class="co"># \donttest{</span>
-<span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span>
-  <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">mo_is_gram_positive</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
-    
-  <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">mo_is_intrinsic_resistant</span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"vanco"</span><span class="op">)</span><span class="op">)</span>
-<span class="op">}</span>
-
-
-<span class="co"># get a list with the complete taxonomy (from kingdom to subspecies)</span>
-<span class="fu">mo_taxonomy</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
-<span class="co"># get a list with the taxonomy, the authors, Gram-stain,</span>
-<span class="co">#   SNOMED codes, and URL to the online database</span>
-<span class="fu">mo_info</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
-<span class="co"># }</span>
-<span class="co"># }</span>
-</code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># taxonomic tree -----------------------------------------------------------</span></span>
+<span><span class="fu">mo_kingdom</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>         <span class="co"># "Bacteria"</span></span>
+<span><span class="fu">mo_phylum</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>          <span class="co"># "Proteobacteria"</span></span>
+<span><span class="fu">mo_class</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>           <span class="co"># "Gammaproteobacteria"</span></span>
+<span><span class="fu">mo_order</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>           <span class="co"># "Enterobacterales"</span></span>
+<span><span class="fu">mo_family</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>          <span class="co"># "Enterobacteriaceae"</span></span>
+<span><span class="fu">mo_genus</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>           <span class="co"># "Escherichia"</span></span>
+<span><span class="fu">mo_species</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>         <span class="co"># "coli"</span></span>
+<span><span class="fu">mo_subspecies</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>      <span class="co"># ""</span></span>
+<span></span>
+<span><span class="co"># colloquial properties ----------------------------------------------------</span></span>
+<span><span class="fu">mo_name</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>            <span class="co"># "Escherichia coli"</span></span>
+<span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>        <span class="co"># "Escherichia coli" - same as mo_name()</span></span>
+<span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>       <span class="co"># "E. coli"</span></span>
+<span></span>
+<span><span class="co"># other properties ---------------------------------------------------------</span></span>
+<span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>       <span class="co"># "Gram-negative"</span></span>
+<span><span class="fu">mo_snomed</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>          <span class="co"># 112283007, 116395006, ... (SNOMED codes)</span></span>
+<span><span class="fu">mo_type</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>            <span class="co"># "Bacteria" (equal to kingdom, but may be translated)</span></span>
+<span><span class="fu">mo_rank</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>            <span class="co"># "species"</span></span>
+<span><span class="fu">mo_url</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>             <span class="co"># get the direct url to the online database entry</span></span>
+<span><span class="fu">mo_synonyms</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>        <span class="co"># get previously accepted taxonomic names</span></span>
+<span></span>
+<span><span class="co"># scientific reference -----------------------------------------------------</span></span>
+<span><span class="fu">mo_ref</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>             <span class="co"># "Castellani et al., 1919"</span></span>
+<span><span class="fu">mo_authors</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>         <span class="co"># "Castellani et al."</span></span>
+<span><span class="fu">mo_year</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>            <span class="co"># 1919</span></span>
+<span><span class="fu">mo_lpsn</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>            <span class="co"># 776057 (LPSN record ID)</span></span>
+<span></span>
+<span><span class="co"># abbreviations known in the field -----------------------------------------</span></span>
+<span><span class="fu">mo_genus</span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>              <span class="co"># "Staphylococcus"</span></span>
+<span><span class="fu">mo_species</span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>            <span class="co"># "aureus"</span></span>
+<span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span>          <span class="co"># "S. aureus"</span></span>
+<span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span>          <span class="co"># "Gram-positive"</span></span>
+<span></span>
+<span><span class="fu">mo_genus</span><span class="op">(</span><span class="st">"EHEC"</span><span class="op">)</span>              <span class="co"># "Escherichia"</span></span>
+<span><span class="fu">mo_species</span><span class="op">(</span><span class="st">"EHEC"</span><span class="op">)</span>            <span class="co"># "coli"</span></span>
+<span></span>
+<span><span class="co"># known subspecies ---------------------------------------------------------</span></span>
+<span><span class="fu">mo_name</span><span class="op">(</span><span class="st">"doylei"</span><span class="op">)</span>             <span class="co"># "Campylobacter jejuni doylei"</span></span>
+<span><span class="fu">mo_genus</span><span class="op">(</span><span class="st">"doylei"</span><span class="op">)</span>            <span class="co"># "Campylobacter"</span></span>
+<span><span class="fu">mo_species</span><span class="op">(</span><span class="st">"doylei"</span><span class="op">)</span>          <span class="co"># "jejuni"</span></span>
+<span><span class="fu">mo_subspecies</span><span class="op">(</span><span class="st">"doylei"</span><span class="op">)</span>       <span class="co"># "doylei"</span></span>
+<span></span>
+<span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"K. pneu rh"</span><span class="op">)</span>     <span class="co"># "Klebsiella pneumoniae rhinoscleromatis"</span></span>
+<span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"K. pneu rh"</span><span class="op">)</span>    <span class="co"># "K. pneumoniae"</span></span>
+<span></span>
+<span><span class="co"># \donttest{</span></span>
+<span><span class="co"># Becker classification, see ?as.mo ----------------------------------------</span></span>
+<span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. epi"</span><span class="op">)</span>                     <span class="co"># "Staphylococcus epidermidis"</span></span>
+<span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. epi"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>      <span class="co"># "Coagulase-negative Staphylococcus (CoNS)"</span></span>
+<span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"S. epi"</span><span class="op">)</span>                    <span class="co"># "S. epidermidis"</span></span>
+<span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"S. epi"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>     <span class="co"># "CoNS"</span></span>
+<span></span>
+<span><span class="co"># Lancefield classification, see ?as.mo ------------------------------------</span></span>
+<span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyo"</span><span class="op">)</span>                     <span class="co"># "Streptococcus pyogenes"</span></span>
+<span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyo"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>  <span class="co"># "Streptococcus group A"</span></span>
+<span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"S. pyo"</span><span class="op">)</span>                    <span class="co"># "S. pyogenes"</span></span>
+<span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"S. pyo"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># "GAS" (='Group A Streptococci')</span></span>
+<span></span>
+<span></span>
+<span><span class="co"># language support  --------------------------------------------------------</span></span>
+<span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"E. coli"</span>, language <span class="op">=</span> <span class="st">"de"</span><span class="op">)</span>  <span class="co"># "Gramnegativ"</span></span>
+<span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"E. coli"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span>  <span class="co"># "Gram-negatief"</span></span>
+<span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"E. coli"</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span>  <span class="co"># "Gram negativo"</span></span>
+<span></span>
+<span><span class="co"># mo_type is equal to mo_kingdom, but mo_kingdom will remain official</span></span>
+<span><span class="fu">mo_kingdom</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>                     <span class="co"># "Bacteria" on a German system</span></span>
+<span><span class="fu">mo_type</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>                        <span class="co"># "Bakterien" on a German system</span></span>
+<span><span class="fu">mo_type</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>                        <span class="co"># "Bacteria" on an English system</span></span>
+<span></span>
+<span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyogenes"</span>,</span>
+<span>            Lancefield <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>            language <span class="op">=</span> <span class="st">"de"</span><span class="op">)</span>              <span class="co"># "Streptococcus Gruppe A"</span></span>
+<span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyogenes"</span>,</span>
+<span>            Lancefield <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>            language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span>              <span class="co"># "Streptococcus groep A"</span></span>
+<span></span>
+<span></span>
+<span><span class="co"># other --------------------------------------------------------------------</span></span>
+<span></span>
+<span><span class="fu">mo_is_yeast</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Candida"</span>, <span class="st">"E. coli"</span><span class="op">)</span><span class="op">)</span>      <span class="co"># TRUE, FALSE</span></span>
+<span></span>
+<span><span class="co"># gram stains and intrinsic resistance can also be used as a filter in dplyr verbs</span></span>
+<span><span class="co"># \donttest{</span></span>
+<span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
+<span>  <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">mo_is_gram_positive</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
+<span>    </span>
+<span>  <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">mo_is_intrinsic_resistant</span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"vanco"</span><span class="op">)</span><span class="op">)</span></span>
+<span><span class="op">}</span></span>
+<span></span>
+<span></span>
+<span><span class="co"># get a list with the complete taxonomy (from kingdom to subspecies)</span></span>
+<span><span class="fu">mo_taxonomy</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span>
+<span><span class="co"># get a list with the taxonomy, the authors, Gram-stain,</span></span>
+<span><span class="co">#   SNOMED codes, and URL to the online database</span></span>
+<span><span class="fu">mo_info</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span>
+<span><span class="co"># }</span></span>
+<span><span class="co"># }</span></span></code></pre></div>
     </div>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -437,7 +449,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer></div>

docs/reference/mo_source.html

@@ -18,7 +18,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9011</span>
       </span>
     </div>
 
@@ -192,56 +192,19 @@ This is the fastest way to have your organisation (or analysis) specific codes p
     
 
 
-<p>Imagine this data on a sheet of an Excel file. The first column contains the organisation specific codes, the second column contains valid taxonomic names:</p><div class="sourceCode"><pre><code>  |         A          |            B          |
---|--------------------|-----------------------|
-1 | Organisation XYZ   | mo                    |
-2 | lab_mo_ecoli       | Escherichia coli      |
-3 | lab_mo_kpneumoniae | Klebsiella pneumoniae |
-4 |                    |                       |
-</code></pre></div>
-
-<p>We save it as <code>"home/me/ourcodes.xlsx"</code>. Now we have to set it as a source:</p><div class="sourceCode"><pre><code><span class="fu"><a href="../reference/mo_source.html">set_mo_source</a></span><span class="op">(</span><span class="st">"home/me/ourcodes.xlsx"</span><span class="op">)</span>
-<span class="co">#&gt; NOTE: Created mo_source file '/Users/me/mo_source.rds' (0.3 kB) from</span>
-<span class="co">#&gt;       '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns </span>
-<span class="co">#&gt;       "Organisation XYZ" and "mo"</span></code></pre></div>
-
+<p>Imagine this data on a sheet of an Excel file. The first column contains the organisation specific codes, the second column contains valid taxonomic names:</p>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
+<p>We save it as <code>"home/me/ourcodes.xlsx"</code>. Now we have to set it as a source:</p>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
 <p>It has now created a file <code>"~/mo_source.rds"</code> with the contents of our Excel file. Only the first column with foreign values and the 'mo' column will be kept when creating the RDS file.</p>
-<p>And now we can use it in our functions:</p><div class="sourceCode"><pre><code><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"lab_mo_ecoli"</span><span class="op">)</span>
-<span class="co">#&gt; Class &lt;mo&gt;</span>
-<span class="co">#&gt; [1] B_ESCHR_COLI</span>
-
-<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"lab_mo_kpneumoniae"</span><span class="op">)</span>
-<span class="co">#&gt; [1] "Klebsiella"</span>
-
-<span class="co"># other input values still work too</span>
-<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span>, <span class="st">"E. coli"</span>, <span class="st">"lab_mo_ecoli"</span><span class="op">)</span><span class="op">)</span>
-<span class="co">#&gt; NOTE: Translation to one microorganism was guessed with uncertainty.</span>
-<span class="co">#&gt;       Use mo_uncertainties() to review it.</span>
-<span class="co">#&gt; Class &lt;mo&gt;</span>
-<span class="co">#&gt; [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI</span></code></pre></div>
-
-<p>If we edit the Excel file by, let's say, adding row 4 like this:</p><div class="sourceCode"><pre><code>  |         A          |            B          |
---|--------------------|-----------------------|
-1 | Organisation XYZ   | mo                    |
-2 | lab_mo_ecoli       | Escherichia coli      |
-3 | lab_mo_kpneumoniae | Klebsiella pneumoniae |
-4 | lab_Staph_aureus   | Staphylococcus aureus |
-5 |                    |                       |
-</code></pre></div>
-
-<p>...any new usage of an MO function in this package will update your data file:</p><div class="sourceCode"><pre><code><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"lab_mo_ecoli"</span><span class="op">)</span>
-<span class="co">#&gt; NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from </span>
-<span class="co">#&gt;       '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns</span>
-<span class="co">#&gt;        "Organisation XYZ" and "mo"</span>
-<span class="co">#&gt; Class &lt;mo&gt;</span>
-<span class="co">#&gt; [1] B_ESCHR_COLI</span>
-
-<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"lab_Staph_aureus"</span><span class="op">)</span>
-<span class="co">#&gt; [1] "Staphylococcus"</span></code></pre></div>
-
-<p>To delete the reference data file, just use <code>""</code>, <code>NULL</code> or <code>FALSE</code> as input for <code>set_mo_source()</code>:</p><div class="sourceCode"><pre><code><span class="fu"><a href="../reference/mo_source.html">set_mo_source</a></span><span class="op">(</span><span class="cn">NULL</span><span class="op">)</span>
-<span class="co">#&gt; Removed mo_source file '/Users/me/mo_source.rds'</span></code></pre></div>
-
+<p>And now we can use it in our functions:</p>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
+<p>If we edit the Excel file by, let's say, adding row 4 like this:</p>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
+<p>...any new usage of an MO function in this package will update your data file:</p>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
+<p>To delete the reference data file, just use <code>""</code>, <code>NULL</code> or <code>FALSE</code> as input for <code>set_mo_source()</code>:</p>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
 <p>If the original file (in the previous case an Excel file) is moved or deleted, the <code>mo_source.rds</code> file will be removed upon the next use of <code><a href="as.mo.html">as.mo()</a></code> or any <code><a href="mo_property.html">mo_*</a></code> function.</p>
     </div>
     <div id="stable-lifecycle">

docs/reference/proportion.html

@@ -18,7 +18,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9011</span>
       </span>
     </div>
 
@@ -239,30 +239,12 @@ resistance() should be used to calculate resistance, susceptibility() should be
     <h2>Combination Therapy</h2>
     
 
-<p>When using more than one variable for <code>...</code> (= combination therapy), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code>susceptibility()</code> works to calculate the %SI:</p><div class="sourceCode"><pre><code>--------------------------------------------------------------------
-                    only_all_tested = FALSE  only_all_tested = TRUE
-                    -----------------------  -----------------------
- Drug A    Drug B   include as  include as   include as  include as
-                    numerator   denominator  numerator   denominator
---------  --------  ----------  -----------  ----------  -----------
- S or I    S or I       X            X            X            X
-   R       S or I       X            X            X            X
-  &lt;NA&gt;     S or I       X            X            -            -
- S or I      R          X            X            X            X
-   R         R          -            X            -            X
-  &lt;NA&gt;       R          -            -            -            -
- S or I     &lt;NA&gt;        X            X            -            -
-   R        &lt;NA&gt;        -            -            -            -
-  &lt;NA&gt;      &lt;NA&gt;        -            -            -            -
---------------------------------------------------------------------
-</code></pre></div>
-
-<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><div class="sourceCode"><pre><code><span class="fu"><a href="../reference/count.html">count_S</a></span><span class="op">(</span><span class="op">)</span>    <span class="op">+</span>   <span class="fu"><a href="../reference/count.html">count_I</a></span><span class="op">(</span><span class="op">)</span>    <span class="op">+</span>   <span class="fu"><a href="../reference/count.html">count_R</a></span><span class="op">(</span><span class="op">)</span>    <span class="op">=</span> <span class="fu"><a href="../reference/count.html">count_all</a></span><span class="op">(</span><span class="op">)</span>
-  <span class="fu"><a href="../reference/proportion.html">proportion_S</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="../reference/proportion.html">proportion_I</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="../reference/proportion.html">proportion_R</a></span><span class="op">(</span><span class="op">)</span> <span class="op">=</span> <span class="fl">1</span></code></pre></div>
-
-<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><div class="sourceCode"><pre><code><span class="fu"><a href="../reference/count.html">count_S</a></span><span class="op">(</span><span class="op">)</span>    <span class="op">+</span>   <span class="fu"><a href="../reference/count.html">count_I</a></span><span class="op">(</span><span class="op">)</span>    <span class="op">+</span>   <span class="fu"><a href="../reference/count.html">count_R</a></span><span class="op">(</span><span class="op">)</span>    <span class="op">&gt;=</span> <span class="fu"><a href="../reference/count.html">count_all</a></span><span class="op">(</span><span class="op">)</span>
-  <span class="fu"><a href="../reference/proportion.html">proportion_S</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="../reference/proportion.html">proportion_I</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="../reference/proportion.html">proportion_R</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&gt;=</span> <span class="fl">1</span></code></pre></div>
-
+<p>When using more than one variable for <code>...</code> (= combination therapy), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code>susceptibility()</code> works to calculate the %SI:</p>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
+<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
+<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p>
+<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
 <p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
     </div>
     <div id="stable-lifecycle">

docs/reference/random.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9011</span>
       </span>
     </div>
 

docs/reference/resistance_predict.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9012</span>
       </span>
     </div>
 
@@ -203,7 +203,7 @@
 <span class="op">)</span>
 
 <span class="co"># S3 method for resistance_predict</span>
-<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span>
+<span class="fu">autoplot</span><span class="op">(</span>
   <span class="va">object</span>,
   main <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Resistance Prediction of"</span>, <span class="va">x_name</span><span class="op">)</span>,
   ribbon <span class="op">=</span> <span class="cn">TRUE</span>,
@@ -228,7 +228,7 @@
 <dt>minimum</dt>
 <dd><p>minimal amount of available isolates per year to include. Years containing less observations will be estimated by the model.</p></dd>
 <dt>model</dt>
-<dd><p>the statistical model of choice. This could be a generalised linear regression model with binomial distribution (i.e. using `glm(..., family = binomial)``, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See <em>Details</em> for all valid options.</p></dd>
+<dd><p>the statistical model of choice. This could be a generalised linear regression model with binomial distribution (i.e. using <code>glm(..., family = binomial)</code>, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See <em>Details</em> for all valid options.</p></dd>
 <dt>I_as_S</dt>
 <dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether values <code>"I"</code> should be treated as <code>"S"</code> (will otherwise be treated as <code>"R"</code>). The default, <code>TRUE</code>, follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section <em>Interpretation of S, I and R</em> below.</p></dd>
 <dt>preserve_measurements</dt>

docs/reference/rsi_translation.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
       </span>
     </div>
 
@@ -162,7 +162,7 @@
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="va">rsi_translation</span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">rsi_translation</span></span></code></pre></div>
     </div>
 
     <div id="format">
@@ -181,21 +181,22 @@
 </ul></div>
     <div id="details">
     <h2>Details</h2>
-    <p>Overview of the data set:</p><div class="sourceCode r"><pre><code><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">rsi_translation</span><span class="op">)</span></code></pre><p></p></div><div class="sourceCode"><pre><code><span class="co">##     guideline method site           mo rank_index  ab     ref_tbl disk_dose</span>
-<span class="co">## 1 EUCAST 2022    MIC &lt;NA&gt; F_ASPRG_MGTS          2 AMB Aspergillus      &lt;NA&gt;</span>
-<span class="co">## 2 EUCAST 2022    MIC &lt;NA&gt; F_ASPRG_NIGR          2 AMB Aspergillus      &lt;NA&gt;</span>
-<span class="co">## 3 EUCAST 2022    MIC &lt;NA&gt;      F_CANDD          3 AMB     Candida      &lt;NA&gt;</span>
-<span class="co">## 4 EUCAST 2022    MIC &lt;NA&gt; F_CANDD_ALBC          2 AMB     Candida      &lt;NA&gt;</span>
-<span class="co">## 5 EUCAST 2022    MIC &lt;NA&gt; F_CANDD_DBLN          2 AMB     Candida      &lt;NA&gt;</span>
-<span class="co">## 6 EUCAST 2022    MIC &lt;NA&gt; F_CANDD_KRUS          2 AMB     Candida      &lt;NA&gt;</span>
-<span class="co">##   breakpoint_S breakpoint_R   uti</span>
-<span class="co">## 1            1            1 FALSE</span>
-<span class="co">## 2            1            1 FALSE</span>
-<span class="co">## 3            1            1 FALSE</span>
-<span class="co">## 4            1            1 FALSE</span>
-<span class="co">## 5            1            1 FALSE</span>
-<span class="co">## 6            1            1 FALSE</span></code></pre></div>
-
+    <p>Overview of the data set:</p>
+<p></p><div class="sourceCode r"><pre><code><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">rsi_translation</span><span class="op">)</span></span>
+<span><span class="co">#&gt;     guideline method site           mo rank_index  ab     ref_tbl disk_dose</span></span>
+<span><span class="co">#&gt; 1 EUCAST 2022    MIC &lt;NA&gt; F_ASPRG_MGTS          2 AMB Aspergillus      &lt;NA&gt;</span></span>
+<span><span class="co">#&gt; 2 EUCAST 2022    MIC &lt;NA&gt; F_ASPRG_NIGR          2 AMB Aspergillus      &lt;NA&gt;</span></span>
+<span><span class="co">#&gt; 3 EUCAST 2022    MIC &lt;NA&gt;      F_CANDD          3 AMB     Candida      &lt;NA&gt;</span></span>
+<span><span class="co">#&gt; 4 EUCAST 2022    MIC &lt;NA&gt; F_CANDD_ALBC          2 AMB     Candida      &lt;NA&gt;</span></span>
+<span><span class="co">#&gt; 5 EUCAST 2022    MIC &lt;NA&gt; F_CANDD_DBLN          2 AMB     Candida      &lt;NA&gt;</span></span>
+<span><span class="co">#&gt; 6 EUCAST 2022    MIC &lt;NA&gt; F_CANDD_KRUS          2 AMB     Candida      &lt;NA&gt;</span></span>
+<span><span class="co">#&gt;   breakpoint_S breakpoint_R   uti</span></span>
+<span><span class="co">#&gt; 1            1            1 FALSE</span></span>
+<span><span class="co">#&gt; 2            1            1 FALSE</span></span>
+<span><span class="co">#&gt; 3            1            1 FALSE</span></span>
+<span><span class="co">#&gt; 4            1            1 FALSE</span></span>
+<span><span class="co">#&gt; 5            1            1 FALSE</span></span>
+<span><span class="co">#&gt; 6            1            1 FALSE</span></span></code></pre><p></p></div>
 <p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href="https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt</a>. This file <strong>allows for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the <code>mo</code> and <code>ab</code> columns have been transformed to contain the full official names instead of codes.</p>
     </div>
     <div id="reference-data-publicly-available">
@@ -227,7 +228,7 @@
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer></div>

docs/survey.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9010</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
       </span>
     </div>
 
@@ -172,7 +172,7 @@
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer></div>

man/as.mic.Rd

@@ -35,7 +35,9 @@ This transforms vectors to a new class \code{\link{mic}}, which treats the input
 \details{
 To interpret MIC values as RSI values, use \code{\link[=as.rsi]{as.rsi()}} on MIC values. It supports guidelines from EUCAST (2011-2022) and CLSI (2011-2022).
 
-This class for MIC values is a quite a special data type: formally it is an ordered \link{factor} with valid MIC values as \link{factor} levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:\preformatted{x <- random_mic(10)
+This class for MIC values is a quite a special data type: formally it is an ordered \link{factor} with valid MIC values as \link{factor} levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{x <- random_mic(10)
 x
 #> Class <mic>
 #>  [1] 16     1      8      8      64     >=128  0.0625 32     32     16
@@ -48,9 +50,11 @@ x[1] * 2
 
 median(x)
 #> [1] 26
-}
+}\if{html}{\out{</div>}}
 
-This makes it possible to maintain operators that often come with MIC values, such ">=" and "<=", even when filtering using \link{numeric} values in data analysis, e.g.:\preformatted{x[x > 4]
+This makes it possible to maintain operators that often come with MIC values, such ">=" and "<=", even when filtering using \link{numeric} values in data analysis, e.g.:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{x[x > 4]
 #> Class <mic>
 #> [1] 16    8     8     64    >=128 32    32    16
 
@@ -63,7 +67,7 @@ subset(df, x > 4) # or with dplyr: df \%>\% filter(x > 4)
 #> 8     32        A
 #> 9     32        A
 #> 10    16        A
-}
+}\if{html}{\out{</div>}}
 
 The following \link[=groupGeneric]{generic functions} are implemented for the MIC class: \code{!}, \code{!=}, \code{\%\%}, \code{\%/\%}, \code{&}, \code{*}, \code{+}, \code{-}, \code{/}, \code{<}, \code{<=}, \code{==}, \code{>}, \code{>=}, \code{^}, \code{|}, \code{\link[=abs]{abs()}}, \code{\link[=acos]{acos()}}, \code{\link[=acosh]{acosh()}}, \code{\link[=all]{all()}}, \code{\link[=any]{any()}}, \code{\link[=asin]{asin()}}, \code{\link[=asinh]{asinh()}}, \code{\link[=atan]{atan()}}, \code{\link[=atanh]{atanh()}}, \code{\link[=ceiling]{ceiling()}}, \code{\link[=cos]{cos()}}, \code{\link[=cosh]{cosh()}}, \code{\link[=cospi]{cospi()}}, \code{\link[=cummax]{cummax()}}, \code{\link[=cummin]{cummin()}}, \code{\link[=cumprod]{cumprod()}}, \code{\link[=cumsum]{cumsum()}}, \code{\link[=digamma]{digamma()}}, \code{\link[=exp]{exp()}}, \code{\link[=expm1]{expm1()}}, \code{\link[=floor]{floor()}}, \code{\link[=gamma]{gamma()}}, \code{\link[=lgamma]{lgamma()}}, \code{\link[=log]{log()}}, \code{\link[=log1p]{log1p()}}, \code{\link[=log2]{log2()}}, \code{\link[=log10]{log10()}}, \code{\link[=max]{max()}}, \code{\link[=mean]{mean()}}, \code{\link[=min]{min()}}, \code{\link[=prod]{prod()}}, \code{\link[=range]{range()}}, \code{\link[=round]{round()}}, \code{\link[=sign]{sign()}}, \code{\link[=signif]{signif()}}, \code{\link[=sin]{sin()}}, \code{\link[=sinh]{sinh()}}, \code{\link[=sinpi]{sinpi()}}, \code{\link[=sqrt]{sqrt()}}, \code{\link[=sum]{sum()}}, \code{\link[=tan]{tan()}}, \code{\link[=tanh]{tanh()}}, \code{\link[=tanpi]{tanpi()}}, \code{\link[=trigamma]{trigamma()}} and \code{\link[=trunc]{trunc()}}. Some functions of the \code{stats} package are also implemented: \code{\link[=median]{median()}}, \code{\link[=quantile]{quantile()}}, \code{\link[=mad]{mad()}}, \code{\link[=IQR]{IQR()}}, \code{\link[=fivenum]{fivenum()}}. Also, \code{\link[=boxplot.stats]{boxplot.stats()}} is supported. Since \code{\link[=sd]{sd()}} and \code{\link[=var]{var()}} are non-generic functions, these could not be extended. Use \code{\link[=mad]{mad()}} as an alternative, or use e.g. \code{sd(as.numeric(x))} where \code{x} is your vector of MIC values.
 

man/as.mo.Rd

@@ -61,7 +61,9 @@ Use this function to determine a valid microorganism code (\code{\link{mo}}). De
 \details{
 \subsection{General Info}{
 
-A microorganism (MO) code from this package (class: \code{\link{mo}}) is human readable and typically looks like these examples:\preformatted{  Code               Full name
+A microorganism (MO) code from this package (class: \code{\link{mo}}) is human readable and typically looks like these examples:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{  Code               Full name
   ---------------    --------------------------------------
   B_KLBSL            Klebsiella
   B_KLBSL_PNMN       Klebsiella pneumoniae
@@ -73,7 +75,7 @@ A microorganism (MO) code from this package (class: \code{\link{mo}}) is human r
   |   \\----> genus, a 5-7 letter acronym
   \\----> taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
                             C (Chromista), F (Fungi), P (Protozoa)
-}
+}\if{html}{\out{</div>}}
 
 Values that cannot be coerced will be considered 'unknown' and will get the MO code \code{UNKNOWN}.
 

man/as.rsi.Rd

@@ -94,16 +94,20 @@ The \code{\link[=as.rsi]{as.rsi()}} function works in four ways:
 \item For \strong{cleaning raw / untransformed data}. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with R/SI interpretations and MIC values such as \code{"<0.25; S"} will be coerced to \code{"S"}. Combined interpretations for multiple test methods (as seen in laboratory records) such as \code{"S; S"} will be coerced to \code{"S"}, but a value like \code{"S; I"} will return \code{NA} with a warning that the input is unclear.
 \item For \strong{interpreting minimum inhibitory concentration (MIC) values} according to EUCAST or CLSI. You must clean your MIC values first using \code{\link[=as.mic]{as.mic()}}, that also gives your columns the new data class \code{\link{mic}}. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the \code{mo} argument.
 \itemize{
-\item Using \code{dplyr}, R/SI interpretation can be done very easily with either:\preformatted{your_data \%>\% mutate_if(is.mic, as.rsi)             # until dplyr 1.0.0
+\item Using \code{dplyr}, R/SI interpretation can be done very easily with either:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{your_data \%>\% mutate_if(is.mic, as.rsi)             # until dplyr 1.0.0
 your_data \%>\% mutate(across(where(is.mic), as.rsi)) # since dplyr 1.0.0
-}
+}\if{html}{\out{</div>}}
 \item Operators like "<=" will be stripped before interpretation. When using \code{conserve_capped_values = TRUE}, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (\code{conserve_capped_values = FALSE}) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".
 }
 \item For \strong{interpreting disk diffusion diameters} according to EUCAST or CLSI. You must clean your disk zones first using \code{\link[=as.disk]{as.disk()}}, that also gives your columns the new data class \code{\link{disk}}. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the \code{mo} argument.
 \itemize{
-\item Using \code{dplyr}, R/SI interpretation can be done very easily with either:\preformatted{your_data \%>\% mutate_if(is.disk, as.rsi)             # until dplyr 1.0.0
+\item Using \code{dplyr}, R/SI interpretation can be done very easily with either:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{your_data \%>\% mutate_if(is.disk, as.rsi)             # until dplyr 1.0.0
 your_data \%>\% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0
-}
+}\if{html}{\out{</div>}}
 }
 \item For \strong{interpreting a complete data set}, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running \code{as.rsi(your_data)}.
 }

man/atc_online.Rd

@@ -59,7 +59,7 @@ Abbreviations of return values when using \code{property = "U"} (unit):
 \itemize{
 \item \code{"g"} = gram
 \item \code{"mg"} = milligram
-\item `"mcg"`` = microgram
+\item \code{"mcg"} = microgram
 \item \code{"U"} = unit
 \item \code{"TU"} = thousand units
 \item \code{"MU"} = million units

man/count.Rd

@@ -97,7 +97,9 @@ This AMR package honours this (new) insight. Use \code{\link[=susceptibility]{su
 
 \section{Combination Therapy}{
 
-When using more than one variable for \code{...} (= combination therapy), use \code{only_all_tested} to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how \code{\link[=susceptibility]{susceptibility()}} works to calculate the \%SI:\preformatted{--------------------------------------------------------------------
+When using more than one variable for \code{...} (= combination therapy), use \code{only_all_tested} to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how \code{\link[=susceptibility]{susceptibility()}} works to calculate the \%SI:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{--------------------------------------------------------------------
                     only_all_tested = FALSE  only_all_tested = TRUE
                     -----------------------  -----------------------
  Drug A    Drug B   include as  include as   include as  include as
@@ -113,15 +115,19 @@ When using more than one variable for \code{...} (= combination therapy), use \c
    R        <NA>        -            -            -            -
   <NA>      <NA>        -            -            -            -
 --------------------------------------------------------------------
-}
+}\if{html}{\out{</div>}}
 
-Please note that, in combination therapies, for \code{only_all_tested = TRUE} applies that:\preformatted{    count_S()    +   count_I()    +   count_R()    = count_all()
+Please note that, in combination therapies, for \code{only_all_tested = TRUE} applies that:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{    count_S()    +   count_I()    +   count_R()    = count_all()
   proportion_S() + proportion_I() + proportion_R() = 1
-}
+}\if{html}{\out{</div>}}
 
-and that, in combination therapies, for \code{only_all_tested = FALSE} applies that:\preformatted{    count_S()    +   count_I()    +   count_R()    >= count_all()
+and that, in combination therapies, for \code{only_all_tested = FALSE} applies that:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{    count_S()    +   count_I()    +   count_R()    >= count_all()
   proportion_S() + proportion_I() + proportion_R() >= 1
-}
+}\if{html}{\out{</div>}}
 
 Using \code{only_all_tested} has no impact when only using one antibiotic as input.
 }

man/custom_eucast_rules.Rd

@@ -7,7 +7,7 @@
 custom_eucast_rules(...)
 }
 \arguments{
-\item{...}{rules in formula notation, see \emph{Examples}}
+\item{...}{rules in \link[=`~`]{formula} notation, see \emph{Examples}}
 }
 \value{
 A \link{list} containing the custom rules
@@ -22,11 +22,15 @@ Some organisations have their own adoption of EUCAST rules. This function can be
 
 \subsection{Basics}{
 
-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")
-}
+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:
 
-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
+\if{html}{\out{<div class="sourceCode">}}\preformatted{x <- custom_eucast_rules(TZP == "S" ~ aminopenicillins == "S",
+                         TZP == "R" ~ aminopenicillins == "R")
+}\if{html}{\out{</div>}}
+
+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:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{x
 #> A set of custom EUCAST rules:
 #> 
 #>   1. If TZP is S then set to S:
@@ -34,9 +38,11 @@ These are two custom EUCAST rules: if TZP (piperacillin/tazobactam) is "S", all
 #> 
 #>   2. If TZP is R then set to R:
 #>      amoxicillin (AMX), ampicillin (AMP)
-}
+}\if{html}{\out{</div>}}
 
-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"),
+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:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{df <- data.frame(mo = c("E. coli", "K. pneumoniae"),
                  TZP = "R",
                  amox = "",
                  AMP = "")
@@ -49,53 +55,55 @@ eucast_rules(df, rules = "custom", custom_rules = x)
 #>              mo TZP amox AMP
 #> 1       E. coli   R    R   R     
 #> 2 K. pneumoniae   R    R   R  
-}
+}\if{html}{\out{</div>}}
 }
 
 \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",
+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: –mo–, –fullname–, –kingdom–, –phylum–, –class–, –order–, –family–, –genus–, –species–, –subspecies–, –rank–, –ref–, –species_id–, –source–, –prevalence– and –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}:
+
+\if{html}{\out{<div class="sourceCode">}}\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
-}
+}\if{html}{\out{</div>}}
 }
 
 \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 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 and tobramycin-high)
-\item \code{aminopenicillins}\cr(amoxicillin and ampicillin)
-\item \code{antifungals}\cr(5-fluorocytosine, amphotericin B, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole and voriconazole)
-\item \code{antimycobacterials}\cr(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, morinamide, p-aminosalicylic acid, pretomanid, prothionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone/isoniazid, tiocarlide and viomycin)
-\item \code{betalactams}\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, 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, 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 and 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 and tebipenem)
-\item \code{cephalosporins}\cr(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, 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 and loracarbef)
-\item \code{cephalosporins_1st}\cr(cefacetrile, cefadroxil, cefaloridine, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, cephalexin, cephalothin, cephapirin and cephradine)
-\item \code{cephalosporins_2nd}\cr(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil and loracarbef)
-\item \code{cephalosporins_3rd}\cr(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 and latamoxef)
-\item \code{cephalosporins_4th}\cr(cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol, cefoselis, cefozopran, cefpirome and cefquinome)
-\item \code{cephalosporins_5th}\cr(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor and ceftolozane/tazobactam)
-\item \code{cephalosporins_except_caz}\cr(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, 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 and loracarbef)
-\item \code{fluoroquinolones}\cr(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)
-\item \code{glycopeptides}\cr(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin and vancomycin-macromethod)
-\item \code{glycopeptides_except_lipo}\cr(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin and vancomycin-macromethod)
-\item \code{lincosamides}\cr(acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin, lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin and tylvalosin)
-\item \code{lipoglycopeptides}\cr(dalbavancin, oritavancin and telavancin)
-\item \code{macrolides}\cr(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin and tylvalosin)
-\item \code{oxazolidinones}\cr(cadazolid, cycloserine, linezolid, tedizolid and thiacetazone)
-\item \code{penicillins}\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, cefepime/nacubactam, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, 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 and ticarcillin/clavulanic acid)
-\item \code{polymyxins}\cr(colistin, polymyxin B and polymyxin B/polysorbate 80)
-\item \code{quinolones}\cr(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)
-\item \code{streptogramins}\cr(pristinamycin and quinupristin/dalfopristin)
-\item \code{tetracyclines}\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline and tigecycline)
-\item \code{tetracyclines_except_tgc}\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline and tetracycline)
-\item \code{trimethoprims}\cr(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim and trimethoprim/sulfamethoxazole)
-\item \code{ureidopenicillins}\cr(azlocillin, mezlocillin, piperacillin and piperacillin/tazobactam)
+\item –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 and tobramycin-high)
+\item –aminopenicillins–\cr(amoxicillin and ampicillin)
+\item –antifungals–\cr(5-fluorocytosine, amphotericin B, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole and voriconazole)
+\item –antimycobacterials–\cr(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, morinamide, p-aminosalicylic acid, pretomanid, prothionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone/isoniazid, tiocarlide and viomycin)
+\item –betalactams–\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, 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, 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 and ticarcillin/clavulanic acid)
+\item –carbapenems–\cr(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil and tebipenem)
+\item –cephalosporins–\cr(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, 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 and loracarbef)
+\item –cephalosporins_1st–\cr(cefacetrile, cefadroxil, cefaloridine, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, cephalexin, cephalothin, cephapirin and cephradine)
+\item –cephalosporins_2nd–\cr(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil and loracarbef)
+\item –cephalosporins_3rd–\cr(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 and latamoxef)
+\item –cephalosporins_4th–\cr(cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol, cefoselis, cefozopran, cefpirome and cefquinome)
+\item –cephalosporins_5th–\cr(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor and ceftolozane/tazobactam)
+\item –cephalosporins_except_caz–\cr(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, 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 and loracarbef)
+\item –fluoroquinolones–\cr(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)
+\item –glycopeptides–\cr(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin and vancomycin-macromethod)
+\item –glycopeptides_except_lipo–\cr(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin and vancomycin-macromethod)
+\item –lincosamides–\cr(acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin, lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin and tylvalosin)
+\item –lipoglycopeptides–\cr(dalbavancin, oritavancin and telavancin)
+\item –macrolides–\cr(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin and tylvalosin)
+\item –oxazolidinones–\cr(cadazolid, cycloserine, linezolid, tedizolid and thiacetazone)
+\item –penicillins–\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, cefepime/nacubactam, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, 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 and ticarcillin/clavulanic acid)
+\item –polymyxins–\cr(colistin, polymyxin B and polymyxin B/polysorbate 80)
+\item –quinolones–\cr(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)
+\item –streptogramins–\cr(pristinamycin and quinupristin/dalfopristin)
+\item –tetracyclines–\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline and tigecycline)
+\item –tetracyclines_except_tgc–\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline and tetracycline)
+\item –trimethoprims–\cr(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim and trimethoprim/sulfamethoxazole)
+\item –ureidopenicillins–\cr(azlocillin, mezlocillin, piperacillin and piperacillin/tazobactam)
 }
 }
 }

man/eucast_rules.Rd

@@ -76,11 +76,13 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
 The file containing all EUCAST rules is located here: \url{https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv}.  \strong{Note:} Old taxonomic names are replaced with the current taxonomy where applicable. For example, \emph{Ochrobactrum anthropi} was renamed to \emph{Brucella anthropi} in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The file used as input for this \code{AMR} package contains the taxonomy updated until \link[=catalogue_of_life]{5 October 2021}.
 \subsection{Custom Rules}{
 
-Custom rules can be created using \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}, e.g.:\preformatted{x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
+Custom rules can be created using \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}, e.g.:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
                          AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
 
 eucast_rules(example_isolates, rules = "custom", custom_rules = x)
-}
+}\if{html}{\out{</div>}}
 }
 
 \subsection{'Other' Rules}{

man/g.test.Rd

@@ -89,8 +89,10 @@ The \emph{G}-test uses the log of the ratio of two likelihoods as the test stati
 
 \eqn{G = 2 * sum(x * log(x / E))}
 
-where \code{E} are the expected values. Since this is chi-square distributed, the p value can be calculated in \R with:\preformatted{p <- stats::pchisq(G, df, lower.tail = FALSE)
-}
+where \code{E} are the expected values. Since this is chi-square distributed, the p value can be calculated in \R with:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{p <- stats::pchisq(G, df, lower.tail = FALSE)
+}\if{html}{\out{</div>}}
 
 where \code{df} are the degrees of freedom.
 

man/key_antimicrobials.Rd

@@ -11,12 +11,12 @@ key_antimicrobials(
   col_mo = NULL,
   universal = c("ampicillin", "amoxicillin/clavulanic acid", "cefuroxime",
     "piperacillin/tazobactam", "ciprofloxacin", "trimethoprim/sulfamethoxazole"),
-  gram_negative = c("gentamicin", "tobramycin", "colistin", "cefotaxime",
-    "ceftazidime", "meropenem"),
+  gram_negative = c("gentamicin", "tobramycin", "colistin", "cefotaxime", "ceftazidime",
+    "meropenem"),
   gram_positive = c("vancomycin", "teicoplanin", "tetracycline", "erythromycin",
     "oxacillin", "rifampin"),
-  antifungal = c("anidulafungin", "caspofungin", "fluconazole", "miconazole",
-    "nystatin", "voriconazole"),
+  antifungal = c("anidulafungin", "caspofungin", "fluconazole", "miconazole", "nystatin",
+    "voriconazole"),
   only_rsi_columns = FALSE,
   ...
 )

man/mdro.Rd

@@ -122,35 +122,43 @@ 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 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",
+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:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{custom <- custom_mdro_guideline(CIP == "R" & age > 60 ~ "Elderly Type A",
                                 ERY == "R" & age > 60 ~ "Elderly Type B")
-}
+}\if{html}{\out{</div>}}
 
 If a row/an isolate matches the first rule, the value after the first \code{~} (in this case \emph{'Elderly Type A'}) will be set as MDRO value. Otherwise, the second rule will be tried and so on. The number of rules is unlimited.
 
-You can print the rules set in the console for an overview. Colours will help reading it if your console supports colours.\preformatted{custom
+You can print the rules set in the console for an overview. Colours will help reading it if your console supports colours.
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{custom
 #> A set of custom MDRO rules:
 #>   1. CIP is "R" and age is higher than 60 -> Elderly Type A
 #>   2. ERY is "R" and age is higher than 60 -> Elderly Type B
 #>   3. Otherwise -> Negative
 #> 
 #> Unmatched rows will return NA.
-}
+}\if{html}{\out{</div>}}
 
-The outcome of the function can be used for the \code{guideline} argument in the \code{\link[=mdro]{mdro()}} function:\preformatted{x <- mdro(example_isolates,
+The outcome of the function can be used for the \code{guideline} argument in the \code{\link[=mdro]{mdro()}} function:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{x <- mdro(example_isolates,
           guideline = custom)
 table(x)
 #>       Negative Elderly Type A Elderly Type B
 #>           1070            198            732
-}
+}\if{html}{\out{</div>}}
 
-Rules can also be combined with other custom rules by using \code{\link[=c]{c()}}:\preformatted{x <- mdro(example_isolates,
+Rules can also be combined with other custom rules by using \code{\link[=c]{c()}}:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{x <- mdro(example_isolates,
           guideline = c(custom, 
                         custom_mdro_guideline(ERY == "R" & age > 50 ~ "Elderly Type C")))
 table(x)
 #>       Negative Elderly Type A Elderly Type B Elderly Type C 
 #>            961            198            732            109
-}
+}\if{html}{\out{</div>}}
 
 The rules set (the \code{custom} object in this case) could be exported to a shared file location using \code{\link[=saveRDS]{saveRDS()}} if you collaborate with multiple users. The custom rules set could then be imported using \code{\link[=readRDS]{readRDS()}}.
 }

man/microorganisms.Rd

@@ -3,9 +3,9 @@
 \docType{data}
 \name{microorganisms}
 \alias{microorganisms}
-\title{Data Set with 70,760 Microorganisms}
+\title{Data Set with 70,764 Microorganisms}
 \format{
-A \link{data.frame} with 70,760 observations and 16 variables:
+A \link{data.frame} with 70,764 observations and 16 variables:
 \itemize{
 \item \code{mo}\cr ID of microorganism as used by this package
 \item \code{fullname}\cr Full name, like \code{"Escherichia coli"}
@@ -54,6 +54,7 @@ For convenience, some entries were added manually:
 \item 11 entries of \emph{Streptococcus} (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)
 \item 2 entries of \emph{Staphylococcus} (coagulase-negative (CoNS) and coagulase-positive (CoPS))
 \item 3 entries of \emph{Trichomonas} (\emph{T. vaginalis}, and its family and genus)
+\item 4 entries of \emph{Toxoplasma} (\emph{T. gondii}, and its order, family and genus)
 \item 1 entry of \emph{Candida} (\emph{C.  krusei}), that is not (yet) in the Catalogue of Life
 \item 1 entry of \emph{Blastocystis} (\emph{B.  hominis}), although it officially does not exist (Noel \emph{et al.} 2005, PMID 15634993)
 \item 1 entry of \emph{Moraxella} (\emph{M. catarrhalis}), which was formally named \emph{Branhamella catarrhalis} (Catlin, 1970) though this change was never accepted within the field of clinical microbiology
@@ -64,15 +65,9 @@ For convenience, some entries were added manually:
 
 \subsection{Direct download}{
 
-This data set is available as 'flat file' for use even without \R - you can find the file here:
-\itemize{
-\item \url{https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt}
-}
+This data set is available as 'flat file' for use even without \R - you can find the file here: \url{https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt}.
 
-The file in \R format (with preserved data structure) can be found here:
-\itemize{
-\item \url{https://github.com/msberends/AMR/raw/main/data/microorganisms.rda}
-}
+The file in \R format (with preserved data structure) can be found here: \url{https://github.com/msberends/AMR/raw/main/data/microorganisms.rda}.
 }
 }
 \section{About the Records from LPSN (see \emph{Source})}{

man/mo_source.Rd

@@ -37,23 +37,29 @@ Reading an Excel file (\code{.xlsx}) with only one row has a size of 8-9 kB. The
 \section{How to Setup}{
 
 
-Imagine this data on a sheet of an Excel file. The first column contains the organisation specific codes, the second column contains valid taxonomic names:\preformatted{  |         A          |            B          |
+Imagine this data on a sheet of an Excel file. The first column contains the organisation specific codes, the second column contains valid taxonomic names:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{  |         A          |            B          |
 --|--------------------|-----------------------|
 1 | Organisation XYZ   | mo                    |
 2 | lab_mo_ecoli       | Escherichia coli      |
 3 | lab_mo_kpneumoniae | Klebsiella pneumoniae |
 4 |                    |                       |
-}
+}\if{html}{\out{</div>}}
 
-We save it as \code{"home/me/ourcodes.xlsx"}. Now we have to set it as a source:\preformatted{set_mo_source("home/me/ourcodes.xlsx")
+We save it as \code{"home/me/ourcodes.xlsx"}. Now we have to set it as a source:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{set_mo_source("home/me/ourcodes.xlsx")
 #> NOTE: Created mo_source file '/Users/me/mo_source.rds' (0.3 kB) from
 #>       '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns 
 #>       "Organisation XYZ" and "mo"
-}
+}\if{html}{\out{</div>}}
 
 It has now created a file \code{"~/mo_source.rds"} with the contents of our Excel file. Only the first column with foreign values and the 'mo' column will be kept when creating the RDS file.
 
-And now we can use it in our functions:\preformatted{as.mo("lab_mo_ecoli")
+And now we can use it in our functions:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{as.mo("lab_mo_ecoli")
 #> Class <mo>
 #> [1] B_ESCHR_COLI
 
@@ -66,18 +72,22 @@ as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli"))
 #>       Use mo_uncertainties() to review it.
 #> Class <mo>
 #> [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI
-}
+}\if{html}{\out{</div>}}
 
-If we edit the Excel file by, let's say, adding row 4 like this:\preformatted{  |         A          |            B          |
+If we edit the Excel file by, let's say, adding row 4 like this:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{  |         A          |            B          |
 --|--------------------|-----------------------|
 1 | Organisation XYZ   | mo                    |
 2 | lab_mo_ecoli       | Escherichia coli      |
 3 | lab_mo_kpneumoniae | Klebsiella pneumoniae |
 4 | lab_Staph_aureus   | Staphylococcus aureus |
 5 |                    |                       |
-}
+}\if{html}{\out{</div>}}
 
-...any new usage of an MO function in this package will update your data file:\preformatted{as.mo("lab_mo_ecoli")
+...any new usage of an MO function in this package will update your data file:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{as.mo("lab_mo_ecoli")
 #> NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from 
 #>       '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns
 #>        "Organisation XYZ" and "mo"
@@ -86,11 +96,13 @@ If we edit the Excel file by, let's say, adding row 4 like this:\preformatted{
 
 mo_genus("lab_Staph_aureus")
 #> [1] "Staphylococcus"
-}
+}\if{html}{\out{</div>}}
 
-To delete the reference data file, just use \code{""}, \code{NULL} or \code{FALSE} as input for \code{\link[=set_mo_source]{set_mo_source()}}:\preformatted{set_mo_source(NULL)
+To delete the reference data file, just use \code{""}, \code{NULL} or \code{FALSE} as input for \code{\link[=set_mo_source]{set_mo_source()}}:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{set_mo_source(NULL)
 #> Removed mo_source file '/Users/me/mo_source.rds'
-}
+}\if{html}{\out{</div>}}
 
 If the original file (in the previous case an Excel file) is moved or deleted, the \code{mo_source.rds} file will be removed upon the next use of \code{\link[=as.mo]{as.mo()}} or any \code{\link[=mo_property]{mo_*}} function.
 }

man/proportion.Rd

@@ -89,7 +89,9 @@ The function \code{\link[=proportion_df]{proportion_df()}} takes any variable fr
 }
 \section{Combination Therapy}{
 
-When using more than one variable for \code{...} (= combination therapy), use \code{only_all_tested} to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how \code{\link[=susceptibility]{susceptibility()}} works to calculate the \%SI:\preformatted{--------------------------------------------------------------------
+When using more than one variable for \code{...} (= combination therapy), use \code{only_all_tested} to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how \code{\link[=susceptibility]{susceptibility()}} works to calculate the \%SI:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{--------------------------------------------------------------------
                     only_all_tested = FALSE  only_all_tested = TRUE
                     -----------------------  -----------------------
  Drug A    Drug B   include as  include as   include as  include as
@@ -105,15 +107,19 @@ When using more than one variable for \code{...} (= combination therapy), use \c
    R        <NA>        -            -            -            -
   <NA>      <NA>        -            -            -            -
 --------------------------------------------------------------------
-}
+}\if{html}{\out{</div>}}
 
-Please note that, in combination therapies, for \code{only_all_tested = TRUE} applies that:\preformatted{    count_S()    +   count_I()    +   count_R()    = count_all()
+Please note that, in combination therapies, for \code{only_all_tested = TRUE} applies that:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{    count_S()    +   count_I()    +   count_R()    = count_all()
   proportion_S() + proportion_I() + proportion_R() = 1
-}
+}\if{html}{\out{</div>}}
 
-and that, in combination therapies, for \code{only_all_tested = FALSE} applies that:\preformatted{    count_S()    +   count_I()    +   count_R()    >= count_all()
+and that, in combination therapies, for \code{only_all_tested = FALSE} applies that:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{    count_S()    +   count_I()    +   count_R()    >= count_all()
   proportion_S() + proportion_I() + proportion_R() >= 1
-}
+}\if{html}{\out{</div>}}
 
 Using \code{only_all_tested} has no impact when only using one antibiotic as input.
 }

man/resistance_predict.Rd

@@ -69,7 +69,7 @@ ggplot_rsi_predict(
 
 \item{minimum}{minimal amount of available isolates per year to include. Years containing less observations will be estimated by the model.}
 
-\item{model}{the statistical model of choice. This could be a generalised linear regression model with binomial distribution (i.e. using `glm(..., family = binomial)``, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See \emph{Details} for all valid options.}
+\item{model}{the statistical model of choice. This could be a generalised linear regression model with binomial distribution (i.e. using \code{glm(..., family = binomial)}, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See \emph{Details} for all valid options.}
 
 \item{I_as_S}{a \link{logical} to indicate whether values \code{"I"} should be treated as \code{"S"} (will otherwise be treated as \code{"R"}). The default, \code{TRUE}, follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section \emph{Interpretation of S, I and R} below.}
 

man/rsi_translation.Rd

@@ -27,22 +27,24 @@ rsi_translation
 Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2022) and CLSI (2011-2022). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values.
 }
 \details{
-Overview of the data set:\if{html}{\out{<div class="sourceCode r">}}\preformatted{head(rsi_translation)
-}\if{html}{\out{</div>}}\preformatted{##     guideline method site           mo rank_index  ab     ref_tbl disk_dose
-## 1 EUCAST 2022    MIC <NA> F_ASPRG_MGTS          2 AMB Aspergillus      <NA>
-## 2 EUCAST 2022    MIC <NA> F_ASPRG_NIGR          2 AMB Aspergillus      <NA>
-## 3 EUCAST 2022    MIC <NA>      F_CANDD          3 AMB     Candida      <NA>
-## 4 EUCAST 2022    MIC <NA> F_CANDD_ALBC          2 AMB     Candida      <NA>
-## 5 EUCAST 2022    MIC <NA> F_CANDD_DBLN          2 AMB     Candida      <NA>
-## 6 EUCAST 2022    MIC <NA> F_CANDD_KRUS          2 AMB     Candida      <NA>
-##   breakpoint_S breakpoint_R   uti
-## 1            1            1 FALSE
-## 2            1            1 FALSE
-## 3            1            1 FALSE
-## 4            1            1 FALSE
-## 5            1            1 FALSE
-## 6            1            1 FALSE
-}
+Overview of the data set:
+
+\if{html}{\out{<div class="sourceCode r">}}\preformatted{head(rsi_translation)
+#>     guideline method site           mo rank_index  ab     ref_tbl disk_dose
+#> 1 EUCAST 2022    MIC <NA> F_ASPRG_MGTS          2 AMB Aspergillus      <NA>
+#> 2 EUCAST 2022    MIC <NA> F_ASPRG_NIGR          2 AMB Aspergillus      <NA>
+#> 3 EUCAST 2022    MIC <NA>      F_CANDD          3 AMB     Candida      <NA>
+#> 4 EUCAST 2022    MIC <NA> F_CANDD_ALBC          2 AMB     Candida      <NA>
+#> 5 EUCAST 2022    MIC <NA> F_CANDD_DBLN          2 AMB     Candida      <NA>
+#> 6 EUCAST 2022    MIC <NA> F_CANDD_KRUS          2 AMB     Candida      <NA>
+#>   breakpoint_S breakpoint_R   uti
+#> 1            1            1 FALSE
+#> 2            1            1 FALSE
+#> 3            1            1 FALSE
+#> 4            1            1 FALSE
+#> 5            1            1 FALSE
+#> 6            1            1 FALSE
+}\if{html}{\out{</div>}}
 
 The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the \code{mo} and \code{ab} columns have been transformed to contain the full official names instead of codes.
 }