(v1.6.0.9063) prepare new release

.github/workflows/check.yaml

@@ -141,7 +141,7 @@ jobs:
           R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
           R_RUN_TINYTEST: true
         run: |
-          R CMD check --no-manual AMR
+          R CMD check --no-manual --run-donttest --run-dontrun AMR
         shell: bash
 
       - name: Show unit tests output

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.6.0.9062
+Version: 1.6.0.9063
 Date: 2021-05-24
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# `AMR` 1.6.0.9062
+# `AMR` 1.6.0.9063
 ## <small>Last updated: 24 May 2021</small>
 
 ### Breaking change

R/ab.R

@@ -82,7 +82,7 @@
 #' # they use as.ab() internally:
 #' ab_name("J01FA01")    # "Erythromycin"
 #' ab_name("eryt")       # "Erythromycin"
-#' 
+#' \donttest{
 #' if (require("dplyr")) {
 #' 
 #'   # you can quickly rename <rsi> columns using dplyr >= 1.0.0:
@@ -90,6 +90,7 @@
 #'     rename_with(as.ab, where(is.rsi))
 #'    
 #' }
+#' }
 as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
   meet_criteria(x, allow_class = c("character", "numeric", "integer", "factor"), allow_NA = TRUE)
   meet_criteria(flag_multiple_results, allow_class = "logical", has_length = 1)

R/ab_class_selectors.R

@@ -70,7 +70,7 @@
 #' 
 #' 
 #' # dplyr -------------------------------------------------------------------
-#' 
+#' \donttest{
 #' if (require("dplyr")) {
 #' 
 #'   # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
@@ -119,6 +119,7 @@
 #'   example_isolates %>% filter(carbapenems() == "R")
 #'   example_isolates %>% filter(across(carbapenems(), ~.x == "R"))
 #' }
+#' }
 ab_class <- function(ab_class, 
                      only_rsi_columns = FALSE) {
   ab_selector(ab_class, function_name = "ab_class", only_rsi_columns = only_rsi_columns)

R/age.R

@@ -88,13 +88,13 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
     # add decimal parts of year
     mod <- n_days_x_rest / n_days_reference_year
     # negative mods are cases where `x_in_reference_year` > `reference` - so 'add' a year
-    mod[mod < 0] <- mod[mod < 0] + 1
+    mod[!is.na(mod) & mod < 0] <- mod[!is.na(mod) & mod < 0] + 1
     # and finally add to ages
     ages <- ages + mod
   }
   
   if (any(ages < 0, na.rm = TRUE)) {
-    ages[ages < 0] <- NA
+    ages[!is.na(ages) & ages < 0] <- NA
     warning_("NAs introduced for ages below 0.", call = TRUE)
   }
   if (any(ages > 120, na.rm = TRUE)) {

R/atc_online.R

@@ -64,7 +64,7 @@
 #' @inheritSection AMR Read more on Our Website!
 #' @source <https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/>
 #' @examples
-#' \donttest{
+#' \dontrun{
 #' # oral DDD (Defined Daily Dose) of amoxicillin
 #' atc_online_property("J01CA04", "DDD", "O")
 #' 

R/availability.R

@@ -35,13 +35,14 @@
 #' @export
 #' @examples
 #' availability(example_isolates)
-#'
+#' \donttest{
 #' if (require("dplyr")) {
 #'   example_isolates %>%
 #'     filter(mo == as.mo("E. coli")) %>%
 #'     select_if(is.rsi) %>%
 #'     availability()
 #' }
+#' }
 availability <- function(tbl, width = NULL) {
   meet_criteria(tbl, allow_class = "data.frame")
   meet_criteria(width, allow_class = c("numeric", "integer"), has_length = 1, allow_NULL = TRUE, is_positive = TRUE, is_finite = TRUE)

R/count.R

@@ -72,7 +72,7 @@
 #' count_susceptible(example_isolates$AMX)
 #' susceptibility(example_isolates$AMX) * n_rsi(example_isolates$AMX)
 #'
-#' 
+#' \donttest{
 #' if (require("dplyr")) {
 #'   example_isolates %>%
 #'     group_by(hospital_id) %>%
@@ -106,6 +106,7 @@
 #'     group_by(hospital_id) %>%
 #'     count_df(translate = FALSE)
 #' }
+#' }
 count_resistant <- function(..., only_all_tested = FALSE) {
   rsi_calc(...,
            ab_result = "R",

R/data.R

@@ -269,12 +269,14 @@
 #' @inheritSection AMR Reference Data Publicly Available
 #' @inheritSection AMR Read more on Our Website!
 #' @examples
+#' \donttest{
 #' if (require("dplyr")) {
 #'   intrinsic_resistant %>%
 #'     filter(antibiotic == "Vancomycin", microorganism %like% "Enterococcus") %>% 
 #'     pull(microorganism)
 #'   # [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
 #' }
+#' }
 "intrinsic_resistant"
 
 #' Data Set with Treatment Dosages as Defined by EUCAST

R/ggplot_pca.R

@@ -65,6 +65,7 @@
 #' # See ?example_isolates.
 #'
 #' # See ?pca for more info about Principal Component Analysis (PCA).
+#' \donttest{
 #' if (require("dplyr")) {
 #'   pca_model <- example_isolates %>% 
 #'     filter(mo_genus(mo) == "Staphylococcus") %>% 
@@ -84,6 +85,7 @@
 #'       labs(title = "Title here")
 #'   }
 #' }
+#' }
 ggplot_pca <- function(x,
                        choices = 1:2,
                        scale = 1,

R/ggplot_rsi.R

@@ -67,6 +67,7 @@
 #' @export
 #' @inheritSection AMR Read more on Our Website!
 #' @examples
+#' \donttest{
 #' if (require("ggplot2") & require("dplyr")) {
 #'  
 #'   # get antimicrobial results for drugs against a UTI:
@@ -116,7 +117,6 @@
 #'     scale_rsi_colours(Value4 = "S", Value5 = "I", Value6 = "R")
 #' }
 #'   
-#' \donttest{
 #' # resistance of ciprofloxacine per age group
 #' example_isolates %>%
 #'   mutate(first_isolate = first_isolate(.)) %>%

R/italicise_taxonomy.R

@@ -45,12 +45,13 @@
 #' 
 #' # since ggplot2 supports no markdown (yet), use
 #' # italicise_taxonomy() and the `ggtext` pkg for titles:
-#' 
+#' \donttest{
 #' if (require("ggplot2") && require("ggtext")) {
 #'   ggplot(example_isolates$AMC,
 #'          title = italicise_taxonomy("Amoxi/clav in E. coli")) +
 #'     theme(plot.title = ggtext::element_markdown())
 #' }
+#' }
 italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
   if (missing(type)) {
     type <- "markdown"

R/mo_property.R

@@ -152,6 +152,7 @@
 #' mo_is_yeast(c("Candida", "E. coli"))      # TRUE, FALSE
 #' 
 #' # gram stains and intrinsic resistance can also be used as a filter in dplyr verbs
+#' \donttest{
 #' if (require("dplyr")) {
 #'   example_isolates %>%
 #'     filter(mo_is_gram_positive())
@@ -167,6 +168,7 @@
 #' #   SNOMED codes, and URL to the online database
 #' mo_info("E. coli")
 #' }
+#' }
 mo_name <- function(x, language = get_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column

R/pca.R

@@ -42,7 +42,6 @@
 #' # See ?example_isolates.
 #'
 #' \donttest{
-#' 
 #' if (require("dplyr")) {
 #'   # calculate the resistance per group first 
 #'   resistance_data <- example_isolates %>% 

R/plot.R

@@ -61,11 +61,13 @@
 #' plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")
 #' plot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
 #' 
+#' \donttest{
 #' if (require("ggplot2")) {
 #'   ggplot(some_mic_values)
 #'   ggplot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
 #'   ggplot(some_rsi_values)
 #' }
+#' }
 NULL
 
 #' @method plot mic

R/proportion.R

@@ -103,6 +103,7 @@
 #' proportion_IR(example_isolates$AMX)
 #' proportion_R(example_isolates$AMX)
 #'
+#' \donttest{
 #' if (require("dplyr")) {
 #'   example_isolates %>%
 #'     group_by(hospital_id) %>%
@@ -161,6 +162,7 @@
 #'     group_by(hospital_id) %>%
 #'     proportion_df(translate = FALSE)
 #' }
+#' }
 resistance <- function(...,
                        minimum = 30,
                        as_percent = FALSE,

R/resistance_predict.R

@@ -70,6 +70,7 @@
 #'                         year_min = 2010,
 #'                         model = "binomial")
 #' plot(x)
+#' \donttest{
 #' if (require("ggplot2")) {
 #'   ggplot_rsi_predict(x)
 #' }
@@ -114,6 +115,7 @@
 #'          x = "Year") +
 #'     theme_minimal(base_size = 13)
 #' }
+#' }
 resistance_predict <- function(x,
                                col_ab,
                                col_date = NULL,

R/rsi.R

@@ -101,12 +101,12 @@
 #' @inheritSection AMR Read more on Our Website!
 #' @examples
 #' summary(example_isolates) # see all R/SI results at a glance
-#' 
+#' \donttest{
 #' if (require("skimr")) {
 #'   # class <rsi> supported in skim() too:
 #'   skim(example_isolates)
 #' }
-#' 
+#' }
 #' # For INTERPRETING disk diffusion and MIC values -----------------------
 #'        
 #' # a whole data set, even with combined MIC values and disk zones

cran-comments.md

@@ -1 +1,3 @@
+* This package has been archived on 22 May 2021 because of errors in the dplyr package, causing the skimr package to fail: <https://github.com/tidyverse/dplyr/issues/5881>. This AMR package contains a fix around this error. Nonetheless, an automated email sent to the maintainer with a warning that the AMR package would be archived would have saved us this archiving. Perhaps an idea for future development of CRAN?
+
 * This package has a tarball size of over 7 MB and an installation size of over 5 MB, which will return a NOTE on R CMD CHECK. The package size is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package. This was written and explained in a manuscript that was accepted for publication in the Journal of Statistical Software 4 weeks ago. We will add the paper as a vignette in the next version. Please allow this exception in package size for CRAN. We already compressed all data sets using `compression = "xz"` to make them as small as possible.

data-raw/_install_deps.R

@@ -24,7 +24,7 @@
 # ==================================================================== #
 
 # some old R instances have trouble installing tinytest, so we ship it too
-install.packages("data-raw/tinytest_1.2.4.patched.tar.gz")
+install.packages("data-raw/tinytest_1.2.4.10.tar.gz")
 install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
 
 pkg_suggests <- gsub("[^a-zA-Z0-9]+", "", unlist(strsplit(packageDescription("AMR", fields = "Suggests"), ", ?")))

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">1.6.0.9062</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9063</span>
       </span>
     </div>
 

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">1.6.0.9062</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9063</span>
       </span>
     </div>
 

docs/articles/datasets.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">1.6.0.9062</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9063</span>
       </span>
     </div>
 

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">1.6.0.9062</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9063</span>
       </span>
     </div>
 

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">1.6.0.9062</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9063</span>
       </span>
     </div>
 

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">1.6.0.9062</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9063</span>
       </span>
     </div>
 

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">1.6.0.9062</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9063</span>
       </span>
     </div>
 
@@ -236,9 +236,9 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1609062" class="section level1">
-<h1 class="page-header" data-toc-text="1.6.0.9062">
-<a href="#amr-1609062" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9062</h1>
+    <div id="amr-1609063" class="section level1">
+<h1 class="page-header" data-toc-text="1.6.0.9063">
+<a href="#amr-1609063" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9063</h1>
 <div id="last-updated-24-may-2021" class="section level2">
 <h2 class="hasAnchor">
 <a href="#last-updated-24-may-2021" class="anchor"></a><small>Last updated: 24 May 2021</small>
@@ -288,7 +288,7 @@
 </ul>
 </li>
 <li>Function <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code> as additional antbiotic column selector and function <code><a href="../reference/AMR-deprecated.html">filter_betalactams()</a></code> as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.</li>
-<li>A <code>ggplot()</code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
+<li>A <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
 </li>
 </ul>
 </div>
@@ -387,7 +387,7 @@
 <span class="co">#&gt; Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
 </li>
 <li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
-<li><p><code>ggplot()</code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
+<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
 <li>
 <p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
@@ -444,7 +444,7 @@
 <li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
 <li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
 <li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
-<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
+<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
 </ul>
 </li>
 <li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>
@@ -461,7 +461,7 @@
 <code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> now detects if the column name resembles an antibiotic name or code and now returns <code>TRUE</code> immediately if the input contains any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.</li>
 <li>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> now support less than a day as value for argument <code>episode_days</code> (e.g., to include one patient/test per hour)</li>
 <li>Argument <code>ampc_cephalosporin_resistance</code> in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> now also applies to value “I” (not only “S”)</li>
-<li>Functions <code><a href="https://rdrr.io/r/base/print.html">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code>
+<li>Functions <code><a href="https://docs.ropensci.org/skimr/reference/print.html">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code>
 </li>
 <li>Improved speed and reliability of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>. As this also internally improves the reliability of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>, this might have a slight impact on the results of those functions.</li>
 <li>Fix for <code><a href="../reference/mo_property.html">mo_name()</a></code> when used in other languages than English</li>

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: 2021-05-23T22:05Z
+last_built: 2021-05-24T06:56Z
 urls:
   reference: https://msberends.github.io/AMR//reference
   article: https://msberends.github.io/AMR//articles

docs/reference/antibiotic_class_selectors.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">1.6.0.9062</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9063</span>
       </span>
     </div>
 
@@ -342,7 +342,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
 
 <span class='co'># dplyr -------------------------------------------------------------------</span>
-
+<span class='co'># \donttest{</span>
 <span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
 
   <span class='co'># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</span>
@@ -391,6 +391,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
   <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span>
   <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span>, <span class='op'>~</span><span class='va'>.x</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span><span class='op'>)</span>
 <span class='op'>}</span>
+<span class='co'># }</span>
 </pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

docs/reference/as.ab.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9063</span>
       </span>
     </div>
 
@@ -347,7 +347,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
 <span class='co'># they use as.ab() internally:</span>
 <span class='fu'><a href='ab_property.html'>ab_name</a></span><span class='op'>(</span><span class='st'>"J01FA01"</span><span class='op'>)</span>    <span class='co'># "Erythromycin"</span>
 <span class='fu'><a href='ab_property.html'>ab_name</a></span><span class='op'>(</span><span class='st'>"eryt"</span><span class='op'>)</span>       <span class='co'># "Erythromycin"</span>
-
+<span class='co'># \donttest{</span>
 <span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
 
   <span class='co'># you can quickly rename &lt;rsi&gt; columns using dplyr &gt;= 1.0.0:</span>
@@ -355,6 +355,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
     <span class='fu'><a href='https://dplyr.tidyverse.org/reference/rename.html'>rename_with</a></span><span class='op'>(</span><span class='va'>as.ab</span>, <span class='fu'>where</span><span class='op'>(</span><span class='va'>is.rsi</span><span class='op'>)</span><span class='op'>)</span>
    
 <span class='op'>}</span>
+<span class='co'># }</span>
 </pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

docs/reference/as.rsi.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">1.6.0.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9063</span>
       </span>
     </div>
 
@@ -419,12 +419,12 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span> <span class='co'># see all R/SI results at a glance</span>
-
+<span class='co'># \donttest{</span>
 <span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://docs.ropensci.org/skimr/'>"skimr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
   <span class='co'># class &lt;rsi&gt; supported in skim() too:</span>
   <span class='fu'><a href='https://docs.ropensci.org/skimr/reference/skim.html'>skim</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>
 <span class='op'>}</span>
-
+<span class='co'># }</span>
 <span class='co'># For INTERPRETING disk diffusion and MIC values -----------------------</span>
        
 <span class='co'># a whole data set, even with combined MIC values and disk zones</span>

docs/reference/atc_online.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">1.6.0.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9063</span>
       </span>
     </div>
 
@@ -327,7 +327,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 <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='co'># \donttest{</span>
+    <pre class="examples"><span class='kw'>if</span> <span class='op'>(</span><span class='cn'>FALSE</span><span class='op'>)</span> <span class='op'>{</span>
 <span class='co'># oral DDD (Defined Daily Dose) of amoxicillin</span>
 <span class='fu'>atc_online_property</span><span class='op'>(</span><span class='st'>"J01CA04"</span>, <span class='st'>"DDD"</span>, <span class='st'>"O"</span><span class='op'>)</span>
 
@@ -335,7 +335,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 <span class='fu'>atc_online_property</span><span class='op'>(</span><span class='st'>"J01CA04"</span>, <span class='st'>"DDD"</span>, <span class='st'>"P"</span><span class='op'>)</span>
 
 <span class='fu'>atc_online_property</span><span class='op'>(</span><span class='st'>"J01CA04"</span>, property <span class='op'>=</span> <span class='st'>"groups"</span><span class='op'>)</span> <span class='co'># search hierarchical groups of amoxicillin</span>
-<span class='co'># }</span>
+<span class='op'>}</span>
 </pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

docs/reference/availability.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">1.6.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9063</span>
       </span>
     </div>
 
@@ -90,14 +90,14 @@
       <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
      
@@ -106,77 +106,77 @@
   <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>
@@ -185,21 +185,21 @@
 </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>
@@ -208,14 +208,14 @@
       <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>
@@ -278,13 +278,14 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='fu'>availability</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>
-
+<span class='co'># \donttest{</span>
 <span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
   <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
     <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>mo</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
     <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select_all.html'>select_if</a></span><span class='op'>(</span><span class='va'>is.rsi</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
     <span class='fu'>availability</span><span class='op'>(</span><span class='op'>)</span>
 <span class='op'>}</span>
+<span class='co'># }</span>
 </pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

docs/reference/count.html

@@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9063</span>
       </span>
     </div>
 
@@ -399,7 +399,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
 <span class='fu'>count_susceptible</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
 <span class='fu'><a href='proportion.html'>susceptibility</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span> <span class='op'>*</span> <span class='fu'>n_rsi</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
 
-
+<span class='co'># \donttest{</span>
 <span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
   <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
     <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
@@ -433,6 +433,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
     <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
     <span class='fu'>count_df</span><span class='op'>(</span>translate <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
 <span class='op'>}</span>
+<span class='co'># }</span>
 </pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

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">1.6.0.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9063</span>
       </span>
     </div>
 
@@ -397,6 +397,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 <span class='co'># See ?example_isolates.</span>
 
 <span class='co'># See ?pca for more info about Principal Component Analysis (PCA).</span>
+<span class='co'># \donttest{</span>
 <span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
   <span class='va'>pca_model</span> <span class='op'>&lt;-</span> <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span> 
     <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='mo_property.html'>mo_genus</a></span><span class='op'>(</span><span class='va'>mo</span><span class='op'>)</span> <span class='op'>==</span> <span class='st'>"Staphylococcus"</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
@@ -416,6 +417,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
       <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span><span class='op'>(</span>title <span class='op'>=</span> <span class='st'>"Title here"</span><span class='op'>)</span>
   <span class='op'>}</span>
 <span class='op'>}</span>
+<span class='co'># }</span>
 </pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

docs/reference/ggplot_rsi.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">1.6.0.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9063</span>
       </span>
     </div>
 
@@ -429,7 +429,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 <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='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://ggplot2.tidyverse.org'>"ggplot2"</a></span><span class='op'>)</span> <span class='op'>&amp;</span> <span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
+    <pre class="examples"><span class='co'># \donttest{</span>
+<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://ggplot2.tidyverse.org'>"ggplot2"</a></span><span class='op'>)</span> <span class='op'>&amp;</span> <span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
  
   <span class='co'># get antimicrobial results for drugs against a UTI:</span>
   <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>+</span>
@@ -478,7 +479,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
     <span class='fu'>scale_rsi_colours</span><span class='op'>(</span>Value4 <span class='op'>=</span> <span class='st'>"S"</span>, Value5 <span class='op'>=</span> <span class='st'>"I"</span>, Value6 <span class='op'>=</span> <span class='st'>"R"</span><span class='op'>)</span>
 <span class='op'>}</span>
   
-<span class='co'># \donttest{</span>
 <span class='co'># resistance of ciprofloxacine per age group</span>
 <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
   <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>first_isolate <span class='op'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span><span class='op'>(</span><span class='va'>.</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>

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">1.6.0.9062</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9063</span>
       </span>
     </div>
 

docs/reference/intrinsic_resistant.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">1.6.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9063</span>
       </span>
     </div>
 
@@ -90,14 +90,14 @@
       <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
      
@@ -106,77 +106,77 @@
   <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>
@@ -185,21 +185,21 @@
 </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>