(v1.8.0.9005) as.rsi() fix

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.0.9004
+Version: 1.8.0.9005
-Date: 2022-03-03
+Date: 2022-03-10
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
     data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,9 +1,10 @@
-# `AMR` 1.8.0.9004
+# `AMR` 1.8.0.9005
-## <small>Last updated:  3 March 2022</small>
+## <small>Last updated: 10 March 2022</small>
 
 All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.
 
 ### Changed
+* Fix for using `as.rsi()` on values containing capped values (such as `>=`), sometimes leading to `NA`
 * Support for antibiotic interpretations of the MIPS laboratory system: `"U"` for S ('susceptible urine'), `"D"` for I ('susceptible dose-dependent')
 * Improved algorithm of `as.mo()`, especially for ignoring non-taxonomic text, such as:
   ```r

R/lifecycle.R

@@ -44,7 +44,7 @@
 #' \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 #' The [lifecycle][AMR::lifecycle] of this function is **stable**. 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.
 #' 
-#' If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+#' If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 #' @section Retired Lifecycle:
 #' \if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:"5"} \cr}
 #' The [lifecycle][AMR::lifecycle] of this function is **retired**. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.

R/mic.R

@@ -243,14 +243,12 @@ droplevels.mic <- function(x, exclude = if (any(is.na(levels(x)))) NULL else NA,
 pillar_shaft.mic <- function(x, ...) {
   crude_numbers <- as.double(x)
   operators <- gsub("[^<=>]+", "", as.character(x))
-  pasted <- trimws(paste0(operators, trimws(format(crude_numbers))))
+  operators[operators != ""] <- font_silver(operators[operators != ""], collapse = NULL)
-  out <- pasted
+  out <- trimws(paste0(operators, trimws(format(crude_numbers))))
   out[is.na(x)] <- font_na(NA)
-  out <- gsub("(<|=|>)", font_silver("\\1"), out)
+  # maketrailing zeroes almost invisible
-  if (any(out %like% "[.]", na.rm = TRUE)) {
+  out[out %like% "[.]"] <- gsub("([.]?0+)$", font_white("\\1"), out[out %like% "[.]"], perl = TRUE)
-    out <- gsub("([.]?0+)$", font_white("\\1"), out)
+  create_pillar_column(out, align = "right", width = max(nchar(font_stripstyle(out))))
-  }
-  create_pillar_column(out, align = "right", width = max(nchar(pasted)))
 }
 
 # will be exported using s3_register() in R/zzz.R

R/rsi.R

@@ -690,7 +690,6 @@ as_rsi_method <- function(method_short = "mic",
            "... ",
            appendLF = FALSE,
            as_note = FALSE)
-  
   result <- exec_as.rsi(method = method_short,
                         x = x,
                         mo = mo_coerced,
@@ -715,7 +714,7 @@ exec_as.rsi <- function(method,
   metadata_mo <- get_mo_failures_uncertainties_renamed()
   
   x_bak <- data.frame(x_mo = paste0(x, mo), stringsAsFactors = FALSE)
-  df <- unique(data.frame(x, mo), stringsAsFactors = FALSE)
+  df <- unique(data.frame(x, mo, x_mo = paste0(x, mo), stringsAsFactors = FALSE))
   x <- df$x
   mo <- df$mo
   
@@ -848,7 +847,7 @@ exec_as.rsi <- function(method,
   }
   
   new_rsi <- x_bak %pm>%
-    pm_left_join(data.frame(x_mo = paste0(df$x, df$mo), new_rsi,
+    pm_left_join(data.frame(x_mo = paste0(x, mo), new_rsi,
                             stringsAsFactors = FALSE),
                  by = "x_mo") %pm>%
     pm_pull(new_rsi)
@@ -907,13 +906,13 @@ freq.rsi <- function(x, ...) {
                           .add_header = list(
                             Drug = paste0(ab_name(ab, language = NULL), " (", ab, ", ", paste(ab_atc(ab), collapse = "/"), ")"),
                             `Drug group` = ab_group(ab, language = NULL),
-                            `%SI` = percentage(susceptibility(x, minimum = 0, as_percent = FALSE),
+                            `%SI` = trimws(percentage(susceptibility(x, minimum = 0, as_percent = FALSE),
-                                               digits = digits)))
+                                                      digits = digits))))
   } else {
     cleaner::freq.default(x = x, ...,
                           .add_header = list(
-                            `%SI` = percentage(susceptibility(x, minimum = 0, as_percent = FALSE),
+                            `%SI` = trimws(percentage(susceptibility(x, minimum = 0, as_percent = FALSE),
-                                               digits = digits)))
+                                                      digits = digits))))
   }
 }
 

docs/404.html

@@ -43,7 +43,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -205,12 +205,14 @@ Content not found. Please use links in the navbar.
 
       <footer><div class="copyright">
   <p></p>
-<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer>

docs/LICENSE-text.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -416,11 +416,13 @@ END OF TERMS AND CONDITIONS
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/articles/datasets.html

@@ -44,7 +44,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -190,7 +190,7 @@
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Data sets for download / own use</h1>
             
-            <h4 data-toc-skip class="date">03 March 2022</h4>
+            <h4 data-toc-skip class="date">10 March 2022</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
       <div class="hidden name"><code>datasets.Rmd</code></div>
@@ -199,42 +199,71 @@
 
     
     
-<p>All reference data (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are reliable, up-to-date and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply tab separated files that are machine-readable and suitable for input in any software program, such as laboratory information systems.</p>
+<p>All reference data (about microorganisms, antibiotics, R/SI
-<p>On this page, we explain how to download them and how the structure of the data sets look like.</p>
+interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are
+reliable, up-to-date and freely available. We continually export our
+data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also
+supply tab separated files that are machine-readable and suitable for
+input in any software program, such as laboratory information
+systems.</p>
+<p>On this page, we explain how to download them and how the structure
+of the data sets look like.</p>
 <p class="dataset-within-r">
-If you are reading this page from within R, please <a href="https://msberends.github.io/AMR/articles/datasets.html">visit our website</a>, which is automatically updated with every code change.
+If you are reading this page from within R, please
+<a href="https://msberends.github.io/AMR/articles/datasets.html">visit
+our website</a>, which is automatically updated with every code change.
 </p>
 <div class="section level2">
 <h2 id="microorganisms-currently-accepted-names">Microorganisms (currently accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-currently-accepted-names"></a>
 </h2>
-<p>A data set with 70,760 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
+<p>A data set with 70,760 rows and 16 columns, containing the following
-<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
+column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>,
-<p>It was last updated on 29 November 2021 11:38:23 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
+<em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>,
+<em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>,
+<em>species_id</em>, <em>source</em>, <em>prevalence</em> and
+<em>snomed</em>.</p>
+<p>This data set is in R available as <code>microorganisms</code>, after
+you load the <code>AMR</code> package.</p>
+<p>It was last updated on 29 November 2021 11:38:23 UTC. Find more info
+about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">R file</a> (1.3 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">R
+file</a> (1.3 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Excel file</a> (6.4 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Excel
+file</a> (6.4 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">plain text file</a> (13.1 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">plain
+text file</a> (13.1 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS file</a> (30.7 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS
+file</a> (30.7 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">SPSS file</a> (16.3 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">SPSS
+file</a> (16.3 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata file</a> (27.5 MB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata
+file</a> (27.5 MB)</li>
 </ul>
-<p><strong>NOTE: The exported files for SAS, SPSS and Stata do not contain SNOMED codes, as their file size would exceed 100 MB; the file size limit of GitHub.</strong> Advice? Use R instead.</p>
+<p><strong>NOTE: The exported files for SAS, SPSS and Stata do not
+contain SNOMED codes, as their file size would exceed 100 MB; the file
+size limit of GitHub.</strong> Advice? Use R instead.</p>
 <div class="section level3">
 <h3 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a>
 </h3>
-<p>Our full taxonomy of microorganisms is based on the authoritative and comprehensive:</p>
+<p>Our full taxonomy of microorganisms is based on the authoritative and
+comprehensive:</p>
 <ul>
 <li>
-<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (included version: 2019)</li>
+<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a>
+(included version: 2019)</li>
 <li>
-<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
+<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with
-<li>US Edition of SNOMED CT from 1 September 2020, retrieved from the <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)</a>, OID 2.16.840.1.114222.4.11.1009, version 12</li>
+Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
+<li>US Edition of SNOMED CT from 1 September 2020, retrieved from the <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">Public
+Health Information Network Vocabulary Access and Distribution System
+(PHIN VADS)</a>, OID 2.16.840.1.114222.4.11.1009, version 12</li>
 </ul>
 </div>
 <div class="section level3">
@@ -427,40 +456,64 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <div class="section level2">
 <h2 id="microorganisms-previously-accepted-names">Microorganisms (previously accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-previously-accepted-names"></a>
 </h2>
-<p>A data set with 14,338 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>prevalence</em>.</p>
+<p>A data set with 14,338 rows and 4 columns, containing the following
-<p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
+column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and
-<p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
+<em>prevalence</em>.</p>
-<p>It was last updated on 6 October 2021 14:38:29 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
+<p><strong>Note:</strong> remember that the ‘ref’ columns contains the
+scientific reference to the old taxonomic entries, i.e. of column
+<em>‘fullname’</em>. For the scientific reference of the new names,
+i.e. of column <em>‘fullname_new’</em>, see the
+<code>microorganisms</code> data set.</p>
+<p>This data set is in R available as <code>microorganisms.old</code>,
+after you load the <code>AMR</code> package.</p>
+<p>It was last updated on 6 October 2021 14:38:29 UTC. Find more info
+about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">R file</a> (0.2 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">R
+file</a> (0.2 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.xlsx" class="external-link">Excel file</a> (0.5 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.xlsx" class="external-link">Excel
+file</a> (0.5 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.txt" class="external-link">plain text file</a> (1 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.txt" class="external-link">plain
+text file</a> (1 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sas" class="external-link">SAS file</a> (2.1 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sas" class="external-link">SAS
+file</a> (2.1 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sav" class="external-link">SPSS file</a> (1.3 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sav" class="external-link">SPSS
+file</a> (1.3 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.dta" class="external-link">Stata file</a> (2 MB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.dta" class="external-link">Stata
+file</a> (2 MB)</li>
 </ul>
 <div class="section level3">
 <h3 id="source-1">Source<a class="anchor" aria-label="anchor" href="#source-1"></a>
 </h3>
-<p>This data set contains old, previously accepted taxonomic names. The data sources are the same as the <code>microorganisms</code> data set:</p>
+<p>This data set contains old, previously accepted taxonomic names. The
+data sources are the same as the <code>microorganisms</code> data
+set:</p>
 <ul>
 <li>
-<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (included version: 2019)</li>
+<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a>
+(included version: 2019)</li>
 <li>
-<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
+<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with
+Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
 </ul>
 </div>
 <div class="section level3">
 <h3 id="example-content-1">Example content<a class="anchor" aria-label="anchor" href="#example-content-1"></a>
 </h3>
 <p>Example rows when filtering on <em>Escherichia</em>:</p>
-<table class="table">
+<table style="width:100%;" class="table">
+<colgroup>
+<col width="31%">
+<col width="30%">
+<col width="24%">
+<col width="13%">
+</colgroup>
 <thead><tr class="header">
 <th align="center">fullname</th>
 <th align="center">fullname_new</th>
@@ -493,31 +546,50 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <div class="section level2">
 <h2 id="antibiotic-agents">Antibiotic agents<a class="anchor" aria-label="anchor" href="#antibiotic-agents"></a>
 </h2>
-<p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
+<p>A data set with 464 rows and 14 columns, containing the following
-<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
+column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>,
-<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
+<em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>,
+<em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>,
+<em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
+<p>This data set is in R available as <code>antibiotics</code>, after
+you load the <code>AMR</code> package.</p>
+<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info
+about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">R file</a> (33 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">R
+file</a> (33 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Excel file</a> (65 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Excel
+file</a> (65 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">plain text file</a> (0.1 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">plain
+text file</a> (0.1 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas" class="external-link">SAS file</a> (1.8 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas" class="external-link">SAS
+file</a> (1.8 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">SPSS file</a> (0.3 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">SPSS
+file</a> (0.3 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata file</a> (0.3 MB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata
+file</a> (0.3 MB)</li>
 </ul>
 <div class="section level3">
 <h3 id="source-2">Source<a class="anchor" aria-label="anchor" href="#source-2"></a>
 </h3>
-<p>This data set contains all EARS-Net and ATC codes gathered from WHO and WHONET, and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
+<p>This data set contains all EARS-Net and ATC codes gathered from WHO
+and WHONET, and all compound IDs from PubChem. It also contains all
+brand names (synonyms) as found on PubChem and Defined Daily Doses
+(DDDs) for oral and parenteral administration.</p>
 <ul>
 <li>
-<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)</li>
+<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO
-<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US National Library of Medicine</a></li>
+Collaborating Centre for Drug Statistics Methodology</a> (note: this may
+not be used for commercial purposes, but is freely available from the
+WHO CC website for personal use)</li>
+<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US
+National Library of Medicine</a></li>
 <li><a href="https://whonet.org" class="external-link">WHONET software 2019</a></li>
 </ul>
 </div>
@@ -597,7 +669,8 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <td align="center">Beta-lactams/penicillins</td>
 <td align="center">J01CR02</td>
 <td align="center">Beta-lactam antibacterials, penicillins</td>
-<td align="center">Combinations of penicillins, incl. beta-lactamase inhibitors</td>
+<td align="center">Combinations of penicillins, incl. beta-lactamase
+inhibitors</td>
 <td align="center">a/c, amcl, aml, …</td>
 <td align="center">amocla, amoclan, amoclav, …</td>
 <td align="center">1.5</td>
@@ -661,31 +734,49 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <div class="section level2">
 <h2 id="antiviral-agents">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents"></a>
 </h2>
-<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
+<p>A data set with 102 rows and 9 columns, containing the following
-<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
+column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>,
-<p>It was last updated on 29 August 2020 19:53:07 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
+<em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>,
+<em>iv_ddd</em> and <em>iv_units</em>.</p>
+<p>This data set is in R available as <code>antivirals</code>, after you
+load the <code>AMR</code> package.</p>
+<p>It was last updated on 29 August 2020 19:53:07 UTC. Find more info
+about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">R file</a> (5 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">R
+file</a> (5 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class="external-link">Excel file</a> (14 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class="external-link">Excel
+file</a> (14 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt" class="external-link">plain text file</a> (16 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt" class="external-link">plain
+text file</a> (16 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas" class="external-link">SAS file</a> (80 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas" class="external-link">SAS
+file</a> (80 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">SPSS file</a> (68 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">SPSS
+file</a> (68 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata file</a> (67 kB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata
+file</a> (67 kB)</li>
 </ul>
 <div class="section level3">
 <h3 id="source-3">Source<a class="anchor" aria-label="anchor" href="#source-3"></a>
 </h3>
-<p>This data set contains all ATC codes gathered from WHO and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
+<p>This data set contains all ATC codes gathered from WHO and all
+compound IDs from PubChem. It also contains all brand names (synonyms)
+as found on PubChem and Defined Daily Doses (DDDs) for oral and
+parenteral administration.</p>
 <ul>
 <li>
-<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)</li>
+<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO
-<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US National Library of Medicine</a></li>
+Collaborating Centre for Drug Statistics Methodology</a> (note: this may
+not be used for commercial purposes, but is freely available from the
+WHO CC website for personal use)</li>
+<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US
+National Library of Medicine</a></li>
 </ul>
 </div>
 <div class="section level3">
@@ -719,7 +810,8 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <td align="center">J05AF06</td>
 <td align="center">441300</td>
 <td align="center">Abacavir</td>
-<td align="center">Nucleoside and nucleotide reverse transcriptase inhibitors</td>
+<td align="center">Nucleoside and nucleotide reverse transcriptase
+inhibitors</td>
 <td align="center">Abacavir, Abacavir sulfate, Ziagen</td>
 <td align="center">0.6</td>
 <td align="center">g</td>
@@ -730,7 +822,8 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <td align="center">J05AB01</td>
 <td align="center">135398513</td>
 <td align="center">Aciclovir</td>
-<td align="center">Nucleosides and nucleotides excl. reverse transcriptase inhibitors</td>
+<td align="center">Nucleosides and nucleotides excl. reverse
+transcriptase inhibitors</td>
 <td align="center">Acicloftal, Aciclovier, Aciclovir, …</td>
 <td align="center">4.0</td>
 <td align="center">g</td>
@@ -741,8 +834,10 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <td align="center">J05AF08</td>
 <td align="center">60871</td>
 <td align="center">Adefovir dipivoxil</td>
-<td align="center">Nucleoside and nucleotide reverse transcriptase inhibitors</td>
+<td align="center">Nucleoside and nucleotide reverse transcriptase
-<td align="center">Adefovir di ester, Adefovir dipivoxil, Adefovir Dipivoxil, …</td>
+inhibitors</td>
+<td align="center">Adefovir di ester, Adefovir dipivoxil, Adefovir
+Dipivoxil, …</td>
 <td align="center">10.0</td>
 <td align="center">mg</td>
 <td align="center"></td>
@@ -788,27 +883,39 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <div class="section level2">
 <h2 id="intrinsic-bacterial-resistance">Intrinsic bacterial resistance<a class="anchor" aria-label="anchor" href="#intrinsic-bacterial-resistance"></a>
 </h2>
-<p>A data set with 134,956 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
+<p>A data set with 134,956 rows and 2 columns, containing the following
-<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
+column names:<br><em>mo</em> and <em>ab</em>.</p>
-<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
+<p>This data set is in R available as <code>intrinsic_resistant</code>,
+after you load the <code>AMR</code> package.</p>
+<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info
+about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">R file</a> (78 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">R
+file</a> (78 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Excel file</a> (0.9 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Excel
+file</a> (0.9 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">plain text file</a> (5.1 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">plain
+text file</a> (5.1 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS file</a> (10.4 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS
+file</a> (10.4 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">SPSS file</a> (7.4 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">SPSS
+file</a> (7.4 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata file</a> (10.2 MB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata
+file</a> (10.2 MB)</li>
 </ul>
 <div class="section level3">
 <h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
 </h3>
-<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">‘EUCAST Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ v3.3</a> (2021).</p>
+<p>This data set contains all defined intrinsic resistance by EUCAST of
+all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">‘EUCAST
+Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’
+v3.3</a> (2021).</p>
 </div>
 <div class="section level3">
 <h3 id="example-content-4">Example content<a class="anchor" aria-label="anchor" href="#example-content-4"></a>
@@ -1055,27 +1162,40 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <div class="section level2">
 <h2 id="interpretation-from-mic-values-disk-diameters-to-rsi">Interpretation from MIC values / disk diameters to R/SI<a class="anchor" aria-label="anchor" href="#interpretation-from-mic-values-disk-diameters-to-rsi"></a>
 </h2>
-<p>A data set with 20,318 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
+<p>A data set with 20,318 rows and 11 columns, containing the following
-<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
+column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>,
-<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
+<em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>,
+<em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
+<p>This data set is in R available as <code>rsi_translation</code>,
+after you load the <code>AMR</code> package.</p>
+<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info
+about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R file</a> (39 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R
+file</a> (39 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Excel file</a> (0.7 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Excel
+file</a> (0.7 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain text file</a> (1.7 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain
+text file</a> (1.7 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS file</a> (3.6 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS
+file</a> (3.6 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS file</a> (2.2 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS
+file</a> (2.2 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata file</a> (3.4 MB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata
+file</a> (3.4 MB)</li>
 </ul>
 <div class="section level3">
 <h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></a>
 </h3>
-<p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST (2011-2021).</p>
+<p>This data set contains interpretation rules for MIC values and disk
+diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
+(2011-2021).</p>
 </div>
 <div class="section level3">
 <h3 id="example-content-5">Example content<a class="anchor" aria-label="anchor" href="#example-content-5"></a>
@@ -1193,33 +1313,57 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <div class="section level2">
 <h2 id="dosage-guidelines-from-eucast">Dosage guidelines from EUCAST<a class="anchor" aria-label="anchor" href="#dosage-guidelines-from-eucast"></a>
 </h2>
-<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
+<p>A data set with 169 rows and 9 columns, containing the following
-<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
+column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>,
-<p>It was last updated on 25 January 2021 20:58:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
+<em>dose_times</em>, <em>administration</em>, <em>notes</em>,
+<em>original_txt</em> and <em>eucast_version</em>.</p>
+<p>This data set is in R available as <code>dosage</code>, after you
+load the <code>AMR</code> package.</p>
+<p>It was last updated on 25 January 2021 20:58:20 UTC. Find more info
+about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">R file</a> (3 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">R
+file</a> (3 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class="external-link">Excel file</a> (14 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class="external-link">Excel
+file</a> (14 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt" class="external-link">plain text file</a> (15 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt" class="external-link">plain
+text file</a> (15 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class="external-link">SAS file</a> (52 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class="external-link">SAS
+file</a> (52 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">SPSS file</a> (45 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">SPSS
+file</a> (45 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata file</a> (44 kB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata
+file</a> (44 kB)</li>
 </ul>
 <div class="section level3">
 <h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
 </h3>
-<p>EUCAST breakpoints used in this package are based on the dosages in this data set.</p>
+<p>EUCAST breakpoints used in this package are based on the dosages in
-<p>Currently included dosages in the data set are meant for: <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical Breakpoint Tables’ v11.0</a> (2021).</p>
+this data set.</p>
+<p>Currently included dosages in the data set are meant for: <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
+Breakpoint Tables’ v11.0</a> (2021).</p>
 </div>
 <div class="section level3">
 <h3 id="example-content-6">Example content<a class="anchor" aria-label="anchor" href="#example-content-6"></a>
 </h3>
 <table class="table">
+<colgroup>
+<col width="4%">
+<col width="10%">
+<col width="15%">
+<col width="10%">
+<col width="9%">
+<col width="13%">
+<col width="5%">
+<col width="16%">
+<col width="13%">
+</colgroup>
 <thead><tr class="header">
 <th align="center">ab</th>
 <th align="center">name</th>
@@ -1316,12 +1460,14 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 
       <footer><div class="copyright">
   <p></p>
-<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer>

docs/articles/index.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -185,11 +185,13 @@
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/authors.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -269,11 +269,13 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/index.html

@@ -47,7 +47,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -195,22 +195,75 @@
 <code>AMR</code> (for R) <img src="./logo.svg" align="right"><a class="anchor" aria-label="anchor" href="#amr-for-r-"></a>
 </h1></div>
 <blockquote>
-<p>Update: The latest <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST guideline for intrinsic resistance</a> (v3.3, October 2021) is now supported, the CLSI 2021 interpretation guideline is now supported, and our taxonomy tables have been updated as well (LPSN, 5 October 2021).</p>
+<p>Update: The latest <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST
+guideline for intrinsic resistance</a> (v3.3, October 2021) is now
+supported, the CLSI 2021 interpretation guideline is now supported, and
+our taxonomy tables have been updated as well (LPSN, 5 October
+2021).</p>
 </blockquote>
 <div class="section level3">
 <h3 id="what-is-amr-for-r">What is <code>AMR</code> (for R)?<a class="anchor" aria-label="anchor" href="#what-is-amr-for-r"></a>
 </h3>
-<p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org" class="external-link">R package</a> (see <a href="#copyright">Copyright</a>) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
+<p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org" class="external-link">R package</a> (see <a href="#copyright">Copyright</a>) to simplify the analysis and prediction
-<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~71,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~570 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, WHONET/EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
+of Antimicrobial Resistance (AMR) and to work with microbial and
-<p>The <code>AMR</code> package is available in <img src="lang_da.svg" style="height: 11px !important; vertical-align: initial !important;"> Danish, <img src="lang_nl.svg" style="height: 11px !important; vertical-align: initial !important;"> Dutch, <img src="lang_en.svg" style="height: 11px !important; vertical-align: initial !important;"> English, <img src="lang_fr.svg" style="height: 11px !important; vertical-align: initial !important;"> French, <img src="lang_de.svg" style="height: 11px !important; vertical-align: initial !important;"> German, <img src="lang_it.svg" style="height: 11px !important; vertical-align: initial !important;"> Italian, <img src="lang_pt.svg" style="height: 11px !important; vertical-align: initial !important;"> Portuguese, <img src="lang_ru.svg" style="height: 11px !important; vertical-align: initial !important;"> Russian, <img src="lang_es.svg" style="height: 11px !important; vertical-align: initial !important;"> Spanish and <img src="lang_sv.svg" style="height: 11px !important; vertical-align: initial !important;"> Swedish. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
+antimicrobial data and properties, by using evidence-based methods.
-<p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">fully independent of any other R package</a> and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>) but is <a href="./news">actively and durably maintained</a> by two public healthcare organisations in the Netherlands.</p>
+<strong>Our aim is to provide a standard</strong> for clean and
+reproducible AMR data analysis, that can therefore empower
+epidemiological analyses to continuously enable surveillance and
+treatment evaluation in any setting.</p>
+<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~71,000 distinct
+microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~570 antibiotic, antimycotic
+and antiviral drugs</strong></a> by name and code (including ATC,
+WHONET/EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about
+valid R/SI and MIC values. It supports any data format, including
+WHONET/EARS-Net data.</p>
+<p>The <code>AMR</code> package is available in
+<img src="lang_da.svg" style="height: 11px !important; vertical-align: initial !important;">
+Danish,
+<img src="lang_nl.svg" style="height: 11px !important; vertical-align: initial !important;">
+Dutch,
+<img src="lang_en.svg" style="height: 11px !important; vertical-align: initial !important;">
+English,
+<img src="lang_fr.svg" style="height: 11px !important; vertical-align: initial !important;">
+French,
+<img src="lang_de.svg" style="height: 11px !important; vertical-align: initial !important;">
+German,
+<img src="lang_it.svg" style="height: 11px !important; vertical-align: initial !important;">
+Italian,
+<img src="lang_pt.svg" style="height: 11px !important; vertical-align: initial !important;">
+Portuguese,
+<img src="lang_ru.svg" style="height: 11px !important; vertical-align: initial !important;">
+Russian,
+<img src="lang_es.svg" style="height: 11px !important; vertical-align: initial !important;">
+Spanish and
+<img src="lang_sv.svg" style="height: 11px !important; vertical-align: initial !important;">
+Swedish. Antimicrobial drug (group) names and colloquial microorganism
+names are provided in these languages.</p>
+<p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">fully independent
+of any other R package</a> and works on Windows, macOS and Linux with
+all versions of R since R-3.0 (April 2013). <strong>It was designed to
+work in any setting, including those with very limited
+resources</strong>. It was created for both routine data analysis and
+academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration
+with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe
+Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This
+R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI
+10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI
+10.33612/diss.192486375</a>) but is <a href="./news">actively and
+durably maintained</a> by two public healthcare organisations in the
+Netherlands.</p>
 <div class="main-content" style="display: inline-block;">
 <p>
-<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in 175 countries</strong><br> Since its first public release in early 2018, this R package has been used in almost all countries in the world. Click the map to enlarge and to see the country names.
+<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a>
+<strong>Used in 175 countries</strong><br> Since its first public
+release in early 2018, this R package has been used in almost all
+countries in the world. Click the map to enlarge and to see the country
+names.
 </p>
 </div>
 <div class="section level5">
-<h5 id="with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side">With <code>AMR</code> (for R), there’s always a knowledgeable microbiologist by your side!<a class="anchor" aria-label="anchor" href="#with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side"></a>
+<h5 id="with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side">With <code>AMR</code> (for R), there’s always a knowledgeable
+microbiologist by your side!<a class="anchor" aria-label="anchor" href="#with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side"></a>
 </h5>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span>
@@ -224,7 +277,12 @@
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>,
          <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,
          <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></code></pre></div>
-<p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p>
+<p>With only having defined a row filter on Gram-negative bacteria with
+intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code>
+and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on
+two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and
+<code><a href="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the
+<code>AMR</code> package make sure you get what you meant:</p>
 <table class="table">
 <thead><tr class="header">
 <th align="left">bacteria</th>
@@ -338,9 +396,14 @@
 <div class="section level4">
 <h4 id="partners">Partners<a class="anchor" aria-label="anchor" href="#partners"></a>
 </h4>
-<p>The development of this package is part of, related to, or made possible by:</p>
+<p>The development of this package is part of, related to, or made
+possible by:</p>
 <div align="center">
-<p><a href="https://www.rug.nl" title="University of Groningen" class="external-link"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen" class="external-link"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation" class="external-link"><img src="./logo_certe.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="EurHealth-1-Health" class="external-link"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG" class="external-link"><img src="./logo_interreg.png" class="partner_logo"></a></p>
+<p><a href="https://www.rug.nl" title="University of Groningen" class="external-link"><img src="./logo_rug.png" class="partner_logo"></a>
+<a href="https://www.umcg.nl" title="University Medical Center Groningen" class="external-link"><img src="./logo_umcg.png" class="partner_logo"></a>
+<a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation" class="external-link"><img src="./logo_certe.png" class="partner_logo"></a>
+<a href="https://www.deutschland-nederland.eu" title="EurHealth-1-Health" class="external-link"><img src="./logo_eh1h.png" class="partner_logo"></a>
+<a href="https://www.deutschland-nederland.eu" title="INTERREG" class="external-link"><img src="./logo_interreg.png" class="partner_logo"></a></p>
 </div>
 </div>
 </div>
@@ -349,21 +412,33 @@
 </h3>
 <p>This package can be used for:</p>
 <ul>
-<li>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> and <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (<a href="./reference/mo_property.html">manual</a>)</li>
+<li>Reference for the taxonomy of microorganisms, since the package
-<li>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines (<a href="./reference/as.rsi.html">manual</a>)</li>
+contains all microbial (sub)species from the <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> and <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in
-<li>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records (<a href="./reference/ab_from_text.html">manual</a>)</li>
+Nomenclature</a> (<a href="./reference/mo_property.html">manual</a>)</li>
+<li>Interpreting raw MIC and disk diffusion values, based on the latest
+CLSI or EUCAST guidelines (<a href="./reference/as.rsi.html">manual</a>)</li>
+<li>Retrieving antimicrobial drug names, doses and forms of
+administration from clinical health care records (<a href="./reference/ab_from_text.html">manual</a>)</li>
 <li>Determining first isolates to be used for AMR data analysis (<a href="./reference/first_isolate.html">manual</a>)</li>
 <li>Calculating antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
-<li>Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO) (<a href="./articles/MDR.html">tutorial</a>)</li>
+<li>Determining multi-drug resistance (MDR) / multi-drug resistant
-<li>Calculating (empirical) susceptibility of both mono therapy and combination therapies (<a href="./articles/AMR.html">tutorial</a>)</li>
+organisms (MDRO) (<a href="./articles/MDR.html">tutorial</a>)</li>
-<li>Predicting future antimicrobial resistance using regression models (<a href="./articles/resistance_predict.html">tutorial</a>)</li>
+<li>Calculating (empirical) susceptibility of both mono therapy and
-<li>Getting properties for any microorganism (like Gram stain, species, genus or family) (<a href="./reference/mo_property.html">manual</a>)</li>
+combination therapies (<a href="./articles/AMR.html">tutorial</a>)</li>
-<li>Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) (<a href="./reference/ab_property.html">manual</a>)</li>
+<li>Predicting future antimicrobial resistance using regression models
+(<a href="./articles/resistance_predict.html">tutorial</a>)</li>
+<li>Getting properties for any microorganism (like Gram stain, species,
+genus or family) (<a href="./reference/mo_property.html">manual</a>)</li>
+<li>Getting properties for any antibiotic (like name, code of
+EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) (<a href="./reference/ab_property.html">manual</a>)</li>
 <li>Plotting antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
 <li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li>
-<li>Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li>
+<li>Getting SNOMED codes of a microorganism, or getting properties of a
-<li>Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
+microorganism based on a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li>
-<li>Machine reading the EUCAST and CLSI guidelines from 2011-2021 to translate MIC values and disk diffusion diameters to R/SI (<a href="./articles/datasets.html">link</a>)</li>
+<li>Getting LOINC codes of an antibiotic, or getting properties of an
+antibiotic based on a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
+<li>Machine reading the EUCAST and CLSI guidelines from 2011-2021 to
+translate MIC values and disk diffusion diameters to R/SI (<a href="./articles/datasets.html">link</a>)</li>
 <li>Principal component analysis for AMR (<a href="./articles/PCA.html">tutorial</a>)</li>
 </ul>
 </div>
@@ -374,17 +449,24 @@
 <h4 id="latest-released-version">Latest released version<a class="anchor" aria-label="anchor" href="#latest-released-version"></a>
 </h4>
 <p><a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://www.r-pkg.org/badges/version-ago/AMR" alt="CRAN"></a> <a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt="CRANlogs"></a></p>
-<p>This package is available <a href="https://cran.r-project.org/package=AMR" class="external-link">here on the official R network (CRAN)</a>. Install this package in R from CRAN by using the command:</p>
+<p>This package is available <a href="https://cran.r-project.org/package=AMR" class="external-link">here on the official R
+network (CRAN)</a>. Install this package in R from CRAN by using the
+command:</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></code></pre></div>
-<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
+<p>It will be downloaded and installed automatically. For RStudio, click
-<p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
+on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type
+in “AMR” and press <kbd>Install</kbd>.</p>
+<p><strong>Note:</strong> Not all functions on this website may be
+available in this latest release. To use all functions and data sets
+mentioned on this website, install the latest development version.</p>
 </div>
 <div class="section level4">
 <h4 id="latest-development-version">Latest development version<a class="anchor" aria-label="anchor" href="#latest-development-version"></a>
 </h4>
 <p><a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=main" alt="R-code-check"></a> <a href="https://www.codefactor.io/repository/github/msberends/amr" class="external-link"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://codecov.io/gh/msberends/AMR/branch/main/graph/badge.svg" alt="Codecov"></a></p>
-<p>The latest and unpublished development version can be installed from GitHub in two ways:</p>
+<p>The latest and unpublished development version can be installed from
+GitHub in two ways:</p>
 <ol style="list-style-type: decimal">
 <li>
 <p>Manually, using:</p>
@@ -393,11 +475,16 @@
 <span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></code></pre></div>
 </li>
 <li>
-<p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our R-universe address</a> to your list of repositories (‘repos’):</p>
+<p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe
+platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our
+R-universe address</a> to your list of repositories (‘repos’):</p>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>,
                   msberends <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
-<p>After this, you can install and update this <code>AMR</code> package like any official release (e.g., using <code>install.packages("AMR")</code> or in RStudio via <em>Tools</em> &gt; <em>Check for Package Updates…</em>).</p>
+<p>After this, you can install and update this <code>AMR</code> package
+like any official release (e.g., using
+<code>install.packages("AMR")</code> or in RStudio via <em>Tools</em>
+&gt; <em>Check for Package Updates…</em>).</p>
 </li>
 </ol>
 <p>You can also download the latest build from our repository: <a href="https://github.com/msberends/AMR/raw/main/data-raw/AMR_latest.tar.gz" class="external-link uri">https://github.com/msberends/AMR/raw/main/data-raw/AMR_latest.tar.gz</a></p>
@@ -406,7 +493,8 @@
 <div class="section level3">
 <h3 id="get-started">Get started<a class="anchor" aria-label="anchor" href="#get-started"></a>
 </h3>
-<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click a link in the <a href="https://msberends.github.io/AMR/articles/">‘How to’ menu</a>.</p>
+<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or
+click a link in the <a href="https://msberends.github.io/AMR/articles/">‘How to’ menu</a>.</p>
 </div>
 <div class="section level3">
 <h3 id="short-introduction">Short introduction<a class="anchor" aria-label="anchor" href="#short-introduction"></a>
@@ -414,66 +502,181 @@
 <div class="section level4">
 <h4 id="microbial-taxonomic-reference-data">Microbial (taxonomic) reference data<a class="anchor" aria-label="anchor" href="#microbial-taxonomic-reference-data"></a>
 </h4>
-<p>This package contains the complete taxonomic tree of almost all ~70,000 microorganisms from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">www.catalogueoflife.org</a>), supplemented by data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/Sp2000/colplus" class="external-link">CoL+ project</a> is finished, which we await. With <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be checked which version of the CoL is included in this package.</p>
+<p>This package contains the complete taxonomic tree of almost all
+~70,000 microorganisms from the authoritative and comprehensive
+Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">www.catalogueoflife.org</a>),
+supplemented by data from the List of Prokaryotic names with Standing in
+Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>).
+This supplementation is needed until the <a href="https://github.com/Sp2000/colplus" class="external-link">CoL+ project</a> is finished,
+which we await. With <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be
+checked which version of the CoL is included in this package.</p>
 <p>Read more about which data from the Catalogue of Life <a href="./reference/catalogue_of_life.html">in our manual</a>.</p>
 </div>
 <div class="section level4">
 <h4 id="antimicrobial-reference-data">Antimicrobial reference data<a class="anchor" aria-label="anchor" href="#antimicrobial-reference-data"></a>
 </h4>
-<p>This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="external-link uri">https://www.whocc.no</a>) and the <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">Pharmaceuticals Community Register of the European Commission</a>.</p>
+<p>This package contains <strong>all ~550 antibiotic, antimycotic and
-<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href="https://www.whocc.no/copyright_disclaimer/" class="external-link uri">https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
+antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC)
+codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the
+World Health Organization Collaborating Centre for Drug Statistics
+Methodology (WHOCC, <a href="https://www.whocc.no" class="external-link uri">https://www.whocc.no</a>) and the <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">Pharmaceuticals
+Community Register of the European Commission</a>.</p>
+<p><strong>NOTE: The WHOCC copyright does not allow use for commercial
+purposes, unlike any other info from this package. See <a href="https://www.whocc.no/copyright_disclaimer/" class="external-link uri">https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
 <p>Read more about the data from WHOCC <a href="./reference/WHOCC.html">in our manual</a>.</p>
 </div>
 <div class="section level4">
 <h4 id="whonet--ears-net">WHONET / EARS-Net<a class="anchor" aria-label="anchor" href="#whonet--ears-net"></a>
 </h4>
-<p>We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a> with the exact same structure as a WHONET export file. Furthermore, this package also contains a <a href="./reference/antibiotics.html">data set antibiotics</a> with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically.</p>
+<p>We support WHONET and EARS-Net data. Exported files from WHONET can
-<p>Read our tutorial about <a href="./articles/WHONET.html">how to work with WHONET data here</a>.</p>
+be imported into R and can be analysed easily using this package. For
+education purposes, we created an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a>
+with the exact same structure as a WHONET export file. Furthermore, this
+package also contains a <a href="./reference/antibiotics.html">data set
+antibiotics</a> with all EARS-Net antibiotic abbreviations, and knows
+almost all WHONET abbreviations for microorganisms. When using WHONET
+data as input for analysis, all input parameters will be set
+automatically.</p>
+<p>Read our tutorial about <a href="./articles/WHONET.html">how to work
+with WHONET data here</a>.</p>
 </div>
 <div class="section level4">
 <h4 id="overview-of-functions">Overview of functions<a class="anchor" aria-label="anchor" href="#overview-of-functions"></a>
 </h4>
-<p>The <code>AMR</code> package basically does four important things:</p>
+<p>The <code>AMR</code> package basically does four important
+things:</p>
 <ol style="list-style-type: decimal">
 <li>
-<p>It <strong>cleanses existing data</strong> by providing new <em>classes</em> for microoganisms, antibiotics and antimicrobial results (both S/I/R and MIC). By installing this package, you teach R everything about microbiology that is needed for analysis. These functions all use intelligent rules to guess results that you would expect:</p>
+<p>It <strong>cleanses existing data</strong> by providing new
+<em>classes</em> for microoganisms, antibiotics and antimicrobial
+results (both S/I/R and MIC). By installing this package, you teach R
+everything about microbiology that is needed for analysis. These
+functions all use intelligent rules to guess results that you would
+expect:</p>
 <ul>
-<li>Use <code><a href="reference/as.mo.html">as.mo()</a></code> to get a microbial ID. The IDs are human readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em> is “B_KLBSL_PNMN” (B stands for Bacteria) and the ID of <em>S. aureus</em> is “B_STPHY_AURS”. The function takes almost any text as input that looks like the name or code of a microorganism like “E. coli”, “esco” or “esccol” and tries to find expected results using intelligent rules combined with the included Catalogue of Life data set. It only takes milliseconds to find results, please see our <a href="./articles/benchmarks.html">benchmarks</a>. Moreover, it can group <em>Staphylococci</em> into coagulase negative and positive (CoNS and CoPS, see <a href="./reference/as.mo.html#source">source</a>) and can categorise <em>Streptococci</em> into Lancefield groups (like beta-haemolytic <em>Streptococcus</em> Group B, <a href="./reference/as.mo.html#source">source</a>).</li>
+<li>Use <code><a href="reference/as.mo.html">as.mo()</a></code> to get a microbial ID. The IDs are human
-<li>Use <code><a href="reference/as.ab.html">as.ab()</a></code> to get an antibiotic ID. Like microbial IDs, these IDs are also human readable based on those used by EARS-Net. For example, the ID of amoxicillin is <code>AMX</code> and the ID of gentamicin is <code>GEN</code>. The <code><a href="reference/as.ab.html">as.ab()</a></code> function also uses intelligent rules to find results like accepting misspelling, trade names and abbrevations used in many laboratory systems. For instance, the values “Furabid”, “Furadantin”, “nitro” all return the ID of Nitrofurantoine. To accomplish this, the package contains a database with most LIS codes, official names, trade names, ATC codes, defined daily doses (DDD) and drug categories of antibiotics.</li>
+readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em>
-<li>Use <code><a href="reference/as.rsi.html">as.rsi()</a></code> to get antibiotic interpretations based on raw MIC values (in mg/L) or disk diffusion values (in mm), or transform existing values to valid antimicrobial results. It produces just S, I or R based on your input and warns about invalid values. Even values like “&lt;=0.002; S” (combined MIC/RSI) will result in “S”.</li>
+is “B_KLBSL_PNMN” (B stands for Bacteria) and the ID of <em>S.
-<li>Use <code><a href="reference/as.mic.html">as.mic()</a></code> to cleanse your MIC values. It produces a so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values as levels. A value like “&lt;=0.002; S” (combined MIC/RSI) will result in “&lt;=0.002”.</li>
+aureus</em> is “B_STPHY_AURS”. The function takes almost any text as
+input that looks like the name or code of a microorganism like “E.
+coli”, “esco” or “esccol” and tries to find expected results using
+intelligent rules combined with the included Catalogue of Life data set.
+It only takes milliseconds to find results, please see our <a href="./articles/benchmarks.html">benchmarks</a>. Moreover, it can group
+<em>Staphylococci</em> into coagulase negative and positive (CoNS and
+CoPS, see <a href="./reference/as.mo.html#source">source</a>) and can
+categorise <em>Streptococci</em> into Lancefield groups (like
+beta-haemolytic <em>Streptococcus</em> Group B, <a href="./reference/as.mo.html#source">source</a>).</li>
+<li>Use <code><a href="reference/as.ab.html">as.ab()</a></code> to get an antibiotic ID. Like microbial
+IDs, these IDs are also human readable based on those used by EARS-Net.
+For example, the ID of amoxicillin is <code>AMX</code> and the ID of
+gentamicin is <code>GEN</code>. The <code><a href="reference/as.ab.html">as.ab()</a></code> function also
+uses intelligent rules to find results like accepting misspelling, trade
+names and abbrevations used in many laboratory systems. For instance,
+the values “Furabid”, “Furadantin”, “nitro” all return the ID of
+Nitrofurantoine. To accomplish this, the package contains a database
+with most LIS codes, official names, trade names, ATC codes, defined
+daily doses (DDD) and drug categories of antibiotics.</li>
+<li>Use <code><a href="reference/as.rsi.html">as.rsi()</a></code> to get antibiotic interpretations based on
+raw MIC values (in mg/L) or disk diffusion values (in mm), or transform
+existing values to valid antimicrobial results. It produces just S, I or
+R based on your input and warns about invalid values. Even values like
+“&lt;=0.002; S” (combined MIC/RSI) will result in “S”.</li>
+<li>Use <code><a href="reference/as.mic.html">as.mic()</a></code> to cleanse your MIC values. It produces a
+so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values
+as levels. A value like “&lt;=0.002; S” (combined MIC/RSI) will result
+in “&lt;=0.002”.</li>
 </ul>
 </li>
 <li>
-<p>It <strong>enhances existing data</strong> and <strong>adds new data</strong> from data sets included in this package.</p>
+<p>It <strong>enhances existing data</strong> and <strong>adds new
+data</strong> from data sets included in this package.</p>
 <ul>
-<li>Use <code><a href="reference/eucast_rules.html">eucast_rules()</a></code> to apply <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST expert rules to isolates</a> (not the translation from MIC to R/SI values, use <code><a href="reference/as.rsi.html">as.rsi()</a></code> for that).</li>
+<li>Use <code><a href="reference/eucast_rules.html">eucast_rules()</a></code> to apply <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST
-<li>Use <code><a href="reference/first_isolate.html">first_isolate()</a></code> to identify the first isolates of every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">using guidelines from the CLSI</a> (Clinical and Laboratory Standards Institute).
+expert rules to isolates</a> (not the translation from MIC to R/SI
+values, use <code><a href="reference/as.rsi.html">as.rsi()</a></code> for that).</li>
+<li>Use <code><a href="reference/first_isolate.html">first_isolate()</a></code> to identify the first isolates of
+every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">using
+guidelines from the CLSI</a> (Clinical and Laboratory Standards
+Institute).
 <ul>
-<li>You can also identify first <em>weighted</em> isolates of every patient, an adjusted version of the CLSI guideline. This takes into account key antibiotics of every strain and compares them.</li>
+<li>You can also identify first <em>weighted</em> isolates of every
+patient, an adjusted version of the CLSI guideline. This takes into
+account key antibiotics of every strain and compares them.</li>
 </ul>
 </li>
-<li>Use <code><a href="reference/mdro.html">mdro()</a></code> to determine which micro-organisms are multi-drug resistant organisms (MDRO). It supports a variety of international guidelines, such as the MDR-paper by Magiorakos <em>et al.</em> (2012, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=21793988" class="external-link">PMID 21793988</a>), the exceptional phenotype definitions of EUCAST and the WHO guideline on multi-drug resistant TB. It also supports the national guidelines of the Netherlands and Germany.</li>
+<li>Use <code><a href="reference/mdro.html">mdro()</a></code> to determine which micro-organisms are
-<li>The <a href="./reference/microorganisms.html">data set microorganisms</a> contains the complete taxonomic tree of ~70,000 microorganisms. Furthermore, some colloquial names and all Gram stains are available, which enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like <code><a href="reference/mo_property.html">mo_genus()</a></code>, <code><a href="reference/mo_property.html">mo_family()</a></code>, <code><a href="reference/mo_property.html">mo_gramstain()</a></code> or even <code><a href="reference/mo_property.html">mo_phylum()</a></code>. Use <code><a href="reference/mo_property.html">mo_snomed()</a></code> to look up any SNOMED CT code associated with a microorganism. As all these function use <code><a href="reference/as.mo.html">as.mo()</a></code> internally, they also use the same intelligent rules for determination. For example, <code>mo_genus("MRSA")</code> and <code>mo_genus("S. aureus")</code> will both return <code>"Staphylococcus"</code>. They also come with support for German, Danish, Dutch, Spanish, Italian, French and Portuguese. These functions can be used to add new variables to your data.</li>
+multi-drug resistant organisms (MDRO). It supports a variety of
-<li>The <a href="./reference/antibiotics.html">data set antibiotics</a> contains ~450 antimicrobial drugs with their EARS-Net code, ATC code, PubChem compound ID, LOINC code, official name, common LIS codes and DDDs of both oral and parenteral administration. It also contains all (thousands of) trade names found in PubChem. Use functions like <code><a href="reference/ab_property.html">ab_name()</a></code>, <code><a href="reference/ab_property.html">ab_group()</a></code>, <code><a href="reference/ab_property.html">ab_atc()</a></code>, <code><a href="reference/ab_property.html">ab_loinc()</a></code> and <code><a href="reference/ab_property.html">ab_tradenames()</a></code> to look up values. The <code>ab_*</code> functions use <code><a href="reference/as.ab.html">as.ab()</a></code> internally so they support the same intelligent rules to guess the most probable result. For example, <code>ab_name("Fluclox")</code>, <code>ab_name("Floxapen")</code> and <code>ab_name("J01CF05")</code> will all return <code>"Flucloxacillin"</code>. These functions can again be used to add new variables to your data.</li>
+international guidelines, such as the MDR-paper by Magiorakos <em>et
+al.</em> (2012, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=21793988" class="external-link">PMID
+21793988</a>), the exceptional phenotype definitions of EUCAST and the
+WHO guideline on multi-drug resistant TB. It also supports the national
+guidelines of the Netherlands and Germany.</li>
+<li>The <a href="./reference/microorganisms.html">data set
+microorganisms</a> contains the complete taxonomic tree of ~70,000
+microorganisms. Furthermore, some colloquial names and all Gram stains
+are available, which enables resistance analysis of e.g. different
+antibiotics per Gram stain. The package also contains functions to look
+up values in this data set like <code><a href="reference/mo_property.html">mo_genus()</a></code>,
+<code><a href="reference/mo_property.html">mo_family()</a></code>, <code><a href="reference/mo_property.html">mo_gramstain()</a></code> or even
+<code><a href="reference/mo_property.html">mo_phylum()</a></code>. Use <code><a href="reference/mo_property.html">mo_snomed()</a></code> to look up any
+SNOMED CT code associated with a microorganism. As all these function
+use <code><a href="reference/as.mo.html">as.mo()</a></code> internally, they also use the same intelligent
+rules for determination. For example, <code>mo_genus("MRSA")</code> and
+<code>mo_genus("S. aureus")</code> will both return
+<code>"Staphylococcus"</code>. They also come with support for German,
+Danish, Dutch, Spanish, Italian, French and Portuguese. These functions
+can be used to add new variables to your data.</li>
+<li>The <a href="./reference/antibiotics.html">data set antibiotics</a>
+contains ~450 antimicrobial drugs with their EARS-Net code, ATC code,
+PubChem compound ID, LOINC code, official name, common LIS codes and
+DDDs of both oral and parenteral administration. It also contains all
+(thousands of) trade names found in PubChem. Use functions like
+<code><a href="reference/ab_property.html">ab_name()</a></code>, <code><a href="reference/ab_property.html">ab_group()</a></code>, <code><a href="reference/ab_property.html">ab_atc()</a></code>,
+<code><a href="reference/ab_property.html">ab_loinc()</a></code> and <code><a href="reference/ab_property.html">ab_tradenames()</a></code> to look up
+values. The <code>ab_*</code> functions use <code><a href="reference/as.ab.html">as.ab()</a></code>
+internally so they support the same intelligent rules to guess the most
+probable result. For example, <code>ab_name("Fluclox")</code>,
+<code>ab_name("Floxapen")</code> and <code>ab_name("J01CF05")</code>
+will all return <code>"Flucloxacillin"</code>. These functions can again
+be used to add new variables to your data.</li>
 </ul>
 </li>
 <li>
-<p>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</p>
+<p>It <strong>analyses the data</strong> with convenient functions
+that use well-known methods.</p>
 <ul>
-<li>Calculate the microbial susceptibility or resistance (and even co-resistance) with the <code><a href="reference/proportion.html">susceptibility()</a></code> and <code><a href="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the <code><a href="reference/proportion.html">proportion_R()</a></code>, <code><a href="reference/proportion.html">proportion_IR()</a></code>, <code><a href="reference/proportion.html">proportion_I()</a></code>, <code><a href="reference/proportion.html">proportion_SI()</a></code> and <code><a href="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><a href="reference/count.html">count_resistant()</a></code>, <code><a href="reference/count.html">count_susceptible()</a></code> and <code><a href="reference/count.html">count_all()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g. in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>)</li>
+<li>Calculate the microbial susceptibility or resistance (and even
-<li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for the <code>ggplot2</code> package</li>
+co-resistance) with the <code><a href="reference/proportion.html">susceptibility()</a></code> and
-<li>Predict antimicrobial resistance for the nextcoming years using logistic regression models with the <code><a href="reference/resistance_predict.html">resistance_predict()</a></code> function</li>
+<code><a href="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the
+<code><a href="reference/proportion.html">proportion_R()</a></code>, <code><a href="reference/proportion.html">proportion_IR()</a></code>,
+<code><a href="reference/proportion.html">proportion_I()</a></code>, <code><a href="reference/proportion.html">proportion_SI()</a></code> and
+<code><a href="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of
+isolates can be determined with the <code><a href="reference/count.html">count_resistant()</a></code>,
+<code><a href="reference/count.html">count_susceptible()</a></code> and <code><a href="reference/count.html">count_all()</a></code> functions.
+All these functions can be used with the <code>dplyr</code> package
+(e.g. in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>)</li>
+<li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for
+the <code>ggplot2</code> package</li>
+<li>Predict antimicrobial resistance for the nextcoming years using
+logistic regression models with the <code><a href="reference/resistance_predict.html">resistance_predict()</a></code>
+function</li>
 </ul>
 </li>
 <li>
-<p>It <strong>teaches the user</strong> how to use all the above actions.</p>
+<p>It <strong>teaches the user</strong> how to use all the above
+actions.</p>
 <ul>
-<li>Aside from this website with many tutorials, the package itself contains extensive help pages with many examples for all functions.</li>
+<li>Aside from this website with many tutorials, the package itself
+contains extensive help pages with many examples for all functions.</li>
 <li>The package also contains example data sets:
 <ul>
-<li>The <a href="./reference/example_isolates.html"><code>example_isolates</code> data set</a>. This data set contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practice AMR data analysis.</li>
+<li>The <a href="./reference/example_isolates.html"><code>example_isolates</code>
-<li>The <a href="./reference/WHONET.html"><code>WHONET</code> data set</a>. This data set only contains fake data, but with the exact same structure as files exported by WHONET. Read more about WHONET <a href="./articles/WHONET.html">on its tutorial page</a>.</li>
+data set</a>. This data set contains 2,000 microbial isolates with their
+full antibiograms. It reflects reality and can be used to practice AMR
+data analysis.</li>
+<li>The <a href="./reference/WHONET.html"><code>WHONET</code> data
+set</a>. This data set only contains fake data, but with the exact same
+structure as files exported by WHONET. Read more about WHONET <a href="./articles/WHONET.html">on its tutorial page</a>.</li>
 </ul>
 </li>
 </ul>
@@ -484,7 +687,9 @@
 <div class="section level3">
 <h3 id="copyright">Copyright<a class="anchor" aria-label="anchor" href="#copyright"></a>
 </h3>
-<p>This R package is free, open-source software and licensed under the <a href="./LICENSE-text.html">GNU General Public License v2.0 (GPL-2)</a>. In a nutshell, this means that this package:</p>
+<p>This R package is free, open-source software and licensed under the
+<a href="./LICENSE-text.html">GNU General Public License v2.0
+(GPL-2)</a>. In a nutshell, this means that this package:</p>
 <ul>
 <li><p>May be used for commercial purposes</p></li>
 <li><p>May be used for private purposes</p></li>
@@ -492,15 +697,18 @@
 <li>
 <p>May be modified, although:</p>
 <ul>
-<li>Modifications <strong>must</strong> be released under the same license when distributing the package</li>
+<li>Modifications <strong>must</strong> be released under the same
+license when distributing the package</li>
 <li>Changes made to the code <strong>must</strong> be documented</li>
 </ul>
 </li>
 <li>
 <p>May be distributed, although:</p>
 <ul>
-<li>Source code <strong>must</strong> be made available when the package is distributed</li>
+<li>Source code <strong>must</strong> be made available when the package
-<li>A copy of the license and copyright notice <strong>must</strong> be included with the package.</li>
+is distributed</li>
+<li>A copy of the license and copyright notice <strong>must</strong> be
+included with the package.</li>
 </ul>
 </li>
 <li><p>Comes with a LIMITATION of liability</p></li>
@@ -556,12 +764,14 @@
 
       <footer><div class="copyright">
   <p></p>
-<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer>

docs/reference/ab_from_text.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -221,7 +221,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -275,11 +275,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/ab_property.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -242,7 +242,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="source">
     <h2>Source</h2>
@@ -344,11 +344,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/age.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -193,7 +193,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -226,11 +226,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/age_groups.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -194,7 +194,7 @@ The default is to split on young children (0-11), youth (12-24), young adults (2
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -250,11 +250,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/antibiotic_class_selectors.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -294,7 +294,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="reference-data-publicly-available">
     <h2>Reference Data Publicly Available</h2>
@@ -430,11 +430,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/as.ab.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -205,7 +205,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="whocc">
     <h2>WHOCC</h2>
@@ -280,11 +280,13 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/as.disk.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -195,7 +195,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -239,11 +239,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/as.mic.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -224,7 +224,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -273,11 +273,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/as.mo.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -283,7 +283,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="matching-score-for-microorganisms">
     <h2>Matching Score for Microorganisms</h2>
@@ -377,11 +377,13 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/as.rsi.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -309,7 +309,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="reference-data-publicly-available">
     <h2>Reference Data Publicly Available</h2>
@@ -423,11 +423,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/atc_online.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -224,7 +224,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -257,11 +257,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/availability.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -186,7 +186,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -216,11 +216,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/bug_drug_combinations.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -230,7 +230,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -265,11 +265,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/count.html

@@ -18,7 +18,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -225,7 +225,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="interpretation-of-r-and-s-i">
     <h2>Interpretation of R and S/I</h2>
@@ -358,11 +358,13 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/custom_eucast_rules.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -269,7 +269,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -301,11 +301,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/eucast_rules.html

@@ -18,7 +18,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -265,7 +265,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="reference-data-publicly-available">
     <h2>Reference Data Publicly Available</h2>
@@ -334,11 +334,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/first_isolate.html

@@ -18,7 +18,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -306,7 +306,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -371,11 +371,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/get_episode.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -193,7 +193,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -278,11 +278,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/ggplot_pca.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
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@@ -264,7 +264,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
 
     <div id="ref-examples">
@@ -304,11 +304,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/ggplot_rsi.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
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@@ -295,7 +295,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -395,11 +395,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
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docs/reference/guess_ab_col.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -195,7 +195,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -243,11 +243,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/index.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -157,7 +157,10 @@
 
     <table class="ref-index"><colgroup><col class="alias"><col class="title"></colgroup><tbody><tr><th colspan="2">
           <h2 id="preparing-data-microorganisms">Preparing data: microorganisms <a href="#preparing-data-microorganisms" class="anchor" aria-hidden="true"></a></h2>
-          <p class="section-desc"></p><p>These functions are meant to get taxonomically valid properties of microorganisms from any input. Use <code><a href="../reference/mo_source.html">mo_source()</a></code> to teach this package how to translate your own codes to valid microorganism codes.</p>
+          <p class="section-desc"></p><p>These functions are meant to get taxonomically valid properties of
+microorganisms from any input. Use <code><a href="../reference/mo_source.html">mo_source()</a></code> to teach
+this package how to translate your own codes to valid microorganism
+codes.</p>
         </th>
       </tr></tbody><tbody><tr><td>
           <p><code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> </p>
@@ -173,7 +176,9 @@
         <td><p>User-Defined Reference Data Set for Microorganisms</p></td>
       </tr></tbody><tbody><tr><th colspan="2">
           <h2 id="preparing-data-antibiotics">Preparing data: antibiotics <a href="#preparing-data-antibiotics" class="anchor" aria-hidden="true"></a></h2>
-          <p class="section-desc"></p><p>Use these functions to get valid properties of antibiotics from any input or to clean your input. You can even retrieve drug names and doses from clinical text records, using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>.</p>
+          <p class="section-desc"></p><p>Use these functions to get valid properties of antibiotics from any
+input or to clean your input. You can even retrieve drug names and doses
+from clinical text records, using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>.</p>
         </th>
       </tr></tbody><tbody><tr><td>
           <p><code><a href="as.ab.html">as.ab()</a></code> <code><a href="as.ab.html">is.ab()</a></code> </p>
@@ -193,7 +198,13 @@
         <td><p>Get ATC Properties from WHOCC Website</p></td>
       </tr></tbody><tbody><tr><th colspan="2">
           <h2 id="preparing-data-antimicrobial-resistance">Preparing data: antimicrobial resistance <a href="#preparing-data-antimicrobial-resistance" class="anchor" aria-hidden="true"></a></h2>
-          <p class="section-desc"></p><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can transform your raw input to valid MIC or disk diffusion values. Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as R/SI based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p>
+          <p class="section-desc"></p><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can
+transform your raw input to valid MIC or disk diffusion values. Use
+<code><a href="../reference/as.rsi.html">as.rsi()</a></code> for cleaning raw data to let it only contain “R”,
+“I” and “S”, or to interpret MIC or disk diffusion values as R/SI based
+on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend
+antibiotic interpretations by applying <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST
+rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p>
         </th>
       </tr></tbody><tbody><tr><td>
           <p><code><a href="as.rsi.html">as.rsi()</a></code> <code><a href="as.rsi.html">NA_rsi_</a></code> <code><a href="as.rsi.html">is.rsi()</a></code> <code><a href="as.rsi.html">is.rsi.eligible()</a></code> </p>
@@ -217,7 +228,14 @@
         <td><p>Define Custom EUCAST Rules</p></td>
       </tr></tbody><tbody><tr><th colspan="2">
           <h2 id="analysing-data-antimicrobial-resistance">Analysing data: antimicrobial resistance <a href="#analysing-data-antimicrobial-resistance" class="anchor" aria-hidden="true"></a></h2>
-          <p class="section-desc"></p><p>Use these function for the analysis part. You can use <code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any antibiotic column. Be sure to first select the isolates that are appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or <code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain resistance in certain antibiotic classes (<code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p>
+          <p class="section-desc"></p><p>Use these function for the analysis part. You can use
+<code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any
+antibiotic column. Be sure to first select the isolates that are
+appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or
+<code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain
+resistance in certain antibiotic classes (<code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>,
+<code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>), or determine multi-drug resistant
+microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p>
         </th>
       </tr></tbody><tbody><tr><td>
           <p><code><a href="proportion.html">resistance()</a></code> <code><a href="proportion.html">susceptibility()</a></code> <code><a href="proportion.html">proportion_R()</a></code> <code><a href="proportion.html">proportion_IR()</a></code> <code><a href="proportion.html">proportion_I()</a></code> <code><a href="proportion.html">proportion_SI()</a></code> <code><a href="proportion.html">proportion_S()</a></code> <code><a href="proportion.html">proportion_df()</a></code> <code><a href="proportion.html">rsi_df()</a></code> </p>
@@ -269,7 +287,9 @@
         <td><p>Guess Antibiotic Column</p></td>
       </tr></tbody><tbody><tr><th colspan="2">
           <h2 id="background-information-on-included-data">Background information on included data <a href="#background-information-on-included-data" class="anchor" aria-hidden="true"></a></h2>
-          <p class="section-desc"></p><p>Some pages about our package and its external sources. Be sure to read our <a href="./../articles/index.html">How To’s</a> for more information about how to work with functions in this package.</p>
+          <p class="section-desc"></p><p>Some pages about our package and its external sources. Be sure to
+read our <a href="./../articles/index.html">How To’s</a> for more
+information about how to work with functions in this package.</p>
         </th>
       </tr></tbody><tbody><tr><td>
           <p><code><a href="AMR.html">AMR</a></code> </p>
@@ -333,7 +353,9 @@
         <td><p>Data Set with 500 Isolates - WHONET Example</p></td>
       </tr></tbody><tbody><tr><th colspan="2">
           <h2 id="other-miscellaneous-functions">Other: miscellaneous functions <a href="#other-miscellaneous-functions" class="anchor" aria-hidden="true"></a></h2>
-          <p class="section-desc"></p><p>These functions are mostly for internal use, but some of them may also be suitable for your analysis. Especially the ‘like’ function can be useful: <code>if (x %like% y) {...}</code>.</p>
+          <p class="section-desc"></p><p>These functions are mostly for internal use, but some of them may
+also be suitable for your analysis. Especially the ‘like’ function can
+be useful: <code>if (x %like% y) {...}</code>.</p>
         </th>
       </tr></tbody><tbody><tr><td>
           <p><code><a href="age_groups.html">age_groups()</a></code> </p>
@@ -381,7 +403,8 @@
         <td><p>Random MIC Values/Disk Zones/RSI Generation</p></td>
       </tr></tbody><tbody><tr><th colspan="2">
           <h2 id="other-statistical-tests">Other: statistical tests <a href="#other-statistical-tests" class="anchor" aria-hidden="true"></a></h2>
-          <p class="section-desc"></p><p>Some statistical tests or methods are not part of base R and were added to this package for convenience.</p>
+          <p class="section-desc"></p><p>Some statistical tests or methods are not part of base R and were
+added to this package for convenience.</p>
         </th>
       </tr></tbody><tbody><tr><td>
           <p><code><a href="g.test.html">g.test()</a></code> </p>
@@ -397,7 +420,9 @@
         <td><p>Skewness of the Sample</p></td>
       </tr></tbody><tbody><tr><th colspan="2">
           <h2 id="other-deprecated-functions">Other: deprecated functions <a href="#other-deprecated-functions" class="anchor" aria-hidden="true"></a></h2>
-          <p class="section-desc"></p><p>These functions are deprecated, meaning that they will still work but show a warning with every use and will be removed in a future version.</p>
+          <p class="section-desc"></p><p>These functions are deprecated, meaning that they will still work but
+show a warning with every use and will be removed in a future
+version.</p>
         </th>
       </tr></tbody><tbody><tr><td>
           <p><code><a href="AMR-deprecated.html">AMR-deprecated</a></code> </p>
@@ -412,11 +437,13 @@
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/italicise_taxonomy.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -186,7 +186,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -221,11 +221,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/join.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -201,7 +201,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -242,11 +242,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/key_antimicrobials.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -252,7 +252,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -308,11 +308,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/kurtosis.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -189,7 +189,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -210,11 +210,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/lifecycle.html

@@ -19,7 +19,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -186,7 +186,7 @@ The lifecycle of this function is <strong>maturing</strong>. The unlying code of
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
 The lifecycle 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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="retired-lifecycle">
     <h2>Retired Lifecycle</h2>
@@ -211,11 +211,13 @@ The lifecycle of this function is <strong>questioning</strong>. This function mi
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/like.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -204,7 +204,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -260,11 +260,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/mdro.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -291,7 +291,7 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="antibiotics">
     <h2>Antibiotics</h2>
@@ -352,11 +352,13 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/mo_matching_score.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -195,7 +195,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="reference-data-publicly-available">
     <h2>Reference Data Publicly Available</h2>
@@ -231,11 +231,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/mo_property.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -264,7 +264,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="matching-score-for-microorganisms">
     <h2>Matching Score for Microorganisms</h2>
@@ -433,11 +433,13 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/mo_source.html

@@ -18,7 +18,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -250,7 +250,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -267,11 +267,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/pca.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
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     </div>
 
@@ -224,7 +224,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -266,11 +266,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/plot.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
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     </div>
 
@@ -292,7 +292,7 @@ The <code><a href="https://ggplot2.tidyverse.org/reference/fortify.html" class="
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -332,11 +332,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/proportion.html

@@ -18,7 +18,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -271,7 +271,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="interpretation-of-r-and-s-i">
     <h2>Interpretation of R and S/I</h2>
@@ -381,11 +381,13 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/random.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -197,7 +197,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -232,11 +232,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/resistance_predict.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -267,7 +267,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="interpretation-of-r-and-s-i">
     <h2>Interpretation of R and S/I</h2>
@@ -358,11 +358,13 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/reference/skewness.html

@@ -18,7 +18,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -189,7 +189,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -210,11 +210,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
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docs/reference/translate.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
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@@ -185,7 +185,7 @@
 
 <p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument 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>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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>
     </div>
     <div id="read-more-on-our-website-">
     <h2>Read more on Our Website!</h2>
@@ -237,11 +237,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

docs/survey.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
       </span>
     </div>
 
@@ -168,11 +168,13 @@
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
+Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
+2.0.2.</p>
 </div>
 
       </footer></div>

man/ab_from_text.Rd

@@ -62,7 +62,7 @@ With using \code{collapse}, this function will return a \link{character}:\cr
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{

man/ab_property.Rd

@@ -100,7 +100,7 @@ The function \code{\link[=set_ab_names]{set_ab_names()}} is a special column ren
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Source}{

man/age.Rd

@@ -33,7 +33,7 @@ This function vectorises over both \code{x} and \code{reference}, meaning that e
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{

man/age_groups.Rd

@@ -38,7 +38,7 @@ The default is to split on young children (0-11), youth (12-24), young adults (2
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{

man/antibiotic_class_selectors.Rd

@@ -169,7 +169,7 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Reference Data Publicly Available}{

man/as.ab.Rd

@@ -52,7 +52,7 @@ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{htt
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{WHOCC}{

man/as.disk.Rd

@@ -38,7 +38,7 @@ Interpret disk values as RSI values with \code{\link[=as.rsi]{as.rsi()}}. It sup
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{

man/as.mic.Rd

@@ -70,7 +70,7 @@ The following \link[=groupGeneric]{generic functions} are implemented for the MI
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{

man/as.mo.Rd

@@ -141,7 +141,7 @@ The intelligent rules consider the prevalence of microorganisms in humans groupe
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Matching Score for Microorganisms}{

man/as.rsi.Rd

@@ -155,7 +155,7 @@ This AMR package honours this (new) insight. Use \code{\link[=susceptibility]{su
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Reference Data Publicly Available}{

man/atc_online.Rd

@@ -74,7 +74,7 @@ Abbreviations of return values when using \code{property = "U"} (unit):
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{

man/availability.Rd

@@ -25,7 +25,7 @@ The function returns a \link{data.frame} with columns \code{"resistant"} and \co
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{

man/bug_drug_combinations.Rd

@@ -68,7 +68,7 @@ The function \code{\link[=format]{format()}} calculates the resistance per bug-d
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{

man/count.Rd

@@ -77,7 +77,7 @@ The function \code{\link[=count_df]{count_df()}} takes any variable from \code{d
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Interpretation of R and S/I}{

man/custom_eucast_rules.Rd

@@ -105,7 +105,7 @@ It is possible to define antibiotic groups instead of single antibiotics for the
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{

man/eucast_rules.Rd

@@ -110,7 +110,7 @@ Amikacin (\code{AMK}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB06&sho
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Reference Data Publicly Available}{

man/first_isolate.Rd

@@ -169,7 +169,7 @@ The default method is phenotype-based (using \code{type = "points"}) and episode
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{

man/get_episode.Rd

@@ -37,7 +37,7 @@ The \code{dplyr} package is not required for these functions to work, but these
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{

man/ggplot_pca.Rd

@@ -113,7 +113,7 @@ The colours for labels and points can be changed by adding another scale layer f
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \examples{

man/ggplot_rsi.Rd

@@ -145,7 +145,7 @@ At default, the names of antibiotics will be shown on the plots using \code{\lin
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{

man/guess_ab_col.Rd

@@ -34,7 +34,7 @@ You can look for an antibiotic (trade) name or abbreviation and it will search \
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{

man/italicise_taxonomy.Rd

@@ -29,7 +29,7 @@ This function also supports abbreviation of the genus if it is followed by a spe
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{

man/join.Rd

@@ -48,7 +48,7 @@ If the \code{dplyr} package is installed, their join functions will be used. Oth
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{

man/key_antimicrobials.Rd

@@ -112,7 +112,7 @@ The default antimicrobial agents used for \strong{fungi} (set in \code{antifunga
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{

man/kurtosis.Rd

@@ -30,7 +30,7 @@ Kurtosis is a measure of the "tailedness" of the probability distribution of a r
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{

man/lifecycle.Rd

@@ -26,7 +26,7 @@ The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unly
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Retired Lifecycle}{

man/like.Rd

@@ -50,7 +50,7 @@ Using RStudio? The \verb{\%like\%}/\verb{\%unlike\%} functions can also be direc
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{

man/mdro.Rd

@@ -160,7 +160,7 @@ The rules set (the \code{custom} object in this case) could be exported to a sha
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Antibiotics}{

man/mo_matching_score.Rd

@@ -44,7 +44,7 @@ Since \code{AMR} version 1.8.1, common microorganism abbreviations are ignored i
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Reference Data Publicly Available}{

man/mo_property.Rd

@@ -144,7 +144,7 @@ SNOMED codes - \code{\link[=mo_snomed]{mo_snomed()}} - are from the US Edition o
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Matching Score for Microorganisms}{

man/mo_source.Rd

@@ -100,7 +100,7 @@ If the original file (in the previous case an Excel file) is moved or deleted, t
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{

man/pca.Rd

@@ -64,7 +64,7 @@ The result of the \code{\link[=pca]{pca()}} function is a \link{prcomp} object,
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{

man/plot.Rd

@@ -134,7 +134,7 @@ Simply using \code{"CLSI"} or \code{"EUCAST"} as input will automatically select
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{

man/proportion.Rd

@@ -123,7 +123,7 @@ Using \code{only_all_tested} has no impact when only using one antibiotic as inp
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Interpretation of R and S/I}{

man/random.Rd

@@ -40,7 +40,7 @@ Generated values are based on the latest EUCAST guideline implemented in the \li
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{

man/resistance_predict.Rd

@@ -115,7 +115,7 @@ Valid options for the statistical model (argument \code{model}) are:
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Interpretation of R and S/I}{

man/skewness.Rd

@@ -30,7 +30,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
 The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. 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.
 
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument 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.
+If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a 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.
 }
 
 \section{Read more on Our Website!}{