(v1.2.0.9007) Tidyverse selections

2020-06-17 01:39:30 +02:00 · 2020-06-17 01:39:30 +02:00 · c4d7412f36
parent 4f94e1312f
commit c4d7412f36
21 changed files with 745 additions and 92 deletions
--- a/4
+++ b/4
@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.2.0.9006
-Date: 2020-06-11
+Version: 1.2.0.9007
+Date: 2020-06-17
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
    person(role = c("aut", "cre"), 
--- a/13
+++ b/13
@ -75,6 +75,7 @@ export(ab_tradenames)
 export(ab_url)
 export(age)
 export(age_groups)
+export(aminoglycosides)
 export(anti_join_microorganisms)
 export(as.ab)
 export(as.disk)
@ -87,7 +88,14 @@ export(atc_online_property)
 export(availability)
 export(brmo)
 export(bug_drug_combinations)
+export(carbapenems)
 export(catalogue_of_life_version)
+export(cephalosporins)
+export(cephalosporins_1st)
+export(cephalosporins_2nd)
+export(cephalosporins_3rd)
+export(cephalosporins_4th)
+export(cephalosporins_5th)
 export(count_I)
 export(count_IR)
 export(count_R)
@ -117,6 +125,7 @@ export(filter_macrolides)
 export(filter_penicillins)
 export(filter_tetracyclines)
 export(first_isolate)
+export(fluoroquinolones)
 export(full_join_microorganisms)
 export(g.test)
 export(geom_rsi)
@ -125,6 +134,7 @@ export(get_mo_source)
 export(ggplot_pca)
 export(ggplot_rsi)
 export(ggplot_rsi_predict)
+export(glycopeptides)
 export(guess_ab_col)
 export(inner_join_microorganisms)
 export(is.ab)
@ -139,6 +149,7 @@ export(kurtosis)
 export(labels_rsi_count)
 export(left_join_microorganisms)
 export(like)
+export(macrolides)
 export(mdr_cmi2012)
 export(mdr_tb)
 export(mdro)
@ -172,6 +183,7 @@ export(mrgn)
 export(n_rsi)
 export(p_symbol)
 export(pca)
+export(penicillins)
 export(portion_I)
 export(portion_IR)
 export(portion_R)
@ -195,6 +207,7 @@ export(semi_join_microorganisms)
 export(set_mo_source)
 export(skewness)
 export(susceptibility)
+export(tetracyclines)
 export(theme_rsi)
 importFrom(graphics,arrows)
 importFrom(graphics,axis)
--- a/NEWS.md
+++ b/NEWS.md
@ -1,15 +1,29 @@
-# AMR 1.2.0.9006
-## <small>Last updated: 11-Jun-2020</small>
+# AMR 1.2.0.9007
+## <small>Last updated: 17-Jun-2020</small>
+
+### New
+* [Tidyverse selections](https://tidyselect.r-lib.org/reference/language.html), that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows Tidyverse selections, like `dplyr::select()` and `tidyr::pivot_longer()`:
+  ```r
+  library(dplyr)
+  
+  example_isolates %>% 
+    select(carbapenems())
+  #> Selecting carbapenems: `IPM` (imipenem), `MEM` (meropenem)
+    
+  tibble(J01CA01 = "S") %>%
+    select(penicillins())
+  #> Selecting beta-lactams/penicillins: `J01CA01` (ampicillin)
+  ```

 ### Changed
 * Fixed a bug where `eucast_rules()` would not work on a tibble when the `tibble` or `dplyr` package was loaded
 * All `*_join_microorganisms()` functions now return the original data class (e.g. tibbles and data.tables)
 * Fixed a bug where `as.ab()` would return an error on invalid input values
-* Fixed a bug for using grouped versions of `rsi_df()`, `proportion_df()` and `count_df()`
+* Fixed a bug for using grouped versions of `rsi_df()`, `proportion_df()` and `count_df()`, and fixed a bug where not all different antimicrobial results were added as rows
 * Added function `filter_penicillins()` to filter isolates on a specific result in any column with a name in the antimicrobial 'penicillins' class (more specific: ATC subgroup *Beta-lactam antibacterials, penicillins*)
 * Added official antimicrobial names to all `filter_ab_class()` functions, such as `filter_aminoglycosides()`
 * Added antibiotics code "FOX1" for cefoxitin screening (abbreviation "cfsc") to the `antibiotics` data set
-* Improved auto-determination for columns of types <mo> and <Date>
+* Improved auto-determination for columns of types `<mo>` and `<Date>`

 # AMR 1.2.0

--- a/R/ab_class_selectors.R
+++ b/R/ab_class_selectors.R
@ -0,0 +1,159 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://gitlab.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+#                                                                      #
+# 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 more info: https://msberends.gitlab.io/AMR.    #
+# ==================================================================== #
+
+#' Antibiotic class selectors
+#' 
+#' Use these selection helpers inside any function that allows [Tidyverse selections](https://tidyselect.r-lib.org/reference/language.html), like `dplyr::select()` or `tidyr::pivot_longer()`. They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.
+#' @details All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.). This means that a selector like e.g. [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
+#' 
+#' These functions only work if the `tidyselect` package is installed, that comes with the `dplyr` package. An error will be thrown if `tidyselect` package is not installed, or if the functions are used outside a function that allows Tidyverse selections like `select()` or `pivot_longer()`.
+#' @rdname antibiotic_class_selectors
+#' @seealso [filter_ab_class()] for the `filter()` equivalent.
+#' @name antibiotic_class_selectors
+#' @export
+#' @examples 
+#' if (require("dplyr")) {
+#' 
+#'   # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
+#'   example_isolates %>% 
+#'     select(carbapenems())
+#'     
+#'     
+#'   # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
+#'   example_isolates %>% 
+#'     select(mo, aminoglycosides())
+#'     
+#'     
+#'   data.frame(irrelevant = "value",
+#'              J01CA01 = "S") %>%   # ATC code of ampicillin
+#'     select(penicillins())         # so the 'J01CA01' column is selected
+#'     
+#' }
+aminoglycosides <- function() {
+  ab_selector("aminoglycoside")
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+carbapenems <- function() {
+  ab_selector("carbapenem")
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+cephalosporins <- function() {
+  ab_selector("cephalosporin")
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+cephalosporins_1st <- function() {
+  ab_selector("cephalosporins.*1")
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+cephalosporins_2nd <- function() {
+  ab_selector("cephalosporins.*2")
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+cephalosporins_3rd <- function() {
+  ab_selector("cephalosporins.*3")
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+cephalosporins_4th <- function() {
+  ab_selector("cephalosporins.*4")
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+cephalosporins_5th <- function() {
+  ab_selector("cephalosporins.*5")
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+fluoroquinolones <- function() {
+  ab_selector("fluoroquinolone")
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+glycopeptides <- function() {
+  ab_selector("glycopeptide")
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+macrolides <- function() {
+  ab_selector("macrolide")
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+penicillins <- function() {
+  ab_selector("penicillin")
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+tetracyclines <- function() {
+  ab_selector("tetracycline")
+}
+
+ab_selector <- function(ab_class, vars = NULL) {
+  
+  stopifnot_installed_package("tidyselect")
+  peek_vars_tidyselect <- get("peek_vars", envir = asNamespace("tidyselect"))
+  
+  vars_vct <- peek_vars_tidyselect(fn = ab_class)
+  vars_df <- data.frame(as.list(vars_vct))[0, , drop = FALSE]
+  colnames(vars_df) <- vars_vct
+  ab_in_data <- suppressMessages(get_column_abx(vars_df))
+
+  if (length(ab_in_data) == 0) {
+    message(font_blue("NOTE: no antimicrobial agents found."))
+    return(NULL)
+  }
+
+  ab_reference <- subset(antibiotics,
+                         group %like% ab_class | 
+                           atc_group1 %like% ab_class | 
+                           atc_group2 %like% ab_class)
+  ab_group <- find_ab_group(ab_class)
+  # get the columns with a group names in the chosen ab class
+  agents <- ab_in_data[names(ab_in_data) %in% ab_reference$ab]
+  if (length(agents) == 0) {
+    message(font_blue(paste0("NOTE: no antimicrobial agents of class ", ab_group, 
+                             " found (such as ", find_ab_names(ab_class, 2), 
+                             ").")))
+  } else {
+    message(font_blue(paste0("Selecting ", ab_group, ": ",
+                             paste(paste0("`", font_bold(agents, collapse = NULL),
+                                          "` (", ab_name(names(agents), tolower = TRUE, language = NULL), ")"),
+                                   collapse = ", "))))
+  }
+  unname(agents)
+}
--- a/R/filter_ab_class.R
+++ b/R/filter_ab_class.R
@ -24,12 +24,13 @@
 #' Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside, or to filter on carbapenem-resistant isolates without the need to specify the drugs.
 #' @inheritSection lifecycle Stable lifecycle
 #' @param x a data set
-#' @param ab_class an antimicrobial class, like `"carbapenems"`, as can be found in [`antibiotics$group`][antibiotics]
+#' @param ab_class an antimicrobial class, like `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value.
 #' @param result an antibiotic result: S, I or R (or a combination of more of them)
 #' @param scope the scope to check which variables to check, can be `"any"` (default) or `"all"`
 #' @param ... parameters passed on to `filter_at` from the `dplyr` package
-#' @details The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched for the input given in `ab_class` (case-insensitive). Next, `x` will be checked for column names with a value in any abbreviation, code or official name found in the [antibiotics] data set.
+#' @details All columns of `x` will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.). This means that a filter function like e.g. [filter_aminoglycosides()] will include column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
 #' @rdname filter_ab_class
+#' @seealso [antibiotic_class_selectors()] for the `select()` equivalent.
 #' @export
 #' @examples
 #' \dontrun{
@ -329,6 +330,7 @@ filter_tetracyclines <- function(x,
 }

 find_ab_group <- function(ab_class) {
+  ab_class <- gsub("[^a-zA-Z0-9]", ".*", ab_class)
  ifelse(ab_class %in% c("aminoglycoside",
                         "carbapenem",
                         "cephalosporin",
@ -344,12 +346,14 @@ find_ab_group <- function(ab_class) {
           pull(group) %>%
           unique() %>%
           tolower() %>%
+           sort() %>% 
           paste(collapse = "/")
  )
 }

 find_ab_names <- function(ab_group, n = 3) {
-  drugs <- antibiotics[which(antibiotics$group %like% ab_group), "name"]
+  ab_group <- gsub("[^a-zA-Z0-9]", ".*", ab_group)
+  drugs <- antibiotics[which(antibiotics$group %like% ab_group & !antibiotics$ab %like% "[0-9]$"), ]$name
  paste0(sort(ab_name(sample(drugs, size = min(n, length(drugs)), replace = FALSE),
                      tolower = TRUE, language = NULL)), 
         collapse = ", ")
--- a/R/rsi_calc.R
+++ b/R/rsi_calc.R
@ -282,7 +282,9 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
  } else if (isTRUE(combine_IR)) {
    out$interpretation <- factor(out$interpretation, levels = c("S", "IR"), ordered = TRUE)
  } else {
-    out$interpretation <- as.rsi(out$interpretation)
+    # don't use as.rsi() here, as it would add the class <rsi> and we would like
+    # the same data structure as output, regardless of input
+    out$interpretation <- factor(out$interpretation, levels = c("S", "I", "R"), ordered = TRUE)
  }
  
  if (data_has_groups) {
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@ -124,6 +124,7 @@ reference:
    - "`bug_drug_combinations`"
    - "`resistance_predict`"
    - "`pca`"
+    - "`antibiotic_class_selectors`"
    - "`filter_ab_class`"
    - "`g.test`"
    - "`ggplot_rsi`"
--- a/docs/404.html
+++ b/docs/404.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9007</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">1.2.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9007</span>
      </span>
    </div>

--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9007</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">1.2.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9007</span>
      </span>
    </div>

--- a/docs/index.html
+++ b/docs/index.html
@ -43,7 +43,7 @@
      </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">1.2.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9007</span>
      </span>
    </div>

--- a/docs/news/index.html
+++ b/docs/news/index.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9007</span>
      </span>
    </div>

@ -229,14 +229,32 @@
      <small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
    </div>

-    <div id="amr-1209006" class="section level1">
-<h1 class="page-header" data-toc-text="1.2.0.9006">
-<a href="#amr-1209006" class="anchor"></a>AMR 1.2.0.9006<small> Unreleased </small>
+    <div id="amr-1209007" class="section level1">
+<h1 class="page-header" data-toc-text="1.2.0.9007">
+<a href="#amr-1209007" class="anchor"></a>AMR 1.2.0.9007<small> Unreleased </small>
 </h1>
-<div id="last-updated-11-jun-2020" class="section level2">
+<div id="last-updated-17-jun-2020" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-11-jun-2020" class="anchor"></a><small>Last updated: 11-Jun-2020</small>
+<a href="#last-updated-17-jun-2020" class="anchor"></a><small>Last updated: 17-Jun-2020</small>
 </h2>
+<div id="new" class="section level3">
+<h3 class="hasAnchor">
+<a href="#new" class="anchor"></a>New</h3>
+<ul>
+<li>
+<p><a href="https://tidyselect.r-lib.org/reference/language.html">Tidyverse selections</a>, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows Tidyverse selections, like <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code> and <code><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html">tidyr::pivot_longer()</a></code>:</p>
+<div class="sourceCode" id="cb1"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
+
+<span class="no">example_isolates</span> <span class="kw">%&gt;%</span>
+  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span>())
+<span class="co">#&gt; Selecting carbapenems: `IPM` (imipenem), `MEM` (meropenem)</span>
+
+<span class="fu"><a href="https://dplyr.tidyverse.org/reference/reexports.html">tibble</a></span>(<span class="kw">J01CA01</span> <span class="kw">=</span> <span class="st">"S"</span>) <span class="kw">%&gt;%</span>
+  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="fu"><a href="../reference/antibiotic_class_selectors.html">penicillins</a></span>())
+<span class="co">#&gt; Selecting beta-lactams/penicillins: `J01CA01` (ampicillin)</span></pre></div>
+</li>
+</ul>
+</div>
 <div id="changed" class="section level3">
 <h3 class="hasAnchor">
 <a href="#changed" class="anchor"></a>Changed</h3>
@ -244,13 +262,12 @@
 <li>Fixed a bug where <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> would not work on a tibble when the <code>tibble</code> or <code>dplyr</code> package was loaded</li>
 <li>All <code>*_join_microorganisms()</code> functions now return the original data class (e.g. tibbles and data.tables)</li>
 <li>Fixed a bug where <code><a href="../reference/as.ab.html">as.ab()</a></code> would return an error on invalid input values</li>
-<li>Fixed a bug for using grouped versions of <code><a href="../reference/proportion.html">rsi_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code> and <code><a href="../reference/count.html">count_df()</a></code>
-</li>
+<li>Fixed a bug for using grouped versions of <code><a href="../reference/proportion.html">rsi_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code> and <code><a href="../reference/count.html">count_df()</a></code>, and fixed a bug where not all different antimicrobial results were added as rows</li>
 <li>Added function <code><a href="../reference/filter_ab_class.html">filter_penicillins()</a></code> to filter isolates on a specific result in any column with a name in the antimicrobial ‘penicillins’ class (more specific: ATC subgroup <em>Beta-lactam antibacterials, penicillins</em>)</li>
 <li>Added official antimicrobial names to all <code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code> functions, such as <code><a href="../reference/filter_ab_class.html">filter_aminoglycosides()</a></code>
 </li>
 <li>Added antibiotics code “FOX1” for cefoxitin screening (abbreviation “cfsc”) to the <code>antibiotics</code> data set</li>
-<li>Improved auto-determination for columns of types <mo> and <date></date></mo>
+<li>Improved auto-determination for columns of types <code>&lt;mo&gt;</code> and <code>&lt;Date&gt;</code>
 </li>
 </ul>
 </div>
@ -324,9 +341,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <h1 class="page-header" data-toc-text="1.1.0">
 <a href="#amr-110" class="anchor"></a>AMR 1.1.0<small> 2020-04-15 </small>
 </h1>
-<div id="new" class="section level3">
+<div id="new-1" class="section level3">
 <h3 class="hasAnchor">
-<a href="#new" class="anchor"></a>New</h3>
+<a href="#new-1" class="anchor"></a>New</h3>
 <ul>
 <li>Support for easy principal component analysis for AMR, using the new <code><a href="../reference/pca.html">pca()</a></code> function</li>
 <li>Plotting biplots for principal component analysis using the new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function</li>
@ -373,11 +390,11 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li>
 <li>
 <p>Interpretation from MIC values (and disk zones) to R/SI can now be used with <code><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at()</a></code> of the <code>dplyr</code> package:</p>
-<div class="sourceCode" id="cb1"><pre class="r"><span class="no">yourdata</span> <span class="kw">%&gt;%</span>
-  <span class="fu">mutate_at</span>(<span class="fu">vars</span>(<span class="no">antibiotic1</span>:<span class="no">antibiotic25</span>), <span class="no">as.rsi</span>, <span class="kw">mo</span> <span class="kw">=</span> <span class="st">"E. coli"</span>)
+<div class="sourceCode" id="cb2"><pre class="r"><span class="no">yourdata</span> <span class="kw">%&gt;%</span>
+  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(<span class="no">antibiotic1</span>:<span class="no">antibiotic25</span>), <span class="no">as.rsi</span>, <span class="kw">mo</span> <span class="kw">=</span> <span class="st">"E. coli"</span>)

 <span class="no">yourdata</span> <span class="kw">%&gt;%</span>
-  <span class="fu">mutate_at</span>(<span class="fu">vars</span>(<span class="no">antibiotic1</span>:<span class="no">antibiotic25</span>), <span class="no">as.rsi</span>, <span class="kw">mo</span> <span class="kw">=</span> <span class="no">.</span>$<span class="no">mybacteria</span>)</pre></div>
+  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(<span class="no">antibiotic1</span>:<span class="no">antibiotic25</span>), <span class="no">as.rsi</span>, <span class="kw">mo</span> <span class="kw">=</span> <span class="no">.</span>$<span class="no">mybacteria</span>)</pre></div>
 </li>
 <li><p>Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole</p></li>
 <li><p>Added <code>uti</code> (as abbreviation of urinary tract infections) as parameter to <code><a href="../reference/as.rsi.html">as.rsi()</a></code>, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs</p></li>
@ -390,9 +407,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <a href="#amr-100" class="anchor"></a>AMR 1.0.0<small> 2020-02-17 </small>
 </h1>
 <p>This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.</p>
-<div id="new-1" class="section level3">
+<div id="new-2" class="section level3">
 <h3 class="hasAnchor">
-<a href="#new-1" class="anchor"></a>New</h3>
+<a href="#new-2" class="anchor"></a>New</h3>
 <ul>
 <li>Support for the newest <a href="http://www.eucast.org/clinical_breakpoints/">EUCAST Clinical Breakpoint Tables v.10.0</a>, valid from 1 January 2020. This affects translation of MIC and disk zones using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> and inferred resistance and susceptibility using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</li>
 <li>The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <a href="https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt" class="uri">https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This <strong>allows for machine reading these guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file <a href="https://gitlab.com/msberends/AMR/blob/master/data-raw/read_EUCAST.R">can be found here</a>.</li>
@ -400,7 +417,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>Support for LOINC codes in the <code>antibiotics</code> data set. Use <code><a href="../reference/ab_property.html">ab_loinc()</a></code> to retrieve LOINC codes, or use a LOINC code for input in any <code>ab_*</code> function:</p>
-<div class="sourceCode" id="cb2"><pre class="r"><span class="fu"><a href="../reference/ab_property.html">ab_loinc</a></span>(<span class="st">"ampicillin"</span>)
+<div class="sourceCode" id="cb3"><pre class="r"><span class="fu"><a href="../reference/ab_property.html">ab_loinc</a></span>(<span class="st">"ampicillin"</span>)
 <span class="co">#&gt; [1] "21066-6" "3355-5"  "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"</span>
 <span class="fu"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="st">"21066-6"</span>)
 <span class="co">#&gt; [1] "Ampicillin"</span>
@ -409,7 +426,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 <li>
 <p>Support for SNOMED CT codes in the <code>microorganisms</code> data set. Use <code><a href="../reference/mo_property.html">mo_snomed()</a></code> to retrieve SNOMED codes, or use a SNOMED code for input in any <code>mo_*</code> function:</p>
-<div class="sourceCode" id="cb3"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_snomed</a></span>(<span class="st">"S. aureus"</span>)
+<div class="sourceCode" id="cb4"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_snomed</a></span>(<span class="st">"S. aureus"</span>)
 <span class="co">#&gt; [1] 115329001   3092008 113961008</span>
 <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="fl">115329001</span>)
 <span class="co">#&gt; [1] "Staphylococcus aureus"</span>
@ -472,21 +489,21 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>If you were dependent on the old Enterobacteriaceae family e.g. by using in your code:</p>
-<div class="sourceCode" id="cb4"><pre class="r"><span class="kw">if</span> (<span class="fu"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="no">somebugs</span>) <span class="kw">==</span> <span class="st">"Enterobacteriaceae"</span>) <span class="no">...</span></pre></div>
+<div class="sourceCode" id="cb5"><pre class="r"><span class="kw">if</span> (<span class="fu"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="no">somebugs</span>) <span class="kw">==</span> <span class="st">"Enterobacteriaceae"</span>) <span class="no">...</span></pre></div>
 <p>then please adjust this to:</p>
-<div class="sourceCode" id="cb5"><pre class="r"><span class="kw">if</span> (<span class="fu"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="no">somebugs</span>) <span class="kw">==</span> <span class="st">"Enterobacterales"</span>) <span class="no">...</span></pre></div>
+<div class="sourceCode" id="cb6"><pre class="r"><span class="kw">if</span> (<span class="fu"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="no">somebugs</span>) <span class="kw">==</span> <span class="st">"Enterobacterales"</span>) <span class="no">...</span></pre></div>
 </li>
 </ul>
 </li>
 </ul>
 </div>
-<div id="new-2" class="section level3">
+<div id="new-3" class="section level3">
 <h3 class="hasAnchor">
-<a href="#new-2" class="anchor"></a>New</h3>
+<a href="#new-3" class="anchor"></a>New</h3>
 <ul>
 <li>
 <p>Functions <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> as aliases of <code><a href="../reference/proportion.html">proportion_SI()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code>, respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.</p>
-<div class="sourceCode" id="cb6"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
+<div class="sourceCode" id="cb7"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
 <span class="no">example_isolates</span> <span class="kw">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">bug</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="no">mo</span>)) <span class="kw">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(<span class="kw">amoxicillin</span> <span class="kw">=</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="no">AMX</span>),
@ -513,7 +530,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>More intelligent way of coping with some consonants like “l” and “r”</p></li>
 <li>
 <p>Added a score (a certainty percentage) to <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code>, that is calculated using the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance">Levenshtein distance</a>:</p>
-<div class="sourceCode" id="cb7"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Stafylococcus aureus"</span>,
+<div class="sourceCode" id="cb8"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Stafylococcus aureus"</span>,
        <span class="st">"staphylokok aureuz"</span>))
 <span class="co">#&gt; Warning: </span>
 <span class="co">#&gt; Results of two values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
@ -570,12 +587,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>Determination of first isolates now <strong>excludes</strong> all ‘unknown’ microorganisms at default, i.e. microbial code <code>"UNKNOWN"</code>. They can be included with the new parameter <code>include_unknown</code>:</p>
-<div class="sourceCode" id="cb8"><pre class="r"><span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="no">...</span>, <span class="kw">include_unknown</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></div>
+<div class="sourceCode" id="cb9"><pre class="r"><span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="no">...</span>, <span class="kw">include_unknown</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></div>
 <p>For WHONET users, this means that all records/isolates with organism code <code>"con"</code> (<em>contamination</em>) will be excluded at default, since <code>as.mo("con") = "UNKNOWN"</code>. The function always shows a note with the number of ‘unknown’ microorganisms that were included or excluded.</p>
 </li>
 <li>
 <p>For code consistency, classes <code>ab</code> and <code>mo</code> will now be preserved in any subsetting or assignment. For the sake of data integrity, this means that invalid assignments will now result in <code>NA</code>:</p>
-<div class="sourceCode" id="cb9"><pre class="r"><span class="co"># how it works in base R:</span>
+<div class="sourceCode" id="cb10"><pre class="r"><span class="co"># how it works in base R:</span>
 <span class="no">x</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html">factor</a></span>(<span class="st">"A"</span>)
 <span class="no">x</span>[<span class="fl">1</span>] <span class="kw">&lt;-</span> <span class="st">"B"</span>
 <span class="co">#&gt; Warning message:</span>
@ -592,13 +609,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
 </ul>
 </div>
-<div id="new-3" class="section level3">
+<div id="new-4" class="section level3">
 <h3 class="hasAnchor">
-<a href="#new-3" class="anchor"></a>New</h3>
+<a href="#new-4" class="anchor"></a>New</h3>
 <ul>
 <li>
 <p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with <code><a href="../reference/mo_property.html">mo_shortname()</a></code> at default:</p>
-<div class="sourceCode" id="cb10"><pre class="r"><span class="no">x</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(<span class="no">example_isolates</span>)
+<div class="sourceCode" id="cb11"><pre class="r"><span class="no">x</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(<span class="no">example_isolates</span>)
 <span class="co">#&gt; NOTE: Using column `mo` as input for `col_mo`.</span>
 <span class="no">x</span>[<span class="fl">1</span>:<span class="fl">4</span>, ]
 <span class="co">#&gt;             mo  ab S I R total</span>
@ -619,11 +636,11 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <span class="co">#&gt; 4 Gram-negative AMX 227  0 405   632</span>
 <span class="co">#&gt; NOTE: Use 'format()' on this result to get a publicable/printable format.</span></pre></div>
 <p>You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R <code><a href="https://rdrr.io/r/base/format.html">format()</a></code> function:</p>
-<div class="sourceCode" id="cb11"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/format.html">format</a></span>(<span class="no">x</span>, <span class="kw">combine_IR</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></div>
+<div class="sourceCode" id="cb12"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/format.html">format</a></span>(<span class="no">x</span>, <span class="kw">combine_IR</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></div>
 </li>
 <li>
 <p>Additional way to calculate co-resistance, i.e. when using multiple antimicrobials as input for <code>portion_*</code> functions or <code>count_*</code> functions. This can be used to determine the empiric susceptibility of a combination therapy. A new parameter <code>only_all_tested</code> (<strong>which defaults to <code>FALSE</code></strong>) replaces the old <code>also_single_tested</code> and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the <code>portion</code> and <code>count</code> help pages), where the %SI is being determined:</p>
-<div class="sourceCode" id="cb12"><pre class="r"># --------------------------------------------------------------------
+<div class="sourceCode" id="cb13"><pre class="r"># --------------------------------------------------------------------
 #                     only_all_tested = FALSE  only_all_tested = TRUE
 #                     -----------------------  -----------------------
 #  Drug A    Drug B   include as  include as   include as  include as
@ -643,7 +660,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 <li>
 <p><code>tibble</code> printing support for classes <code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code> <code>mo</code>. When using <code>tibble</code>s containing antimicrobial columns, values <code>S</code> will print in green, values <code>I</code> will print in yellow and values <code>R</code> will print in red. Microbial IDs (class <code>mo</code>) will emphasise on the genus and species, not on the kingdom.</p>
-<div class="sourceCode" id="cb13"><pre class="r"><span class="co"># (run this on your own console, as this page does not support colour printing)</span>
+<div class="sourceCode" id="cb14"><pre class="r"><span class="co"># (run this on your own console, as this page does not support colour printing)</span>
 <span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
 <span class="no">example_isolates</span> <span class="kw">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="no">mo</span>:<span class="no">AMC</span>) <span class="kw">%&gt;%</span>
@ -718,13 +735,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <h1 class="page-header" data-toc-text="0.7.1">
 <a href="#amr-071" class="anchor"></a>AMR 0.7.1<small> 2019-06-23 </small>
 </h1>
-<div id="new-4" class="section level4">
+<div id="new-5" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-4" class="anchor"></a>New</h4>
+<a href="#new-5" class="anchor"></a>New</h4>
 <ul>
 <li>
 <p>Function <code><a href="../reference/proportion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/AMR-deprecated.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p>
-<div class="sourceCode" id="cb14"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
+<div class="sourceCode" id="cb15"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="no">AMX</span>, <span class="no">CIP</span>) <span class="kw">%&gt;%</span>
  <span class="fu"><a href="../reference/proportion.html">rsi_df</a></span>()
 <span class="co">#      antibiotic  interpretation      value  isolates</span>
@ -749,7 +766,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>UPEC (Uropathogenic <em>E. coli</em>)</li>
 </ul>
 <p>All these lead to the microbial ID of <em>E. coli</em>:</p>
-<div class="sourceCode" id="cb15"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)
+<div class="sourceCode" id="cb16"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)
 <span class="co"># B_ESCHR_COL</span>
 <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"UPEC"</span>)
 <span class="co"># "Escherichia coli"</span>
@ -799,9 +816,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <h1 class="page-header" data-toc-text="0.7.0">
 <a href="#amr-070" class="anchor"></a>AMR 0.7.0<small> 2019-06-03 </small>
 </h1>
-<div id="new-5" class="section level4">
+<div id="new-6" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-5" class="anchor"></a>New</h4>
+<a href="#new-6" class="anchor"></a>New</h4>
 <ul>
 <li>Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on an MIC value (created with <code><a href="../reference/as.mic.html">as.mic()</a></code>), a disk diffusion value (created with the new <code><a href="../reference/as.disk.html">as.disk()</a></code>) or on a complete date set containing columns with MIC or disk diffusion values.</li>
 <li>Function <code><a href="../reference/mo_property.html">mo_name()</a></code> as alias of <code><a href="../reference/mo_property.html">mo_fullname()</a></code>
@ -856,7 +873,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>when all values are unique it now shows a message instead of a warning</p></li>
 <li>
 <p>support for boxplots:</p>
-<div class="sourceCode" id="cb16"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
+<div class="sourceCode" id="cb17"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
  <span class="fu">freq</span>(<span class="no">age</span>) <span class="kw">%&gt;%</span>
  <span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()
 <span class="co"># grouped boxplots:</span>
@ -916,9 +933,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>Contains the complete manual of this package and all of its functions with an explanation of their parameters</li>
 <li>Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis, import data from WHONET or SPSS and many more.</li>
 </ul>
-<div id="new-6" class="section level4">
+<div id="new-7" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-6" class="anchor"></a>New</h4>
+<a href="#new-7" class="anchor"></a>New</h4>
 <ul>
 <li><p><strong>BREAKING</strong>: removed deprecated functions, parameters and references to ‘bactid’. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> to identify an MO code.</p></li>
 <li>
@ -947,7 +964,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 <li>
 <p>New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:</p>
-<div class="sourceCode" id="cb17"><pre class="r"><span class="fu"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()
+<div class="sourceCode" id="cb18"><pre class="r"><span class="fu"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()
 <span class="fu"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()
 <span class="fu"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()
 <span class="fu"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()
@ -959,14 +976,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <span class="fu"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()
 <span class="fu"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</pre></div>
 <p>The <code>antibiotics</code> data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set. For example:</p>
-<div class="sourceCode" id="cb18"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="kw">result</span> <span class="kw">=</span> <span class="st">"R"</span>)
+<div class="sourceCode" id="cb19"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="kw">result</span> <span class="kw">=</span> <span class="st">"R"</span>)
 <span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span>
 <span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="kw">result</span> <span class="kw">=</span> <span class="st">"R"</span>, <span class="kw">scope</span> <span class="kw">=</span> <span class="st">"all"</span>)
 <span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></pre></div>
 </li>
 <li>
 <p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
-<div class="sourceCode" id="cb19"><pre class="r"><span class="no">ab_property</span> <span class="kw">-&gt;</span> <span class="fu">atc_property</span>()
+<div class="sourceCode" id="cb20"><pre class="r"><span class="no">ab_property</span> <span class="kw">-&gt;</span> <span class="fu">atc_property</span>()
 <span class="no">ab_name</span> <span class="kw">-&gt;</span> <span class="fu">atc_name</span>()
 <span class="no">ab_official</span> <span class="kw">-&gt;</span> <span class="fu">atc_official</span>()
 <span class="no">ab_trivial_nl</span> <span class="kw">-&gt;</span> <span class="fu">atc_trivial_nl</span>()
@ -985,17 +1002,17 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</p></li>
 <li>
 <p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="https://rdrr.io/r/base/plot.html">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
-<div class="sourceCode" id="cb20"><pre class="r"><span class="no">x</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="no">septic_patients</span>, <span class="kw">col_ab</span> <span class="kw">=</span> <span class="st">"amox"</span>)
+<div class="sourceCode" id="cb21"><pre class="r"><span class="no">x</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="no">septic_patients</span>, <span class="kw">col_ab</span> <span class="kw">=</span> <span class="st">"amox"</span>)
 <span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">x</span>)
 <span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(<span class="no">x</span>)</pre></div>
 </li>
 <li>
 <p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
-<div class="sourceCode" id="cb21"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(<span class="no">...</span>)
+<div class="sourceCode" id="cb22"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(<span class="no">...</span>)
 <span class="co"># or</span>
 <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(<span class="no">septic_patients</span>, <span class="no">...</span>)</pre></div>
 <p>is equal to:</p>
-<div class="sourceCode" id="cb22"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
+<div class="sourceCode" id="cb23"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="kw">only_firsts</span> <span class="kw">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="no">septic_patients</span>, <span class="no">...</span>)) <span class="kw">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="no">only_firsts</span> <span class="kw">==</span> <span class="fl">TRUE</span>) <span class="kw">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(-<span class="no">only_firsts</span>)</pre></div>
@ -1026,7 +1043,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>Now handles incorrect spelling, like <code>i</code> instead of <code>y</code> and <code>f</code> instead of <code>ph</code>:</p>
-<div class="sourceCode" id="cb23"><pre class="r"><span class="co"># mo_fullname() uses as.mo() internally</span>
+<div class="sourceCode" id="cb24"><pre class="r"><span class="co"># mo_fullname() uses as.mo() internally</span>

 <span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)
 <span class="co">#&gt; [1] "Staphylococcus aureus"</span>
@ -1036,7 +1053,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 <li>
 <p>Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default <code>allow_uncertain = TRUE</code> is equal to uncertainty level 2. Run <code><a href="../reference/as.mo.html">?as.mo</a></code> for more info about these levels.</p>
-<div class="sourceCode" id="cb24"><pre class="r"><span class="co"># equal:</span>
+<div class="sourceCode" id="cb25"><pre class="r"><span class="co"># equal:</span>
 <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="no">...</span>, <span class="kw">allow_uncertain</span> <span class="kw">=</span> <span class="fl">TRUE</span>)
 <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="no">...</span>, <span class="kw">allow_uncertain</span> <span class="kw">=</span> <span class="fl">2</span>)

@ -1049,7 +1066,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>All microbial IDs that found are now saved to a local file <code>~/.Rhistory_mo</code>. Use the new function <code>clean_mo_history()</code> to delete this file, which resets the algorithms.</p></li>
 <li>
 <p>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</p>
-<div class="sourceCode" id="cb25"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"es"</span>)
+<div class="sourceCode" id="cb26"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"es"</span>)
 <span class="co"># Warning: </span>
 <span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span>
 <span class="co">#&gt; [1] "(género desconocido)"</span></pre></div>
@ -1097,7 +1114,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
-<div class="sourceCode" id="cb26"><pre class="r"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span>
+<div class="sourceCode" id="cb27"><pre class="r"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span>
 <span class="co"># OLD WAY</span>
 <span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="kw">genus</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="no">mo</span>)) <span class="kw">%&gt;%</span>
@ -1142,9 +1159,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <h1 class="page-header" data-toc-text="0.5.0">
 <a href="#amr-050" class="anchor"></a>AMR 0.5.0<small> 2018-11-30 </small>
 </h1>
-<div id="new-7" class="section level4">
+<div id="new-8" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-7" class="anchor"></a>New</h4>
+<a href="#new-8" class="anchor"></a>New</h4>
 <ul>
 <li>Repository moved to GitLab: <a href="https://gitlab.com/msberends/AMR" class="uri">https://gitlab.com/msberends/AMR</a>
 </li>
@ -1180,7 +1197,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Fewer than 3 characters as input for <code>as.mo</code> will return NA</p></li>
 <li>
 <p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
-<div class="sourceCode" id="cb27"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>)        <span class="co"># B_ESCHR</span>
+<div class="sourceCode" id="cb28"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>)        <span class="co"># B_ESCHR</span>
 <span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>)     <span class="co"># "Escherichia species"</span>
 <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>)            <span class="co"># B_STPHY</span>
 <span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>)  <span class="co"># "Staphylococcus species"</span></pre></div>
@ -1195,13 +1212,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>
 <p>Support for grouping variables, test with:</p>
-<div class="sourceCode" id="cb28"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
+<div class="sourceCode" id="cb29"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="no">hospital_id</span>) <span class="kw">%&gt;%</span>
  <span class="fu">freq</span>(<span class="no">gender</span>)</pre></div>
 </li>
 <li>
 <p>Support for (un)selecting columns:</p>
-<div class="sourceCode" id="cb29"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
+<div class="sourceCode" id="cb30"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
  <span class="fu">freq</span>(<span class="no">hospital_id</span>) <span class="kw">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(-<span class="no">count</span>, -<span class="no">cum_count</span>) <span class="co"># only get item, percent, cum_percent</span></pre></div>
 </li>
@ -1261,9 +1278,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <h1 class="page-header" data-toc-text="0.4.0">
 <a href="#amr-040" class="anchor"></a>AMR 0.4.0<small> 2018-10-01 </small>
 </h1>
-<div id="new-8" class="section level4">
+<div id="new-9" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-8" class="anchor"></a>New</h4>
+<a href="#new-9" class="anchor"></a>New</h4>
 <ul>
 <li><p>The data set <code>microorganisms</code> now contains <strong>all microbial taxonomic data from ITIS</strong> (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via <a href="https://itis.gov" class="uri">https://itis.gov</a>. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set <code>microorganisms.old</code> contains all previously known taxonomic names from those kingdoms.</p></li>
 <li>
@ -1279,7 +1296,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 </ul>
 <p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
-<div class="sourceCode" id="cb30"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)
+<div class="sourceCode" id="cb31"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)
 <span class="co"># [1] "Gram negative"</span>
 <span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"de"</span>) <span class="co"># German</span>
 <span class="co"># [1] "Gramnegativ"</span>
@ -1288,7 +1305,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span>
 <span class="co"># [1] "Streptococcus grupo A"</span></pre></div>
 <p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
-<div class="sourceCode" id="cb31"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)
+<div class="sourceCode" id="cb32"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)
 <span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span>
 <span class="co"># [1] "Gram negative"</span></pre></div>
 </li>
@ -1301,14 +1318,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Function <code>is.rsi.eligible</code> to check for columns that have valid antimicrobial results, but do not have the <code>rsi</code> class yet. Transform the columns of your raw data with: <code>data %&gt;% mutate_if(is.rsi.eligible, as.rsi)</code></p></li>
 <li>
 <p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using intelligent rules:</p>
-<div class="sourceCode" id="cb32"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)
+<div class="sourceCode" id="cb33"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)
 <span class="co"># [1] B_ESCHR_COL</span>
 <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)
 <span class="co"># [1] B_STPHY_AUR</span>
 <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)
 <span class="co"># [1] B_STRPTC_GRA</span></pre></div>
 <p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p>
-<div class="sourceCode" id="cb33"><pre class="r"><span class="no">thousands_of_E_colis</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="st">"E. coli"</span>, <span class="fl">25000</span>)
+<div class="sourceCode" id="cb34"><pre class="r"><span class="no">thousands_of_E_colis</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="st">"E. coli"</span>, <span class="fl">25000</span>)
 <span class="kw pkg">microbenchmark</span><span class="kw ns">::</span><span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="no">thousands_of_E_colis</span>), <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"s"</span>)
 <span class="co"># Unit: seconds</span>
 <span class="co">#         min       median         max  neval</span>
@ -1340,7 +1357,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</p></li>
 <li>
 <p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
-<div class="sourceCode" id="cb34"><pre class="r"><span class="fu">ab_official</span>(<span class="st">"Bactroban"</span>)
+<div class="sourceCode" id="cb35"><pre class="r"><span class="fu">ab_official</span>(<span class="st">"Bactroban"</span>)
 <span class="co"># [1] "Mupirocin"</span>
 <span class="fu"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))
 <span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span>
@ -1355,7 +1372,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Added parameters <code>minimum</code> and <code>as_percent</code> to <code>portion_df</code></p></li>
 <li>
 <p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
-<div class="sourceCode" id="cb35"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="no">amox</span>, <span class="no">cipr</span>) <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span>()
+<div class="sourceCode" id="cb36"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="no">amox</span>, <span class="no">cipr</span>) <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span>()
 <span class="co"># which is the same as:</span>
 <span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span>(<span class="no">amox</span>, <span class="no">cipr</span>)

@ -1373,10 +1390,10 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Added longest en shortest character length in the frequency table (<code>freq</code>) header of class <code>character</code></p></li>
 <li>
 <p>Support for types (classes) list and matrix for <code>freq</code></p>
-<div class="sourceCode" id="cb36"><pre class="r"><span class="no">my_matrix</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span>(<span class="no">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">age</span>, <span class="no">gender</span>), <span class="kw">ncol</span> <span class="kw">=</span> <span class="fl">2</span>))
+<div class="sourceCode" id="cb37"><pre class="r"><span class="no">my_matrix</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span>(<span class="no">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">age</span>, <span class="no">gender</span>), <span class="kw">ncol</span> <span class="kw">=</span> <span class="fl">2</span>))
 <span class="fu">freq</span>(<span class="no">my_matrix</span>)</pre></div>
 <p>For lists, subsetting is possible:</p>
-<div class="sourceCode" id="cb37"><pre class="r"><span class="no">my_list</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="kw">age</span> <span class="kw">=</span> <span class="no">septic_patients</span>$<span class="no">age</span>, <span class="kw">gender</span> <span class="kw">=</span> <span class="no">septic_patients</span>$<span class="no">gender</span>)
+<div class="sourceCode" id="cb38"><pre class="r"><span class="no">my_list</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="kw">age</span> <span class="kw">=</span> <span class="no">septic_patients</span>$<span class="no">age</span>, <span class="kw">gender</span> <span class="kw">=</span> <span class="no">septic_patients</span>$<span class="no">gender</span>)
 <span class="no">my_list</span> <span class="kw">%&gt;%</span> <span class="fu">freq</span>(<span class="no">age</span>)
 <span class="no">my_list</span> <span class="kw">%&gt;%</span> <span class="fu">freq</span>(<span class="no">gender</span>)</pre></div>
 </li>
@ -1394,9 +1411,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <h1 class="page-header" data-toc-text="0.3.0">
 <a href="#amr-030" class="anchor"></a>AMR 0.3.0<small> 2018-08-14 </small>
 </h1>
-<div id="new-9" class="section level4">
+<div id="new-10" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-9" class="anchor"></a>New</h4>
+<a href="#new-10" class="anchor"></a>New</h4>
 <ul>
 <li>
 <strong>BREAKING</strong>: <code>rsi_df</code> was removed in favour of new functions <code>portion_R</code>, <code>portion_IR</code>, <code>portion_I</code>, <code>portion_SI</code> and <code>portion_S</code> to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old <code>rsi</code> function. The old function still works, but is deprecated.
@ -1531,9 +1548,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <h1 class="page-header" data-toc-text="0.2.0">
 <a href="#amr-020" class="anchor"></a>AMR 0.2.0<small> 2018-05-03 </small>
 </h1>
-<div id="new-10" class="section level4">
+<div id="new-11" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-10" class="anchor"></a>New</h4>
+<a href="#new-11" class="anchor"></a>New</h4>
 <ul>
 <li>Full support for Windows, Linux and macOS</li>
 <li>Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)</li>
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@ -10,7 +10,7 @@ articles:
  WHONET: WHONET.html
  benchmarks: benchmarks.html
  resistance_predict: resistance_predict.html
-last_built: 2020-06-11T17:56Z
+last_built: 2020-06-16T23:38Z
 urls:
  reference: https://msberends.gitlab.io/AMR/reference
  article: https://msberends.gitlab.io/AMR/articles
--- a/docs/reference/antibiotic_class_selectors.html
+++ b/docs/reference/antibiotic_class_selectors.html
@ -0,0 +1,318 @@
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+<meta property="og:description" content="Use these selection helpers inside any function that allows Tidyverse selections, like dplyr::select() or tidyr::pivot_longer(). They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations." />
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+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Antibiotic class selectors</h1>
+    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ab_class_selectors.R'><code>R/ab_class_selectors.R</code></a></small>
+    <div class="hidden name"><code>antibiotic_class_selectors.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Use these selection helpers inside any function that allows <a href='https://tidyselect.r-lib.org/reference/language.html'>Tidyverse selections</a>, like <code><a href='https://dplyr.tidyverse.org/reference/select.html'>dplyr::select()</a></code> or <code><a href='https://tidyr.tidyverse.org/reference/pivot_longer.html'>tidyr::pivot_longer()</a></code>. They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.</p>
+    </div>
+
+    <pre class="usage"><span class='fu'>aminoglycosides</span>()
+
+<span class='fu'>carbapenems</span>()
+
+<span class='fu'>cephalosporins</span>()
+
+<span class='fu'>cephalosporins_1st</span>()
+
+<span class='fu'>cephalosporins_2nd</span>()
+
+<span class='fu'>cephalosporins_3rd</span>()
+
+<span class='fu'>cephalosporins_4th</span>()
+
+<span class='fu'>cephalosporins_5th</span>()
+
+<span class='fu'>fluoroquinolones</span>()
+
+<span class='fu'>glycopeptides</span>()
+
+<span class='fu'>macrolides</span>()
+
+<span class='fu'>penicillins</span>()
+
+<span class='fu'>tetracyclines</span>()</pre>
+
+
+    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+    <p>All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.). This means that a selector like e.g. <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.</p>
+<p>These functions only work if the <code>tidyselect</code> package is installed, that comes with the <code>dplyr</code> package. An error will be thrown if <code>tidyselect</code> package is not installed, or if the functions are used outside a function that allows Tidyverse selections like <code><a href='https://dplyr.tidyverse.org/reference/select.html'>select()</a></code> or <code>pivot_longer()</code>.</p>
+    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+    <div class='dont-index'><p><code><a href='filter_ab_class.html'>filter_ab_class()</a></code> for the <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code> equivalent.</p></div>
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
+
+  <span class='co'># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</span>
+  <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
+    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='fu'>carbapenems</span>())
+
+
+  <span class='co'># this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':</span>
+  <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
+    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>, <span class='fu'>aminoglycosides</span>())
+
+
+  <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>irrelevant</span> <span class='kw'>=</span> <span class='st'>"value"</span>,
+             <span class='kw'>J01CA01</span> <span class='kw'>=</span> <span class='st'>"S"</span>) <span class='kw'>%&gt;%</span>   <span class='co'># ATC code of ampicillin</span>
+    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='fu'>penicillins</span>())         <span class='co'># so the 'J01CA01' column is selected</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>
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--- a/docs/reference/filter_ab_class.html
+++ b/docs/reference/filter_ab_class.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">1.2.0.9003</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9007</span>
      </span>
    </div>

@ -272,7 +272,7 @@
    </tr>
    <tr>
      <th>ab_class</th>
-      <td><p>an antimicrobial class, like <code>"carbapenems"</code>, as can be found in <code><a href='antibiotics.html'>antibiotics$group</a></code></p></td>
+      <td><p>an antimicrobial class, like <code>"carbapenems"</code>. The columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code> of the <a href='antibiotics.html'>antibiotics</a> data set will be searched (case-insensitive) for this value.</p></td>
    </tr>
    <tr>
      <th>result</th>
@ -290,7 +290,7 @@

    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>

-    <p>The columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code> of the <a href='antibiotics.html'>antibiotics</a> data set will be searched for the input given in <code>ab_class</code> (case-insensitive). Next, <code>x</code> will be checked for column names with a value in any abbreviation, code or official name found in the <a href='antibiotics.html'>antibiotics</a> data set.</p>
+    <p>All columns of <code>x</code> will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.). This means that a filter function like e.g. <code>filter_aminoglycosides()</code> will include column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.</p>
    <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>

    
@ -298,6 +298,9 @@
 <p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
 The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
 <p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
+    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+    <div class='dont-index'><p><code><a href='antibiotic_class_selectors.html'>antibiotic_class_selectors()</a></code> for the <code><a href='https://dplyr.tidyverse.org/reference/select.html'>select()</a></code> equivalent.</p></div>

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
--- 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">1.2.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9007</span>
      </span>
    </div>

--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@ -24,6 +24,9 @@
  <url>
    <loc>https://msberends.gitlab.io/AMR/reference/age_groups.html</loc>
  </url>
+  <url>
+    <loc>https://msberends.gitlab.io/AMR/reference/antibiotic_class_selectors.html</loc>
+  </url>
  <url>
    <loc>https://msberends.gitlab.io/AMR/reference/antibiotics.html</loc>
  </url>
--- a/man/antibiotic_class_selectors.Rd
+++ b/man/antibiotic_class_selectors.Rd
@ -0,0 +1,75 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ab_class_selectors.R
+\name{antibiotic_class_selectors}
+\alias{antibiotic_class_selectors}
+\alias{aminoglycosides}
+\alias{carbapenems}
+\alias{cephalosporins}
+\alias{cephalosporins_1st}
+\alias{cephalosporins_2nd}
+\alias{cephalosporins_3rd}
+\alias{cephalosporins_4th}
+\alias{cephalosporins_5th}
+\alias{fluoroquinolones}
+\alias{glycopeptides}
+\alias{macrolides}
+\alias{penicillins}
+\alias{tetracyclines}
+\title{Antibiotic class selectors}
+\usage{
+aminoglycosides()
+
+carbapenems()
+
+cephalosporins()
+
+cephalosporins_1st()
+
+cephalosporins_2nd()
+
+cephalosporins_3rd()
+
+cephalosporins_4th()
+
+cephalosporins_5th()
+
+fluoroquinolones()
+
+glycopeptides()
+
+macrolides()
+
+penicillins()
+
+tetracyclines()
+}
+\description{
+Use these selection helpers inside any function that allows \href{https://tidyselect.r-lib.org/reference/language.html}{Tidyverse selections}, like \code{dplyr::select()} or \code{tidyr::pivot_longer()}. They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.
+}
+\details{
+All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.). This means that a selector like e.g. \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
+
+These functions only work if the \code{tidyselect} package is installed, that comes with the \code{dplyr} package. An error will be thrown if \code{tidyselect} package is not installed, or if the functions are used outside a function that allows Tidyverse selections like \code{select()} or \code{pivot_longer()}.
+}
+\examples{
+if (require("dplyr")) {
+
+  # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
+  example_isolates \%>\% 
+    select(carbapenems())
+    
+    
+  # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
+  example_isolates \%>\% 
+    select(mo, aminoglycosides())
+    
+    
+  data.frame(irrelevant = "value",
+             J01CA01 = "S") \%>\%   # ATC code of ampicillin
+    select(penicillins())         # so the 'J01CA01' column is selected
+    
+}
+}
+\seealso{
+\code{\link[=filter_ab_class]{filter_ab_class()}} for the \code{filter()} equivalent.
+}
--- a/man/filter_ab_class.Rd
+++ b/man/filter_ab_class.Rd
@ -48,7 +48,7 @@ filter_tetracyclines(x, result = NULL, scope = "any", ...)
 \arguments{
 \item{x}{a data set}

-\item{ab_class}{an antimicrobial class, like \code{"carbapenems"}, as can be found in \code{\link[=antibiotics]{antibiotics$group}}}
+\item{ab_class}{an antimicrobial class, like \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched (case-insensitive) for this value.}

 \item{result}{an antibiotic result: S, I or R (or a combination of more of them)}

@ -60,7 +60,7 @@ filter_tetracyclines(x, result = NULL, scope = "any", ...)
 Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside, or to filter on carbapenem-resistant isolates without the need to specify the drugs.
 }
 \details{
-The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched for the input given in \code{ab_class} (case-insensitive). Next, \code{x} will be checked for column names with a value in any abbreviation, code or official name found in the \link{antibiotics} data set.
+All columns of \code{x} will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.). This means that a filter function like e.g. \code{\link[=filter_aminoglycosides]{filter_aminoglycosides()}} will include column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
 }
 \section{Stable lifecycle}{

@ -103,3 +103,6 @@ example_isolates \%>\%
  filter_fluoroquinolones("R", "all")
 }
 }
+\seealso{
+\code{\link[=antibiotic_class_selectors]{antibiotic_class_selectors()}} for the \code{select()} equivalent.
+}
--- a/tests/testthat/test-antibiotic_class_selectors.R
+++ b/tests/testthat/test-antibiotic_class_selectors.R
@ -0,0 +1,41 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://gitlab.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+#                                                                      #
+# 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 more info: https://msberends.gitlab.io/AMR.    #
+# ==================================================================== #
+
+context("ab_class_selectors.R")
+
+test_that("Antibiotic class selectors work", {
+  skip_on_cran()
+  
+  expect_lt(example_isolates %>% dplyr::select(aminoglycosides()) %>% ncol(), ncol(example_isolates))
+  expect_lt(example_isolates %>% dplyr::select(carbapenems()) %>% ncol(), ncol(example_isolates))
+  expect_lt(example_isolates %>% dplyr::select(cephalosporins()) %>% ncol(), ncol(example_isolates))
+  expect_lt(example_isolates %>% dplyr::select(cephalosporins_1st()) %>% ncol(), ncol(example_isolates))
+  expect_lt(example_isolates %>% dplyr::select(cephalosporins_2nd()) %>% ncol(), ncol(example_isolates))
+  expect_lt(example_isolates %>% dplyr::select(cephalosporins_3rd()) %>% ncol(), ncol(example_isolates))
+  expect_lt(example_isolates %>% dplyr::select(cephalosporins_4th()) %>% ncol(), ncol(example_isolates))
+  expect_lt(example_isolates %>% dplyr::select(cephalosporins_5th()) %>% ncol(), ncol(example_isolates))
+  expect_lt(example_isolates %>% dplyr::select(fluoroquinolones()) %>% ncol(), ncol(example_isolates))
+  expect_lt(example_isolates %>% dplyr::select(glycopeptides()) %>% ncol(), ncol(example_isolates))
+  expect_lt(example_isolates %>% dplyr::select(macrolides()) %>% ncol(), ncol(example_isolates))
+  expect_lt(example_isolates %>% dplyr::select(penicillins()) %>% ncol(), ncol(example_isolates))
+  expect_lt(example_isolates %>% dplyr::select(tetracyclines()) %>% ncol(), ncol(example_isolates))
+  
+})