P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-25 05:35:38 +02:00
Code Releases Activity

(v1.6.0.9000) custom EUCAST rules

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-04-07 08:37:42 +02:00
parent 551f99dc8f
commit 7a3139f7cc
49 changed files with 1363 additions and 594 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
docs/404.html
View File

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
</span>
</div>

2
docs/LICENSE-text.html
View File

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
</span>
</div>

2
docs/articles/index.html
View File

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
</span>
</div>

2
docs/authors.html
View File

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
</span>
</div>

13
docs/index.html
View File

@ -19,11 +19,10 @@
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
<script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet">
<script src="extra.js"></script><meta property="og:title" content="Antimicrobial Resistance Data Analysis">
<meta property="og:description" content="Functions to simplify the analysis and prediction of Antimicrobial
Resistance (AMR) and to work with microbial and antimicrobial properties by
using evidence-based methods, like those defined by Leclercq et al. (2013)
&lt;doi:10.1111/j.1469-0691.2011.03703.x&gt; and containing reference data such as
LPSN &lt;doi:10.1099/ijsem.0.004332&gt;.">
<meta property="og:description" content="Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by
using evidence-based methods and reliable reference data such as LPSN
&lt;doi:10.1099/ijsem.0.004332&gt;.">
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@ -43,7 +42,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
</span>
</div>
@ -197,7 +196,7 @@
<div class="page-header"><h1 class="hasAnchor">
<a href="#amr-for-r-" class="anchor"></a><code>AMR</code> (for R) <img src="./logo.png" align="right" height="120px">
</h1></div>
<p><em>Note: the rules of ‘EUCAST Clinical Breakpoints v11.0 (2021)’ are now implemented</em></p>
<p><em>Note: the rules of ‘EUCAST Clinical Breakpoints v11.0 (2021)’ are now implemented.</em></p>
<blockquote>
<p><span class="fa fa-clipboard-list" style="color: #128f76; font-size: 20pt; margin-right: 5px;"></span> <strong>PLEASE TAKE PART IN OUR SURVEY!</strong><br>
Since you are one of our users, we would like to know how you use the package and what it brought you or your organisation. <strong>If you have a minute, please <a href="./survey.html">anonymously fill in this short questionnaire</a></strong>. Your valuable input will help to improve the package and its functionalities. You can answer the open questions in either English, Spanish, French, Dutch, or German. Thank you very much in advance! <br><a class="btn btn-info btn-amr" href="./survey.html">Take me to the 5-min survey!</a></p>

148
docs/news/index.html
View File

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
</span>
</div>
@ -236,14 +236,32 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-160" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0">
<a href="#amr-160" class="anchor"></a>AMR 1.6.0<small> Unreleased </small>
<div id="amr-1609000" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9000">
<a href="#amr-1609000" class="anchor"></a>AMR 1.6.0.9000<small> Unreleased </small>
</h1>
<div id="last-updated-7-april-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-7-april-2021" class="anchor"></a><small>Last updated: 7 April 2021</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h3>
<ul>
<li>Function <code><a href="../reference/custom_eucast_rules.html">custom_eucast_rules()</a></code> that brings support for custom AMR rules in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>
</li>
</ul>
</div>
</div>
</div>
<div id="amr-160" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0">
<a href="#amr-160" class="anchor"></a>AMR 1.6.0<small> 2021-03-14 </small>
</h1>
<div id="new-1" class="section level3">
<h3 class="hasAnchor">
<a href="#new-1" class="anchor"></a>New</h3>
<ul>
<li>
<p>Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function and in <code><a href="../reference/as.rsi.html">as.rsi()</a></code> to interpret MIC and disk diffusion values. This is now the default guideline in this package.</p>
<ul>
@ -316,11 +334,11 @@
</li>
</ul>
</div>
<div id="changed" class="section level3">
<div id="changed-1" class="section level3">
<h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3>
<a href="#changed-1" class="anchor"></a>Changed</h3>
<ul>
<li>Updated the bacterial taxonomy to 3 March 2021 (using <a href="https://lpsn.dsmz.de">LSPN</a>)
<li>Updated the bacterial taxonomy to 3 March 2021 (using <a href="https://lpsn.dsmz.de">LPSN</a>)
<ul>
<li>Added 3,372 new species and 1,523 existing species became synomyms</li>
<li>The URL of a bacterial species (<code><a href="../reference/mo_property.html">mo_url()</a></code>) will now lead to <a href="https://lpsn.dsmz.de" class="uri">https://lpsn.dsmz.de</a>
@ -378,9 +396,9 @@
<h1 class="page-header" data-toc-text="1.5.0">
<a href="#amr-150" class="anchor"></a>AMR 1.5.0<small> 2021-01-06 </small>
</h1>
<div id="new-1" class="section level3">
<div id="new-2" class="section level3">
<h3 class="hasAnchor">
<a href="#new-1" class="anchor"></a>New</h3>
<a href="#new-2" class="anchor"></a>New</h3>
<ul>
<li>
<p>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> to determine (patient) episodes which are not necessarily based on microorganisms. The <code><a href="../reference/get_episode.html">get_episode()</a></code> function returns the index number of the episode per group, while the <code><a href="../reference/get_episode.html">is_new_episode()</a></code> function returns values <code>TRUE</code>/<code>FALSE</code> to indicate whether an item in a vector is the start of a new episode. They also support <code>dplyr</code>s grouping (i.e. using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code>):</p>
@ -396,9 +414,9 @@
<li><p>Functions <code><a href="../reference/random.html">random_mic()</a></code>, <code><a href="../reference/random.html">random_disk()</a></code> and <code><a href="../reference/random.html">random_rsi()</a></code> for random value generation. The functions <code><a href="../reference/random.html">random_mic()</a></code> and <code><a href="../reference/random.html">random_disk()</a></code> take microorganism names and antibiotic names as input to make generation more realistic.</p></li>
</ul>
</div>
<div id="changed-1" class="section level3">
<div id="changed-2" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-1" class="anchor"></a>Changed</h3>
<a href="#changed-2" class="anchor"></a>Changed</h3>
<ul>
<li><p>New argument <code>ampc_cephalosporin_resistance</code> in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> to correct for AmpC de-repressed cephalosporin-resistant mutants</p></li>
<li>
@ -492,9 +510,9 @@
<h1 class="page-header" data-toc-text="1.4.0">
<a href="#amr-140" class="anchor"></a>AMR 1.4.0<small> 2020-10-08 </small>
</h1>
<div id="new-2" class="section level3">
<div id="new-3" class="section level3">
<h3 class="hasAnchor">
<a href="#new-2" class="anchor"></a>New</h3>
<a href="#new-3" class="anchor"></a>New</h3>
<ul>
<li><p>Support for ‘EUCAST Expert Rules’ / ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ version 3.2 of May 2020. With this addition to the previously implemented version 3.1 of 2016, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function can now correct for more than 180 different antibiotics and the <code><a href="../reference/mdro.html">mdro()</a></code> function can determine multidrug resistance based on more than 150 different antibiotics. All previously implemented versions of the EUCAST rules are now maintained and kept available in this package. The <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function consequently gained the arguments <code>version_breakpoints</code> (at the moment defaults to v10.0, 2020) and <code>version_expertrules</code> (at the moment defaults to v3.2, 2020). The <code>example_isolates</code> data set now also reflects the change from v3.1 to v3.2. The <code><a href="../reference/mdro.html">mdro()</a></code> function now accepts <code>guideline == "EUCAST3.1"</code> and <code>guideline == "EUCAST3.2"</code>.</p></li>
<li><p>A new vignette and website page with info about all our public and freely available data sets, that can be downloaded as flat files or in formats for use in R, SPSS, SAS, Stata and Excel: <a href="https://msberends.github.io/AMR/articles/datasets.html" class="uri">https://msberends.github.io/AMR/articles/datasets.html</a></p></li>
@ -514,9 +532,9 @@
<li><p>Support for skimming classes <code>&lt;rsi&gt;</code>, <code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code> and <code>&lt;mo&gt;</code> with the <code>skimr</code> package</p></li>
</ul>
</div>
<div id="changed-2" class="section level3">
<div id="changed-3" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-2" class="anchor"></a>Changed</h3>
<a href="#changed-3" class="anchor"></a>Changed</h3>
<ul>
<li><p>Although advertised that this package should work under R 3.0.0, we still had a dependency on R 3.6.0. This is fixed, meaning that our package should now work under R 3.0.0.</p></li>
<li>
@ -596,9 +614,9 @@
<h1 class="page-header" data-toc-text="1.3.0">
<a href="#amr-130" class="anchor"></a>AMR 1.3.0<small> 2020-07-31 </small>
</h1>
<div id="new-3" class="section level3">
<div id="new-4" class="section level3">
<h3 class="hasAnchor">
<a href="#new-3" class="anchor"></a>New</h3>
<a href="#new-4" class="anchor"></a>New</h3>
<ul>
<li><p>Function <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code> to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses <code><a href="../reference/as.ab.html">as.ab()</a></code> internally</p></li>
<li>
@ -620,9 +638,9 @@
<li><p>Added argument <code>conserve_capped_values</code> to <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for interpreting MIC values - it makes sure that values starting with “&lt;” (but not “&lt;=”) will always return “S” and values starting with “&gt;” (but not “&gt;=”) will always return “R”. The default behaviour of <code><a href="../reference/as.rsi.html">as.rsi()</a></code> has not changed, so you need to specifically do <code><a href="../reference/as.rsi.html">as.rsi(..., conserve_capped_values = TRUE)</a></code>.</p></li>
</ul>
</div>
<div id="changed-3" class="section level3">
<div id="changed-4" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-3" class="anchor"></a>Changed</h3>
<a href="#changed-4" class="anchor"></a>Changed</h3>
<ul>
<li>
<p>Big speed improvement for using any function on microorganism codes from earlier package versions (prior to <code>AMR</code> v1.2.0), such as <code><a href="../reference/as.mo.html">as.mo()</a></code>, <code><a href="../reference/mo_property.html">mo_name()</a></code>, <code><a href="../reference/first_isolate.html">first_isolate()</a></code>, <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, <code><a href="../reference/mdro.html">mdro()</a></code>, etc.</p>
@ -696,9 +714,9 @@
</li>
</ul>
</div>
<div id="changed-4" class="section level3">
<div id="changed-5" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-4" class="anchor"></a>Changed</h3>
<a href="#changed-5" class="anchor"></a>Changed</h3>
<ul>
<li>Taxonomy:
<ul>
@ -743,17 +761,17 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<h1 class="page-header" data-toc-text="1.1.0">
<a href="#amr-110" class="anchor"></a>AMR 1.1.0<small> 2020-04-15 </small>
</h1>
<div id="new-4" class="section level3">
<div id="new-5" class="section level3">
<h3 class="hasAnchor">
<a href="#new-4" class="anchor"></a>New</h3>
<a href="#new-5" class="anchor"></a>New</h3>
<ul>
<li>Support for easy principal component analysis for AMR, using the new <code><a href="../reference/pca.html">pca()</a></code> function</li>
<li>Plotting biplots for principal component analysis using the new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function</li>
</ul>
</div>
<div id="changed-5" class="section level3">
<div id="changed-6" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-5" class="anchor"></a>Changed</h3>
<a href="#changed-6" class="anchor"></a>Changed</h3>
<ul>
<li>Improvements for the algorithm used by <code><a href="../reference/as.mo.html">as.mo()</a></code> (and consequently all <code>mo_*</code> functions, that use <code><a href="../reference/as.mo.html">as.mo()</a></code> internally):
<ul>
@ -785,9 +803,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<h1 class="page-header" data-toc-text="1.0.1">
<a href="#amr-101" class="anchor"></a>AMR 1.0.1<small> 2020-02-23 </small>
</h1>
<div id="changed-6" class="section level3">
<div id="changed-7" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-6" class="anchor"></a>Changed</h3>
<a href="#changed-7" class="anchor"></a>Changed</h3>
<ul>
<li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li>
<li>
@ -811,9 +829,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<a href="#amr-100" class="anchor"></a>AMR 1.0.0<small> 2020-02-17 </small>
</h1>
<p>This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.</p>
<div id="new-5" class="section level3">
<div id="new-6" class="section level3">
<h3 class="hasAnchor">
<a href="#new-5" class="anchor"></a>New</h3>
<a href="#new-6" class="anchor"></a>New</h3>
<ul>
<li>Support for the newest <a href="https://www.eucast.org/clinical_breakpoints/">EUCAST Clinical Breakpoint Tables v.10.0</a>, valid from 1 January 2020. This affects translation of MIC and disk zones using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> and inferred resistance and susceptibility using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</li>
<li>The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <a href="https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt" class="uri">https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This <strong>allows for machine reading these guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file <a href="https://github.com/msberends/AMR/blob/master/data-raw/read_EUCAST.R">can be found here</a>.</li>
@ -909,9 +927,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
</div>
<div id="new-6" class="section level3">
<div id="new-7" class="section level3">
<h3 class="hasAnchor">
<a href="#new-6" class="anchor"></a>New</h3>
<a href="#new-7" class="anchor"></a>New</h3>
<ul>
<li>
<p>Functions <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> as aliases of <code><a href="../reference/proportion.html">proportion_SI()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code>, respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.</p>
@ -1029,9 +1047,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
</ul>
</div>
<div id="new-7" class="section level3">
<div id="new-8" class="section level3">
<h3 class="hasAnchor">
<a href="#new-7" class="anchor"></a>New</h3>
<a href="#new-8" class="anchor"></a>New</h3>
<ul>
<li>
<p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with <code><a href="../reference/mo_property.html">mo_shortname()</a></code> at default:</p>
@ -1096,9 +1114,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
</div>
<div id="changed-7" class="section level3">
<div id="changed-8" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-7" class="anchor"></a>Changed</h3>
<a href="#changed-8" class="anchor"></a>Changed</h3>
<ul>
<li>Many algorithm improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code> (of which some led to additions to the <code>microorganisms</code> data set). Many thanks to all contributors that helped improving the algorithms.
<ul>
@ -1163,9 +1181,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<h1 class="page-header" data-toc-text="0.7.1">
<a href="#amr-071" class="anchor"></a>AMR 0.7.1<small> 2019-06-23 </small>
</h1>
<div id="new-8" class="section level4">
<div id="new-9" class="section level4">
<h4 class="hasAnchor">
<a href="#new-8" class="anchor"></a>New</h4>
<a href="#new-9" class="anchor"></a>New</h4>
<ul>
<li>
<p>Function <code><a href="../reference/proportion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code>portion_df()</code> to immediately show resistance percentages and number of available isolates:</p>
@ -1209,9 +1227,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Function <code><a href="../reference/mo_property.html">mo_synonyms()</a></code> to get all previously accepted taxonomic names of a microorganism</p></li>
</ul>
</div>
<div id="changed-8" class="section level4">
<div id="changed-9" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-8" class="anchor"></a>Changed</h4>
<a href="#changed-9" class="anchor"></a>Changed</h4>
<ul>
<li>Column names of output <code><a href="../reference/count.html">count_df()</a></code> and <code>portion_df()</code> are now lowercase</li>
<li>Fixed bug in translation of microorganism names</li>
@ -1248,9 +1266,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<h1 class="page-header" data-toc-text="0.7.0">
<a href="#amr-070" class="anchor"></a>AMR 0.7.0<small> 2019-06-03 </small>
</h1>
<div id="new-9" class="section level4">
<div id="new-10" class="section level4">
<h4 class="hasAnchor">
<a href="#new-9" class="anchor"></a>New</h4>
<a href="#new-10" class="anchor"></a>New</h4>
<ul>
<li>Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on an MIC value (created with <code><a href="../reference/as.mic.html">as.mic()</a></code>), a disk diffusion value (created with the new <code><a href="../reference/as.disk.html">as.disk()</a></code>) or on a complete date set containing columns with MIC or disk diffusion values.</li>
<li>Function <code><a href="../reference/mo_property.html">mo_name()</a></code> as alias of <code><a href="../reference/mo_property.html">mo_fullname()</a></code>
@ -1258,9 +1276,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Added guidelines of the WHO to determine multi-drug resistance (MDR) for TB (<code><a href="../reference/mdro.html">mdr_tb()</a></code>) and added a new vignette about MDR. Read this tutorial <a href="https://msberends.gitlab.io/AMR/articles/MDR.html">here on our website</a>.</li>
</ul>
</div>
<div id="changed-9" class="section level4">
<div id="changed-10" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-9" class="anchor"></a>Changed</h4>
<a href="#changed-10" class="anchor"></a>Changed</h4>
<ul>
<li>Fixed a critical bug in <code><a href="../reference/first_isolate.html">first_isolate()</a></code> where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1.</li>
<li>Fixed a bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> where antibiotics from WHONET software would not be recognised</li>
@ -1345,9 +1363,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<h1 class="page-header" data-toc-text="0.6.1">
<a href="#amr-061" class="anchor"></a>AMR 0.6.1<small> 2019-03-29 </small>
</h1>
<div id="changed-10" class="section level4">
<div id="changed-11" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-10" class="anchor"></a>Changed</h4>
<a href="#changed-11" class="anchor"></a>Changed</h4>
<ul>
<li>Fixed a critical bug when using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> with <code>verbose = TRUE</code>
</li>
@ -1365,9 +1383,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Contains the complete manual of this package and all of its functions with an explanation of their arguments</li>
<li>Contains a comprehensive tutorial about how to conduct AMR data analysis, import data from WHONET or SPSS and many more.</li>
</ul>
<div id="new-10" class="section level4">
<div id="new-11" class="section level4">
<h4 class="hasAnchor">
<a href="#new-10" class="anchor"></a>New</h4>
<a href="#new-11" class="anchor"></a>New</h4>
<ul>
<li><p><strong>BREAKING</strong>: removed deprecated functions, arguments and references to ‘bactid’. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> to identify an MO code.</p></li>
<li>
@ -1465,9 +1483,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a>.</p></li>
</ul>
</div>
<div id="changed-11" class="section level4">
<div id="changed-12" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-11" class="anchor"></a>Changed</h4>
<a href="#changed-12" class="anchor"></a>Changed</h4>
<ul>
<li>Function <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:
<ul>
@ -1611,9 +1629,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<h1 class="page-header" data-toc-text="0.5.0">
<a href="#amr-050" class="anchor"></a>AMR 0.5.0<small> 2018-11-30 </small>
</h1>
<div id="new-11" class="section level4">
<div id="new-12" class="section level4">
<h4 class="hasAnchor">
<a href="#new-11" class="anchor"></a>New</h4>
<a href="#new-12" class="anchor"></a>New</h4>
<ul>
<li>Repository moved to GitLab</li>
<li>Function <code>count_all</code> to get all available isolates (that like all <code>portion_*</code> and <code>count_*</code> functions also supports <code>summarise</code> and <code>group_by</code>), the old <code>n_rsi</code> is now an alias of <code>count_all</code>
@ -1624,9 +1642,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Functions <code>mo_authors</code> and <code>mo_year</code> to get specific values about the scientific reference of a taxonomic entry</li>
</ul>
</div>
<div id="changed-12" class="section level4">
<div id="changed-13" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-12" class="anchor"></a>Changed</h4>
<a href="#changed-13" class="anchor"></a>Changed</h4>
<ul>
<li><p>Functions <code>MDRO</code>, <code>BRMO</code>, <code>MRGN</code> and <code>EUCAST_exceptional_phenotypes</code> were renamed to <code>mdro</code>, <code>brmo</code>, <code>mrgn</code> and <code>eucast_exceptional_phenotypes</code></p></li>
<li><p><code>EUCAST_rules</code> was renamed to <code>eucast_rules</code>, the old function still exists as a deprecated function</p></li>
@ -1735,9 +1753,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<h1 class="page-header" data-toc-text="0.4.0">
<a href="#amr-040" class="anchor"></a>AMR 0.4.0<small> 2018-10-01 </small>
</h1>
<div id="new-12" class="section level4">
<div id="new-13" class="section level4">
<h4 class="hasAnchor">
<a href="#new-12" class="anchor"></a>New</h4>
<a href="#new-13" class="anchor"></a>New</h4>
<ul>
<li><p>The data set <code>microorganisms</code> now contains <strong>all microbial taxonomic data from ITIS</strong> (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via <a href="https://itis.gov" class="uri">https://itis.gov</a>. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set <code>microorganisms.old</code> contains all previously known taxonomic names from those kingdoms.</p></li>
<li>
@ -1815,9 +1833,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Renamed <code>septic_patients$sex</code> to <code>septic_patients$gender</code></p></li>
</ul>
</div>
<div id="changed-13" class="section level4">
<div id="changed-14" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-13" class="anchor"></a>Changed</h4>
<a href="#changed-14" class="anchor"></a>Changed</h4>
<ul>
<li><p>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</p></li>
<li>
@ -1884,9 +1902,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<h1 class="page-header" data-toc-text="0.3.0">
<a href="#amr-030" class="anchor"></a>AMR 0.3.0<small> 2018-08-14 </small>
</h1>
<div id="new-13" class="section level4">
<div id="new-14" class="section level4">
<h4 class="hasAnchor">
<a href="#new-13" class="anchor"></a>New</h4>
<a href="#new-14" class="anchor"></a>New</h4>
<ul>
<li>
<strong>BREAKING</strong>: <code>rsi_df</code> was removed in favour of new functions <code>portion_R</code>, <code>portion_IR</code>, <code>portion_I</code>, <code>portion_SI</code> and <code>portion_S</code> to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old <code>rsi</code> function. The old function still works, but is deprecated.
@ -1957,9 +1975,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
</div>
<div id="changed-14" class="section level4">
<div id="changed-15" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-14" class="anchor"></a>Changed</h4>
<a href="#changed-15" class="anchor"></a>Changed</h4>
<ul>
<li>Improvements for forecasting with <code>resistance_predict</code> and added more examples</li>
<li>More antibiotics added as arguments for EUCAST rules</li>
@ -2021,9 +2039,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<h1 class="page-header" data-toc-text="0.2.0">
<a href="#amr-020" class="anchor"></a>AMR 0.2.0<small> 2018-05-03 </small>
</h1>
<div id="new-14" class="section level4">
<div id="new-15" class="section level4">
<h4 class="hasAnchor">
<a href="#new-14" class="anchor"></a>New</h4>
<a href="#new-15" class="anchor"></a>New</h4>
<ul>
<li>Full support for Windows, Linux and macOS</li>
<li>Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)</li>
@ -2043,9 +2061,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>New print format for <code>tibble</code>s and <code>data.table</code>s</li>
</ul>
</div>
<div id="changed-15" class="section level4">
<div id="changed-16" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-15" class="anchor"></a>Changed</h4>
<a href="#changed-16" class="anchor"></a>Changed</h4>
<ul>
<li>Fixed <code>rsi</code> class for vectors that contain only invalid antimicrobial interpretations</li>
<li>Renamed dataset <code>ablist</code> to <code>antibiotics</code>

2
docs/pkgdown.yml
View File

@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-03-14T08:55Z
last_built: 2021-04-07T06:37Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

2
docs/reference/antibiotic_class_selectors.html
View File

@ -83,7 +83,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
</span>
</div>

312
docs/reference/custom_eucast_rules.html Normal file
View File

@ -0,0 +1,312 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Create Custom EUCAST Rules — custom_eucast_rules • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png" />
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script>
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Create Custom EUCAST Rules — custom_eucast_rules" />
<meta property="og:description" content="Create Custom EUCAST Rules" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fas fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question-circle"></span>
How to
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
</li>
</ul>
</li>
<li>
<a href="../reference/index.html">
<span class="fas fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fas fa-users"></span>
Authors
</a>
</li>
<li>
<a href="../news/index.html">
<span class="far fa-newspaper"></span>
Changelog
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
Survey
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
</header>
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Create Custom EUCAST Rules</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/custom_eucast_rules.R'><code>R/custom_eucast_rules.R</code></a></small>
<div class="hidden name"><code>custom_eucast_rules.Rd</code></div>
</div>
<div class="ref-description">
<p>Create Custom EUCAST Rules</p>
</div>
<pre class="usage"><span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>...</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>...</th>
<td><p>rules in formula notation, see <em>Examples</em></p></td>
</tr>
</table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>This documentation page will be updated shortly. <strong>This function is experimental.</strong></p>
<h2 class="hasAnchor" id="how-it-works"><a class="anchor" href="#how-it-works"></a>How it works</h2>
<p>..</p>
<p>It is also possible to define antibiotic groups instead of single antibiotics. The following groups are allowed (case-insensitive): <code>aminoglycosides</code>, <code>aminopenicillins</code>, <code>betalactams</code>, <code>carbapenems</code>, <code>cephalosporins</code>, <code>cephalosporins_1st</code>, <code>cephalosporins_2nd</code>, <code>cephalosporins_3rd</code>, <code>cephalosporins_except_caz</code>, <code>fluoroquinolones</code>, <code>glycopeptides</code>, <code>glycopeptides_except_lipo</code>, <code>lincosamides</code>, <code>lipoglycopeptides</code>, <code>macrolides</code>, <code>oxazolidinones</code>, <code>penicillins</code>, <code>polymyxins</code>, <code>streptogramins</code>, <code>tetracyclines</code>, <code>tetracyclines_except_tgc</code> and <code>ureidopenicillins</code>.</p>
<h2 class="hasAnchor" id="experimental-lifecycle"><a class="anchor" href="#experimental-lifecycle"></a>Experimental Lifecycle</h2>
<p><img src='figures/lifecycle_experimental.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>experimental</strong>. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this <code>AMR</code> package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span>,
<span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"I"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"I"</span><span class='op'>)</span>
<span class='fu'><a href='eucast_rules.html'>eucast_rules</a></span><span class='op'>(</span><span class='va'>example_isolates</span>,
rules <span class='op'>=</span> <span class='st'>"custom"</span>,
custom_rules <span class='op'>=</span> <span class='va'>x</span>,
info <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='co'># combine rule sets</span>
<span class='va'>x2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='va'>x</span>,
<span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>~</span> <span class='va'>carbapenems</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span><span class='op'>)</span>
<span class='va'>x2</span>
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>
</div>
</body>
</html>

21
docs/reference/eucast_rules.html
View File

@ -83,7 +83,7 @@ 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="Latest development version">1.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
</span>
</div>
@ -254,6 +254,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
version_expertrules <span class='op'>=</span> <span class='fl'>3.2</span>,
ampc_cephalosporin_resistance <span class='op'>=</span> <span class='cn'>NA</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
custom_rules <span class='op'>=</span> <span class='cn'>NULL</span>,
<span class='va'>...</span>
<span class='op'>)</span>
@ -276,7 +277,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</tr>
<tr>
<th>rules</th>
<td><p>a character vector that specifies which rules should be applied. Must be one or more of <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"all"</code>, and defaults to <code><a href='https://rdrr.io/r/base/c.html'>c("breakpoints", "expert")</a></code>. The default value can be set to another value, e.g. using <code><a href='https://rdrr.io/r/base/options.html'>options(AMR_eucastrules = "all")</a></code>.</p></td>
<td><p>a character vector that specifies which rules should be applied. Must be one or more of <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"custom"</code>, <code>"all"</code>, and defaults to <code><a href='https://rdrr.io/r/base/c.html'>c("breakpoints", "expert")</a></code>. The default value can be set to another value, e.g. using <code><a href='https://rdrr.io/r/base/options.html'>options(AMR_eucastrules = "all")</a></code>. If using <code>"custom"</code>, be sure to fill in argument <code>custom_rules</code> too. Custom rules can be created with <code><a href='custom_eucast_rules.html'>custom_eucast_rules()</a></code>.</p></td>
</tr>
<tr>
<th>verbose</th>
@ -298,6 +299,10 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<th>only_rsi_columns</th>
<td><p>a logical to indicate whether only antibiotic columns must be detected that were transformed to class <code>&lt;rsi&gt;</code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></td>
</tr>
<tr>
<th>custom_rules</th>
<td><p>custom rules to apply, created with <code><a href='custom_eucast_rules.html'>custom_eucast_rules()</a></code></p></td>
</tr>
<tr>
<th>...</th>
<td><p>column name of an antibiotic, see section <em>Antibiotics</em> below</p></td>
@ -332,7 +337,17 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<p><strong>Note:</strong> This function does not translate MIC values to RSI values. Use <code><a href='as.rsi.html'>as.rsi()</a></code> for that. <br />
<strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.</p>
<p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>'Other' Rules</h3>
<p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Custom Rules</h3>
<p>Custom rules can be created using <code><a href='custom_eucast_rules.html'>custom_eucast_rules()</a></code>, e.g.:</p><pre><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'><a href='custom_eucast_rules.html'>custom_eucast_rules</a></span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span>,
<span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"I"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"I"</span><span class='op'>)</span>
<span class='fu'>eucast_rules</span><span class='op'>(</span><span class='va'>example_isolates</span>, rules <span class='op'>=</span> <span class='st'>"custom"</span>, custom_rules <span class='op'>=</span> <span class='va'>x</span><span class='op'>)</span>
</pre>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>'Other' Rules</h3>
<p>Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:</p><ol>

2
docs/reference/ggplot_pca.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
</span>
</div>

10
docs/reference/index.html
View File

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
</span>
</div>
@ -450,6 +450,12 @@
<p><code><a href="eucast_rules.html">eucast_rules()</a></code> <code><a href="eucast_rules.html">eucast_dosage()</a></code> </p>
</td>
<td><p>Apply EUCAST Rules</p></td>
</tr><tr>
<td>
<p><code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code> </p>
</td>
<td><p>Create Custom EUCAST Rules</p></td>
</tr>
</tbody><tbody>
<tr>
@ -595,7 +601,7 @@
<td>
<p><code><a href="like.html">like()</a></code> <code><a href="like.html">`%like%`</a></code> <code><a href="like.html">`%like_case%`</a></code> </p>
</td>
<td><p>Pattern Matching with Keyboard Shortcut</p></td>
<td><p>Vectorised Pattern Matching with Keyboard Shortcut</p></td>
</tr><tr>
<td>

16
docs/reference/like.html
View File

@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Pattern Matching with Keyboard Shortcut — like • AMR (for R)</title>
<title>Vectorised Pattern Matching with Keyboard Shortcut — like • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Pattern Matching with Keyboard Shortcut — like" />
<meta property="og:title" content="Vectorised Pattern Matching with Keyboard Shortcut — like" />
<meta property="og:description" content="Convenient wrapper around grepl() to match a pattern: x %like% pattern. It always returns a logical vector and is always case-insensitive (use x %like_case% pattern for case-sensitive matching). Also, pattern can be as long as x to compare items of each index in both vectors, or they both can have the same length to iterate over all cases." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
</span>
</div>
@ -233,7 +233,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Pattern Matching with Keyboard Shortcut</h1>
<h1>Vectorised Pattern Matching with Keyboard Shortcut</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/like.R'><code>R/like.R</code></a></small>
<div class="hidden name"><code>like.Rd</code></div>
</div>
@ -267,17 +267,17 @@
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>Idea from the <a href='https://github.com/Rdatatable/data.table/blob/master/R/like.R'><code>like</code> function from the <code>data.table</code> package</a></p>
<p>Idea from the <a href='https://github.com/Rdatatable/data.table/blob/ec1259af1bf13fc0c96a1d3f9e84d55d8106a9a4/R/like.R'><code>like</code> function from the <code>data.table</code> package</a></p>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A <code><a href='https://rdrr.io/r/base/logical.html'>logical</a></code> vector</p>
<p>A <a href='https://rdrr.io/r/base/logical.html'>logical</a> vector</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The <code>%like%</code> function:</p><ul>
<li><p>Is case-insensitive (use <code>%like_case%</code> for case-sensitive matching)</p></li>
<li><p>Supports multiple patterns</p></li>
<li><p>Checks if <code>pattern</code> is a regular expression and sets <code>fixed = TRUE</code> if not, to greatly improve speed</p></li>
<li><p>Always uses compatibility with Perl</p></li>
<li><p>Always uses compatibility with Perl unless <code>fixed = TRUE</code>, to greatly improve speed</p></li>
</ul>
<p>Using RStudio? The text <code>%like%</code> can also be directly inserted in your code from the Addins menu and can have its own Keyboard Shortcut like <code>Ctrl+Shift+L</code> or <code>Cmd+Shift+L</code> (see <code>Tools</code> &gt; <code>Modify Keyboard Shortcuts...</code>).</p>
@ -320,7 +320,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='va'>mo</span><span class='op'>)</span> <span class='op'>%like%</span> <span class='st'>"^ent"</span><span class='op'>)</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%like%</span> <span class='st'>"^ent"</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>

17
docs/reference/mdro.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
</span>
</div>
@ -374,10 +374,19 @@ Ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with levels <cod
<span class='co'>#&gt; Unmatched rows will return NA.</span>
</pre>
<p>The outcome of the function can be used for the <code>guideline</code> argument in the <code>mdro()</code> function:</p><pre><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>mdro</span><span class='op'>(</span><span class='va'>example_isolates</span>, guideline <span class='op'>=</span> <span class='va'>custom</span><span class='op'>)</span>
<p>The outcome of the function can be used for the <code>guideline</code> argument in the <code>mdro()</code> function:</p><pre><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>mdro</span><span class='op'>(</span><span class='va'>example_isolates</span>,
guideline <span class='op'>=</span> <span class='va'>custom</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/table.html'>table</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
<span class='co'>#&gt; Elderly Type A Elderly Type B Negative </span>
<span class='co'>#&gt; 43 891 1066 </span>
<span class='co'>#&gt; Negative Elderly Type A Elderly Type B</span>
<span class='co'>#&gt; 1070 198 732</span>
</pre>
<p>Rules can also be combined with other custom rules by using <code><a href='https://rdrr.io/r/base/c.html'>c()</a></code>:</p><pre><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>mdro</span><span class='op'>(</span><span class='va'>example_isolates</span>,
guideline <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='va'>custom</span>,
<span class='fu'>custom_mdro_guideline</span><span class='op'>(</span><span class='va'>ERY</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>age</span> <span class='op'>&gt;</span> <span class='fl'>50</span> <span class='op'>~</span> <span class='st'>"Elderly Type C"</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/table.html'>table</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
<span class='co'>#&gt; Negative Elderly Type A Elderly Type B Elderly Type C </span>
<span class='co'>#&gt; 961 198 732 109</span>
</pre>
<p>The rules set (the <code>custom</code> object in this case) could be exported to a shared file location using <code><a href='https://rdrr.io/r/base/readRDS.html'>saveRDS()</a></code> if you collaborate with multiple users. The custom rules set could then be imported using <code><a href='https://rdrr.io/r/base/readRDS.html'>readRDS()</a></code>.</p>

5
docs/reference/plot.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
</span>
</div>
@ -321,6 +321,7 @@
xlab <span class='op'>=</span> <span class='st'>"Antimicrobial Interpretation"</span>,
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
colours_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"#ED553B"</span>, <span class='st'>"#3CAEA3"</span>, <span class='st'>"#F6D55C"</span><span class='op'>)</span>,
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
@ -407,7 +408,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'>plot</span><span class='op'>(</span><span class='va'>some_mic_values</span>, mo <span class='op'>=</span> <span class='st'>"S. aureus"</span>, ab <span class='op'>=</span> <span class='st'>"ampicillin"</span><span class='op'>)</span>
<span class='fu'>plot</span><span class='op'>(</span><span class='va'>some_disk_values</span>, mo <span class='op'>=</span> <span class='st'>"Escherichia coli"</span>, ab <span class='op'>=</span> <span class='st'>"cipro"</span><span class='op'>)</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='http://ggplot2.tidyverse.org'>"ggplot2"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://ggplot2.tidyverse.org'>"ggplot2"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>some_mic_values</span><span class='op'>)</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>some_disk_values</span>, mo <span class='op'>=</span> <span class='st'>"Escherichia coli"</span>, ab <span class='op'>=</span> <span class='st'>"cipro"</span><span class='op'>)</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>some_rsi_values</span><span class='op'>)</span>

3
docs/sitemap.xml
View File

@ -66,6 +66,9 @@
<url>
<loc>https://msberends.github.io/AMR//reference/count.html</loc>
</url>
<url>
<loc>https://msberends.github.io/AMR//reference/custom_eucast_rules.html</loc>
</url>
<url>
<loc>https://msberends.github.io/AMR//reference/dosage.html</loc>
</url>

2
docs/survey.html
View File

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
</span>
</div>