(v1.6.0.9016) website update and c() fixes

(v1.6.0.9015) italicise_taxonomy
2024-12-27 09:26:11 +01:00 · 2021-05-03 13:06:43 +02:00 · 2021-05-03 10:47:32 +02:00
45 changed files with 703 additions and 154 deletions
--- a/4
+++ b/4
@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.6.0.9014
-Date: 2021-04-30
+Version: 1.6.0.9016
+Date: 2021-05-03
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(
    person(role = c("aut", "cre"), 
--- a/2
+++ b/2
@ -237,6 +237,8 @@ export(is.mo)
 export(is.rsi)
 export(is.rsi.eligible)
 export(is_new_episode)
+export(italicise_taxonomy)
+export(italicize_taxonomy)
 export(key_antibiotics)
 export(key_antibiotics_equal)
 export(key_antimicrobials)
--- a/NEWS.md
+++ b/NEWS.md
@ -1,8 +1,9 @@
-# `AMR` 1.6.0.9014
-## <small>Last updated: 30 April 2021</small>
+# `AMR` 1.6.0.9016
+## <small>Last updated:  3 May 2021</small>

 ### New
 * Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()`
+* Function `italicise_taxonomy()` to make taxonomic names within a string italic, with support for markdown and ANSI
 * Support for all four methods to determine first isolates as summarised by Hindler *et al* (doi: [10.1086/511864](https://doi.org/10.1086/511864)): isolate-based, patient-based, episode-based and phenotype-based. The last method is now the default.
  * The `first_isolate()` function gained the argument `method` that has to be "phenotype-based", "episode-based", "patient-based", or "isolate-based". The old behaviour is equal to "episode-based". The new default is "phenotype-based" if antimicrobial test results are available, and "episode-based" otherwise. This new default will yield slightly more isolates for selection (which is a good thing).
  * Since fungal isolates can also be selected, the functions `key_antibiotics()` and `key_antibiotics_equal()` are now deprecated in favour of the `key_antimicrobials()` and `antimicrobial_equal()` functions. Also, the new `all_antimicrobials()` function works like the old `key_antibiotics()` function, but includes any column with antimicrobial test results. Using `key_antimicrobials()` still only selects six preferred antibiotics for Gram-negatives, six for Gram-positives, and six universal antibiotics. It has a new `antifungal` argument to set antifungal agents (antimycotics).
--- a/R/aa_helper_functions.R
+++ b/R/aa_helper_functions.R
@ -458,7 +458,7 @@ stop_ifnot <- function(expr, ..., call = TRUE) {
         ifelse(!is.na(y), y, NA))
 }

-class_integrity_check <- function(value, type, check_vector) {
+return_after_integrity_check <- function(value, type, check_vector) {
  if (!all(value[!is.na(value)] %in% check_vector)) {
    warning_(paste0("invalid ", type, ", NA generated"), call = FALSE)
    value[!value %in% check_vector] <- NA
--- a/R/ab.R
+++ b/R/ab.R
@ -477,7 +477,6 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
  if (length(x_unknown) > 0 & fast_mode == FALSE) {
    warning_("These values could not be coerced to a valid antimicrobial ID: ",
             vector_and(x_unknown), ".",
-             ".",
             call = FALSE)
  }
  
@ -552,7 +551,7 @@ as.data.frame.ab <- function(x, ...) {
 "[<-.ab" <- function(i, j, ..., value) {
  y <- NextMethod()
  attributes(y) <- attributes(i)
-  class_integrity_check(y, "antimicrobial code", antibiotics$ab)
+  return_after_integrity_check(y, "antimicrobial code", antibiotics$ab)
 }
 #' @method [[<- ab
 #' @export
@ -560,15 +559,16 @@ as.data.frame.ab <- function(x, ...) {
 "[[<-.ab" <- function(i, j, ..., value) {
  y <- NextMethod()
  attributes(y) <- attributes(i)
-  class_integrity_check(y, "antimicrobial code", antibiotics$ab)
+  return_after_integrity_check(y, "antimicrobial code", antibiotics$ab)
 }
 #' @method c ab
 #' @export
 #' @noRd
-c.ab <- function(x, ...) {
+c.ab <- function(...) {
+  x <- list(...)[[1L]]
  y <- NextMethod()
  attributes(y) <- attributes(x)
-  class_integrity_check(y, "antimicrobial code", antibiotics$ab)
+  return_after_integrity_check(y, "antimicrobial code", antibiotics$ab)
 }

 #' @method unique ab
--- a/R/custom_eucast_rules.R
+++ b/R/custom_eucast_rules.R
@ -93,6 +93,7 @@
 #' 
 #' `r paste0("  * ", sapply(DEFINED_AB_GROUPS, function(x) paste0("``", tolower(x), "``\\cr(", paste0(sort(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE)), collapse = ", "), ")"), USE.NAMES = FALSE), "\n", collapse = "")`
 #' @returns A [list] containing the custom rules
+#' @inheritSection AMR Read more on Our Website!
 #' @export
 #' @examples
 #' x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
--- a/R/disk.R
+++ b/R/disk.R
@ -182,11 +182,8 @@ print.disk <- function(x, ...) {
 #' @method c disk
 #' @export
 #' @noRd
-c.disk <- function(x, ...) {
-  y <- NextMethod()
-  y <- as.disk(y)
-  attributes(y) <- attributes(x)
-  y
+c.disk <- function(...) {
+  as.disk(unlist(lapply(list(...), as.character)))
 }

 #' @method unique disk
--- a/R/eucast_rules.R
+++ b/R/eucast_rules.R
@ -65,7 +65,6 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
 #' @details
 #' **Note:** This function does not translate MIC values to RSI values. Use [as.rsi()] for that. \cr
 #' **Note:** When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. \cr
-
 #'
 #' The file containing all EUCAST rules is located here: <https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv>.  **Note:** Old taxonomic names are replaced with the current taxonomy where applicable. For example, *Ochrobactrum anthropi* was renamed to *Brucella anthropi* in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The file used as input for this `AMR` package contains the taxonomy updated until [`r CATALOGUE_OF_LIFE$yearmonth_LPSN`][catalogue_of_life()].
 #' 
@ -322,17 +321,6 @@ eucast_rules <- function(x,
    }
    cols_ab[match(x_new, names(cols_ab))]
  }
-  markup_italics_where_needed <- function(x) {
-    # returns names found in family, genus or species as italics
-    if (!has_colour()) {
-      return(x)
-    }
-    x <- unlist(strsplit(x, " "))
-    ind <- gsub("[)(:]", "", x) %in% c(MO_lookup[which(MO_lookup$rank %in% c("family", "genus")), ]$fullname,
-                                       MO_lookup[which(MO_lookup$rank == "species"), ]$species)
-    x[ind] <- font_italic(x[ind], collapse = NULL)
-    paste(x, collapse = " ")
-  }
  get_antibiotic_names <- function(x) {
    x <- x %pm>%
      strsplit(",") %pm>%
@ -343,6 +331,7 @@ eucast_rules <- function(x,
      paste(collapse = ", ")
    x <- gsub("_", " ", x, fixed = TRUE)
    x <- gsub("except CAZ", paste("except", ab_name("CAZ", language = NULL, tolower = TRUE)), x, fixed = TRUE)
+    x <- gsub("except TGC", paste("except", ab_name("TGC", language = NULL, tolower = TRUE)), x, fixed = TRUE)
    x <- gsub("cephalosporins (1st|2nd|3rd|4th|5th)", "cephalosporins (\\1 gen.)", x)
    x
  }
@ -655,9 +644,10 @@ eucast_rules <- function(x,
      # Print rule  -------------------------------------------------------------
      if (rule_current != rule_previous) {
        # is new rule within group, print its name
-        cat(markup_italics_where_needed(word_wrap(rule_current, 
-                                                  width = getOption("width") - 30,
-                                                  extra_indent = 6)))
+        cat(italicise_taxonomy(word_wrap(rule_current, 
+                                         width = getOption("width") - 30,
+                                         extra_indent = 6),
+                               type = "ansi"))
        warned <- FALSE
      }
    }
@ -795,9 +785,10 @@ eucast_rules <- function(x,
                          get_antibiotic_names(cols))
      if (info == TRUE) {
        # print rule
-        cat(markup_italics_where_needed(word_wrap(format_custom_query_rule(rule$query, colours = FALSE), 
-                                                  width = getOption("width") - 30,
-                                                  extra_indent = 6)))
+        cat(italicise_taxonomy(word_wrap(format_custom_query_rule(rule$query, colours = FALSE), 
+                                         width = getOption("width") - 30,
+                                         extra_indent = 6),
+                               type = "ansi"))
        warned <- FALSE
      }
      run_changes <- edit_rsi(x = x,
--- a/R/italicise_taxonomy.R
+++ b/R/italicise_taxonomy.R
@ -0,0 +1,122 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Data Analysis for R                   #
+#                                                                      #
+# SOURCE                                                               #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# Developed at the University of Groningen, the Netherlands, in        #
+# collaboration with non-profit organisations Certe Medical            #
+# Diagnostics & Advice, and University Medical Center Groningen.       # 
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+# We created this package for both routine data analysis and academic  #
+# research and it was publicly released in the hope that it will be    #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+#                                                                      #
+# Visit our website for the full manual and a complete tutorial about  #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
+# ==================================================================== #
+
+#' Italicise Taxonomic Families, Genera, Species, Subspecies
+#' 
+#' According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italic. This function finds taxonomic names within strings and makes them italic.
+#' @inheritSection lifecycle Maturing Lifecycle
+#' @param string a character (vector)
+#' @param type type of conversion of the taxonomic names, either "markdown" or "ansi", see *Details*
+#' @details 
+#' This function finds the taxonomic names and makes them italic based on the [microorganisms] data set.
+#' 
+#' The taxonomic names can be italicised using markdown (the default) by adding `*` before and after the taxonomic names, or using ANSI colours by adding `\033[3m` before and `\033[23m` after the taxonomic names. If multiple ANSI colours are not available, no conversion will occur.
+#' 
+#' This function also supports abbreviation of the genus if it is followed by a species, such as "E. coli" and "K. pneumoniae ozaenae".
+#' @inheritSection AMR Read more on Our Website!
+#' @export
+#' @examples
+#' italicise_taxonomy("An overview of Staphylococcus aureus isolates")
+#' italicise_taxonomy("An overview of S. aureus isolates")
+#' 
+#' cat(italicise_taxonomy("An overview of S. aureus isolates", type = "ansi"))
+italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
+  if (missing(type)) {
+    type <- "markdown"
+  }
+  meet_criteria(string, allow_class = "character")
+  meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("markdown", "ansi"))
+  
+  if (type == "markdown") {
+    before <- "*"
+    after <- "*"
+  } else if (type == "ansi") {
+    if (!has_colour()) {
+      return(string)
+    }
+    before <- "\033[3m"
+    after <- "\033[23m"
+  }
+  
+  vapply(FUN.VALUE = character(1),
+         string,
+         function(s) {
+           s_split <- unlist(strsplit(s, " "))
+           
+           search_strings <- gsub("[^a-zA-Z-]", "", s_split)
+           
+           ind_species <- search_strings != "" &
+             search_strings %in% MO_lookup[which(MO_lookup$rank %in% c("family",
+                                                                       "genus",
+                                                                       "species",
+                                                                       "subspecies",
+                                                                       "infraspecies",
+                                                                       "subsp.")),
+                                           "species",
+                                           drop = TRUE]
+           
+           ind_fullname <- search_strings != "" &
+             search_strings %in% c(MO_lookup[which(MO_lookup$rank %in% c("family",
+                                                                         "genus",
+                                                                         "species",
+                                                                         "subspecies",
+                                                                         "infraspecies",
+                                                                         "subsp.")),
+                                             "fullname",
+                                             drop = TRUE],
+                                   MO_lookup[which(MO_lookup$rank %in% c("family",
+                                                                         "genus",
+                                                                         "species",
+                                                                         "subspecies",
+                                                                         "infraspecies",
+                                                                         "subsp.")),
+                                             "subspecies",
+                                             drop = TRUE])
+
+           # also support E. coli, add "E." to indices
+           has_previous_genera_abbr <- s_split[which(ind_species) - 1] %like_case% "^[A-Z][.]?$"
+           ind_species <- c(which(ind_species), which(ind_species)[has_previous_genera_abbr] - 1)
+           
+           ind <- c(ind_species, which(ind_fullname))
+           
+           s_split[ind] <- paste0(before, s_split[ind], after)
+           s_paste <- paste(s_split, collapse = " ")
+           
+           # clean up a bit
+           s_paste <- gsub(paste0(after, " ", before), " ", s_paste, fixed = TRUE)
+           
+           s_paste
+         },
+         USE.NAMES = FALSE)
+}
+
+#' @rdname italicise_taxonomy
+#' @export
+italicize_taxonomy <- function(string, type = c("markdown", "ansi")) {
+  if (missing(type)) {
+    type <- "markdown"
+  }
+  italicise_taxonomy(string = string, type = type)
+}
--- a/R/mic.R
+++ b/R/mic.R
@ -307,10 +307,8 @@ as.matrix.mic <- function(x, ...) {
 #' @method c mic
 #' @export
 #' @noRd
-c.mic <- function(x, ...) {
-  y <- unlist(lapply(list(...), as.character))
-  x <- as.character(x)
-  as.mic(c(x, y))
+c.mic <- function(...) {
+  as.mic(unlist(lapply(list(...), as.character)))
 }

 #' @method unique mic
--- a/R/mo.R
+++ b/R/mo.R
@ -1677,7 +1677,7 @@ pillar_shaft.mo <- function(x, ...) {
    } else {
      col <- "The data"
    }
-    warning_(col, " contains old microbial codes (from a previous AMR package version). ",
+    warning_(col, " contains old MO codes (from a previous AMR package version). ",
             "Please update your MO codes with `as.mo()`.",
             call = FALSE)
  }
@ -1751,6 +1751,11 @@ print.mo <- function(x, print.shortnames = FALSE, ...) {
  }
  x <- as.character(x)
  names(x) <- x_names
+  if (!all(x[!is.na(x)] %in% MO_lookup$mo)) {
+    warning_("Some MO codes are from a previous AMR package version. ",
+             "Please update these MO codes with `as.mo()`.",
+             call = FALSE)
+  }
  print.default(x, quote = FALSE)
 }

@ -1777,7 +1782,7 @@ summary.mo <- function(object, ...) {
 #' @noRd
 as.data.frame.mo <- function(x, ...) {
  if (!all(x[!is.na(x)] %in% MO_lookup$mo)) {
-    warning_("The data contains old microbial codes (from a previous AMR package version). ",
+    warning_("The data contains old MO codes (from a previous AMR package version). ",
             "Please update your MO codes with `as.mo()`.",
             call = FALSE)
  }
@ -1812,8 +1817,8 @@ as.data.frame.mo <- function(x, ...) {
  y <- NextMethod()
  attributes(y) <- attributes(i)
  # must only contain valid MOs
-  class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
-                                                   as.character(microorganisms.translation$mo_old)))
+  return_after_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
+                                                          as.character(microorganisms.translation$mo_old)))
 }
 #' @method [[<- mo
 #' @export
@ -1822,18 +1827,18 @@ as.data.frame.mo <- function(x, ...) {
  y <- NextMethod()
  attributes(y) <- attributes(i)
  # must only contain valid MOs
-  class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
-                                                   as.character(microorganisms.translation$mo_old)))
+  return_after_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
+                                                          as.character(microorganisms.translation$mo_old)))
 }
 #' @method c mo
 #' @export
 #' @noRd
-c.mo <- function(x, ...) {
+c.mo <- function(...) {
+  x <- list(...)[[1L]]
  y <- NextMethod()
  attributes(y) <- attributes(x)
-  # must only contain valid MOs
-  class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
-                                                   as.character(microorganisms.translation$mo_old)))
+  return_after_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
+                                                          as.character(microorganisms.translation$mo_old)))
 }

 #' @method unique mo
@ -2058,10 +2063,10 @@ replace_old_mo_codes <- function(x, property) {
    n_matched <- length(matched[!is.na(matched)])
    if (property != "mo") {
      message_(font_blue(paste0("The input contained ", n_matched,
-                                " old microbial code", ifelse(n_matched == 1, "", "s"),
+                                " old MO code", ifelse(n_matched == 1, "", "s"),
                                " (from a previous AMR package version). Please update your MO codes with `as.mo()`.")))
    } else {
-      message_(font_blue(paste0(n_matched, " old microbial code", ifelse(n_matched == 1, "", "s"), 
+      message_(font_blue(paste0(n_matched, " old MO code", ifelse(n_matched == 1, "", "s"), 
                                " (from a previous AMR package version) ", 
                                ifelse(n_matched == 1, "was", "were"), 
                                " updated to ", ifelse(n_matched == 1, "a ", ""), 
@ -2100,7 +2105,7 @@ repair_reference_df <- function(reference_df) {
  reference_df[, "x"] <- as.character(reference_df[, "x", drop = TRUE])
  reference_df[, "mo"] <- as.character(reference_df[, "mo", drop = TRUE])
  
-  # some microbial codes might be old
+  # some MO codes might be old
  reference_df[, "mo"] <- as.mo(reference_df[, "mo", drop = TRUE])
  reference_df
 }
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@ -177,6 +177,7 @@ reference:
    - "`availability`"
    - "`get_locale`"
    - "`ggplot_pca`"
+    - "`italicise_taxonomy`"
    - "`join`"
    - "`like`"
    - "`mo_matching_score`"
--- a/data-raw/AMR_latest.tar.gz
+++ b/data-raw/AMR_latest.tar.gz
--- a/docs/404.html
+++ b/docs/404.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9016</span>
      </span>
    </div>

--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9016</span>
      </span>
    </div>

--- a/docs/articles/benchmarks.html
+++ b/docs/articles/benchmarks.html
@ -39,7 +39,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9015</span>
      </span>
    </div>

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

      

-      </header><link href="benchmarks_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
-<script src="benchmarks_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
+      </header><script src="benchmarks_files/header-attrs-2.7/header-attrs.js"></script><div class="row">
  <div class="col-md-9 contents">
    <div class="page-header toc-ignore">
      <h1 data-toc-skip>Benchmarks</h1>
@ -203,15 +202,15 @@
    
 <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">Catalogue of Life</a> (CoL) and the <a href="https://lpsn.dsmz.de">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">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">
-<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/joshuaulrich/microbenchmark/">microbenchmark</a></span><span class="op">)</span>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/joshuaulrich/microbenchmark/">microbenchmark</a></span><span class="op">)</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
-<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span></pre></div>
+<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">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>But the calculation time differs a lot:</p>
-<div class="sourceCode" id="cb2"><pre class="downlit">
-<span class="va">S.aureus</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span><span class="op">(</span>
+<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">microbenchmark</a></span><span class="op">(</span>
  <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"sau"</span><span class="op">)</span>, <span class="co"># WHONET code</span>
  <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"stau"</span><span class="op">)</span>,
  <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"STAU"</span><span class="op">)</span>,
@ -225,21 +224,21 @@
  <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">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">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")  25.0  25.0   30   26.0  26.0  83    25</span>
-<span class="co">#                          as.mo("stau") 120.0 130.0  150  130.0 180.0 390    25</span>
-<span class="co">#                          as.mo("STAU") 120.0 130.0  150  130.0 180.0 190    25</span>
-<span class="co">#                        as.mo("staaur")  25.0  26.0   33   26.0  26.0  83    25</span>
-<span class="co">#                        as.mo("STAAUR")  25.0  26.0   33   26.0  26.0  83    25</span>
-<span class="co">#                     as.mo("S. aureus")  66.0  66.0   89   67.0 120.0 150    25</span>
-<span class="co">#                      as.mo("S aureus")  66.0  66.0   74   66.0  67.0 120    25</span>
-<span class="co">#         as.mo("Staphylococcus aureus")   6.8   6.9   14    6.9   7.5  63    25</span>
-<span class="co">#  as.mo("Staphylococcus aureus (MRSA)") 550.0 550.0  560  550.0 560.0 620    25</span>
-<span class="co">#       as.mo("Sthafilokkockus aaureuz") 410.0 420.0  430  420.0 420.0 620    25</span>
-<span class="co">#                          as.mo("MRSA")  25.0  26.0   31   26.0  26.0  83    25</span>
-<span class="co">#                          as.mo("VISA")  46.0  47.0   65   47.0  98.0 110    25</span></pre></div>
+<span class="co">#                                   expr   min    lq  mean median    uq max neval</span>
+<span class="co">#                           as.mo("sau")   9.6  10.0  12.0     10  11.0  42    25</span>
+<span class="co">#                          as.mo("stau")  52.0  55.0  74.0     59  94.0 110    25</span>
+<span class="co">#                          as.mo("STAU")  51.0  53.0  73.0     57  91.0 100    25</span>
+<span class="co">#                        as.mo("staaur")   9.5   9.9  11.0     10  12.0  13    25</span>
+<span class="co">#                        as.mo("STAAUR")   9.4  10.0  18.0     10  12.0  52    25</span>
+<span class="co">#                     as.mo("S. aureus")  24.0  26.0  31.0     26  29.0  62    25</span>
+<span class="co">#                      as.mo("S aureus")  25.0  25.0  42.0     29  62.0  68    25</span>
+<span class="co">#         as.mo("Staphylococcus aureus")   2.5   2.9   3.2      3   3.5   4    25</span>
+<span class="co">#  as.mo("Staphylococcus aureus (MRSA)") 240.0 240.0 260.0    250 260.0 390    25</span>
+<span class="co">#       as.mo("Sthafilokkockus aaureuz") 150.0 190.0 190.0    190 190.0 250    25</span>
+<span class="co">#                          as.mo("MRSA")   8.7  10.0  15.0     11  12.0  49    25</span>
+<span class="co">#                          as.mo("VISA")  17.0  19.0  25.0     21  22.0  57    25</span></code></pre></div>
 <p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="750"></p>
 <p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 200 times slower to determine.</p>
 <p>To improve performance, we implemented two important algorithms to save unnecessary calculations: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
@ -248,8 +247,8 @@
 <a href="#repetitive-results" class="anchor"></a>Repetitive results</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><a href="../reference/as.mo.html">as.mo(c("E. coli", "E. coli"))</a></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">
-<span class="co"># start with the example_isolates data set</span>
+<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">%&gt;%</span> 
  <span class="co"># take all MO codes from the 'mo' column</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/pull.html">pull</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span> <span class="op">%&gt;%</span>
@ -261,8 +260,8 @@
 <span class="co"># what do these values look like? They are of class &lt;mo&gt;:</span>
 <span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
 <span class="co"># Class &lt;mo&gt;</span>
-<span class="co"># [1] B_STPHY_EPDR B_STPHY_EPDR B_STPHY_CONS B_STPHY_CONS B_STPHY_EPDR</span>
-<span class="co"># [6] B_ESCHR_COLI</span>
+<span class="co"># [1] B_KLBSL_PNMN B_STPHY_EPDR B_STRPT_PNMN B_STRPT_EQNS B_ESCHR_COLI</span>
+<span class="co"># [6] B_KLBSL_PNMN</span>
  
 <span class="co"># as the example_isolates data set has 2,000 rows, we should have 2 million items</span>
 <span class="fu"><a href="https://rdrr.io/r/base/length.html">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
@ -275,30 +274,30 @@
 <span class="co"># now let's see:</span>
 <span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>,
                         times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
-<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
+<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
 <span class="co">#        expr min  lq mean median  uq max neval</span>
-<span class="co">#  mo_name(x) 321 378  443    410 438 713    10</span></pre></div>
-<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.41 seconds. That is 205 nanoseconds on average. You only lose time on your unique input values.</p>
+<span class="co">#  mo_name(x) 155 182  233    228 242 350    10</span></code></pre></div>
+<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.228 seconds. That is 114 nanoseconds on average. You only lose time on your unique input values.</p>
 </div>
 <div id="precalculated-results" class="section level3">
 <h3 class="hasAnchor">
 <a href="#precalculated-results" class="anchor"></a>Precalculated results</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>
-<div class="sourceCode" id="cb4"><pre class="downlit">
-<span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"STAAUR"</span><span class="op">)</span>,
+<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">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">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">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 17.00 17.1 17.10  17.10 17.20  17.20    10</span>
-<span class="co">#     B 57.20 57.3 68.90  57.60 58.40 117.00    10</span>
-<span class="co">#     C  3.66  3.7  3.74   3.74  3.77   3.89    10</span></pre></div>
-<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0037 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">
-<span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
+<span class="co">#  expr   min    lq  mean median    uq   max neval</span>
+<span class="co">#     A  6.62  6.84  7.30   6.91  8.10  8.74    10</span>
+<span class="co">#     B 22.20 23.10 33.20  24.50 27.70 70.80    10</span>
+<span class="co">#     C  1.37  1.50  1.66   1.71  1.81  1.84    10</span></code></pre></div>
+<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0017 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
                         B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"Staphylococcus"</span><span class="op">)</span>,
                         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>,
                         D <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_family</a></span><span class="op">(</span><span class="st">"Staphylococcaceae"</span><span class="op">)</span>,
@ -307,25 +306,25 @@
                         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">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">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 3.70 3.71 3.81   3.74 3.82 4.14    10</span>
-<span class="co">#     B 3.66 3.67 3.76   3.69 3.76 4.10    10</span>
-<span class="co">#     C 3.66 3.70 3.72   3.72 3.73 3.76    10</span>
-<span class="co">#     D 3.63 3.67 3.77   3.71 3.88 4.09    10</span>
-<span class="co">#     E 3.62 3.67 3.75   3.70 3.78 4.07    10</span>
-<span class="co">#     F 3.62 3.64 3.66   3.65 3.65 3.74    10</span>
-<span class="co">#     G 3.63 3.64 3.67   3.67 3.68 3.75    10</span>
-<span class="co">#     H 3.63 3.64 3.74   3.67 3.84 4.07    10</span></pre></div>
+<span class="co">#     A 1.19 1.21 1.43   1.28 1.65 2.03    10</span>
+<span class="co">#     B 1.19 1.24 1.38   1.26 1.53 1.83    10</span>
+<span class="co">#     C 1.24 1.28 1.45   1.36 1.41 2.24    10</span>
+<span class="co">#     D 1.20 1.22 1.33   1.23 1.41 1.77    10</span>
+<span class="co">#     E 1.21 1.22 1.35   1.27 1.38 1.69    10</span>
+<span class="co">#     F 1.20 1.21 1.34   1.26 1.37 1.71    10</span>
+<span class="co">#     G 1.17 1.22 1.31   1.27 1.31 1.71    10</span>
+<span class="co">#     H 1.21 1.27 1.42   1.37 1.47 1.84    10</span></code></pre></div>
 <p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package contains all phyla of all known bacteria, it can just return the initial value immediately.</p>
 </div>
 <div id="results-in-other-languages" class="section level3">
 <h3 class="hasAnchor">
 <a href="#results-in-other-languages" class="anchor"></a>Results in other languages</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:</p>
-<div class="sourceCode" id="cb6"><pre class="downlit">
-<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"en"</span><span class="op">)</span> <span class="co"># or just mo_name("CoNS") on an English system</span>
+<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"en"</span><span class="op">)</span> <span class="co"># or just mo_name("CoNS") on an English system</span>
 <span class="co"># [1] "Coagulase-negative Staphylococcus (CoNS)"</span>

 <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span> <span class="co"># or just mo_name("CoNS") on a Spanish system</span>
@ -342,16 +341,16 @@
                         fr <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"fr"</span><span class="op">)</span>,
                         pt <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"pt"</span><span class="op">)</span>,
                         times <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
-<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
+<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
-<span class="co">#  expr   min    lq  mean median    uq   max neval</span>
-<span class="co">#    en 43.15 43.49 48.88  43.66 43.81 122.3   100</span>
-<span class="co">#    de 79.59 80.39 88.27  80.89 81.11 135.8   100</span>
-<span class="co">#    nl 79.69 80.45 87.16  80.81 81.07 136.6   100</span>
-<span class="co">#    es 79.28 80.12 89.84  80.51 81.02 159.5   100</span>
-<span class="co">#    it 51.74 52.20 55.59  52.39 52.61 109.1   100</span>
-<span class="co">#    fr 51.43 51.88 54.83  52.05 52.29 105.5   100</span>
-<span class="co">#    pt 51.58 51.93 59.25  52.28 52.55 111.8   100</span></pre></div>
+<span class="co">#  expr   min    lq  mean median    uq    max neval</span>
+<span class="co">#    en 17.19 17.50 22.00  17.76 18.54  61.02   100</span>
+<span class="co">#    de 31.08 31.53 39.66  32.04 35.34  76.23   100</span>
+<span class="co">#    nl 30.19 31.41 40.64  32.30 35.93  79.53   100</span>
+<span class="co">#    es 30.50 31.33 41.70  31.84 35.90 181.80   100</span>
+<span class="co">#    it 20.94 21.37 25.27  21.63 22.44  69.84   100</span>
+<span class="co">#    fr 20.62 21.00 27.09  21.41 23.12  79.50   100</span>
+<span class="co">#    pt 20.41 21.23 25.33  21.56 22.22  70.65   100</span></code></pre></div>
 <p>Currently supported non-English languages are German, Dutch, Spanish, Italian, French and Portuguese.</p>
 </div>
  </div>
--- a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png
+++ b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png
--- a/docs/articles/benchmarks_files/header-attrs-2.7/header-attrs.js
+++ b/docs/articles/benchmarks_files/header-attrs-2.7/header-attrs.js
@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9016</span>
      </span>
    </div>

--- a/docs/authors.html
+++ b/docs/authors.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9016</span>
      </span>
    </div>

--- a/docs/countries.png
+++ b/docs/countries.png
--- a/docs/countries_large.png
+++ b/docs/countries_large.png
--- a/docs/extra.js
+++ b/docs/extra.js
@ -52,7 +52,10 @@ $(document).ready(function() {
    $("pre.examples").html($("pre.examples").html().replaceAll("# \\dontrun{", ""));
    $("pre.examples").html($("pre.examples").html().replaceAll("# }", ""));
  }
-
+  
+  // remove leading newline in code examples on changelog
+  $("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R">\n<span', 'sourceCode R"><span'));
+  
  // PR for 'R for Data Science' on How To pages
  if ($(".template-article").length > 0) {
    $('#pkgdown-sidebar').prepend(
--- a/docs/index.html
+++ b/docs/index.html
@ -42,7 +42,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9016</span>
      </span>
    </div>

@ -206,7 +206,7 @@
 <p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell">fully independent of any other R package</a> and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (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">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl">University Medical Center Groningen</a>. This R package is <a href="./news">actively maintained</a> and is free software (see <a href="#copyright">Copyright</a>).</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 155 countries</strong><br> Since its first public release in early 2018, this package has been downloaded from 155 countries. 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 162 countries</strong><br> Since its first public release in early 2018, this package has been downloaded from 162 countries. Click the map to enlarge and to see the country names.
 </p>
 </div>
 <div id="with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side" class="section level5">
--- a/docs/news/index.html
+++ b/docs/news/index.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9016</span>
      </span>
    </div>

@ -236,12 +236,12 @@
      <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
    </div>

-    <div id="amr-1609014" class="section level1">
-<h1 class="page-header" data-toc-text="1.6.0.9014">
-<a href="#amr-1609014" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9014</h1>
-<div id="last-updated-30-april-2021" class="section level2">
+    <div id="amr-1609016" class="section level1">
+<h1 class="page-header" data-toc-text="1.6.0.9016">
+<a href="#amr-1609016" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9016</h1>
+<div id="last-updated-3-may-2021" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-30-april-2021" class="anchor"></a><small>Last updated: 30 April 2021</small>
+<a href="#last-updated-3-may-2021" class="anchor"></a><small>Last updated: 3 May 2021</small>
 </h2>
 <div id="new" class="section level3">
 <h3 class="hasAnchor">
@ -249,6 +249,7 @@
 <ul>
 <li>Function <code><a href="../reference/custom_eucast_rules.html">custom_eucast_rules()</a></code> that brings support for custom AMR rules in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>
 </li>
+<li>Function <code><a href="../reference/italicise_taxonomy.html">italicise_taxonomy()</a></code> to make taxonomic names within a string italic, with support for markdown and ANSI</li>
 <li>Support for all four methods to determine first isolates as summarised by Hindler <em>et al</em> (doi: <a href="https://doi.org/10.1086/511864">10.1086/511864</a>): isolate-based, patient-based, episode-based and phenotype-based. The last method is now the default.
 <ul>
 <li>The <code><a href="../reference/first_isolate.html">first_isolate()</a></code> function gained the argument <code>method</code> that has to be “phenotype-based”, “episode-based”, “patient-based”, or “isolate-based”. The old behaviour is equal to “episode-based”. The new default is “phenotype-based” if antimicrobial test results are available, and “episode-based” otherwise. This new default will yield slightly more isolates for selection (which is a good thing).</li>
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@ -12,7 +12,7 @@ articles:
  datasets: datasets.html
  resistance_predict: resistance_predict.html
  welcome_to_AMR: welcome_to_AMR.html
-last_built: 2021-04-30T08:14Z
+last_built: 2021-05-03T11:04Z
 urls:
  reference: https://msberends.github.io/AMR//reference
  article: https://msberends.github.io/AMR//articles
--- a/docs/reference/AMR-deprecated.html
+++ b/docs/reference/AMR-deprecated.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9015</span>
      </span>
    </div>

--- a/docs/reference/custom_eucast_rules.html
+++ b/docs/reference/custom_eucast_rules.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9010</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9015</span>
      </span>
    </div>

@ -344,6 +344,11 @@

 <p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
 The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
+    <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
+
+    
+
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span>,
--- a/docs/reference/first_isolate.html
+++ b/docs/reference/first_isolate.html
@ -83,7 +83,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9015</span>
      </span>
    </div>

--- a/docs/reference/get_episode.html
+++ b/docs/reference/get_episode.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9015</span>
      </span>
    </div>

--- a/docs/reference/ggplot_pca.html
+++ b/docs/reference/ggplot_pca.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9015</span>
      </span>
    </div>

--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9016</span>
      </span>
    </div>

@ -592,6 +592,12 @@
        <td><p>PCA Biplot with <code>ggplot2</code></p></td>
      </tr><tr>
        
+        <td>
+          <p><code><a href="italicise_taxonomy.html">italicise_taxonomy()</a></code> <code><a href="italicise_taxonomy.html">italicize_taxonomy()</a></code> </p>
+        </td>
+        <td><p>Italicise Taxonomic Families, Genera, Species, Subspecies</p></td>
+      </tr><tr>
+        
        <td>
          <p><code><a href="join.html">inner_join_microorganisms()</a></code> <code><a href="join.html">left_join_microorganisms()</a></code> <code><a href="join.html">right_join_microorganisms()</a></code> <code><a href="join.html">full_join_microorganisms()</a></code> <code><a href="join.html">semi_join_microorganisms()</a></code> <code><a href="join.html">anti_join_microorganisms()</a></code> </p>
        </td>
--- a/docs/reference/italicise_taxonomy.html
+++ b/docs/reference/italicise_taxonomy.html
@ -0,0 +1,312 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+  <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy • AMR (for R)</title>
+
+<!-- favicons -->
+<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png" />
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+  <link href="../extra.css" rel="stylesheet">
+  <script src="../extra.js"></script>
+
+<meta property="og:title" content="Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy" />
+<meta property="og:description" content="According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italic. This function finds taxonomic names within strings and makes them italic." />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+
+  </head>
+
+  <body data-spy="scroll" data-target="#toc">
+    <div class="container template-reference-topic">
+      <header>
+      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">AMR (for R)</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9015</span>
+      </span>
+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav">
+        <li>
+  <a href="../index.html">
+    <span class="fas fa-home"></span>
+     
+    Home
+  </a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    <span class="fas fa-question-circle"></span>
+     
+    How to
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="../articles/AMR.html">
+        <span class="fas fa-directions"></span>
+         
+        Conduct AMR analysis
+      </a>
+    </li>
+    <li>
+      <a href="../articles/resistance_predict.html">
+        <span class="fas fa-dice"></span>
+         
+        Predict antimicrobial resistance
+      </a>
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+      <a href="../articles/datasets.html">
+        <span class="fas fa-database"></span>
+         
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+    <li>
+      <a href="../articles/PCA.html">
+        <span class="fas fa-compress"></span>
+         
+        Conduct principal component analysis for AMR
+      </a>
+    </li>
+    <li>
+      <a href="../articles/MDR.html">
+        <span class="fas fa-skull-crossbones"></span>
+         
+        Determine multi-drug resistance (MDR)
+      </a>
+    </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fas fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
+    <li>
+      <a href="../articles/SPSS.html">
+        <span class="fas fa-file-upload"></span>
+         
+        Import data from SPSS/SAS/Stata
+      </a>
+    </li>
+    <li>
+      <a href="../articles/EUCAST.html">
+        <span class="fas fa-exchange-alt"></span>
+         
+        Apply EUCAST rules
+      </a>
+    </li>
+    <li>
+      <a href="../reference/mo_property.html">
+        <span class="fas fa-bug"></span>
+         
+        Get properties of a microorganism
+      </a>
+    </li>
+    <li>
+      <a href="../reference/ab_property.html">
+        <span class="fas fa-capsules"></span>
+         
+        Get properties of an antibiotic
+      </a>
+    </li>
+    <li>
+      <a href="../articles/benchmarks.html">
+        <span class="fas fa-shipping-fast"></span>
+         
+        Other: benchmarks
+      </a>
+    </li>
+  </ul>
+</li>
+<li>
+  <a href="../reference/index.html">
+    <span class="fas fa-book-open"></span>
+     
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+  </a>
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+    <span class="fas fa-users"></span>
+     
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+  </a>
+</li>
+<li>
+  <a href="../news/index.html">
+    <span class="far fa-newspaper"></span>
+     
+    Changelog
+  </a>
+</li>
+      </ul>
+      <ul class="nav navbar-nav navbar-right">
+        <li>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa-github"></span>
+     
+    Source Code
+  </a>
+</li>
+<li>
+  <a href="../survey.html">
+    <span class="fas fa-clipboard-list"></span>
+     
+    Survey
+  </a>
+</li>
+      </ul>
+      
+    </div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header>
+
+<div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Italicise Taxonomic Families, Genera, Species, Subspecies</h1>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/italicise_taxonomy.R'><code>R/italicise_taxonomy.R</code></a></small>
+    <div class="hidden name"><code>italicise_taxonomy.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italic. This function finds taxonomic names within strings and makes them italic.</p>
+    </div>
+
+    <pre class="usage"><span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='va'>string</span>, type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"markdown"</span>, <span class='st'>"ansi"</span><span class='op'>)</span><span class='op'>)</span>
+
+<span class='fu'>italicize_taxonomy</span><span class='op'>(</span><span class='va'>string</span>, type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"markdown"</span>, <span class='st'>"ansi"</span><span class='op'>)</span><span class='op'>)</span></pre>
+
+    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+    <table class="ref-arguments">
+    <colgroup><col class="name" /><col class="desc" /></colgroup>
+    <tr>
+      <th>string</th>
+      <td><p>a character (vector)</p></td>
+    </tr>
+    <tr>
+      <th>type</th>
+      <td><p>type of conversion of the taxonomic names, either "markdown" or "ansi", see <em>Details</em></p></td>
+    </tr>
+    </table>
+
+    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+    <p>This function finds the taxonomic names and makes them italic based on the <a href='microorganisms.html'>microorganisms</a> data set.</p>
+<p>The taxonomic names can be italicised using markdown (the default) by adding <code><a href='https://rdrr.io/r/base/Arithmetic.html'>*</a></code> before and after the taxonomic names, or using ANSI colours by adding <code>\033[3m</code> before and <code>\033[23m</code> after the taxonomic names. If multiple ANSI colours are not available, no conversion will occur.</p>
+<p>This function also supports abbreviation of the genus if it is followed by a species, such as "E. coli" and "K. pneumoniae ozaenae".</p>
+    <h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing Lifecycle</h2>
+
+    
+
+<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
+    <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
+
+    
+
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"An overview of Staphylococcus aureus isolates"</span><span class='op'>)</span>
+<span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"An overview of S. aureus isolates"</span><span class='op'>)</span>
+
+<span class='fu'><a href='https://rdrr.io/r/base/cat.html'>cat</a></span><span class='op'>(</span><span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"An overview of S. aureus isolates"</span>, type <span class='op'>=</span> <span class='st'>"ansi"</span><span class='op'>)</span><span class='op'>)</span>
+</pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
+  </div>
+</div>
+
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+</div>
+
+      </footer>
+   </div>
+
+  
+
+
+  </body>
+</html>
+
+
--- a/docs/reference/join.html
+++ b/docs/reference/join.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9015</span>
      </span>
    </div>

--- a/docs/reference/key_antimicrobials.html
+++ b/docs/reference/key_antimicrobials.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9015</span>
      </span>
    </div>

--- a/docs/reference/random.html
+++ b/docs/reference/random.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9015</span>
      </span>
    </div>

--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@ -105,6 +105,9 @@
  <url>
    <loc>https://msberends.github.io/AMR//reference/intrinsic_resistant.html</loc>
  </url>
+  <url>
+    <loc>https://msberends.github.io/AMR//reference/italicise_taxonomy.html</loc>
+  </url>
  <url>
    <loc>https://msberends.github.io/AMR//reference/join.html</loc>
  </url>
--- a/docs/survey.html
+++ b/docs/survey.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9016</span>
      </span>
    </div>

--- a/index.md
+++ b/index.md
@ -15,8 +15,8 @@ This package is [fully independent of any other R package](https://en.wikipedia.
 <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 155 countries</strong><br>
-    Since its first public release in early 2018, this package has been downloaded from 155 countries. Click the map to enlarge and to see the country names.</p>
+    <strong>Used in 162 countries</strong><br>
+    Since its first public release in early 2018, this package has been downloaded from 162 countries. Click the map to enlarge and to see the country names.</p>
 </div>

 ##### With `AMR` (for R), there's always a knowledgeable microbiologist by your side!
--- a/man/custom_eucast_rules.Rd
+++ b/man/custom_eucast_rules.Rd
@ -100,6 +100,11 @@ It is possible to define antibiotic groups instead of single antibiotics for the
 The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
 }

+\section{Read more on Our Website!}{
+
+On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
+}
+
 \examples{
 x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
                         AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
--- a/man/italicise_taxonomy.Rd
+++ b/man/italicise_taxonomy.Rd
@ -0,0 +1,43 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/italicise_taxonomy.R
+\name{italicise_taxonomy}
+\alias{italicise_taxonomy}
+\alias{italicize_taxonomy}
+\title{Italicise Taxonomic Families, Genera, Species, Subspecies}
+\usage{
+italicise_taxonomy(string, type = c("markdown", "ansi"))
+
+italicize_taxonomy(string, type = c("markdown", "ansi"))
+}
+\arguments{
+\item{string}{a character (vector)}
+
+\item{type}{type of conversion of the taxonomic names, either "markdown" or "ansi", see \emph{Details}}
+}
+\description{
+According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italic. This function finds taxonomic names within strings and makes them italic.
+}
+\details{
+This function finds the taxonomic names and makes them italic based on the \link{microorganisms} data set.
+
+The taxonomic names can be italicised using markdown (the default) by adding \code{*} before and after the taxonomic names, or using ANSI colours by adding \verb{\\033[3m} before and \verb{\\033[23m} after the taxonomic names. If multiple ANSI colours are not available, no conversion will occur.
+
+This function also supports abbreviation of the genus if it is followed by a species, such as "E. coli" and "K. pneumoniae ozaenae".
+}
+\section{Maturing Lifecycle}{
+
+\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
+The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
+}
+
+\section{Read more on Our Website!}{
+
+On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
+}
+
+\examples{
+italicise_taxonomy("An overview of Staphylococcus aureus isolates")
+italicise_taxonomy("An overview of S. aureus isolates")
+
+cat(italicise_taxonomy("An overview of S. aureus isolates", type = "ansi"))
+}
--- a/pkgdown/extra.js
+++ b/pkgdown/extra.js
@ -52,7 +52,10 @@ $(document).ready(function() {
    $("pre.examples").html($("pre.examples").html().replaceAll("# \\dontrun{", ""));
    $("pre.examples").html($("pre.examples").html().replaceAll("# }", ""));
  }
-
+  
+  // remove leading newline in code examples on changelog
+  $("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R">\n<span', 'sourceCode R"><span'));
+  
  // PR for 'R for Data Science' on How To pages
  if ($(".template-article").length > 0) {
    $('#pkgdown-sidebar').prepend(
--- a/pkgdown/logos/countries.png
+++ b/pkgdown/logos/countries.png
--- a/pkgdown/logos/countries_large.png
+++ b/pkgdown/logos/countries_large.png
--- a/tests/testthat/test-italicise_taxonomy.R
+++ b/tests/testthat/test-italicise_taxonomy.R
@ -0,0 +1,39 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Data Analysis for R                   #
+#                                                                      #
+# SOURCE                                                               #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# Developed at the University of Groningen, the Netherlands, in        #
+# collaboration with non-profit organisations Certe Medical            #
+# Diagnostics & Advice, and University Medical Center Groningen.       # 
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+# We created this package for both routine data analysis and academic  #
+# research and it was publicly released in the hope that it will be    #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+#                                                                      #
+# Visit our website for the full manual and a complete tutorial about  #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
+# ==================================================================== #
+
+context("italicise_taxonomy.R")
+
+test_that("italic taxonomy works", {
+  skip_on_cran()
+  
+  expect_identical(italicise_taxonomy("test for E. coli"),
+                   "test for *E. coli*")
+  expect_identical(italicise_taxonomy("test for E. coli"),
+                   italicize_taxonomy("test for E. coli"))
+  if (has_colour()) {
+    expect_identical(italicise_taxonomy("test for E. coli", type = "ansi"),
+                     "test for \033[3mE. coli\033[23m")
+  }
+})
Author	SHA1	Message	Date
dr. M.S. (Matthijs) Berends	f33e61bac7	(v1.6.0.9016) website update and c() fixes	2021-05-03 13:06:43 +02:00
dr. M.S. (Matthijs) Berends	12a8d59869	(v1.6.0.9015) italicise_taxonomy	2021-05-03 10:47:32 +02:00