(v1.8.1.9014) add Toxoplasma

.github/workflows/check.yaml

@@ -57,8 +57,8 @@ jobs:
           - {os: macOS-latest,   r: '3.6',     allowfail: false}
           - {os: macOS-latest,   r: '3.5',     allowfail: false}
           - {os: macOS-latest,   r: '3.4',     allowfail: false}
-          - {os: macOS-latest,   r: '3.3',     allowfail: false}
-          - {os: macOS-latest,   r: '3.2',     allowfail: false}
+          # - {os: macOS-latest,   r: '3.3',     allowfail: false}
+          # - {os: macOS-latest,   r: '3.2',     allowfail: false}
           # - {os: macOS-latest,   r: '3.1',     allowfail: true}
           # - {os: macOS-latest,   r: '3.0',     allowfail: true}
           - {os: ubuntu-20.04,   r: 'devel',   allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
@@ -77,7 +77,7 @@ jobs:
           - {os: windows-latest, r: '3.6',     allowfail: false}
           - {os: windows-latest, r: '3.5',     allowfail: false}
           - {os: windows-latest, r: '3.4',     allowfail: false}
-          - {os: windows-latest, r: '3.3',     allowfail: false}
+          # - {os: windows-latest, r: '3.3',     allowfail: false}
           # - {os: windows-latest, r: '3.2',     allowfail: true}
           # - {os: windows-latest, r: '3.1',     allowfail: true}
           # - {os: windows-latest, r: '3.0',     allowfail: true}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.1
-Date: 2022-03-17
+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)

NAMESPACE

@@ -50,7 +50,6 @@ S3method(any,mic)
 S3method(as.data.frame,ab)
 S3method(as.data.frame,mo)
 S3method(as.double,mic)
-S3method(as.integer,mic)
 S3method(as.list,custom_eucast_rules)
 S3method(as.list,custom_mdro_guideline)
 S3method(as.matrix,mic)

NEWS.md

@@ -1,8 +1,21 @@
+# `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.
+
+### Changed
+* Fix for `as.rsi()` on certain EUCAST breakpoints for MIC values
+* Removed `as.integer()` for MIC values, since MIC are not integer values and running `table()` on MIC values  consequently failed for not being able to retrieve the level position (as that's how normally `as.integer()` on `factor`s work)
+* `droplevels()` on MIC will now return a common `factor` at default and will lose the `<mic>` class. Use `droplevels(..., as.mic = TRUE)` to keep the `<mic>` class.
+* 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
 
-
-All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.
-
 ### Changed
 * Fix for using `as.rsi()` on values containing capped values (such as `>=`), sometimes leading to `NA`
 * Support for antibiotic interpretations of the MIPS laboratory system: `"U"` for S ('susceptible urine'), `"D"` for I ('susceptible dose-dependent')

R/aa_helper_functions.R

@@ -638,7 +638,7 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_ca
   if (isTRUE(initial_captital)) {
     v[1] <- gsub("^([a-z])", "\\U\\1", v[1], perl = TRUE)
   }
-  if (length(v) == 1) {
+  if (length(v) <= 1) {
     return(paste0(quotes, v, quotes))
   }
   if (identical(v, c("I", "R", "S"))) {

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.
 #' 
@@ -251,7 +249,14 @@
 #' - `breakpoint_S`\cr Lowest MIC value or highest number of millimetres that leads to "S"
 #' - `breakpoint_R`\cr Highest MIC value or lowest number of millimetres that leads to "R"
 #' - `uti`\cr A [logical] value (`TRUE`/`FALSE`) to indicate whether the rule applies to a urinary tract infection (UTI)
-#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt>. This file **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 `mo` and `ab` columns have been transformed to contain the full official names instead of codes.
+#' @details 
+#' Overview of the data set:
+#' 
+#' ```{r}
+#' head(rsi_translation)
+#' ```
+#' 
+#' The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt>. This file **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 `mo` and `ab` columns have been transformed to contain the full official names instead of codes.
 #' @inheritSection AMR Reference Data Publicly Available
 #' @inheritSection AMR Read more on Our Website!
 #' @seealso [intrinsic_resistant]

R/mic.R

@@ -47,7 +47,8 @@ valid_mic_levels <- c(c(t(vapply(FUN.VALUE = character(9), ops,
 #' @rdname as.mic
 #' @param x a [character] or [numeric] vector
 #' @param na.rm a [logical] indicating whether missing values should be removed
-#' @details To interpret MIC values as RSI values, use [as.rsi()] on MIC values. It supports guidelines from EUCAST and CLSI.
+#' @param ... arguments passed on to methods
+#' @details To interpret MIC values as RSI values, use [as.rsi()] on MIC values. It supports guidelines from EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`).
 #' 
 #' This class for MIC values is a quite a special data type: formally it is an ordered [factor] with valid MIC values as [factor] levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:
 #' 
@@ -86,6 +87,10 @@ valid_mic_levels <- c(c(t(vapply(FUN.VALUE = character(9), ops,
 #' ```
 #' 
 #' The following [generic functions][groupGeneric()] are implemented for the MIC class: `!`, `!=`, `%%`, `%/%`, `&`, `*`, `+`, `-`, `/`, `<`, `<=`, `==`, `>`, `>=`, `^`, `|`, [abs()], [acos()], [acosh()], [all()], [any()], [asin()], [asinh()], [atan()], [atanh()], [ceiling()], [cos()], [cosh()], [cospi()], [cummax()], [cummin()], [cumprod()], [cumsum()], [digamma()], [exp()], [expm1()], [floor()], [gamma()], [lgamma()], [log()], [log1p()], [log2()], [log10()], [max()], [mean()], [min()], [prod()], [range()], [round()], [sign()], [signif()], [sin()], [sinh()], [sinpi()], [sqrt()], [sum()], [tan()], [tanh()], [tanpi()], [trigamma()] and [trunc()]. Some functions of the `stats` package are also implemented: [median()], [quantile()], [mad()], [IQR()], [fivenum()]. Also, [boxplot.stats()] is supported. Since [sd()] and [var()] are non-generic functions, these could not be extended. Use [mad()] as an alternative, or use e.g. `sd(as.numeric(x))` where `x` is your vector of MIC values.
+#' 
+#' Using [as.double()] or [as.numeric()] on MIC values will remove the operators and return a numeric vector. Do **not** use [as.integer()] on MIC values as by the \R convention on [factor]s, it will return the index of the factor levels (which is often useless for regular users).
+#' 
+#' Use [droplevels()] to drop unused levels. At default, it will return a plain factor. Use `droplevels(..., as.mic = TRUE)` to maintain the `<mic>` class.
 #' @return Ordered [factor] with additional class [`mic`], that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a [numeric] value.
 #' @aliases mic
 #' @export
@@ -196,7 +201,8 @@ all_valid_mics <- function(x) {
 }
 
 #' @rdname as.mic
-#' @details `NA_mic_` is a missing value of the new `<mic>` class.
+#' @details `NA_mic_` is a missing value of the new `<mic>` class, analogous to e.g. base \R's [`NA_character_`][base::NA].
+#' @format NULL
 #' @export
 NA_mic_ <- set_clean_class(factor(NA, levels = valid_mic_levels, ordered = TRUE),
                            new_class =  c("mic", "ordered", "factor"))
@@ -214,13 +220,6 @@ as.double.mic <- function(x, ...) {
   as.double(gsub("[<=>]+", "", as.character(x), perl = TRUE))
 }
 
-#' @method as.integer mic
-#' @export
-#' @noRd
-as.integer.mic <- function(x, ...) {
-  as.integer(gsub("[<=>]+", "", as.character(x), perl = TRUE))
-}
-
 #' @method as.numeric mic
 #' @export
 #' @noRd
@@ -228,11 +227,12 @@ as.numeric.mic <- function(x, ...) {
   as.numeric(gsub("[<=>]+", "", as.character(x), perl = TRUE))
 }
 
+#' @rdname as.mic
 #' @method droplevels mic
+#' @param as.mic a [logical] to indicate whether the `<mic>` class should be kept, defaults to `FALSE`
 #' @export
-#' @noRd
-droplevels.mic <- function(x, exclude = if (any(is.na(levels(x)))) NULL else NA, as.mic = TRUE, ...) {
-  x <- droplevels.factor(x, exclude = exclude, ...)
+droplevels.mic <- function(x, as.mic = FALSE, ...) {
+  x <- droplevels.factor(x, ...)
   if (as.mic == TRUE) {
     class(x) <- c("mic", "ordered", "factor")
   }
@@ -260,7 +260,9 @@ type_sum.mic <- function(x, ...) {
 #' @export
 #' @noRd
 print.mic <- function(x, ...) {
-  cat("Class <mic>\n")
+  cat("Class <mic>",
+      ifelse(length(levels(x)) < length(valid_mic_levels), font_red(" with dropped levels"), ""),
+      "\n", sep = "")
   print(as.character(x), quote = FALSE)
   att <- attributes(x)
   if ("na.action" %in% names(att)) {

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/mo_source.R

@@ -29,16 +29,16 @@
 #'
 #' This is **the fastest way** to have your organisation (or analysis) specific codes picked up and translated by this package, since you don't have to bother about it again after setting it up once.
 #' @inheritSection lifecycle Stable Lifecycle
-#' @param path location of your reference file, see *Details*. Can be `""`, `NULL` or `FALSE` to delete the reference file.
+#' @param path location of your reference file, this can be any text file (comma-, tab- or pipe-separated) or an Excel file (see *Details*). Can also be `""`, `NULL` or `FALSE` to delete the reference file.
 #' @param destination destination of the compressed data file, default to the user's home directory.
 #' @rdname mo_source
 #' @name mo_source
 #' @aliases set_mo_source get_mo_source
 #' @details The reference file can be a text file separated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an \R object file (extension '.rds'). To use an Excel file, you will need to have the `readxl` package installed.
 #'
-#' [set_mo_source()] will check the file for validity: it must be a [data.frame], must have a column named `"mo"` which contains values from [`microorganisms$mo`][microorganisms] and must have a reference column with your own defined values. If all tests pass, [set_mo_source()] will read the file into \R and will ask to export it to `"~/mo_source.rds"`. The CRAN policy disallows packages to write to the file system, although '*exceptions may be allowed in interactive sessions if the package obtains confirmation from the user*'. For this reason, this function only works in interactive sessions so that the user can **specifically confirm and allow** that this file will be created. The destination of this file can be set with the `destination` argument and defaults to the user's home directory. It can also be set as an \R option, using `options(AMR_mo_source = "my/location/file.rds")`.
+#' [set_mo_source()] will check the file for validity: it must be a [data.frame], must have a column named `"mo"` which contains values from [`microorganisms$mo`][microorganisms] or [`microorganisms$fullname`][microorganisms] and must have a reference column with your own defined values. If all tests pass, [set_mo_source()] will read the file into \R and will ask to export it to `"~/mo_source.rds"`. The CRAN policy disallows packages to write to the file system, although '*exceptions may be allowed in interactive sessions if the package obtains confirmation from the user*'. For this reason, this function only works in interactive sessions so that the user can **specifically confirm and allow** that this file will be created. The destination of this file can be set with the `destination` argument and defaults to the user's home directory. It can also be set as an \R option, using `options(AMR_mo_source = "my/location/file.rds")`.
 #' 
-#' The created compressed data file `"mo_source.rds"` will be used at default for MO determination (function [as.mo()] and consequently all `mo_*` functions like [mo_genus()] and [mo_gramstain()]). The location and timestamp of the original file will be saved as an attribute to the compressed data file. 
+#' The created compressed data file `"mo_source.rds"` will be used at default for MO determination (function [as.mo()] and consequently all `mo_*` functions like [mo_genus()] and [mo_gramstain()]). The location and timestamp of the original file will be saved as an [attribute][base::attributes()] to the compressed data file. 
 #' 
 #' The function [get_mo_source()] will return the data set by reading `"mo_source.rds"` with [readRDS()]. If the original file has changed (by checking the location and timestamp of the original file), it will call [set_mo_source()] to update the data file automatically if used in an interactive session.
 #'
@@ -46,14 +46,14 @@
 #' 
 #' @section How to Setup:
 #' 
-#' Imagine this data on a sheet of an Excel file (mo codes were looked up in the [microorganisms] data set). The first column contains the organisation specific codes, the second column contains an MO code from this package:
+#' 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:
 #' 
 #' ```
 #'   |         A          |            B          |
-#' --|--------------------|--------------|
+#' --|--------------------|-----------------------|
 #' 1 | Organisation XYZ   | mo                    |
-#' 2 | lab_mo_ecoli       | B_ESCHR_COLI |
-#' 3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
+#' 2 | lab_mo_ecoli       | Escherichia coli      |
+#' 3 | lab_mo_kpneumoniae | Klebsiella pneumoniae |
 #' 4 |                    |                       |
 #' ```
 #'
@@ -90,11 +90,11 @@
 #' 
 #' ```
 #'   |         A          |            B          |
-#' --|--------------------|--------------|
+#' --|--------------------|-----------------------|
 #' 1 | Organisation XYZ   | mo                    |
-#' 2 | lab_mo_ecoli       | B_ESCHR_COLI |
-#' 3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
-#' 4 | lab_Staph_aureus   | B_STPHY_AURS |
+#' 2 | lab_mo_ecoli       | Escherichia coli      |
+#' 3 | lab_mo_kpneumoniae | Klebsiella pneumoniae |
+#' 4 | lab_Staph_aureus   | Staphylococcus aureus |
 #' 5 |                    |                       |
 #' ```
 #'
@@ -144,6 +144,7 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s
   
   stop_ifnot(file.exists(path), "file not found: ", path)
   
+  df <- NULL
   if (path %like% "[.]rds$") {
     df <- readRDS(path)
     
@@ -153,28 +154,34 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s
     df <- readxl::read_excel(path)
     
   } else if (path %like% "[.]tsv$") {
-    df <- utils::read.table(header = TRUE, sep = "\t", stringsAsFactors = FALSE)
+    df <- utils::read.table(file = path, header = TRUE, sep = "\t", stringsAsFactors = FALSE)
+    
+  } else if (path %like% "[.]csv$") {
+    df <- utils::read.table(file = path, header = TRUE, sep = ",", stringsAsFactors = FALSE)
     
   } else {
     # try comma first
     try(
-      df <- utils::read.table(header = TRUE, sep = ",", stringsAsFactors = FALSE),
+      df <- utils::read.table(file = path, header = TRUE, sep = ",", stringsAsFactors = FALSE),
       silent = TRUE)
     if (!check_validity_mo_source(df, stop_on_error = FALSE)) {
       # try tab
       try(
-        df <- utils::read.table(header = TRUE, sep = "\t", stringsAsFactors = FALSE),
+        df <- utils::read.table(file = path, header = TRUE, sep = "\t", stringsAsFactors = FALSE),
         silent = TRUE)
     }
     if (!check_validity_mo_source(df, stop_on_error = FALSE)) {
       # try pipe
       try(
-        df <- utils::read.table(header = TRUE, sep = "|", stringsAsFactors = FALSE),
+        df <- utils::read.table(file = path, header = TRUE, sep = "|", stringsAsFactors = FALSE),
         silent = TRUE)
     }
   }
   
   # check integrity
+  if (is.null(df)) {
+    stop_("the path '", path, "' could not be imported as a dataset.")
+  }
   check_validity_mo_source(df)
   
   df <- subset(df, !is.na(mo))
@@ -187,7 +194,7 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s
   }
   
   df <- as.data.frame(df, stringAsFactors = FALSE)
-  df[, "mo"] <- set_clean_class(df[, "mo", drop = TRUE], c("mo", "character"))
+  df[, "mo"] <- as.mo(df[, "mo", drop = TRUE])
   
   # success
   if (file.exists(mo_source_destination)) {
@@ -275,9 +282,9 @@ check_validity_mo_source <- function(x, refer_to_name = "`reference_df`", stop_o
       return(FALSE)
     }
   }
-  if (!all(x$mo %in% c("", microorganisms$mo), na.rm = TRUE)) {
+  if (!all(x$mo %in% c("", microorganisms$mo, microorganisms$fullname), na.rm = TRUE)) {
     if (stop_on_error == TRUE) {
-      invalid <- x[which(!x$mo %in% c("", microorganisms$mo)), , drop = FALSE]
+      invalid <- x[which(!x$mo %in% c("", microorganisms$mo, microorganisms$fullname)), , drop = FALSE]
       if (nrow(invalid) > 1) {
         plural <- "s"
       } else {

R/plot.R

@@ -79,7 +79,7 @@ plot.mic <- function(x,
                      mo = NULL,
                      ab = NULL,
                      guideline = "EUCAST",
-                     main = paste("MIC values of", deparse(substitute(x))),
+                     main = deparse(substitute(x)),
                      ylab = "Frequency",
                      xlab = "Minimum Inhibitory Concentration (mg/L)",
                      colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
@@ -166,7 +166,7 @@ barplot.mic <- function(height,
                         mo = NULL,
                         ab = NULL,
                         guideline = "EUCAST",
-                        main = paste("MIC values of", deparse(substitute(height))),
+                        main = deparse(substitute(height)),
                         ylab = "Frequency",
                         xlab = "Minimum Inhibitory Concentration (mg/L)",
                         colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
@@ -299,7 +299,7 @@ fortify.mic <- function(object, ...) {
 #' @importFrom graphics barplot axis mtext legend
 #' @rdname plot
 plot.disk <- function(x,
-                      main = paste("Disk zones of", deparse(substitute(x))),
+                      main = deparse(substitute(x)),
                       ylab = "Frequency",
                       xlab = "Disk diffusion diameter (mm)",
                       mo = NULL,
@@ -386,7 +386,7 @@ plot.disk <- function(x,
 #' @export
 #' @noRd
 barplot.disk <- function(height,
-                         main = paste("Disk zones of", deparse(substitute(height))),
+                         main = deparse(substitute(height)),
                          ylab = "Frequency",
                          xlab = "Disk diffusion diameter (mm)",
                          mo = NULL,
@@ -525,7 +525,7 @@ fortify.disk <- function(object, ...) {
 plot.rsi <- function(x,
                      ylab = "Percentage",
                      xlab = "Antimicrobial Interpretation",
-                     main = paste("Resistance Overview of", deparse(substitute(x))),
+                     main = deparse(substitute(x)),
                      ...) {
   meet_criteria(ylab, allow_class = "character", has_length = 1)
   meet_criteria(xlab, allow_class = "character", has_length = 1)
@@ -576,7 +576,7 @@ plot.rsi <- function(x,
 #' @export
 #' @noRd
 barplot.rsi <- function(height,
-                        main = paste("Resistance Overview of", deparse(substitute(height))),
+                        main = deparse(substitute(height)),
                         xlab = "Antimicrobial Interpretation",
                         ylab = "Frequency",
                         colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
@@ -738,7 +738,11 @@ plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_RSI, f
                ab_name(ab, language = NULL, tolower = TRUE), " in ", moname)
       guideline_txt <- ""
     } else {
-      guideline_txt <- paste0("(", guideline, ")")
+      guideline_txt <- guideline
+      if (isTRUE(list(...)$uti)) {
+        guideline_txt <- paste("UTIs,", guideline_txt)
+      }
+      guideline_txt <- paste0("(", guideline_txt, ")")
     }
     sub <- bquote(.(abname)~"-"~italic(.(moname))~.(guideline_txt))
   } else {

R/random.R

@@ -34,7 +34,7 @@
 #' @param ... ignored, only in place to allow future extensions
 #' @details The base \R function [sample()] is used for generating values.
 #' 
-#' Generated values are based on the latest EUCAST guideline implemented in the [rsi_translation] data set. To create specific generated values per bug or drug, set the `mo` and/or `ab` argument.
+#' Generated values are based on the EUCAST `r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))` guideline as implemented in the [rsi_translation] data set. To create specific generated values per bug or drug, set the `mo` and/or `ab` argument.
 #' @return class `<mic>` for [random_mic()] (see [as.mic()]) and class `<disk>` for [random_disk()] (see [as.disk()])
 #' @name random
 #' @rdname random
@@ -89,6 +89,7 @@ random_rsi <- function(size = NULL, prob_RSI = c(0.33, 0.33, 0.33), ...) {
 }
 
 random_exec <- function(type, size, mo = NULL, ab = NULL) {
+  check_dataset_integrity()
   df <- rsi_translation %pm>%
     pm_filter(guideline %like% "EUCAST") %pm>%
     pm_arrange(pm_desc(guideline)) %pm>%

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/rsi.R

@@ -33,7 +33,7 @@
 #' @param ab any (vector of) text that can be coerced to a valid antimicrobial code with [as.ab()]
 #' @param uti (Urinary Tract Infection) A vector with [logical]s (`TRUE` or `FALSE`) to specify whether a UTI specific interpretation from the guideline should be chosen. For using [as.rsi()] on a [data.frame], this can also be a column containing [logical]s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See *Examples*.
 #' @inheritParams first_isolate
-#' @param guideline defaults to the latest included EUCAST guideline, see *Details* for all options
+#' @param guideline defaults to EUCAST `r  max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))` (the latest implemented EUCAST guideline in the [rsi_translation] data set), supports EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`), see *Details*
 #' @param conserve_capped_values a [logical] to indicate that MIC values starting with `">"` (but not `">="`) must always return "R" , and that MIC values starting with `"<"` (but not `"<="`) must always return "S"
 #' @param add_intrinsic_resistance *(only useful when using a EUCAST guideline)* a [logical] to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in *Klebsiella* species. Determination is based on the [intrinsic_resistant] data set, that itself is based on `r format_eucast_version_nr(3.3)`.
 #' @param reference_data a [data.frame] to be used for interpretation, which defaults to the [rsi_translation] data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the [rsi_translation] data set (same column names and column types). Please note that the `guideline` argument will be ignored when `reference_data` is manually set.
@@ -179,7 +179,7 @@
 #'   example_isolates %>%
 #'     mutate_if(is.rsi.eligible, as.rsi)
 #'     
-#'   # note: from dplyr 1.0.0 on, this will be: 
+#'   # since dplyr 1.0.0, this can also be: 
 #'   # example_isolates %>%
 #'   #   mutate(across(where(is.rsi.eligible), as.rsi))
 #' }
@@ -189,7 +189,7 @@ as.rsi <- function(x, ...) {
 }
 
 #' @rdname as.rsi
-#' @details `NA_rsi_` is a missing value of the new `<rsi>` class.
+#' @details `NA_rsi_` is a missing value of the new `<rsi>` class, analogous to e.g. base \R's [`NA_character_`][base::NA].
 #' @export
 NA_rsi_ <- set_clean_class(factor(NA, levels = c("S", "I", "R"), ordered = TRUE),
                            new_class =  c("rsi", "ordered", "factor"))
@@ -818,18 +818,20 @@ exec_as.rsi <- function(method,
       if (is.na(x[i]) | (is.na(get_record$breakpoint_S) & is.na(get_record$breakpoint_R))) {
         new_rsi[i] <- NA_character_
       } else if (method == "mic") {
-        new_rsi[i] <- quick_case_when(isTRUE(conserve_capped_values) & x[i] %like% "^<[0-9]" ~ "S",
-                                      isTRUE(conserve_capped_values) & x[i] %like% "^>[0-9]" ~ "R",
+        new_rsi[i] <- quick_case_when(isTRUE(conserve_capped_values) & isTRUE(x[i] %like% "^<[0-9]") ~ "S",
+                                      isTRUE(conserve_capped_values) & isTRUE(x[i] %like% "^>[0-9]") ~ "R",
                                       # these basically call `<=.mic()` and `>=.mic()`:
-                                      x[i] <= get_record$breakpoint_S ~ "S",
-                                      x[i] >= get_record$breakpoint_R ~ "R",
+                                      isTRUE(x[i] <= get_record$breakpoint_S) ~ "S",
+                                      guideline_coerced %like% "EUCAST" & isTRUE(x[i] > get_record$breakpoint_R) ~ "R",
+                                      guideline_coerced %like% "CLSI" & isTRUE(x[i] >= get_record$breakpoint_R) ~ "R",
                                       # return "I" when not match the bottom or top
                                       !is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I",
                                       # and NA otherwise
                                       TRUE ~ NA_character_)
       } else if (method == "disk") {
         new_rsi[i] <- quick_case_when(isTRUE(as.double(x[i]) >= as.double(get_record$breakpoint_S)) ~ "S",
-                                      isTRUE(as.double(x[i]) <= as.double(get_record$breakpoint_R)) ~ "R",
+                                      guideline_coerced %like% "EUCAST" & isTRUE(as.double(x[i]) < as.double(get_record$breakpoint_R)) ~ "R",
+                                      guideline_coerced %like% "CLSI" & isTRUE(as.double(x[i]) <= as.double(get_record$breakpoint_R)) ~ "R",
                                       # return "I" when not match the bottom or top
                                       !is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I",
                                       # and NA otherwise

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.
+  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,
@@ -252,7 +276,9 @@ changed_md5 <- function(object) {
 }
 
 # give official names to ABs and MOs
-rsi <- dplyr::mutate(rsi_translation, ab = ab_name(ab), mo = mo_name(mo))
+rsi <- AMR::rsi_translation %>% 
+  mutate(mo_name = mo_name(mo, language = NULL), .after = mo) %>% 
+  mutate(ab_name = ab_name(ab, language = NULL), .after = ab)
 if (changed_md5(rsi)) {
   usethis::ui_info(paste0("Saving {usethis::ui_value('rsi_translation')} to {usethis::ui_value('/data-raw/')}"))
   write_md5(rsi)
@@ -273,7 +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)) {
@@ -312,8 +338,8 @@ if (changed_md5(av)) {
 }
 
 # give official names to ABs and MOs
-intrinsicR <- data.frame(microorganism = mo_name(intrinsic_resistant$mo),
-                         antibiotic = ab_name(intrinsic_resistant$ab),
+intrinsicR <- data.frame(microorganism = mo_name(intrinsic_resistant$mo, language = NULL),
+                         antibiotic = ab_name(intrinsic_resistant$ab, language = NULL),
                          stringsAsFactors = FALSE)
 if (changed_md5(intrinsicR)) {
   usethis::ui_info(paste0("Saving {usethis::ui_value('intrinsic_resistant')} to {usethis::ui_value('/data-raw/')}"))

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/reproduction_of_rsi_translation.R

@@ -24,6 +24,7 @@
 # ==================================================================== #
 
 # This script runs in under a minute and renews all guidelines of CLSI and EUCAST!
+# Run it with source("data-raw/reproduction_of_rsi_translation.R")
 
 library(dplyr)
 library(readr)
@@ -32,9 +33,9 @@ library(AMR)
 
 # Install the WHONET software on Windows (http://www.whonet.org/software.html),
 # and copy the folder C:\WHONET\Codes to data-raw/WHONET/Codes
-DRGLST <- readr::read_tsv("data-raw/WHONET/Codes/DRGLST.txt", na = c("", "NA", "-"))
-DRGLST1 <- readr::read_tsv("data-raw/WHONET/Codes/DRGLST1.txt", na = c("", "NA", "-"))
-ORGLIST <- readr::read_tsv("data-raw/WHONET/Codes/ORGLIST.txt", na = c("", "NA", "-"))
+DRGLST <- read_tsv("data-raw/WHONET/Codes/DRGLST.txt", na = c("", "NA", "-"), show_col_types = FALSE)
+DRGLST1 <- read_tsv("data-raw/WHONET/Codes/DRGLST1.txt", na = c("", "NA", "-"), show_col_types = FALSE)
+ORGLIST <- read_tsv("data-raw/WHONET/Codes/ORGLIST.txt", na = c("", "NA", "-"), show_col_types = FALSE)
 
 # create data set for generic rules (i.e., AB-specific but not MO-specific)
 rsi_generic <- DRGLST %>%
@@ -128,11 +129,30 @@ rsi_translation[which(rsi_translation$breakpoint_R == 257), "breakpoint_R"] <- m
 rsi_translation[which(rsi_translation$breakpoint_R == 513), "breakpoint_R"] <- m[which(m == 512) + 1]
 rsi_translation[which(rsi_translation$breakpoint_R == 1025), "breakpoint_R"] <- m[which(m == 1024) + 1]
 
+# WHONET adds one log2 level to the R breakpoint for their software, e.g. in AMC in Enterobacterales:
+# EUCAST 2021 guideline: S <= 8 and R > 8
+#           WHONET file: S <= 8 and R >= 16
+# this will make an MIC of 12 I, which should be R, so:
+eucast_mics <- which(rsi_translation$guideline %like% "EUCAST" &
+                       rsi_translation$method == "MIC" &
+                       log2(as.double(rsi_translation$breakpoint_R)) - log2(as.double(rsi_translation$breakpoint_S)) != 0 &
+                       !is.na(rsi_translation$breakpoint_R))
+old_R <- rsi_translation[eucast_mics, "breakpoint_R", drop = TRUE]
+old_S <- rsi_translation[eucast_mics, "breakpoint_S", drop = TRUE]
+new_R <- 2 ^ (log2(old_R) - 1)
+new_R[new_R < old_S | is.na(as.mic(new_R))] <- old_S[new_R < old_S | is.na(as.mic(new_R))]
+rsi_translation[eucast_mics, "breakpoint_R"] <- new_R
+eucast_disks <- which(rsi_translation$guideline %like% "EUCAST" &
+                        rsi_translation$method == "DISK" &
+                        rsi_translation$breakpoint_S - rsi_translation$breakpoint_R != 0 &
+                        !is.na(rsi_translation$breakpoint_R))
+rsi_translation[eucast_disks, "breakpoint_R"] <- rsi_translation[eucast_disks, "breakpoint_R", drop = TRUE] + 1
+
 # Greek symbols and EM dash symbols are not allowed by CRAN, so replace them with ASCII:
 rsi_translation$disk_dose <- gsub("μ", "u", rsi_translation$disk_dose, fixed = TRUE)
 rsi_translation$disk_dose <- gsub("–", "-", rsi_translation$disk_dose, fixed = TRUE)
 
 # save to package
-usethis::use_data(rsi_translation, overwrite = TRUE)
+usethis::use_data(rsi_translation, overwrite = TRUE, compress = "xz")
 rm(rsi_translation)
 devtools::load_all(".")

data-raw/rsi.md5

@@ -1 +1 @@
-d8083b68d4e492ea8e87c1eae4da4196
+75a10b41a8bd4f4788520f3407431e66

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">1.8.0.9010</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
       </span>
     </div>
 
@@ -57,7 +57,7 @@
   </a>
 </li>
 <li class="dropdown">
-  <a href="https://msberends.github.io/AMR/#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="https://msberends.github.io/AMR/#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
     <span class="fa fa-question-circle"></span>
      
     How to
@@ -205,14 +205,12 @@ Content not found. Please use links in the navbar.
 
       <footer><div class="copyright">
   <p></p>
-<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
-Erwin E. A. Hassing.</p>
+<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
-2.0.2.</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">1.8.0.9010</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
       </span>
     </div>
 
@@ -30,7 +30,7 @@
   </a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
     <span class="fa fa-question-circle"></span>
      
     How to
@@ -416,13 +416,11 @@ END OF TERMS AND CONDITIONS
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
-Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
-2.0.2.</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/AMR.html

@@ -44,7 +44,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9008</span>
       </span>
     </div>
 
@@ -58,7 +58,7 @@
   </a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
     <span class="fa fa-question-circle"></span>
      
     How to
@@ -192,7 +192,7 @@
                         <h4 data-toc-skip class="author">Dr Matthijs
 Berends</h4>
             
-            <h4 data-toc-skip class="date">14 March 2022</h4>
+            <h4 data-toc-skip class="date">11 mei 2022</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
       <div class="hidden name"><code>AMR.Rmd</code></div>
@@ -205,7 +205,7 @@ Berends</h4>
 website update since they are based on randomly created values and the
 page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
 Markdown</a>. However, the methodology remains unchanged. This page was
-generated on 14 March 2022.</p>
+generated on 11 mei 2022.</p>
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
@@ -261,21 +261,21 @@ make the structure of your data generally look like this:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2022-03-14</td>
+<td align="center">2022-05-11</td>
 <td align="center">abcd</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">S</td>
 </tr>
 <tr class="even">
-<td align="center">2022-03-14</td>
+<td align="center">2022-05-11</td>
 <td align="center">abcd</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">R</td>
 </tr>
 <tr class="odd">
-<td align="center">2022-03-14</td>
+<td align="center">2022-05-11</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@@ -392,12 +392,12 @@ data set:</p>
 <col width="13%">
 <col width="13%">
 <col width="13%">
-<col width="28%">
+<col width="26%">
 <col width="5%">
 <col width="5%">
 <col width="5%">
 <col width="5%">
-<col width="8%">
+<col width="9%">
 </colgroup>
 <thead><tr class="header">
 <th align="center">date</th>
@@ -412,69 +412,69 @@ data set:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2015-06-11</td>
-<td align="center">R8</td>
-<td align="center">Hospital A</td>
-<td align="center">Streptococcus pneumoniae</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">F</td>
-</tr>
-<tr class="even">
-<td align="center">2016-12-29</td>
-<td align="center">E9</td>
-<td align="center">Hospital A</td>
-<td align="center">Escherichia coli</td>
-<td align="center">R</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">M</td>
-</tr>
-<tr class="odd">
-<td align="center">2011-11-10</td>
-<td align="center">L4</td>
-<td align="center">Hospital A</td>
-<td align="center">Streptococcus pneumoniae</td>
-<td align="center">S</td>
-<td align="center">R</td>
-<td align="center">R</td>
-<td align="center">R</td>
-<td align="center">M</td>
-</tr>
-<tr class="even">
-<td align="center">2013-03-20</td>
-<td align="center">G10</td>
-<td align="center">Hospital A</td>
-<td align="center">Streptococcus pneumoniae</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">R</td>
-<td align="center">S</td>
-<td align="center">M</td>
-</tr>
-<tr class="odd">
-<td align="center">2010-03-14</td>
-<td align="center">N6</td>
-<td align="center">Hospital A</td>
-<td align="center">Escherichia coli</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">R</td>
-<td align="center">S</td>
-<td align="center">F</td>
-</tr>
-<tr class="even">
-<td align="center">2010-09-24</td>
+<td align="center">2012-05-19</td>
 <td align="center">T9</td>
-<td align="center">Hospital A</td>
+<td align="center">Hospital D</td>
+<td align="center">Escherichia coli</td>
+<td align="center">I</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">F</td>
+</tr>
+<tr class="even">
+<td align="center">2014-09-16</td>
+<td align="center">D6</td>
+<td align="center">Hospital C</td>
+<td align="center">Klebsiella pneumoniae</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">M</td>
+</tr>
+<tr class="odd">
+<td align="center">2017-03-16</td>
+<td align="center">D10</td>
+<td align="center">Hospital C</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
+<td align="center">I</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">M</td>
+</tr>
+<tr class="even">
+<td align="center">2014-05-04</td>
+<td align="center">S5</td>
+<td align="center">Hospital B</td>
+<td align="center">Staphylococcus aureus</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">F</td>
+</tr>
+<tr class="odd">
+<td align="center">2011-06-06</td>
+<td align="center">N10</td>
+<td align="center">Hospital B</td>
+<td align="center">Staphylococcus aureus</td>
+<td align="center">I</td>
+<td align="center">I</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">F</td>
+</tr>
+<tr class="even">
+<td align="center">2016-05-12</td>
+<td align="center">R3</td>
+<td align="center">Hospital D</td>
+<td align="center">Klebsiella pneumoniae</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
 <td align="center">S</td>
-<td align="center">R</td>
-<td align="center">R</td>
 <td align="center">F</td>
 </tr>
 </tbody>
@@ -511,16 +511,16 @@ Longest: 1</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">M</td>
-<td align="right">10,365</td>
-<td align="right">51.83%</td>
-<td align="right">10,365</td>
-<td align="right">51.83%</td>
+<td align="right">10,452</td>
+<td align="right">52.26%</td>
+<td align="right">10,452</td>
+<td align="right">52.26%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">F</td>
-<td align="right">9,635</td>
-<td align="right">48.18%</td>
+<td align="right">9,548</td>
+<td align="right">47.74%</td>
 <td align="right">20,000</td>
 <td align="right">100.00%</td>
 </tr>
@@ -630,9 +630,9 @@ takes into account the antimicrobial susceptibility test results using
 <span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span>
 <span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span>
 <span class="co"># 2</span>
-<span class="co"># =&gt; Found 10,676 'phenotype-based' first isolates (53.4% of total where a</span>
+<span class="co"># =&gt; Found 10,708 'phenotype-based' first isolates (53.5% of total where a</span>
 <span class="co">#    microbial ID was available)</span></code></pre></div>
-<p>So only 53.4% is suitable for resistance analysis! We can now filter
+<p>So only 53.5% is suitable for resistance analysis! We can now filter
 on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
 <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
@@ -642,11 +642,11 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
 <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
   <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
-<p>So we end up with 10,676 isolates for analysis. Now our data looks
+<p>So we end up with 10,708 isolates for analysis. Now our data looks
 like:</p>
 <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></code></pre></div>
-<table class="table">
+<table style="width:100%;" class="table">
 <colgroup>
 <col width="2%">
 <col width="9%">
@@ -659,7 +659,7 @@ like:</p>
 <col width="3%">
 <col width="6%">
 <col width="11%">
-<col width="11%">
+<col width="12%">
 <col width="9%">
 <col width="5%">
 </colgroup>
@@ -681,58 +681,58 @@ like:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="left">1</td>
-<td align="center">2015-06-11</td>
-<td align="center">R8</td>
-<td align="center">Hospital A</td>
-<td align="center">B_STRPT_PNMN</td>
-<td align="center">S</td>
-<td align="center">S</td>
+<td align="left">2</td>
+<td align="center">2014-09-16</td>
+<td align="center">D6</td>
+<td align="center">Hospital C</td>
+<td align="center">B_KLBSL_PNMN</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
-<td align="center">F</td>
-<td align="center">Gram-positive</td>
-<td align="center">Streptococcus</td>
-<td align="center">pneumoniae</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="even">
-<td align="left">3</td>
-<td align="center">2011-11-10</td>
-<td align="center">L4</td>
-<td align="center">Hospital A</td>
-<td align="center">B_STRPT_PNMN</td>
-<td align="center">R</td>
-<td align="center">R</td>
-<td align="center">R</td>
-<td align="center">R</td>
+<td align="center">S</td>
 <td align="center">M</td>
-<td align="center">Gram-positive</td>
-<td align="center">Streptococcus</td>
-<td align="center">pneumoniae</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="odd">
-<td align="left">4</td>
-<td align="center">2013-03-20</td>
-<td align="center">G10</td>
-<td align="center">Hospital A</td>
-<td align="center">B_STRPT_PNMN</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">R</td>
-<td align="center">R</td>
-<td align="center">M</td>
-<td align="center">Gram-positive</td>
-<td align="center">Streptococcus</td>
+<td align="center">Gram-negative</td>
+<td align="center">Klebsiella</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="left">5</td>
-<td align="center">2010-03-14</td>
-<td align="center">N6</td>
-<td align="center">Hospital A</td>
+<td align="center">2011-06-06</td>
+<td align="center">N10</td>
+<td align="center">Hospital B</td>
+<td align="center">B_STPHY_AURS</td>
+<td align="center">I</td>
+<td align="center">I</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">F</td>
+<td align="center">Gram-positive</td>
+<td align="center">Staphylococcus</td>
+<td align="center">aureus</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="odd">
+<td align="left">6</td>
+<td align="center">2016-05-12</td>
+<td align="center">R3</td>
+<td align="center">Hospital D</td>
+<td align="center">B_KLBSL_PNMN</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">F</td>
+<td align="center">Gram-negative</td>
+<td align="center">Klebsiella</td>
+<td align="center">pneumoniae</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="even">
+<td align="left">8</td>
+<td align="center">2010-02-19</td>
+<td align="center">U1</td>
+<td align="center">Hospital D</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@@ -745,35 +745,35 @@ like:</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
-<td align="left">6</td>
-<td align="center">2010-09-24</td>
-<td align="center">T9</td>
-<td align="center">Hospital A</td>
-<td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
-<td align="center">S</td>
+<td align="left">11</td>
+<td align="center">2012-02-09</td>
+<td align="center">G7</td>
+<td align="center">Hospital D</td>
+<td align="center">B_STPHY_AURS</td>
 <td align="center">R</td>
 <td align="center">R</td>
-<td align="center">F</td>
-<td align="center">Gram-negative</td>
-<td align="center">Escherichia</td>
-<td align="center">coli</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">M</td>
+<td align="center">Gram-positive</td>
+<td align="center">Staphylococcus</td>
+<td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="left">10</td>
-<td align="center">2011-01-26</td>
-<td align="center">K5</td>
-<td align="center">Hospital A</td>
-<td align="center">B_ESCHR_COLI</td>
+<td align="left">12</td>
+<td align="center">2012-04-12</td>
+<td align="center">Q10</td>
+<td align="center">Hospital D</td>
+<td align="center">B_STRPT_PNMN</td>
+<td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
-<td align="center">S</td>
-<td align="center">M</td>
-<td align="center">Gram-negative</td>
-<td align="center">Escherichia</td>
-<td align="center">coli</td>
+<td align="center">F</td>
+<td align="center">Gram-positive</td>
+<td align="center">Streptococcus</td>
+<td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 </tbody>
@@ -809,8 +809,8 @@ readable:</p>
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></code></pre></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: character<br>
-Length: 10,676<br>
-Available: 10,676 (100%, NA: 0 = 0%)<br>
+Length: 10,708<br>
+Available: 10,708 (100%, NA: 0 = 0%)<br>
 Unique: 4</p>
 <p>Shortest: 16<br>
 Longest: 24</p>
@@ -835,33 +835,33 @@ Longest: 24</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Escherichia coli</td>
-<td align="right">4,677</td>
-<td align="right">43.81%</td>
-<td align="right">4,677</td>
-<td align="right">43.81%</td>
+<td align="right">4,664</td>
+<td align="right">43.56%</td>
+<td align="right">4,664</td>
+<td align="right">43.56%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Staphylococcus aureus</td>
-<td align="right">2,652</td>
-<td align="right">24.84%</td>
-<td align="right">7,329</td>
-<td align="right">68.65%</td>
+<td align="right">2,713</td>
+<td align="right">25.34%</td>
+<td align="right">7,377</td>
+<td align="right">68.89%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Streptococcus pneumoniae</td>
-<td align="right">2,144</td>
-<td align="right">20.08%</td>
-<td align="right">9,473</td>
-<td align="right">88.73%</td>
+<td align="right">2,154</td>
+<td align="right">20.12%</td>
+<td align="right">9,531</td>
+<td align="right">89.01%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Klebsiella pneumoniae</td>
-<td align="right">1,203</td>
-<td align="right">11.27%</td>
-<td align="right">10,676</td>
+<td align="right">1,177</td>
+<td align="right">10.99%</td>
+<td align="right">10,708</td>
 <td align="right">100.00%</td>
 </tr>
 </tbody>
@@ -882,14 +882,14 @@ antibiotic class they are in:</p>
 <col width="9%">
 <col width="9%">
 <col width="9%">
-<col width="10%">
+<col width="11%">
 <col width="3%">
 <col width="3%">
 <col width="3%">
 <col width="3%">
 <col width="6%">
 <col width="11%">
-<col width="12%">
+<col width="11%">
 <col width="9%">
 <col width="5%">
 </colgroup>
@@ -910,12 +910,12 @@ antibiotic class they are in:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2015-06-11</td>
-<td align="center">R8</td>
-<td align="center">Hospital A</td>
+<td align="center">2012-04-12</td>
+<td align="center">Q10</td>
+<td align="center">Hospital D</td>
 <td align="center">B_STRPT_PNMN</td>
-<td align="center">S</td>
-<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">F</td>
@@ -925,39 +925,24 @@ antibiotic class they are in:</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="center">2011-11-10</td>
-<td align="center">L4</td>
-<td align="center">Hospital A</td>
+<td align="center">2011-03-17</td>
+<td align="center">Z4</td>
+<td align="center">Hospital C</td>
 <td align="center">B_STRPT_PNMN</td>
+<td align="center">S</td>
+<td align="center">S</td>
 <td align="center">R</td>
 <td align="center">R</td>
-<td align="center">R</td>
-<td align="center">R</td>
-<td align="center">M</td>
+<td align="center">F</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
-<td align="center">2013-03-20</td>
-<td align="center">G10</td>
-<td align="center">Hospital A</td>
-<td align="center">B_STRPT_PNMN</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">R</td>
-<td align="center">R</td>
-<td align="center">M</td>
-<td align="center">Gram-positive</td>
-<td align="center">Streptococcus</td>
-<td align="center">pneumoniae</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="even">
-<td align="center">2010-09-24</td>
-<td align="center">T9</td>
-<td align="center">Hospital A</td>
+<td align="center">2010-09-07</td>
+<td align="center">P9</td>
+<td align="center">Hospital B</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@@ -969,31 +954,46 @@ antibiotic class they are in:</p>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="odd">
-<td align="center">2014-12-18</td>
-<td align="center">D8</td>
-<td align="center">Hospital B</td>
-<td align="center">B_STPHY_AURS</td>
+<tr class="even">
+<td align="center">2013-08-06</td>
+<td align="center">Z6</td>
+<td align="center">Hospital A</td>
+<td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">F</td>
+<td align="center">Gram-negative</td>
+<td align="center">Escherichia</td>
+<td align="center">coli</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="odd">
+<td align="center">2017-02-20</td>
+<td align="center">K5</td>
+<td align="center">Hospital D</td>
+<td align="center">B_ESCHR_COLI</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
-<td align="center">Gram-positive</td>
-<td align="center">Staphylococcus</td>
-<td align="center">aureus</td>
+<td align="center">Gram-negative</td>
+<td align="center">Escherichia</td>
+<td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="center">2014-10-24</td>
-<td align="center">V7</td>
+<td align="center">2015-08-23</td>
+<td align="center">G1</td>
 <td align="center">Hospital A</td>
 <td align="center">B_STRPT_PNMN</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
 <td align="center">R</td>
-<td align="center">R</td>
-<td align="center">R</td>
-<td align="center">R</td>
-<td align="center">F</td>
+<td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
@@ -1022,50 +1022,50 @@ different bug/drug combinations, you can use the
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">AMX</td>
-<td align="center">2208</td>
-<td align="center">135</td>
-<td align="center">2334</td>
-<td align="center">4677</td>
+<td align="center">2171</td>
+<td align="center">132</td>
+<td align="center">2361</td>
+<td align="center">4664</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">AMC</td>
-<td align="center">3416</td>
-<td align="center">135</td>
-<td align="center">1126</td>
-<td align="center">4677</td>
+<td align="center">3389</td>
+<td align="center">168</td>
+<td align="center">1107</td>
+<td align="center">4664</td>
 </tr>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">CIP</td>
-<td align="center">3415</td>
+<td align="center">3428</td>
 <td align="center">0</td>
-<td align="center">1262</td>
-<td align="center">4677</td>
+<td align="center">1236</td>
+<td align="center">4664</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">4110</td>
+<td align="center">4083</td>
 <td align="center">0</td>
-<td align="center">567</td>
-<td align="center">4677</td>
+<td align="center">581</td>
+<td align="center">4664</td>
 </tr>
 <tr class="odd">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMX</td>
 <td align="center">0</td>
 <td align="center">0</td>
-<td align="center">1203</td>
-<td align="center">1203</td>
+<td align="center">1177</td>
+<td align="center">1177</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMC</td>
-<td align="center">926</td>
-<td align="center">38</td>
-<td align="center">239</td>
-<td align="center">1203</td>
+<td align="center">935</td>
+<td align="center">30</td>
+<td align="center">212</td>
+<td align="center">1177</td>
 </tr>
 </tbody>
 </table>
@@ -1088,34 +1088,34 @@ different bug/drug combinations, you can use the
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">4110</td>
+<td align="center">4083</td>
 <td align="center">0</td>
-<td align="center">567</td>
-<td align="center">4677</td>
+<td align="center">581</td>
+<td align="center">4664</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">GEN</td>
-<td align="center">1083</td>
+<td align="center">1074</td>
 <td align="center">0</td>
-<td align="center">120</td>
-<td align="center">1203</td>
+<td align="center">103</td>
+<td align="center">1177</td>
 </tr>
 <tr class="odd">
 <td align="center">S. aureus</td>
 <td align="center">GEN</td>
-<td align="center">2348</td>
+<td align="center">2426</td>
 <td align="center">0</td>
-<td align="center">304</td>
-<td align="center">2652</td>
+<td align="center">287</td>
+<td align="center">2713</td>
 </tr>
 <tr class="even">
 <td align="center">S. pneumoniae</td>
 <td align="center">GEN</td>
 <td align="center">0</td>
 <td align="center">0</td>
-<td align="center">2144</td>
-<td align="center">2144</td>
+<td align="center">2154</td>
+<td align="center">2154</td>
 </tr>
 </tbody>
 </table>
@@ -1147,7 +1147,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
 own:</p>
 <div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>
-<span class="co"># [1] 0.5491757</span></code></pre></div>
+<span class="co"># [1] 0.5473478</span></code></pre></div>
 <p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
 <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
@@ -1162,19 +1162,19 @@ own:</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5442031</td>
+<td align="center">0.5482456</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5462647</td>
+<td align="center">0.5499477</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5565553</td>
+<td align="center">0.5403687</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5569745</td>
+<td align="center">0.5464842</td>
 </tr>
 </tbody>
 </table>
@@ -1197,23 +1197,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5442031</td>
-<td align="center">3269</td>
+<td align="center">0.5482456</td>
+<td align="center">3192</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5462647</td>
-<td align="center">3815</td>
+<td align="center">0.5499477</td>
+<td align="center">3824</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5565553</td>
-<td align="center">1556</td>
+<td align="center">0.5403687</td>
+<td align="center">1573</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5569745</td>
-<td align="center">2036</td>
+<td align="center">0.5464842</td>
+<td align="center">2119</td>
 </tr>
 </tbody>
 </table>
@@ -1236,27 +1236,27 @@ therapies very easily:</p>
 <tbody>
 <tr class="odd">
 <td align="center">Escherichia</td>
-<td align="center">0.7592474</td>
-<td align="center">0.8787684</td>
-<td align="center">0.9775497</td>
+<td align="center">0.7626501</td>
+<td align="center">0.8754288</td>
+<td align="center">0.9774871</td>
 </tr>
 <tr class="even">
 <td align="center">Klebsiella</td>
-<td align="center">0.8013300</td>
-<td align="center">0.9002494</td>
-<td align="center">0.9758936</td>
+<td align="center">0.8198811</td>
+<td align="center">0.9124894</td>
+<td align="center">0.9821580</td>
 </tr>
 <tr class="odd">
 <td align="center">Staphylococcus</td>
-<td align="center">0.7929864</td>
-<td align="center">0.8853695</td>
-<td align="center">0.9807692</td>
+<td align="center">0.7983782</td>
+<td align="center">0.8942130</td>
+<td align="center">0.9834132</td>
 </tr>
 <tr class="even">
 <td align="center">Streptococcus</td>
-<td align="center">0.5247201</td>
+<td align="center">0.5329619</td>
 <td align="center">0.0000000</td>
-<td align="center">0.5247201</td>
+<td align="center">0.5329619</td>
 </tr>
 </tbody>
 </table>
@@ -1284,23 +1284,23 @@ classes, use a antibiotic class selector such as
 <tbody>
 <tr class="odd">
 <td align="left">Hospital A</td>
-<td align="right">54.4%</td>
-<td align="right">26.2%</td>
+<td align="right">54.8%</td>
+<td align="right">28.0%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital B</td>
-<td align="right">54.6%</td>
-<td align="right">28.2%</td>
+<td align="right">55.0%</td>
+<td align="right">26.3%</td>
 </tr>
 <tr class="odd">
 <td align="left">Hospital C</td>
-<td align="right">55.7%</td>
-<td align="right">26.6%</td>
+<td align="right">54.0%</td>
+<td align="right">26.2%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital D</td>
-<td align="right">55.7%</td>
-<td align="right">28.9%</td>
+<td align="right">54.6%</td>
+<td align="right">26.4%</td>
 </tr>
 </tbody>
 </table>
@@ -1402,18 +1402,18 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
 <code class="sourceCode R"><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
 <span class="va">mic_values</span>
 <span class="co"># Class &lt;mic&gt;</span>
-<span class="co">#   [1] 0.5     0.25    32      &lt;=0.001 0.002   0.0625  0.025   256     1      </span>
-<span class="co">#  [10] 1       0.25    0.25    1       128     0.125   256     0.025   0.002  </span>
-<span class="co">#  [19] 128     0.25    0.5     &lt;=0.001 0.01    256     0.25    0.0625  0.005  </span>
-<span class="co">#  [28] 32      8       0.002   64      4       0.125   4       128     &lt;=0.001</span>
-<span class="co">#  [37] 32      1       4       0.002   0.25    0.5     16      0.25    128    </span>
-<span class="co">#  [46] 256     0.01    16      0.25    0.002   0.5     16      128     0.5    </span>
-<span class="co">#  [55] 0.005   128     64      0.25    2       4       16      16      2      </span>
-<span class="co">#  [64] 0.0625  1       0.0625  8       0.5     &lt;=0.001 8       4       0.002  </span>
-<span class="co">#  [73] 16      0.002   0.5     0.01    &lt;=0.001 128     0.025   0.025   0.01   </span>
-<span class="co">#  [82] 4       0.25    64      4       0.25    32      0.0625  1       128    </span>
-<span class="co">#  [91] &lt;=0.001 &lt;=0.001 0.005   8       0.25    0.25    64      16      0.01   </span>
-<span class="co"># [100] 128</span></code></pre></div>
+<span class="co">#   [1] 4       4       &lt;=0.001 2       256     32      32      0.002   4      </span>
+<span class="co">#  [10] 0.002   0.125   0.005   &lt;=0.001 4       0.002   128     16      32     </span>
+<span class="co">#  [19] 256     8       256     0.25    0.025   0.25    0.002   64      &lt;=0.001</span>
+<span class="co">#  [28] 0.25    256     2       0.0625  2       0.25    0.01    0.005   2      </span>
+<span class="co">#  [37] 0.0625  1       64      32      0.0625  0.002   0.0625  0.125   0.005  </span>
+<span class="co">#  [46] 1       256     0.025   256     0.005   16      64      0.25    2      </span>
+<span class="co">#  [55] 0.25    1       128     0.0625  0.005   0.5     0.5     &lt;=0.001 0.025  </span>
+<span class="co">#  [64] 2       64      0.005   0.0625  0.5     128     0.0625  8       4      </span>
+<span class="co">#  [73] 0.002   128     0.01    &lt;=0.001 2       64      64      128     32     </span>
+<span class="co">#  [82] 0.005   256     64      0.0625  0.5     32      0.002   &lt;=0.001 1      </span>
+<span class="co">#  [91] 16      0.25    0.005   16      2       64      0.005   &lt;=0.001 256    </span>
+<span class="co"># [100] 32</span></code></pre></div>
 <div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="co"># base R:</span>
 <span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></code></pre></div>
@@ -1449,10 +1449,10 @@ plotting:</p>
 <span class="co">#   coli). Run `mo_uncertainties()` to review this.</span>
 <span class="va">disk_values</span>
 <span class="co"># Class &lt;disk&gt;</span>
-<span class="co">#   [1] 30 17 16 29 29 24 20 21 22 19 31 28 19 22 20 19 19 17 27 17 29 31 24 27 21</span>
-<span class="co">#  [26] 18 19 29 22 20 22 31 28 23 24 24 25 20 17 29 17 31 20 29 31 27 18 27 23 22</span>
-<span class="co">#  [51] 24 18 17 19 18 23 16 28 19 28 23 27 16 19 26 28 24 22 22 20 23 30 25 27 27</span>
-<span class="co">#  [76] 18 31 21 27 30 23 24 26 19 19 23 17 17 28 16 23 26 27 29 22 27 17 27 28 21</span></code></pre></div>
+<span class="co">#   [1] 28 27 24 30 31 28 30 27 21 22 18 28 20 25 29 18 31 20 31 28 26 31 25 30 29</span>
+<span class="co">#  [26] 21 20 25 24 29 23 26 27 26 20 18 29 21 17 31 18 30 30 26 19 17 18 23 30 31</span>
+<span class="co">#  [51] 24 22 27 29 17 27 29 20 31 30 19 28 30 21 21 19 19 25 24 30 29 19 21 27 22</span>
+<span class="co">#  [76] 30 17 26 21 18 31 29 26 21 23 31 27 30 19 18 20 20 23 28 25 24 31 18 17 28</span></code></pre></div>
 <div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="co"># base R:</span>
 <span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></code></pre></div>
@@ -1531,14 +1531,12 @@ really different.</p>
 
       <footer><div class="copyright">
   <p></p>
-<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
-Erwin E. A. Hassing.</p>
+<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
-2.0.2.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
 </div>
 
       </footer>

docs/articles/AMR_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

docs/articles/EUCAST.html

@@ -44,7 +44,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9008</span>
       </span>
     </div>
 
@@ -58,7 +58,7 @@
   </a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
     <span class="fa fa-question-circle"></span>
      
     How to
@@ -425,14 +425,12 @@ reading</em>, is basically a form of imputation, and is part of the
 
       <footer><div class="copyright">
   <p></p>
-<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
-Erwin E. A. Hassing.</p>
+<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
-2.0.2.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
 </div>
 
       </footer>

docs/articles/EUCAST_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

docs/articles/MDR.html

@@ -44,7 +44,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9008</span>
       </span>
     </div>
 
@@ -58,7 +58,7 @@
   </a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
     <span class="fa fa-question-circle"></span>
      
     How to
@@ -422,18 +422,18 @@ names or codes, this would have worked exactly the same way:</p>
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
 <span class="co">#   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
-<span class="co"># 1          I         S            I          I            S            S</span>
-<span class="co"># 2          R         S            I          S            R            R</span>
-<span class="co"># 3          I         R            I          S            R            S</span>
-<span class="co"># 4          I         I            I          R            S            R</span>
-<span class="co"># 5          R         S            I          R            S            I</span>
-<span class="co"># 6          S         S            I          S            R            R</span>
+<span class="co"># 1          R         I            R          R            I            S</span>
+<span class="co"># 2          I         I            S          S            R            S</span>
+<span class="co"># 3          I         S            R          R            S            R</span>
+<span class="co"># 4          R         I            S          R            R            I</span>
+<span class="co"># 5          R         I            I          I            R            I</span>
+<span class="co"># 6          R         I            R          S            R            I</span>
 <span class="co">#   kanamycin</span>
 <span class="co"># 1         R</span>
-<span class="co"># 2         I</span>
+<span class="co"># 2         R</span>
 <span class="co"># 3         S</span>
-<span class="co"># 4         S</span>
-<span class="co"># 5         S</span>
+<span class="co"># 4         I</span>
+<span class="co"># 5         I</span>
 <span class="co"># 6         R</span></code></pre></div>
 <p>We can now add the interpretation of MDR-TB to our data set. You can
 use:</p>
@@ -455,7 +455,7 @@ use:</p>
 <span class="co">#            management of drug-resistant tuberculosis</span>
 <span class="co"># Author(s): WHO (World Health Organization)</span>
 <span class="co"># Version:   WHO/HTM/TB/2014.11, 2014</span>
-<span class="co"># Source:    https://www.who.int/tb/publications/pmdt_companionhandbook/en/</span></code></pre></div>
+<span class="co"># Source:    https://www.who.int/publications/i/item/9789241548809</span></code></pre></div>
 <p>Create a frequency table of the results:</p>
 <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span><span class="op">)</span></code></pre></div>
@@ -487,40 +487,40 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistant</td>
-<td align="right">3261</td>
-<td align="right">65.22%</td>
-<td align="right">3261</td>
-<td align="right">65.22%</td>
+<td align="right">3218</td>
+<td align="right">64.36%</td>
+<td align="right">3218</td>
+<td align="right">64.36%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">987</td>
-<td align="right">19.74%</td>
-<td align="right">4248</td>
-<td align="right">84.96%</td>
+<td align="right">979</td>
+<td align="right">19.58%</td>
+<td align="right">4197</td>
+<td align="right">83.94%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Multi-drug-resistant</td>
-<td align="right">437</td>
-<td align="right">8.74%</td>
-<td align="right">4685</td>
-<td align="right">93.70%</td>
+<td align="right">458</td>
+<td align="right">9.16%</td>
+<td align="right">4655</td>
+<td align="right">93.10%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistant</td>
-<td align="right">218</td>
-<td align="right">4.36%</td>
-<td align="right">4903</td>
-<td align="right">98.06%</td>
+<td align="right">237</td>
+<td align="right">4.74%</td>
+<td align="right">4892</td>
+<td align="right">97.84%</td>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
 <td align="left">Extensively drug-resistant</td>
-<td align="right">97</td>
-<td align="right">1.94%</td>
+<td align="right">108</td>
+<td align="right">2.16%</td>
 <td align="right">5000</td>
 <td align="right">100.00%</td>
 </tr>
@@ -539,14 +539,12 @@ Unique: 5</p>
 
       <footer><div class="copyright">
   <p></p>
-<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
-Erwin E. A. Hassing.</p>
+<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
-2.0.2.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
 </div>
 
       </footer>

docs/articles/MDR_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

docs/articles/PCA.html

@@ -44,7 +44,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9008</span>
       </span>
     </div>
 
@@ -58,7 +58,7 @@
   </a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
     <span class="fa fa-question-circle"></span>
      
     How to
@@ -213,7 +213,7 @@ is currently being developed.</strong></p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
-<span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
+<span class="fu"><a href="https://dplyr.tidyverse.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
 <span class="co"># Rows: 2,000</span>
 <span class="co"># Columns: 49</span>
 <span class="co"># $ date            <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-…</span>
@@ -305,7 +305,7 @@ function:</p>
 <span class="co"># [1] "Caryophanales"    "Enterobacterales" "Lactobacillales"  "Pseudomonadales"</span>
 <span class="co"># Importance of components:</span>
 <span class="co">#                           PC1    PC2    PC3     PC4     PC5     PC6       PC7</span>
-<span class="co"># Standard deviation     2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 5.121e-17</span>
+<span class="co"># Standard deviation     2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 5.674e-17</span>
 <span class="co"># Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span>
 <span class="co"># Cumulative Proportion  0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></code></pre></div>
 <pre><code><span class="co"># Groups (n=4, named as 'order'):</span>
@@ -348,14 +348,12 @@ automatically adds the right labels and even groups:</p>
 
       <footer><div class="copyright">
   <p></p>
-<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
-Erwin E. A. Hassing.</p>
+<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
-2.0.2.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
 </div>
 
       </footer>

docs/articles/PCA_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

docs/articles/SPSS.html

@@ -44,7 +44,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9008</span>
       </span>
     </div>
 
@@ -58,7 +58,7 @@
   </a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
     <span class="fa fa-question-circle"></span>
      
     How to
@@ -192,7 +192,7 @@
                         <h4 data-toc-skip class="author">Dr. Matthijs
 Berends</h4>
             
-            <h4 data-toc-skip class="date">14 March 2022</h4>
+            <h4 data-toc-skip class="date">11 mei 2022</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
       <div class="hidden name"><code>SPSS.Rmd</code></div>
@@ -272,7 +272,7 @@ data using a custom made website. The webdesign knowledge needed
 <li>
 <p><strong>R has a huge community.</strong></p>
 <p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest
-online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">439,954
+online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">447,735
 R-related questions</a> have already been asked on this platform (that
 covers questions and answers for any programming language). In my own
 experience, most questions are answered within a couple of
@@ -511,14 +511,12 @@ yourself:</p>
 
       <footer><div class="copyright">
   <p></p>
-<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
-Erwin E. A. Hassing.</p>
+<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
-2.0.2.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
 </div>
 
       </footer>

docs/articles/SPSS_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

docs/articles/WHONET.html

@@ -44,7 +44,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9008</span>
       </span>
     </div>
 
@@ -58,7 +58,7 @@
   </a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
     <span class="fa fa-question-circle"></span>
      
     How to
@@ -436,14 +436,12 @@ using the included <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a>
 
       <footer><div class="copyright">
   <p></p>
-<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
-Erwin E. A. Hassing.</p>
+<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
-2.0.2.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
 </div>
 
       </footer>

docs/articles/WHONET_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

docs/articles/benchmarks.html

@@ -185,7 +185,7 @@
 
       
 
-      </header><div class="row">
+      </header><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Benchmarks</h1>
@@ -198,30 +198,14 @@
 
     
     
-<p>One of the most important features of this package is the complete
-microbial taxonomic database, supplied by the <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (CoL) and
-the <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with
-Standing in Nomenclature</a> (LPSN). We created a function
-<code><a href="../reference/as.mo.html">as.mo()</a></code> that transforms any user input value to a valid
-microbial ID by using intelligent rules combined with the microbial
-taxonomy.</p>
-<p>Using the <code>microbenchmark</code> package, we can review the
-calculation performance of this function. Its function
-<code><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark()</a></code> runs different input expressions
-independently of each other and measures their time-to-result.</p>
+<p>One of the most important features of this package is the complete microbial taxonomic database, supplied by the <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (CoL) and the <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN). We created a function <code><a href="../reference/as.mo.html">as.mo()</a></code> that transforms any user input value to a valid microbial ID by using intelligent rules combined with the microbial taxonomy.</p>
+<p>Using the <code>microbenchmark</code> package, we can review the calculation performance of this function. Its function <code><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark()</a></code> runs different input expressions independently of each other and measures their time-to-result.</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/joshuaulrich/microbenchmark/" class="external-link">microbenchmark</a></span><span class="op">)</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></code></pre></div>
-<p>In the next test, we try to ‘coerce’ different input values into the
-microbial code of <em>Staphylococcus aureus</em>. Coercion is a
-computational process of forcing output based on an input. For
-microorganism names, coercing user input to taxonomically valid
-microorganism names is crucial to ensure correct interpretation and to
-enable grouping based on taxonomic properties.</p>
-<p>The actual result is the same every time: it returns its
-microorganism code <code>B_STPHY_AURS</code> (<em>B</em> stands for
-<em>Bacteria</em>, its taxonomic kingdom).</p>
+<p>In the next test, we try to ‘coerce’ different input values into the microbial code of <em>Staphylococcus aureus</em>. Coercion is a computational process of forcing output based on an input. For microorganism names, coercing user input to taxonomically valid microorganism names is crucial to ensure correct interpretation and to enable grouping based on taxonomic properties.</p>
+<p>The actual result is the same every time: it returns its microorganism code <code>B_STPHY_AURS</code> (<em>B</em> stands for <em>Bacteria</em>, its taxonomic kingdom).</p>
 <p>But the calculation time differs a lot:</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">S.aureus</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span>
@@ -238,42 +222,29 @@ microorganism code <code>B_STPHY_AURS</code> (<em>B</em> stands for
   <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>, <span class="co"># Methicillin Resistant S. aureus</span>
   <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span>, <span class="co"># Vancomycin Intermediate S. aureus</span>
   times <span class="op">=</span> <span class="fl">25</span><span class="op">)</span>
-<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
+<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
 <span class="co">#                                   expr   min    lq  mean median    uq max neval</span>
-<span class="co">#                           as.mo("sau")  12.0  13.0  17.0   14.0  15  53    25</span>
-<span class="co">#                          as.mo("stau")  51.0  59.0  74.0   71.0  90  97    25</span>
-<span class="co">#                          as.mo("STAU")  53.0  60.0  77.0   87.0  91  96    25</span>
-<span class="co">#                        as.mo("staaur")  11.0  13.0  16.0   14.0  15  48    25</span>
-<span class="co">#                        as.mo("STAAUR")  13.0  14.0  19.0   15.0  16  48    25</span>
-<span class="co">#                     as.mo("S. aureus")  28.0  31.0  48.0   59.0  63  70    25</span>
-<span class="co">#                      as.mo("S aureus")  28.0  29.0  42.0   33.0  58  83    25</span>
-<span class="co">#         as.mo("Staphylococcus aureus")   3.9   4.1   6.1    4.4   5  43    25</span>
-<span class="co">#  as.mo("Staphylococcus aureus (MRSA)") 250.0 260.0 270.0  270.0 270 390    25</span>
-<span class="co">#       as.mo("Sthafilokkockus aaureuz") 160.0 190.0 200.0  200.0 220 240    25</span>
-<span class="co">#                          as.mo("MRSA")  13.0  13.0  19.0   14.0  15  50    25</span>
-<span class="co">#                          as.mo("VISA")  21.0  22.0  29.0   24.0  27  61    25</span></code></pre></div>
+<span class="co">#                           as.mo("sau")  19.0  20.0  25.0   20.0  26.0  55    25</span>
+<span class="co">#                          as.mo("stau")  94.0  95.0 110.0  100.0 130.0 140    25</span>
+<span class="co">#                          as.mo("STAU")  92.0  97.0 110.0  110.0 120.0 140    25</span>
+<span class="co">#                        as.mo("staaur")  19.0  19.0  24.0   20.0  21.0  56    25</span>
+<span class="co">#                        as.mo("STAAUR")  19.0  20.0  21.0   20.0  20.0  49    25</span>
+<span class="co">#                     as.mo("S. aureus")  54.0  57.0  72.0   64.0  86.0  96    25</span>
+<span class="co">#                      as.mo("S aureus")  55.0  55.0  72.0   57.0  90.0 100    25</span>
+<span class="co">#         as.mo("Staphylococcus aureus")   5.6   5.7   8.5    5.8   6.2  40    25</span>
+<span class="co">#  as.mo("Staphylococcus aureus (MRSA)") 360.0 370.0 400.0  400.0 420.0 550    25</span>
+<span class="co">#       as.mo("Sthafilokkockus aaureuz") 280.0 290.0 300.0  300.0 320.0 350    25</span>
+<span class="co">#                          as.mo("MRSA")  19.0  20.0  24.0   20.0  21.0  51    25</span>
+<span class="co">#                          as.mo("VISA")  34.0  34.0  48.0   36.0  65.0  73    25</span></code></pre></div>
 <p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="750"></p>
-<p>In the table above, all measurements are shown in milliseconds
-(thousands of seconds). A value of 5 milliseconds means it can determine
-200 input values per second. It case of 200 milliseconds, this is only 5
-input values per second. It is clear that accepted taxonomic names are
-extremely fast, but some variations are up to 61 times slower to
-determine.</p>
-<p>To improve performance, we implemented two important algorithms to
-save unnecessary calculations: <strong>repetitive results</strong> and
-<strong>already precalculated results</strong>.</p>
+<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 69 times slower to determine.</p>
+<p>To improve performance, we implemented two important algorithms to save unnecessary calculations: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
 <div class="section level3">
 <h3 id="repetitive-results">Repetitive results<a class="anchor" aria-label="anchor" href="#repetitive-results"></a>
 </h3>
-<p>Repetitive results are values that are present more than once in a
-vector. Unique values will only be calculated once by
-<code><a href="../reference/as.mo.html">as.mo()</a></code>. So running
-<code>as.mo(c("E. coli", "E. coli"))</code> will check the value
-<code>"E. coli"</code> only once.</p>
-<p>To prove this, we will use <code><a href="../reference/mo_property.html">mo_name()</a></code> for testing - a
-helper function that returns the full microbial name (genus, species and
-possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()</a></code> internally.</p>
+<p>Repetitive results are values that are present more than once in a vector. Unique values will only be calculated once by <code><a href="../reference/as.mo.html">as.mo()</a></code>. So running <code>as.mo(c("E. coli", "E. coli"))</code> will check the value <code>"E. coli"</code> only once.</p>
+<p>To prove this, we will use <code><a href="../reference/mo_property.html">mo_name()</a></code> for testing - a helper function that returns the full microbial name (genus, species and possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()</a></code> internally.</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="co"># start with the example_isolates data set</span>
 <span class="va">x</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
@@ -287,8 +258,8 @@ possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()<
 <span class="co"># what do these values look like? They are of class &lt;mo&gt;:</span>
 <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
 <span class="co"># Class &lt;mo&gt;</span>
-<span class="co"># [1] B_ACNTB      B_ESCHR_COLI B_STRPT_GRPC B_STPHY_HMNS B_STPHY_CONS</span>
-<span class="co"># [6] B_ESCHR_COLI</span>
+<span class="co"># [1] B_ENTRBC_CLOC B_ESCHR_COLI  B_STRPT_PYGN  B_STPHY_AURS  B_ESCHR_COLI </span>
+<span class="co"># [6] B_STRPT_PNMN</span>
   
 <span class="co"># as the example_isolates data set has 2,000 rows, we should have 2 million items</span>
 <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
@@ -301,38 +272,28 @@ possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()<
 <span class="co"># now let's see:</span>
 <span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>,
                          times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
-<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
+<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
 <span class="co">#        expr min  lq mean median  uq max neval</span>
-<span class="co">#  mo_name(x) 200 204  265    225 320 392    10</span></code></pre></div>
-<p>So getting official taxonomic names of 2,000,000 (!!) items
-consisting of 90 unique values only takes 0.225 seconds. That is 112
-nanoseconds on average. You only lose time on your unique input
-values.</p>
+<span class="co">#  mo_name(x) 259 264  357    299 451 509    10</span></code></pre></div>
+<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.299 seconds. That is 149 nanoseconds on average. You only lose time on your unique input values.</p>
 </div>
 <div class="section level3">
 <h3 id="precalculated-results">Precalculated results<a class="anchor" aria-label="anchor" href="#precalculated-results"></a>
 </h3>
-<p>What about precalculated results? If the input is an already
-precalculated result of a helper function such as
-<code><a href="../reference/mo_property.html">mo_name()</a></code>, it almost doesn’t take any time at all. In other
-words, if you run <code><a href="../reference/mo_property.html">mo_name()</a></code> on a valid taxonomic name, it
-will return the results immediately (see ‘C’ below):</p>
+<p>What about precalculated results? If the input is an already precalculated result of a helper function such as <code><a href="../reference/mo_property.html">mo_name()</a></code>, it almost doesn’t take any time at all. In other words, if you run <code><a href="../reference/mo_property.html">mo_name()</a></code> on a valid taxonomic name, it will return the results immediately (see ‘C’ below):</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"STAAUR"</span><span class="op">)</span>,
                          B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>,
                          C <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span>,
                          times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
-<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
+<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
 <span class="co">#  expr   min    lq mean median    uq   max neval</span>
-<span class="co">#     A  8.35  8.84  9.10   9.01  9.32 10.20    10</span>
-<span class="co">#     B 23.00 24.70 30.30  25.00 26.90 72.70    10</span>
-<span class="co">#     C  2.05  2.07  2.44   2.41  2.83  3.05    10</span></code></pre></div>
-<p>So going from <code>mo_name("Staphylococcus aureus")</code> to
-<code>"Staphylococcus aureus"</code> takes 0.0024 seconds - it doesn’t
-even start calculating <em>if the result would be the same as the
-expected resulting value</em>. That goes for all helper functions:</p>
+<span class="co">#     A 11.90 12.10 13.0  13.50 13.70 13.80    10</span>
+<span class="co">#     B 60.90 61.20 67.7  66.20 66.90 99.70    10</span>
+<span class="co">#     C  2.91  2.94  3.2   3.32  3.38  3.46    10</span></code></pre></div>
+<p>So going from <code>mo_name("Staphylococcus aureus")</code> to <code>"Staphylococcus aureus"</code> takes 0.0033 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
                          B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"Staphylococcus"</span><span class="op">)</span>,
@@ -343,31 +304,23 @@ expected resulting value</em>. That goes for all helper functions:</p>
                          G <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_phylum</a></span><span class="op">(</span><span class="st">"Firmicutes"</span><span class="op">)</span>,
                          H <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span><span class="op">(</span><span class="st">"Bacteria"</span><span class="op">)</span>,
                          times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
-<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
+<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
 <span class="co">#  expr  min   lq mean median   uq  max neval</span>
-<span class="co">#     A 1.89 1.93 2.09   2.05 2.17 2.40    10</span>
-<span class="co">#     B 1.89 1.93 2.08   2.00 2.19 2.63    10</span>
-<span class="co">#     C 1.91 1.92 2.10   1.97 2.30 2.43    10</span>
-<span class="co">#     D 1.90 1.94 2.21   2.02 2.53 2.88    10</span>
-<span class="co">#     E 1.87 1.95 2.09   2.04 2.22 2.33    10</span>
-<span class="co">#     F 1.84 1.91 1.97   1.92 2.04 2.14    10</span>
-<span class="co">#     G 1.87 1.92 2.10   1.96 2.12 2.96    10</span>
-<span class="co">#     H 1.90 1.96 2.12   2.06 2.21 2.47    10</span></code></pre></div>
-<p>Of course, when running <code>mo_phylum("Firmicutes")</code> the
-function has zero knowledge about the actual microorganism, namely
-<em>S. aureus</em>. But since the result would be
-<code>"Firmicutes"</code> anyway, there is no point in calculating the
-result. And because this package contains all phyla of all known
-bacteria, it can just return the initial value immediately.</p>
+<span class="co">#     A 2.92 2.93 3.02   2.94 3.02 3.40    10</span>
+<span class="co">#     B 2.87 2.90 3.14   3.09 3.32 3.71    10</span>
+<span class="co">#     C 2.91 2.94 3.15   3.12 3.33 3.46    10</span>
+<span class="co">#     D 2.86 2.90 3.05   2.96 3.27 3.30    10</span>
+<span class="co">#     E 2.87 2.88 3.03   2.96 3.16 3.29    10</span>
+<span class="co">#     F 2.92 2.95 3.08   2.98 3.29 3.35    10</span>
+<span class="co">#     G 2.89 2.96 3.04   2.99 3.11 3.29    10</span>
+<span class="co">#     H 2.85 2.95 3.11   3.08 3.31 3.38    10</span></code></pre></div>
+<p>Of course, when running <code>mo_phylum("Firmicutes")</code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package contains all phyla of all known bacteria, it can just return the initial value immediately.</p>
 </div>
 <div class="section level3">
 <h3 id="results-in-other-languages">Results in other languages<a class="anchor" aria-label="anchor" href="#results-in-other-languages"></a>
 </h3>
-<p>When the system language is non-English and supported by this
-<code>AMR</code> package, some functions will have a translated result.
-This almost does’t take extra time (compare “en” from the table below
-with the other languages):</p>
+<p>When the system language is non-English and supported by this <code>AMR</code> package, some functions will have a translated result. This almost does’t take extra time (compare “en” from the table below with the other languages):</p>
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">CoNS</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"CoNS"</span><span class="op">)</span>
 <span class="va">CoNS</span>
@@ -394,21 +347,20 @@ with the other languages):</p>
                          ru <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"ru"</span><span class="op">)</span>,
                          sv <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"sv"</span><span class="op">)</span>,
                          times <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
-<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
+<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
 <span class="co">#  expr   min    lq  mean median    uq    max neval</span>
-<span class="co">#    da 2.133 2.304 3.442  2.494 2.816 46.020   100</span>
-<span class="co">#    de 2.128 2.312 3.068  2.520 2.699 53.220   100</span>
-<span class="co">#    en 1.014 1.115 1.262  1.227 1.362  2.424   100</span>
-<span class="co">#    es 2.133 2.338 2.981  2.570 2.737 43.770   100</span>
-<span class="co">#    fr 1.986 2.149 3.139  2.377 2.567 41.610   100</span>
-<span class="co">#    it 2.072 2.268 2.911  2.468 2.656 44.560   100</span>
-<span class="co">#    nl 2.115 2.286 2.962  2.521 2.723 43.240   100</span>
-<span class="co">#    pt 2.055 2.205 2.912  2.520 2.687 39.520   100</span>
-<span class="co">#    ru 1.998 2.210 2.866  2.474 2.631 39.820   100</span>
-<span class="co">#    sv 2.022 2.187 2.759  2.357 2.536 38.560   100</span></code></pre></div>
-<p>Currently supported languages are Danish, Dutch, English, French,
-German, Italian, Portuguese, Russian, Spanish and Swedish.</p>
+<span class="co">#    da 3.546 3.643 4.072  3.704 3.832 35.930   100</span>
+<span class="co">#    de 3.597 3.659 4.422  3.734 3.839 36.400   100</span>
+<span class="co">#    en 1.672 1.726 1.804  1.767 1.794  2.259   100</span>
+<span class="co">#    es 3.609 3.685 4.496  3.760 3.843 36.540   100</span>
+<span class="co">#    fr 3.484 3.567 3.725  3.654 3.713  6.281   100</span>
+<span class="co">#    it 3.523 3.615 4.419  3.720 3.787 36.720   100</span>
+<span class="co">#    nl 3.614 3.676 3.805  3.732 3.838  4.703   100</span>
+<span class="co">#    pt 3.512 3.595 4.077  3.659 3.789 37.310   100</span>
+<span class="co">#    ru 3.556 3.647 4.057  3.680 3.812 35.230   100</span>
+<span class="co">#    sv 3.540 3.642 4.093  3.732 3.803 36.340   100</span></code></pre></div>
+<p>Currently supported languages are Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish.</p>
 </div>
   </div>
 
@@ -422,14 +374,12 @@ German, Italian, Portuguese, Russian, Spanish and Swedish.</p>
 
       <footer><div class="copyright">
   <p></p>
-<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
-Erwin E. A. Hassing.</p>
+<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
-2.0.2.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer>

docs/articles/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

docs/articles/datasets.html

@@ -44,7 +44,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9010</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
       </span>
     </div>
 
@@ -58,7 +58,7 @@
   </a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
     <span class="fa fa-question-circle"></span>
      
     How to
@@ -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">15 March 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
@@ -881,6 +881,173 @@ Dipivoxil, …</td>
 </div>
 </div>
 <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 20,369 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>
+<p>This data set is in R available as <code>rsi_translation</code>,
+after you load the <code>AMR</code> package.</p>
+<p>It was last updated on 10 May 2022 19:42:39 UTC. Find more info about
+the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
+<p><strong>Direct download links:</strong></p>
+<ul>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R
+file</a> (49 kB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Excel
+file</a> (0.9 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain
+text file</a> (2 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS
+file</a> (4 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS
+file</a> (2.6 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata
+file</a> (3.8 MB)</li>
+</ul>
+<div class="section level3">
+<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
+</h3>
+<p>This data set contains interpretation rules for MIC values and disk
+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>
+</h3>
+<table style="width:100%;" class="table">
+<colgroup>
+<col width="8%">
+<col width="5%">
+<col width="3%">
+<col width="8%">
+<col width="14%">
+<col width="7%">
+<col width="3%">
+<col width="10%">
+<col width="8%">
+<col width="7%">
+<col width="8%">
+<col width="8%">
+<col width="4%">
+</colgroup>
+<thead><tr class="header">
+<th align="center">guideline</th>
+<th align="center">method</th>
+<th align="center">site</th>
+<th align="center">mo</th>
+<th align="center">mo_name</th>
+<th align="center">rank_index</th>
+<th align="center">ab</th>
+<th align="center">ab_name</th>
+<th align="center">ref_tbl</th>
+<th align="center">disk_dose</th>
+<th align="center">breakpoint_S</th>
+<th align="center">breakpoint_R</th>
+<th align="center">uti</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td align="center">EUCAST 2022</td>
+<td align="center">MIC</td>
+<td align="center"></td>
+<td align="center">F_ASPRG_MGTS</td>
+<td align="center">Aspergillus fumigatus</td>
+<td align="center">2</td>
+<td align="center">AMB</td>
+<td align="center">Amphotericin B</td>
+<td align="center">Aspergillus</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_ASPRG_NIGR</td>
+<td align="center">Aspergillus niger</td>
+<td align="center">2</td>
+<td align="center">AMB</td>
+<td align="center">Amphotericin B</td>
+<td align="center">Aspergillus</td>
+<td align="center"></td>
+<td align="center">1</td>
+<td align="center">1</td>
+<td align="center">FALSE</td>
+</tr>
+<tr class="odd">
+<td align="center">EUCAST 2022</td>
+<td align="center">MIC</td>
+<td align="center"></td>
+<td align="center">F_CANDD</td>
+<td align="center">Candida</td>
+<td align="center">3</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_ALBC</td>
+<td align="center">Candida albicans</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="odd">
+<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>
+<td align="center">Candida krusei</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>
+</tbody>
+</table>
+</div>
+</div>
+<div class="section level2">
 <h2 id="intrinsic-bacterial-resistance">Intrinsic bacterial resistance<a class="anchor" aria-label="anchor" href="#intrinsic-bacterial-resistance"></a>
 </h2>
 <p>A data set with 134,956 rows and 2 columns, containing the following
@@ -895,7 +1062,7 @@ about the structure of this data set <a href="https://msberends.github.io/AMR/re
 file</a> (78 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Excel
-file</a> (0.9 MB)<br>
+file</a> (1.3 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">plain
 text file</a> (5.1 MB)<br>
@@ -910,15 +1077,15 @@ file</a> (7.4 MB)<br>
 file</a> (10.2 MB)</li>
 </ul>
 <div class="section level3">
-<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
+<h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></a>
 </h3>
 <p>This data set contains all defined intrinsic resistance by EUCAST of
-all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">‘EUCAST
+all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes/" class="external-link">‘EUCAST
 Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’
 v3.3</a> (2021).</p>
 </div>
 <div class="section level3">
-<h3 id="example-content-4">Example content<a class="anchor" aria-label="anchor" href="#example-content-4"></a>
+<h3 id="example-content-5">Example content<a class="anchor" aria-label="anchor" href="#example-content-5"></a>
 </h3>
 <p>Example rows when filtering on <em>Enterobacter cloacae</em>:</p>
 <table class="table">
@@ -933,6 +1100,14 @@ v3.3</a> (2021).</p>
 </tr>
 <tr class="even">
 <td align="center">Enterobacter cloacae</td>
+<td align="center">Acetylspiramycin</td>
+</tr>
+<tr class="odd">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Amoxicillin</td>
+</tr>
+<tr class="even">
+<td align="center">Enterobacter cloacae</td>
 <td align="center">Amoxicillin/clavulanic acid</td>
 </tr>
 <tr class="odd">
@@ -941,35 +1116,43 @@ v3.3</a> (2021).</p>
 </tr>
 <tr class="even">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Amoxicillin</td>
+<td align="center">Ampicillin/sulbactam</td>
 </tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Acetylspiramycin</td>
-</tr>
-<tr class="even">
-<td align="center">Enterobacter cloacae</td>
 <td align="center">Avoparcin</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Azithromycin</td>
 </tr>
+<tr class="odd">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Benzylpenicillin</td>
+</tr>
 <tr class="even">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Cadazolid</td>
 </tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Cephalothin</td>
+<td align="center">Cefadroxil</td>
 </tr>
 <tr class="even">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Cefadroxil</td>
+<td align="center">Cefazolin</td>
 </tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Clindamycin</td>
+<td align="center">Cefoxitin</td>
+</tr>
+<tr class="even">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Cephalexin</td>
+</tr>
+<tr class="odd">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Cephalothin</td>
 </tr>
 <tr class="even">
 <td align="center">Enterobacter cloacae</td>
@@ -977,11 +1160,11 @@ v3.3</a> (2021).</p>
 </tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Cycloserine</td>
+<td align="center">Clindamycin</td>
 </tr>
 <tr class="even">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Cefazolin</td>
+<td align="center">Cycloserine</td>
 </tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
@@ -1001,27 +1184,19 @@ v3.3</a> (2021).</p>
 </tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Cefoxitin</td>
-</tr>
-<tr class="even">
-<td align="center">Enterobacter cloacae</td>
 <td align="center">Fusidic acid</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Gamithromycin</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Josamycin</td>
 </tr>
-<tr class="odd">
-<td align="center">Enterobacter cloacae</td>
-<td align="center">Kitasamycin</td>
-</tr>
 <tr class="even">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Cephalexin</td>
+<td align="center">Kitasamycin</td>
 </tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
@@ -1033,31 +1208,39 @@ v3.3</a> (2021).</p>
 </tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
+<td align="center">Meleumycin</td>
+</tr>
+<tr class="even">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Midecamycin</td>
+</tr>
+<tr class="odd">
+<td align="center">Enterobacter cloacae</td>
 <td align="center">Miocamycin</td>
 </tr>
 <tr class="even">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Meleumycin</td>
+<td align="center">Nafithromycin</td>
 </tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Midecamycin</td>
-</tr>
-<tr class="even">
-<td align="center">Enterobacter cloacae</td>
 <td align="center">Norvancomycin</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Oleandomycin</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Oritavancin</td>
 </tr>
+<tr class="even">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Pirlimycin</td>
+</tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Benzylpenicillin</td>
+<td align="center">Primycin</td>
 </tr>
 <tr class="even">
 <td align="center">Enterobacter cloacae</td>
@@ -1065,14 +1248,6 @@ v3.3</a> (2021).</p>
 </tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Pirlimycin</td>
-</tr>
-<tr class="even">
-<td align="center">Enterobacter cloacae</td>
-<td align="center">Primycin</td>
-</tr>
-<tr class="odd">
-<td align="center">Enterobacter cloacae</td>
 <td align="center">Quinupristin/dalfopristin</td>
 </tr>
 <tr class="even">
@@ -1093,15 +1268,15 @@ v3.3</a> (2021).</p>
 </tr>
 <tr class="even">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Ampicillin/sulbactam</td>
+<td align="center">Solithromycin</td>
 </tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Solithromycin</td>
+<td align="center">Spiramycin</td>
 </tr>
 <tr class="even">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Spiramycin</td>
+<td align="center">Tedizolid</td>
 </tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
@@ -1109,15 +1284,7 @@ v3.3</a> (2021).</p>
 </tr>
 <tr class="even">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Thiacetazone</td>
-</tr>
-<tr class="odd">
-<td align="center">Enterobacter cloacae</td>
-<td align="center">Tilmicosin</td>
-</tr>
-<tr class="even">
-<td align="center">Enterobacter cloacae</td>
-<td align="center">Tildipirosin</td>
+<td align="center">Telavancin</td>
 </tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
@@ -1125,7 +1292,15 @@ v3.3</a> (2021).</p>
 </tr>
 <tr class="even">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Telavancin</td>
+<td align="center">Thiacetazone</td>
+</tr>
+<tr class="odd">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Tildipirosin</td>
+</tr>
+<tr class="even">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Tilmicosin</td>
 </tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
@@ -1145,167 +1320,8 @@ v3.3</a> (2021).</p>
 </tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Tedizolid</td>
-</tr>
-<tr class="even">
-<td align="center">Enterobacter cloacae</td>
 <td align="center">Vancomycin</td>
 </tr>
-<tr class="odd">
-<td align="center">Enterobacter cloacae</td>
-<td align="center">Nafithromycin</td>
-</tr>
-</tbody>
-</table>
-</div>
-</div>
-<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
-column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>,
-<em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>,
-<em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
-<p>This data set is in R available as <code>rsi_translation</code>,
-after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info
-about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
-<p><strong>Direct download links:</strong></p>
-<ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R
-file</a> (39 kB)<br>
-</li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Excel
-file</a> (0.7 MB)<br>
-</li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain
-text file</a> (1.7 MB)<br>
-</li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS
-file</a> (3.6 MB)<br>
-</li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS
-file</a> (2.2 MB)<br>
-</li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata
-file</a> (3.4 MB)</li>
-</ul>
-<div class="section level3">
-<h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></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>
-</div>
-<div class="section level3">
-<h3 id="example-content-5">Example content<a class="anchor" aria-label="anchor" href="#example-content-5"></a>
-</h3>
-<table class="table">
-<colgroup>
-<col width="9%">
-<col width="5%">
-<col width="4%">
-<col width="16%">
-<col width="8%">
-<col width="11%">
-<col width="9%">
-<col width="8%">
-<col width="10%">
-<col width="10%">
-<col width="5%">
-</colgroup>
-<thead><tr class="header">
-<th align="center">guideline</th>
-<th align="center">method</th>
-<th align="center">site</th>
-<th align="center">mo</th>
-<th align="center">rank_index</th>
-<th align="center">ab</th>
-<th align="center">ref_tbl</th>
-<th align="center">disk_dose</th>
-<th align="center">breakpoint_S</th>
-<th align="center">breakpoint_R</th>
-<th align="center">uti</th>
-</tr></thead>
-<tbody>
-<tr class="odd">
-<td align="center">EUCAST 2021</td>
-<td align="center">MIC</td>
-<td align="center"></td>
-<td align="center">Aspergillus fumigatus</td>
-<td align="center">2</td>
-<td align="center">Amphotericin B</td>
-<td align="center">Aspergillus</td>
-<td align="center"></td>
-<td align="center">1</td>
-<td align="center">4</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">Aspergillus niger</td>
-<td align="center">2</td>
-<td align="center">Amphotericin B</td>
-<td align="center">Aspergillus</td>
-<td align="center"></td>
-<td align="center">1</td>
-<td align="center">4</td>
-<td align="center">FALSE</td>
-</tr>
-<tr class="odd">
-<td align="center">EUCAST 2021</td>
-<td align="center">MIC</td>
-<td align="center"></td>
-<td align="center">Candida</td>
-<td align="center">3</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>
-<tr class="even">
-<td align="center">EUCAST 2021</td>
-<td align="center">MIC</td>
-<td align="center"></td>
-<td align="center">Candida albicans</td>
-<td align="center">2</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>
-<tr class="odd">
-<td align="center">EUCAST 2021</td>
-<td align="center">MIC</td>
-<td align="center"></td>
-<td align="center">Candida krusei</td>
-<td align="center">2</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>
-<tr class="even">
-<td align="center">EUCAST 2021</td>
-<td align="center">MIC</td>
-<td align="center"></td>
-<td align="center">Candida parapsilosis</td>
-<td align="center">2</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>
 </table>
 </div>
@@ -1460,14 +1476,12 @@ Breakpoint Tables’ v11.0</a> (2021).</p>
 
       <footer><div class="copyright">
   <p></p>
-<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
-Erwin E. A. Hassing.</p>
+<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
-2.0.2.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer>

docs/articles/datasets_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

docs/articles/index.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9008</span>
       </span>
     </div>
 
@@ -30,7 +30,7 @@
   </a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
     <span class="fa fa-question-circle"></span>
      
     How to
@@ -185,13 +185,11 @@
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
-Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
-2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
 </div>
 
       </footer></div>

docs/articles/resistance_predict.html

@@ -185,7 +185,7 @@
 
       
 
-      </header><div class="row">
+      </header><script src="resistance_predict_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>How to predict antimicrobial resistance</h1>
@@ -201,13 +201,8 @@
 <div class="section level2">
 <h2 id="needed-r-packages">Needed R packages<a class="anchor" aria-label="anchor" href="#needed-r-packages"></a>
 </h2>
-<p>As with many uses in R, we need some additional packages for AMR data
-analysis. Our package works closely together with the <a href="https://www.tidyverse.org" class="external-link">tidyverse packages</a> <a href="https://dplyr.tidyverse.org/" class="external-link"><code>dplyr</code></a> and <a href="https://ggplot2.tidyverse.org" class="external-link"><code>ggplot2</code></a> by Dr
-Hadley Wickham. The tidyverse tremendously improves the way we conduct
-data science - it allows for a very natural way of writing syntaxes and
-creating beautiful plots in R.</p>
-<p>Our <code>AMR</code> package depends on these packages and even
-extends their use and functions.</p>
+<p>As with many uses in R, we need some additional packages for AMR data analysis. Our package works closely together with the <a href="https://www.tidyverse.org" class="external-link">tidyverse packages</a> <a href="https://dplyr.tidyverse.org/" class="external-link"><code>dplyr</code></a> and <a href="https://ggplot2.tidyverse.org" class="external-link"><code>ggplot2</code></a> by Dr Hadley Wickham. The tidyverse tremendously improves the way we conduct data science - it allows for a very natural way of writing syntaxes and creating beautiful plots in R.</p>
+<p>Our <code>AMR</code> package depends on these packages and even extends their use and functions.</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span>
@@ -219,34 +214,24 @@ extends their use and functions.</p>
 <div class="section level2">
 <h2 id="prediction-analysis">Prediction analysis<a class="anchor" aria-label="anchor" href="#prediction-analysis"></a>
 </h2>
-<p>Our package contains a function <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>,
-which takes the same input as functions for <a href="./AMR.html">other
-AMR data analysis</a>. Based on a date column, it calculates cases per
-year and uses a regression model to predict antimicrobial
-resistance.</p>
+<p>Our package contains a function <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>, which takes the same input as functions for <a href="./AMR.html">other AMR data analysis</a>. Based on a date column, it calculates cases per year and uses a regression model to predict antimicrobial resistance.</p>
 <p>It is basically as easy as:</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="co"># resistance prediction of piperacillin/tazobactam (TZP):</span></span>
-<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="fu">resistance_predict</span>(<span class="at">tbl =</span> example_isolates, <span class="at">col_date =</span> <span class="st">"date"</span>, <span class="at">col_ab =</span> <span class="st">"TZP"</span>, <span class="at">model =</span> <span class="st">"binomial"</span>)</span>
-<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a><span class="co"># or:</span></span>
-<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a>example_isolates <span class="sc">%&gt;%</span> </span>
-<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a>  <span class="fu">resistance_predict</span>(<span class="at">col_ab =</span> <span class="st">"TZP"</span>,</span>
-<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a>                     model  <span class="st">"binomial"</span>)</span>
-<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a><span class="co"># to bind it to object 'predict_TZP' for example:</span></span>
-<span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a>predict_TZP <span class="ot">&lt;-</span> example_isolates <span class="sc">%&gt;%</span> </span>
-<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a>  <span class="fu">resistance_predict</span>(<span class="at">col_ab =</span> <span class="st">"TZP"</span>,</span>
-<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a>                     <span class="at">model =</span> <span class="st">"binomial"</span>)</span></code></pre></div>
-<p>The function will look for a date column itself if
-<code>col_date</code> is not set.</p>
-<p>When running any of these commands, a summary of the regression model
-will be printed unless using
-<code>resistance_predict(..., info = FALSE)</code>.</p>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true"></a><span class="co"># resistance prediction of piperacillin/tazobactam (TZP):</span></span>
+<span id="cb2-2"><a href="#cb2-2" aria-hidden="true"></a><span class="kw">resistance_predict</span>(<span class="dt">tbl =</span> example_isolates, <span class="dt">col_date =</span> <span class="st">"date"</span>, <span class="dt">col_ab =</span> <span class="st">"TZP"</span>, <span class="dt">model =</span> <span class="st">"binomial"</span>)</span>
+<span id="cb2-3"><a href="#cb2-3" aria-hidden="true"></a></span>
+<span id="cb2-4"><a href="#cb2-4" aria-hidden="true"></a><span class="co"># or:</span></span>
+<span id="cb2-5"><a href="#cb2-5" aria-hidden="true"></a>example_isolates <span class="op">%&gt;%</span><span class="st"> </span></span>
+<span id="cb2-6"><a href="#cb2-6" aria-hidden="true"></a><span class="st">  </span><span class="kw">resistance_predict</span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>,</span>
+<span id="cb2-7"><a href="#cb2-7" aria-hidden="true"></a>                     model  <span class="st">"binomial"</span>)</span>
+<span id="cb2-8"><a href="#cb2-8" aria-hidden="true"></a></span>
+<span id="cb2-9"><a href="#cb2-9" aria-hidden="true"></a><span class="co"># to bind it to object 'predict_TZP' for example:</span></span>
+<span id="cb2-10"><a href="#cb2-10" aria-hidden="true"></a>predict_TZP &lt;-<span class="st"> </span>example_isolates <span class="op">%&gt;%</span><span class="st"> </span></span>
+<span id="cb2-11"><a href="#cb2-11" aria-hidden="true"></a><span class="st">  </span><span class="kw">resistance_predict</span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>,</span>
+<span id="cb2-12"><a href="#cb2-12" aria-hidden="true"></a>                     <span class="dt">model =</span> <span class="st">"binomial"</span>)</span></code></pre></div>
+<p>The function will look for a date column itself if <code>col_date</code> is not set.</p>
+<p>When running any of these commands, a summary of the regression model will be printed unless using <code>resistance_predict(..., info = FALSE)</code>.</p>
 <pre><code><span class="co"># ℹ Using column 'date' as input for `col_date`.</span></code></pre>
-<p>This text is only a printed summary - the actual result (output) of
-the function is a <code>data.frame</code> containing for each year: the
-number of observations, the actual observed resistance, the estimated
-resistance and the standard error below and above the estimation:</p>
+<p>This text is only a printed summary - the actual result (output) of the function is a <code>data.frame</code> containing for each year: the number of observations, the actual observed resistance, the estimated resistance and the standard error below and above the estimation:</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">predict_TZP</span>
 <span class="co">#    year      value    se_min    se_max observations   observed  estimated</span>
@@ -281,18 +266,12 @@ resistance and the standard error below and above the estimation:</p>
 <span class="co"># 29 2030 0.48639359 0.3782932 0.5944939           NA         NA 0.48639359</span>
 <span class="co"># 30 2031 0.51109592 0.3973697 0.6248221           NA         NA 0.51109592</span>
 <span class="co"># 31 2032 0.53574417 0.4169574 0.6545309           NA         NA 0.53574417</span></code></pre></div>
-<p>The function <code>plot</code> is available in base R, and can be
-extended by other packages to depend the output based on the type of
-input. We extended its function to cope with resistance predictions:</p>
+<p>The function <code>plot</code> is available in base R, and can be extended by other packages to depend the output based on the type of input. We extended its function to cope with resistance predictions:</p>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span></code></pre></div>
 <p><img src="resistance_predict_files/figure-html/unnamed-chunk-4-1.png" width="720"></p>
-<p>This is the fastest way to plot the result. It automatically adds the
-right axes, error bars, titles, number of available observations and
-type of model.</p>
-<p>We also support the <code>ggplot2</code> package with our custom
-function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> to create more appealing
-plots:</p>
+<p>This is the fastest way to plot the result. It automatically adds the right axes, error bars, titles, number of available observations and type of model.</p>
+<p>We also support the <code>ggplot2</code> package with our custom function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> to create more appealing plots:</p>
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span></code></pre></div>
 <p><img src="resistance_predict_files/figure-html/unnamed-chunk-5-1.png" width="720"></p>
@@ -304,9 +283,7 @@ plots:</p>
 <div class="section level3">
 <h3 id="choosing-the-right-model">Choosing the right model<a class="anchor" aria-label="anchor" href="#choosing-the-right-model"></a>
 </h3>
-<p>Resistance is not easily predicted; if we look at vancomycin
-resistance in Gram-positive bacteria, the spread (i.e. standard error)
-is enormous:</p>
+<p>Resistance is not easily predicted; if we look at vancomycin resistance in Gram-positive bacteria, the spread (i.e. standard error) is enormous:</p>
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
   <span class="fu"><a href="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_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
@@ -314,13 +291,8 @@ is enormous:</p>
   <span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span>
 <span class="co"># ℹ Using column 'date' as input for `col_date`.</span></code></pre></div>
 <p><img src="resistance_predict_files/figure-html/unnamed-chunk-6-1.png" width="720"></p>
-<p>Vancomycin resistance could be 100% in ten years, but might also stay
-around 0%.</p>
-<p>You can define the model with the <code>model</code> parameter. The
-model chosen above is a generalised linear regression model using a
-binomial distribution, assuming that a period of zero resistance was
-followed by a period of increasing resistance leading slowly to more and
-more resistance.</p>
+<p>Vancomycin resistance could be 100% in ten years, but might also stay around 0%.</p>
+<p>You can define the model with the <code>model</code> parameter. The model chosen above is a generalised linear regression model using a binomial distribution, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance.</p>
 <p>Valid values are:</p>
 <table class="table">
 <colgroup>
@@ -336,8 +308,7 @@ more resistance.</p>
 <tbody>
 <tr class="odd">
 <td>
-<code>"binomial"</code> or <code>"binom"</code> or
-<code>"logit"</code>
+<code>"binomial"</code> or <code>"binom"</code> or <code>"logit"</code>
 </td>
 <td><code>glm(..., family = binomial)</code></td>
 <td>Generalised linear model with binomial distribution</td>
@@ -358,9 +329,7 @@ more resistance.</p>
 </tr>
 </tbody>
 </table>
-<p>For the vancomycin resistance in Gram-positive bacteria, a linear
-model might be more appropriate since no binomial distribution is to be
-expected based on the observed years:</p>
+<p>For the vancomycin resistance in Gram-positive bacteria, a linear model might be more appropriate since no binomial distribution is to be expected based on the observed years:</p>
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
   <span class="fu"><a href="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_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
@@ -369,8 +338,7 @@ expected based on the observed years:</p>
 <span class="co"># ℹ Using column 'date' as input for `col_date`.</span></code></pre></div>
 <p><img src="resistance_predict_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
 <p>This seems more likely, doesn’t it?</p>
-<p>The model itself is also available from the object, as an
-<code>attribute</code>:</p>
+<p>The model itself is also available from the object, as an <code>attribute</code>:</p>
 <div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">model</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/attributes.html" class="external-link">attributes</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span><span class="op">$</span><span class="va">model</span>
 
@@ -399,14 +367,12 @@ expected based on the observed years:</p>
 
       <footer><div class="copyright">
   <p></p>
-<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
-Erwin E. A. Hassing.</p>
+<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
-2.0.2.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer>

docs/articles/resistance_predict_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

docs/articles/welcome_to_AMR.html

@@ -185,7 +185,7 @@
 
       
 
-      </header><div class="row">
+      </header><script src="welcome_to_AMR_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Welcome to the <code>AMR</code> package</h1>
@@ -198,83 +198,33 @@
 
     
     
-<p>Note: to keep the package size as small as possible, we only included
-this vignette on CRAN. You can read more vignettes on our website about
-how to conduct AMR data analysis, determine MDRO’s, find explanation of
-EUCAST rules, and much more: <a href="https://msberends.github.io/AMR/articles/" class="uri">https://msberends.github.io/AMR/articles/</a>.</p>
+<p>Note: to keep the package size as small as possible, we only included this vignette on CRAN. You can read more vignettes on our website about how to conduct AMR data analysis, determine MDRO’s, find explanation of EUCAST rules, and much more: <a href="https://msberends.github.io/AMR/articles/" class="uri">https://msberends.github.io/AMR/articles/</a>.</p>
 <hr>
-<p><code>AMR</code> is a free, open-source and independent R package
-(see <a href="https://msberends.github.io/AMR/#copyright">Copyright</a>)
-to simplify the analysis and prediction of Antimicrobial Resistance
-(AMR) and to work with microbial and antimicrobial data and properties,
-by using evidence-based methods. <strong>Our aim is to provide a
-standard</strong> for clean and reproducible antimicrobial resistance
-data analysis, that can therefore empower epidemiological analyses to
-continuously enable surveillance and treatment evaluation in any
-setting.</p>
-<p>After installing this package, R knows ~71,000 distinct microbial
-species and all ~570 antibiotic, antimycotic and antiviral drugs by name
-and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and
-knows all about valid R/SI and MIC values. It supports any data format,
-including WHONET/EARS-Net data.</p>
-<p>The <code>AMR</code> package is available in Danish, Dutch, English,
-French, German, Italian, Portuguese, Russian, Spanish and Swedish.
-Antimicrobial drug (group) names and colloquial microorganism names are
-provided in these languages.</p>
-<p>This package is fully independent of any other R package and works on
-Windows, macOS and Linux with all versions of R since R-3.0 (April
-2013). <strong>It was designed to work in any setting, including those
-with very limited resources</strong>. Since its first public release in
-early 2018, this package has been downloaded from more than 175
-countries.</p>
+<p><code>AMR</code> is a free, open-source and independent R package (see <a href="https://msberends.github.io/AMR/#copyright">Copyright</a>) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
+<p>After installing this package, R knows ~71,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
+<p>The <code>AMR</code> package is available in Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
+<p>This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. Since its first public release in early 2018, this package has been downloaded from more than 175 countries.</p>
 <p>This package can be used for:</p>
 <ul>
-<li>Reference for the taxonomy of microorganisms, since the package
-contains all microbial (sub)species from the Catalogue of Life and List
-of Prokaryotic names with Standing in Nomenclature</li>
-<li>Interpreting raw MIC and disk diffusion values, based on the latest
-CLSI or EUCAST guidelines</li>
-<li>Retrieving antimicrobial drug names, doses and forms of
-administration from clinical health care records</li>
+<li>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the Catalogue of Life and List of Prokaryotic names with Standing in Nomenclature</li>
+<li>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines</li>
+<li>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records</li>
 <li>Determining first isolates to be used for AMR data analysis</li>
 <li>Calculating antimicrobial resistance</li>
-<li>Determining multi-drug resistance (MDR) / multi-drug resistant
-organisms (MDRO)</li>
-<li>Calculating (empirical) susceptibility of both mono therapy and
-combination therapies</li>
-<li>Predicting future antimicrobial resistance using regression
-models</li>
-<li>Getting properties for any microorganism (like Gram stain, species,
-genus or family)</li>
-<li>Getting properties for any antibiotic (like name, code of
-EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name)</li>
+<li>Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO)</li>
+<li>Calculating (empirical) susceptibility of both mono therapy and combination therapies</li>
+<li>Predicting future antimicrobial resistance using regression models</li>
+<li>Getting properties for any microorganism (like Gram stain, species, genus or family)</li>
+<li>Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name)</li>
 <li>Plotting antimicrobial resistance</li>
 <li>Applying EUCAST expert rules</li>
-<li>Getting SNOMED codes of a microorganism, or getting properties of a
-microorganism based on a SNOMED code</li>
-<li>Getting LOINC codes of an antibiotic, or getting properties of an
-antibiotic based on a LOINC code</li>
-<li>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to
-translate MIC values and disk diffusion diameters to R/SI</li>
+<li>Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code</li>
+<li>Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code</li>
+<li>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI</li>
 <li>Principal component analysis for AMR</li>
 </ul>
-<p>All reference data sets (about microorganisms, antibiotics, R/SI
-interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are
-publicly and freely available. We continually export our data sets to
-formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat
-files that are machine-readable and suitable for input in any software
-program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all
-download links on our website</a>, which is automatically updated with
-every code change.</p>
-<p>This R package was created for both routine data analysis and
-academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration
-with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe
-Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This
-R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI
-10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI
-10.33612/diss.192486375</a>) but is actively and durably maintained (see
-<a href="https://msberends.github.io/AMR/news/index.html">changelog)</a>)
-by two public healthcare organisations in the Netherlands.</p>
+<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
+<p>This R package was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>) but is actively and durably maintained (see <a href="https://msberends.github.io/AMR/news/index.html">changelog)</a>) by two public healthcare organisations in the Netherlands.</p>
   </div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -287,14 +237,12 @@ by two public healthcare organisations in the Netherlands.</p>
 
       <footer><div class="copyright">
   <p></p>
-<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
-Erwin E. A. Hassing.</p>
+<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
-2.0.2.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer>

docs/articles/welcome_to_AMR_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

docs/authors.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9010</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
       </span>
     </div>
 
@@ -30,7 +30,7 @@
   </a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
     <span class="fa fa-question-circle"></span>
      
     How to
@@ -269,13 +269,11 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
-Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
-2.0.2.</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">1.8.0.9010</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
       </span>
     </div>
 
@@ -61,7 +61,7 @@
   </a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
     <span class="fa fa-question-circle"></span>
      
     How to
@@ -195,94 +195,37 @@
 <code>AMR</code> (for R) <img src="./logo.svg" align="right"><a class="anchor" aria-label="anchor" href="#amr-for-r-"></a>
 </h1></div>
 <blockquote>
-<p>Update: The latest <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST
-guideline for intrinsic resistance</a> (v3.3, October 2021) is now
-supported, the CLSI 2021 interpretation guideline is now supported, and
-our taxonomy tables have been updated as well (LPSN, 5 October
-2021).</p>
+<p>Update May 2022: EUCAST 2022 and CLSI 2022 guidelines have been added for <code><a href="reference/as.rsi.html">as.rsi()</a></code>!</p>
+<p>Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.</p>
 </blockquote>
 <div class="section level3">
 <h3 id="what-is-amr-for-r">What is <code>AMR</code> (for R)?<a class="anchor" aria-label="anchor" href="#what-is-amr-for-r"></a>
 </h3>
-<p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org" class="external-link">R package</a> (see <a href="#copyright">Copyright</a>) to simplify the analysis and prediction
-of Antimicrobial Resistance (AMR) and to work with microbial and
-antimicrobial data and properties, by using evidence-based methods.
-<strong>Our aim is to provide a standard</strong> for clean and
-reproducible AMR data analysis, that can therefore empower
-epidemiological analyses to continuously enable surveillance and
-treatment evaluation in any setting.</p>
-<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~71,000 distinct
-microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~570 antibiotic, antimycotic
-and antiviral drugs</strong></a> by name and code (including ATC,
-WHONET/EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about
-valid R/SI and MIC values. It supports any data format, including
-WHONET/EARS-Net data.</p>
-<p>The <code>AMR</code> package is available in
-<img src="lang_da.svg" style="height: 11px !important; vertical-align: initial !important;">
-Danish,
-<img src="lang_nl.svg" style="height: 11px !important; vertical-align: initial !important;">
-Dutch,
-<img src="lang_en.svg" style="height: 11px !important; vertical-align: initial !important;">
-English,
-<img src="lang_fr.svg" style="height: 11px !important; vertical-align: initial !important;">
-French,
-<img src="lang_de.svg" style="height: 11px !important; vertical-align: initial !important;">
-German,
-<img src="lang_it.svg" style="height: 11px !important; vertical-align: initial !important;">
-Italian,
-<img src="lang_pt.svg" style="height: 11px !important; vertical-align: initial !important;">
-Portuguese,
-<img src="lang_ru.svg" style="height: 11px !important; vertical-align: initial !important;">
-Russian,
-<img src="lang_es.svg" style="height: 11px !important; vertical-align: initial !important;">
-Spanish and
-<img src="lang_sv.svg" style="height: 11px !important; vertical-align: initial !important;">
-Swedish. Antimicrobial drug (group) names and colloquial microorganism
-names are provided in these languages.</p>
-<p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">fully independent
-of any other R package</a> and works on Windows, macOS and Linux with
-all versions of R since R-3.0 (April 2013). <strong>It was designed to
-work in any setting, including those with very limited
-resources</strong>. It was created for both routine data analysis and
-academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration
-with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe
-Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This
-R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI
-10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI
-10.33612/diss.192486375</a>) but is <a href="./news">actively and
-durably maintained</a> by two public healthcare organisations in the
-Netherlands.</p>
+<p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org" class="external-link">R package</a> (see <a href="#copyright">Copyright</a>) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
+<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~71,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~570 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, WHONET/EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
+<p>The <code>AMR</code> package is available in <img src="lang_da.svg" style="height: 11px !important; vertical-align: initial !important;"> Danish, <img src="lang_nl.svg" style="height: 11px !important; vertical-align: initial !important;"> Dutch, <img src="lang_en.svg" style="height: 11px !important; vertical-align: initial !important;"> English, <img src="lang_fr.svg" style="height: 11px !important; vertical-align: initial !important;"> French, <img src="lang_de.svg" style="height: 11px !important; vertical-align: initial !important;"> German, <img src="lang_it.svg" style="height: 11px !important; vertical-align: initial !important;"> Italian, <img src="lang_pt.svg" style="height: 11px !important; vertical-align: initial !important;"> Portuguese, <img src="lang_ru.svg" style="height: 11px !important; vertical-align: initial !important;"> Russian, <img src="lang_es.svg" style="height: 11px !important; vertical-align: initial !important;"> Spanish and <img src="lang_sv.svg" style="height: 11px !important; vertical-align: initial !important;"> Swedish. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
+<p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">fully independent of any other R package</a> and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>) but is <a href="./news">actively and durably maintained</a> by two public healthcare organisations in the Netherlands.</p>
 <div class="main-content" style="display: inline-block;">
 <p>
-<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a>
-<strong>Used in 175 countries</strong><br> Since its first public
-release in early 2018, this R package has been used in almost all
-countries in the world. Click the map to enlarge and to see the country
-names.
+<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in 175 countries</strong><br> Since its first public release in early 2018, this R package has been used in almost all countries in the world. Click the map to enlarge and to see the country names.
 </p>
 </div>
 <div class="section level5">
-<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 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>
-<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>
+<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">
 <th align="left">bacteria</th>
@@ -388,22 +331,17 @@ two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html"
 </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>
 </h4>
-<p>The development of this package is part of, related to, or made
-possible by:</p>
+<p>The development of this package is part of, related to, or made possible by:</p>
 <div align="center">
-<p><a href="https://www.rug.nl" title="University of Groningen" class="external-link"><img src="./logo_rug.png" class="partner_logo"></a>
-<a href="https://www.umcg.nl" title="University Medical Center Groningen" class="external-link"><img src="./logo_umcg.png" class="partner_logo"></a>
-<a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation" class="external-link"><img src="./logo_certe.png" class="partner_logo"></a>
-<a href="https://www.deutschland-nederland.eu" title="EurHealth-1-Health" class="external-link"><img src="./logo_eh1h.png" class="partner_logo"></a>
-<a href="https://www.deutschland-nederland.eu" title="INTERREG" class="external-link"><img src="./logo_interreg.png" class="partner_logo"></a></p>
+<p><a href="https://www.rug.nl" title="University of Groningen" class="external-link"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen" class="external-link"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation" class="external-link"><img src="./logo_certe.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="EurHealth-1-Health" class="external-link"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG" class="external-link"><img src="./logo_interreg.png" class="partner_logo"></a></p>
 </div>
 </div>
 </div>
@@ -412,33 +350,21 @@ possible by:</p>
 </h3>
 <p>This package can be used for:</p>
 <ul>
-<li>Reference for the taxonomy of microorganisms, since the package
-contains all microbial (sub)species from the <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> and <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in
-Nomenclature</a> (<a href="./reference/mo_property.html">manual</a>)</li>
-<li>Interpreting raw MIC and disk diffusion values, based on the latest
-CLSI or EUCAST guidelines (<a href="./reference/as.rsi.html">manual</a>)</li>
-<li>Retrieving antimicrobial drug names, doses and forms of
-administration from clinical health care records (<a href="./reference/ab_from_text.html">manual</a>)</li>
+<li>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> and <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (<a href="./reference/mo_property.html">manual</a>)</li>
+<li>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines (<a href="./reference/as.rsi.html">manual</a>)</li>
+<li>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records (<a href="./reference/ab_from_text.html">manual</a>)</li>
 <li>Determining first isolates to be used for AMR data analysis (<a href="./reference/first_isolate.html">manual</a>)</li>
 <li>Calculating antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
-<li>Determining multi-drug resistance (MDR) / multi-drug resistant
-organisms (MDRO) (<a href="./articles/MDR.html">tutorial</a>)</li>
-<li>Calculating (empirical) susceptibility of both mono therapy and
-combination therapies (<a href="./articles/AMR.html">tutorial</a>)</li>
-<li>Predicting future antimicrobial resistance using regression models
-(<a href="./articles/resistance_predict.html">tutorial</a>)</li>
-<li>Getting properties for any microorganism (like Gram stain, species,
-genus or family) (<a href="./reference/mo_property.html">manual</a>)</li>
-<li>Getting properties for any antibiotic (like name, code of
-EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) (<a href="./reference/ab_property.html">manual</a>)</li>
+<li>Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO) (<a href="./articles/MDR.html">tutorial</a>)</li>
+<li>Calculating (empirical) susceptibility of both mono therapy and combination therapies (<a href="./articles/AMR.html">tutorial</a>)</li>
+<li>Predicting future antimicrobial resistance using regression models (<a href="./articles/resistance_predict.html">tutorial</a>)</li>
+<li>Getting properties for any microorganism (like Gram stain, species, genus or family) (<a href="./reference/mo_property.html">manual</a>)</li>
+<li>Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) (<a href="./reference/ab_property.html">manual</a>)</li>
 <li>Plotting antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
 <li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li>
-<li>Getting SNOMED codes of a microorganism, or getting properties of a
-microorganism based on a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li>
-<li>Getting LOINC codes of an antibiotic, or getting properties of an
-antibiotic based on a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
-<li>Machine reading the EUCAST and CLSI guidelines from 2011-2021 to
-translate MIC values and disk diffusion diameters to R/SI (<a href="./articles/datasets.html">link</a>)</li>
+<li>Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li>
+<li>Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
+<li>Machine reading the EUCAST and CLSI guidelines from 2011-2021 to translate MIC values and disk diffusion diameters to R/SI (<a href="./articles/datasets.html">link</a>)</li>
 <li>Principal component analysis for AMR (<a href="./articles/PCA.html">tutorial</a>)</li>
 </ul>
 </div>
@@ -449,42 +375,30 @@ translate MIC values and disk diffusion diameters to R/SI (<a href="./articles/d
 <h4 id="latest-released-version">Latest released version<a class="anchor" aria-label="anchor" href="#latest-released-version"></a>
 </h4>
 <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>
+<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>
-<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>
+<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>
 <div class="section level4">
 <h4 id="latest-development-version">Latest development version<a class="anchor" aria-label="anchor" href="#latest-development-version"></a>
 </h4>
 <p><a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=main" alt="R-code-check"></a> <a href="https://www.codefactor.io/repository/github/msberends/amr" class="external-link"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://codecov.io/gh/msberends/AMR/branch/main/graph/badge.svg" alt="Codecov"></a></p>
-<p>The latest and unpublished development version can be installed from
-GitHub in two ways:</p>
+<p>The latest and unpublished development version can be installed from GitHub in two ways:</p>
 <ol style="list-style-type: decimal">
 <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>
+<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>
-<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>
+<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>
 <p>You can also download the latest build from our repository: <a href="https://github.com/msberends/AMR/raw/main/data-raw/AMR_latest.tar.gz" class="external-link uri">https://github.com/msberends/AMR/raw/main/data-raw/AMR_latest.tar.gz</a></p>
@@ -493,8 +407,7 @@ like any official release (e.g., using
 <div class="section level3">
 <h3 id="get-started">Get started<a class="anchor" aria-label="anchor" href="#get-started"></a>
 </h3>
-<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or
-click a link in the <a href="https://msberends.github.io/AMR/articles/">‘How to’ menu</a>.</p>
+<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click a link in the <a href="https://msberends.github.io/AMR/articles/">‘How to’ menu</a>.</p>
 </div>
 <div class="section level3">
 <h3 id="short-introduction">Short introduction<a class="anchor" aria-label="anchor" href="#short-introduction"></a>
@@ -502,181 +415,66 @@ click a link in the <a href="https://msberends.github.io/AMR/articles/">‘How t
 <div class="section level4">
 <h4 id="microbial-taxonomic-reference-data">Microbial (taxonomic) reference data<a class="anchor" aria-label="anchor" href="#microbial-taxonomic-reference-data"></a>
 </h4>
-<p>This package contains the complete taxonomic tree of almost all
-~71,000 microorganisms from the authoritative and comprehensive
-Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">www.catalogueoflife.org</a>),
-supplemented by data from the List of Prokaryotic names with Standing in
-Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>).
-This supplementation is needed until the <a href="https://github.com/Sp2000/colplus" class="external-link">CoL+ project</a> is finished,
-which we await. With <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be
-checked which version of the CoL is included in this package.</p>
+<p>This package contains the complete taxonomic tree of almost all ~71,000 microorganisms from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">www.catalogueoflife.org</a>), supplemented by data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/Sp2000/colplus" class="external-link">CoL+ project</a> is finished, which we await. With <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be checked which version of the CoL is included in this package.</p>
 <p>Read more about which data from the Catalogue of Life <a href="./reference/catalogue_of_life.html">in our manual</a>.</p>
 </div>
 <div class="section level4">
 <h4 id="antimicrobial-reference-data">Antimicrobial reference data<a class="anchor" aria-label="anchor" href="#antimicrobial-reference-data"></a>
 </h4>
-<p>This package contains <strong>all ~570 antibiotic, antimycotic and
-antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC)
-codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the
-World Health Organization Collaborating Centre for Drug Statistics
-Methodology (WHOCC, <a href="https://www.whocc.no" class="external-link uri">https://www.whocc.no</a>) and the <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">Pharmaceuticals
-Community Register of the European Commission</a>.</p>
-<p><strong>NOTE: The WHOCC copyright does not allow use for commercial
-purposes, unlike any other info from this package. See <a href="https://www.whocc.no/copyright_disclaimer/" class="external-link uri">https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
+<p>This package contains <strong>all ~570 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="external-link uri">https://www.whocc.no</a>) and the <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">Pharmaceuticals Community Register of the European Commission</a>.</p>
+<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href="https://www.whocc.no/copyright_disclaimer/" class="external-link uri">https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
 <p>Read more about the data from WHOCC <a href="./reference/WHOCC.html">in our manual</a>.</p>
 </div>
 <div class="section level4">
 <h4 id="whonet--ears-net">WHONET / EARS-Net<a class="anchor" aria-label="anchor" href="#whonet--ears-net"></a>
 </h4>
-<p>We support WHONET and EARS-Net data. Exported files from WHONET can
-be imported into R and can be analysed easily using this package. For
-education purposes, we created an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a>
-with the exact same structure as a WHONET export file. Furthermore, this
-package also contains a <a href="./reference/antibiotics.html">data set
-antibiotics</a> with all EARS-Net antibiotic abbreviations, and knows
-almost all WHONET abbreviations for microorganisms. When using WHONET
-data as input for analysis, all input parameters will be set
-automatically.</p>
-<p>Read our tutorial about <a href="./articles/WHONET.html">how to work
-with WHONET data here</a>.</p>
+<p>We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a> with the exact same structure as a WHONET export file. Furthermore, this package also contains a <a href="./reference/antibiotics.html">data set antibiotics</a> with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically.</p>
+<p>Read our tutorial about <a href="./articles/WHONET.html">how to work with WHONET data here</a>.</p>
 </div>
 <div class="section level4">
 <h4 id="overview-of-functions">Overview of functions<a class="anchor" aria-label="anchor" href="#overview-of-functions"></a>
 </h4>
-<p>The <code>AMR</code> package basically does four important
-things:</p>
+<p>The <code>AMR</code> package basically does four important things:</p>
 <ol style="list-style-type: decimal">
 <li>
-<p>It <strong>cleanses existing data</strong> by providing new
-<em>classes</em> for microoganisms, antibiotics and antimicrobial
-results (both S/I/R and MIC). By installing this package, you teach R
-everything about microbiology that is needed for analysis. These
-functions all use intelligent rules to guess results that you would
-expect:</p>
+<p>It <strong>cleanses existing data</strong> by providing new <em>classes</em> for microoganisms, antibiotics and antimicrobial results (both S/I/R and MIC). By installing this package, you teach R everything about microbiology that is needed for analysis. These functions all use intelligent rules to guess results that you would expect:</p>
 <ul>
-<li>Use <code><a href="reference/as.mo.html">as.mo()</a></code> to get a microbial ID. The IDs are human
-readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em>
-is “B_KLBSL_PNMN” (B stands for Bacteria) and the ID of <em>S.
-aureus</em> is “B_STPHY_AURS”. The function takes almost any text as
-input that looks like the name or code of a microorganism like “E.
-coli”, “esco” or “esccol” and tries to find expected results using
-intelligent rules combined with the included Catalogue of Life data set.
-It only takes milliseconds to find results, please see our <a href="./articles/benchmarks.html">benchmarks</a>. Moreover, it can group
-<em>Staphylococci</em> into coagulase negative and positive (CoNS and
-CoPS, see <a href="./reference/as.mo.html#source">source</a>) and can
-categorise <em>Streptococci</em> into Lancefield groups (like
-beta-haemolytic <em>Streptococcus</em> Group B, <a href="./reference/as.mo.html#source">source</a>).</li>
-<li>Use <code><a href="reference/as.ab.html">as.ab()</a></code> to get an antibiotic ID. Like microbial
-IDs, these IDs are also human readable based on those used by EARS-Net.
-For example, the ID of amoxicillin is <code>AMX</code> and the ID of
-gentamicin is <code>GEN</code>. The <code><a href="reference/as.ab.html">as.ab()</a></code> function also
-uses intelligent rules to find results like accepting misspelling, trade
-names and abbrevations used in many laboratory systems. For instance,
-the values “Furabid”, “Furadantin”, “nitro” all return the ID of
-Nitrofurantoine. To accomplish this, the package contains a database
-with most LIS codes, official names, trade names, ATC codes, defined
-daily doses (DDD) and drug categories of antibiotics.</li>
-<li>Use <code><a href="reference/as.rsi.html">as.rsi()</a></code> to get antibiotic interpretations based on
-raw MIC values (in mg/L) or disk diffusion values (in mm), or transform
-existing values to valid antimicrobial results. It produces just S, I or
-R based on your input and warns about invalid values. Even values like
-“&lt;=0.002; S” (combined MIC/RSI) will result in “S”.</li>
-<li>Use <code><a href="reference/as.mic.html">as.mic()</a></code> to cleanse your MIC values. It produces a
-so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values
-as levels. A value like “&lt;=0.002; S” (combined MIC/RSI) will result
-in “&lt;=0.002”.</li>
+<li>Use <code><a href="reference/as.mo.html">as.mo()</a></code> to get a microbial ID. The IDs are human readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em> is “B_KLBSL_PNMN” (B stands for Bacteria) and the ID of <em>S. aureus</em> is “B_STPHY_AURS”. The function takes almost any text as input that looks like the name or code of a microorganism like “E. coli”, “esco” or “esccol” and tries to find expected results using intelligent rules combined with the included Catalogue of Life data set. It only takes milliseconds to find results, please see our <a href="./articles/benchmarks.html">benchmarks</a>. Moreover, it can group <em>Staphylococci</em> into coagulase negative and positive (CoNS and CoPS, see <a href="./reference/as.mo.html#source">source</a>) and can categorise <em>Streptococci</em> into Lancefield groups (like beta-haemolytic <em>Streptococcus</em> Group B, <a href="./reference/as.mo.html#source">source</a>).</li>
+<li>Use <code><a href="reference/as.ab.html">as.ab()</a></code> to get an antibiotic ID. Like microbial IDs, these IDs are also human readable based on those used by EARS-Net. For example, the ID of amoxicillin is <code>AMX</code> and the ID of gentamicin is <code>GEN</code>. The <code><a href="reference/as.ab.html">as.ab()</a></code> function also uses intelligent rules to find results like accepting misspelling, trade names and abbrevations used in many laboratory systems. For instance, the values “Furabid”, “Furadantin”, “nitro” all return the ID of Nitrofurantoine. To accomplish this, the package contains a database with most LIS codes, official names, trade names, ATC codes, defined daily doses (DDD) and drug categories of antibiotics.</li>
+<li>Use <code><a href="reference/as.rsi.html">as.rsi()</a></code> to get antibiotic interpretations based on raw MIC values (in mg/L) or disk diffusion values (in mm), or transform existing values to valid antimicrobial results. It produces just S, I or R based on your input and warns about invalid values. Even values like “&lt;=0.002; S” (combined MIC/RSI) will result in “S”.</li>
+<li>Use <code><a href="reference/as.mic.html">as.mic()</a></code> to cleanse your MIC values. It produces a so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values as levels. A value like “&lt;=0.002; S” (combined MIC/RSI) will result in “&lt;=0.002”.</li>
 </ul>
 </li>
 <li>
-<p>It <strong>enhances existing data</strong> and <strong>adds new
-data</strong> from data sets included in this package.</p>
+<p>It <strong>enhances existing data</strong> and <strong>adds new data</strong> from data sets included in this package.</p>
 <ul>
-<li>Use <code><a href="reference/eucast_rules.html">eucast_rules()</a></code> to apply <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST
-expert rules to isolates</a> (not the translation from MIC to R/SI
-values, use <code><a href="reference/as.rsi.html">as.rsi()</a></code> for that).</li>
-<li>Use <code><a href="reference/first_isolate.html">first_isolate()</a></code> to identify the first isolates of
-every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">using
-guidelines from the CLSI</a> (Clinical and Laboratory Standards
-Institute).
+<li>Use <code><a href="reference/eucast_rules.html">eucast_rules()</a></code> to apply <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST expert rules to isolates</a> (not the translation from MIC to R/SI values, use <code><a href="reference/as.rsi.html">as.rsi()</a></code> for that).</li>
+<li>Use <code><a href="reference/first_isolate.html">first_isolate()</a></code> to identify the first isolates of every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">using guidelines from the CLSI</a> (Clinical and Laboratory Standards Institute).
 <ul>
-<li>You can also identify first <em>weighted</em> isolates of every
-patient, an adjusted version of the CLSI guideline. This takes into
-account key antibiotics of every strain and compares them.</li>
+<li>You can also identify first <em>weighted</em> isolates of every patient, an adjusted version of the CLSI guideline. This takes into account key antibiotics of every strain and compares them.</li>
 </ul>
 </li>
-<li>Use <code><a href="reference/mdro.html">mdro()</a></code> to determine which micro-organisms are
-multi-drug resistant organisms (MDRO). It supports a variety of
-international guidelines, such as the MDR-paper by Magiorakos <em>et
-al.</em> (2012, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=21793988" class="external-link">PMID
-21793988</a>), the exceptional phenotype definitions of EUCAST and the
-WHO guideline on multi-drug resistant TB. It also supports the national
-guidelines of the Netherlands and Germany.</li>
-<li>The <a href="./reference/microorganisms.html">data set
-microorganisms</a> contains the complete taxonomic tree of ~70,000
-microorganisms. Furthermore, some colloquial names and all Gram stains
-are available, which enables resistance analysis of e.g. different
-antibiotics per Gram stain. The package also contains functions to look
-up values in this data set like <code><a href="reference/mo_property.html">mo_genus()</a></code>,
-<code><a href="reference/mo_property.html">mo_family()</a></code>, <code><a href="reference/mo_property.html">mo_gramstain()</a></code> or even
-<code><a href="reference/mo_property.html">mo_phylum()</a></code>. Use <code><a href="reference/mo_property.html">mo_snomed()</a></code> to look up any
-SNOMED CT code associated with a microorganism. As all these function
-use <code><a href="reference/as.mo.html">as.mo()</a></code> internally, they also use the same intelligent
-rules for determination. For example, <code>mo_genus("MRSA")</code> and
-<code>mo_genus("S. aureus")</code> will both return
-<code>"Staphylococcus"</code>. They also come with support for German,
-Danish, Dutch, Spanish, Italian, French and Portuguese. These functions
-can be used to add new variables to your data.</li>
-<li>The <a href="./reference/antibiotics.html">data set antibiotics</a>
-contains ~450 antimicrobial drugs with their EARS-Net code, ATC code,
-PubChem compound ID, LOINC code, official name, common LIS codes and
-DDDs of both oral and parenteral administration. It also contains all
-(thousands of) trade names found in PubChem. Use functions like
-<code><a href="reference/ab_property.html">ab_name()</a></code>, <code><a href="reference/ab_property.html">ab_group()</a></code>, <code><a href="reference/ab_property.html">ab_atc()</a></code>,
-<code><a href="reference/ab_property.html">ab_loinc()</a></code> and <code><a href="reference/ab_property.html">ab_tradenames()</a></code> to look up
-values. The <code>ab_*</code> functions use <code><a href="reference/as.ab.html">as.ab()</a></code>
-internally so they support the same intelligent rules to guess the most
-probable result. For example, <code>ab_name("Fluclox")</code>,
-<code>ab_name("Floxapen")</code> and <code>ab_name("J01CF05")</code>
-will all return <code>"Flucloxacillin"</code>. These functions can again
-be used to add new variables to your data.</li>
+<li>Use <code><a href="reference/mdro.html">mdro()</a></code> to determine which micro-organisms are multi-drug resistant organisms (MDRO). It supports a variety of international guidelines, such as the MDR-paper by Magiorakos <em>et al.</em> (2012, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=21793988" class="external-link">PMID 21793988</a>), the exceptional phenotype definitions of EUCAST and the WHO guideline on multi-drug resistant TB. It also supports the national guidelines of the Netherlands and Germany.</li>
+<li>The <a href="./reference/microorganisms.html">data set microorganisms</a> contains the complete taxonomic tree of ~70,000 microorganisms. Furthermore, some colloquial names and all Gram stains are available, which enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like <code><a href="reference/mo_property.html">mo_genus()</a></code>, <code><a href="reference/mo_property.html">mo_family()</a></code>, <code><a href="reference/mo_property.html">mo_gramstain()</a></code> or even <code><a href="reference/mo_property.html">mo_phylum()</a></code>. Use <code><a href="reference/mo_property.html">mo_snomed()</a></code> to look up any SNOMED CT code associated with a microorganism. As all these function use <code><a href="reference/as.mo.html">as.mo()</a></code> internally, they also use the same intelligent rules for determination. For example, <code>mo_genus("MRSA")</code> and <code>mo_genus("S. aureus")</code> will both return <code>"Staphylococcus"</code>. They also come with support for German, Danish, Dutch, Spanish, Italian, French and Portuguese. These functions can be used to add new variables to your data.</li>
+<li>The <a href="./reference/antibiotics.html">data set antibiotics</a> contains ~450 antimicrobial drugs with their EARS-Net code, ATC code, PubChem compound ID, LOINC code, official name, common LIS codes and DDDs of both oral and parenteral administration. It also contains all (thousands of) trade names found in PubChem. Use functions like <code><a href="reference/ab_property.html">ab_name()</a></code>, <code><a href="reference/ab_property.html">ab_group()</a></code>, <code><a href="reference/ab_property.html">ab_atc()</a></code>, <code><a href="reference/ab_property.html">ab_loinc()</a></code> and <code><a href="reference/ab_property.html">ab_tradenames()</a></code> to look up values. The <code>ab_*</code> functions use <code><a href="reference/as.ab.html">as.ab()</a></code> internally so they support the same intelligent rules to guess the most probable result. For example, <code>ab_name("Fluclox")</code>, <code>ab_name("Floxapen")</code> and <code>ab_name("J01CF05")</code> will all return <code>"Flucloxacillin"</code>. These functions can again be used to add new variables to your data.</li>
 </ul>
 </li>
 <li>
-<p>It <strong>analyses the data</strong> with convenient functions
-that use well-known methods.</p>
+<p>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</p>
 <ul>
-<li>Calculate the microbial susceptibility or resistance (and even
-co-resistance) with the <code><a href="reference/proportion.html">susceptibility()</a></code> and
-<code><a href="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the
-<code><a href="reference/proportion.html">proportion_R()</a></code>, <code><a href="reference/proportion.html">proportion_IR()</a></code>,
-<code><a href="reference/proportion.html">proportion_I()</a></code>, <code><a href="reference/proportion.html">proportion_SI()</a></code> and
-<code><a href="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of
-isolates can be determined with the <code><a href="reference/count.html">count_resistant()</a></code>,
-<code><a href="reference/count.html">count_susceptible()</a></code> and <code><a href="reference/count.html">count_all()</a></code> functions.
-All these functions can be used with the <code>dplyr</code> package
-(e.g. in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>)</li>
-<li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for
-the <code>ggplot2</code> package</li>
-<li>Predict antimicrobial resistance for the nextcoming years using
-logistic regression models with the <code><a href="reference/resistance_predict.html">resistance_predict()</a></code>
-function</li>
+<li>Calculate the microbial susceptibility or resistance (and even co-resistance) with the <code><a href="reference/proportion.html">susceptibility()</a></code> and <code><a href="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the <code><a href="reference/proportion.html">proportion_R()</a></code>, <code><a href="reference/proportion.html">proportion_IR()</a></code>, <code><a href="reference/proportion.html">proportion_I()</a></code>, <code><a href="reference/proportion.html">proportion_SI()</a></code> and <code><a href="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><a href="reference/count.html">count_resistant()</a></code>, <code><a href="reference/count.html">count_susceptible()</a></code> and <code><a href="reference/count.html">count_all()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g. in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>)</li>
+<li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for the <code>ggplot2</code> package</li>
+<li>Predict antimicrobial resistance for the nextcoming years using logistic regression models with the <code><a href="reference/resistance_predict.html">resistance_predict()</a></code> function</li>
 </ul>
 </li>
 <li>
-<p>It <strong>teaches the user</strong> how to use all the above
-actions.</p>
+<p>It <strong>teaches the user</strong> how to use all the above actions.</p>
 <ul>
-<li>Aside from this website with many tutorials, the package itself
-contains extensive help pages with many examples for all functions.</li>
+<li>Aside from this website with many tutorials, the package itself contains extensive help pages with many examples for all functions.</li>
 <li>The package also contains example data sets:
 <ul>
-<li>The <a href="./reference/example_isolates.html"><code>example_isolates</code>
-data set</a>. This data set contains 2,000 microbial isolates with their
-full antibiograms. It reflects reality and can be used to practice AMR
-data analysis.</li>
-<li>The <a href="./reference/WHONET.html"><code>WHONET</code> data
-set</a>. This data set only contains fake data, but with the exact same
-structure as files exported by WHONET. Read more about WHONET <a href="./articles/WHONET.html">on its tutorial page</a>.</li>
+<li>The <a href="./reference/example_isolates.html"><code>example_isolates</code> data set</a>. This data set contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practice AMR data analysis.</li>
+<li>The <a href="./reference/WHONET.html"><code>WHONET</code> data set</a>. This data set only contains fake data, but with the exact same structure as files exported by WHONET. Read more about WHONET <a href="./articles/WHONET.html">on its tutorial page</a>.</li>
 </ul>
 </li>
 </ul>
@@ -687,9 +485,7 @@ structure as files exported by WHONET. Read more about WHONET <a href="./article
 <div class="section level3">
 <h3 id="copyright">Copyright<a class="anchor" aria-label="anchor" href="#copyright"></a>
 </h3>
-<p>This R package is free, open-source software and licensed under the
-<a href="./LICENSE-text.html">GNU General Public License v2.0
-(GPL-2)</a>. In a nutshell, this means that this package:</p>
+<p>This R package is free, open-source software and licensed under the <a href="./LICENSE-text.html">GNU General Public License v2.0 (GPL-2)</a>. In a nutshell, this means that this package:</p>
 <ul>
 <li><p>May be used for commercial purposes</p></li>
 <li><p>May be used for private purposes</p></li>
@@ -697,18 +493,15 @@ structure as files exported by WHONET. Read more about WHONET <a href="./article
 <li>
 <p>May be modified, although:</p>
 <ul>
-<li>Modifications <strong>must</strong> be released under the same
-license when distributing the package</li>
+<li>Modifications <strong>must</strong> be released under the same license when distributing the package</li>
 <li>Changes made to the code <strong>must</strong> be documented</li>
 </ul>
 </li>
 <li>
 <p>May be distributed, although:</p>
 <ul>
-<li>Source code <strong>must</strong> be made available when the package
-is distributed</li>
-<li>A copy of the license and copyright notice <strong>must</strong> be
-included with the package.</li>
+<li>Source code <strong>must</strong> be made available when the package is distributed</li>
+<li>A copy of the license and copyright notice <strong>must</strong> be included with the package.</li>
 </ul>
 </li>
 <li><p>Comes with a LIMITATION of liability</p></li>
@@ -764,14 +557,12 @@ included with the package.</li>
 
       <footer><div class="copyright">
   <p></p>
-<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
-Erwin E. A. Hassing.</p>
+<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
-2.0.2.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer>

docs/pkgdown.yml

@@ -1,4 +1,4 @@
-pandoc: 2.17.1.1
+pandoc: 2.9.2.1
 pkgdown: 2.0.2
 pkgdown_sha: ~
 articles:
@@ -12,7 +12,7 @@ articles:
   datasets: datasets.html
   resistance_predict: resistance_predict.html
   welcome_to_AMR: welcome_to_AMR.html
-last_built: 2022-03-14T15:38Z
+last_built: 2022-03-27T07:33Z
 urls:
   reference: https://msberends.github.io/AMR/reference
   article: https://msberends.github.io/AMR/articles

docs/reference/AMR-deprecated.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
       </span>
     </div>
 
@@ -30,7 +30,7 @@
   </a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
     <span class="fa fa-question-circle"></span>
      
     How to
@@ -184,13 +184,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>retired</
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
-Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
-2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
 </div>
 
       </footer></div>