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prerelease 1.8.1

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Merge branch 'development' of https://github.com/msberends/AMR into development

# Conflicts:
#	docs/articles/AMR.html
#	docs/articles/AMR_files/figure-html/disk_plots-1.png
#	docs/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png
#	docs/articles/AMR_files/figure-html/mic_plots-1.png
#	docs/articles/AMR_files/figure-html/mic_plots-2.png
#	docs/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png
#	docs/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png
#	docs/articles/AMR_files/figure-html/plot 1-1.png
#	docs/articles/AMR_files/figure-html/plot 3-1.png
#	docs/articles/AMR_files/figure-html/plot 4-1.png
#	docs/articles/AMR_files/figure-html/plot 5-1.png
#	docs/articles/EUCAST.html
#	docs/articles/MDR.html
#	docs/articles/PCA.html
#	docs/articles/PCA_files/figure-html/unnamed-chunk-6-1.png
#	docs/articles/PCA_files/figure-html/unnamed-chunk-7-1.png
#	docs/articles/SPSS.html
#	docs/articles/WHONET.html
#	docs/articles/WHONET_files/figure-html/unnamed-chunk-7-1.png
#	docs/articles/benchmarks.html
#	docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png
#	docs/articles/datasets.html
#	docs/articles/resistance_predict.html
#	docs/articles/resistance_predict_files/figure-html/unnamed-chunk-4-1.png
#	docs/articles/resistance_predict_files/figure-html/unnamed-chunk-5-1.png
#	docs/articles/resistance_predict_files/figure-html/unnamed-chunk-5-2.png
#	docs/articles/resistance_predict_files/figure-html/unnamed-chunk-6-1.png
#	docs/articles/resistance_predict_files/figure-html/unnamed-chunk-7-1.png
#	docs/articles/welcome_to_AMR.html
#	docs/news/index.html
#	docs/pkgdown.yml
#	docs/reference/AMR-deprecated.html
#	docs/reference/AMR.html
#	docs/reference/WHOCC.html
#	docs/reference/WHONET.html
#	docs/reference/antibiotics.html
#	docs/reference/catalogue_of_life.html
#	docs/reference/catalogue_of_life_version.html
#	docs/reference/dosage.html
#	docs/reference/example_isolates.html
#	docs/reference/example_isolates_unclean.html
#	docs/reference/g.test.html
#	docs/reference/intrinsic_resistant.html
#	docs/reference/microorganisms.codes.html
#	docs/reference/microorganisms.html
#	docs/reference/microorganisms.old.html
#	docs/reference/rsi_translation.html
This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-03-14 16:37:37 +01:00
parent 1b0983e382 8c9feea087
commit 45e9546538
73 changed files with 1231 additions and 1020 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
docs/reference/AMR-deprecated.html
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@ -17,7 +17,11 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span>
</div>

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docs/reference/AMR.html
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@ -17,7 +17,11 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span>
</div>
@ -226,8 +230,12 @@ Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<<<<<<< HEAD
<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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</div>
</footer></div>

4
docs/reference/WHOCC.html
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@ -17,7 +17,11 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span>
</div>

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docs/reference/WHONET.html
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@ -17,7 +17,11 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span>
</div>
@ -220,8 +224,12 @@ Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<<<<<<< HEAD
<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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</div>
</footer></div>

6
docs/reference/ab_from_text.html
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@ -275,13 +275,11 @@ 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>

6
docs/reference/ab_property.html
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@ -344,13 +344,11 @@ 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>

6
docs/reference/age.html
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@ -226,13 +226,11 @@ 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>

6
docs/reference/age_groups.html
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@ -250,13 +250,11 @@ 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>

6
docs/reference/antibiotic_class_selectors.html
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@ -430,13 +430,11 @@ 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>

4
docs/reference/antibiotics.html
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@ -17,7 +17,11 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span>
</div>

6
docs/reference/as.ab.html
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@ -280,13 +280,11 @@ 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>

6
docs/reference/as.disk.html
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@ -239,13 +239,11 @@ 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>

6
docs/reference/as.mic.html
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@ -273,13 +273,11 @@ 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>

6
docs/reference/as.mo.html
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@ -377,13 +377,11 @@ 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>

8
docs/reference/as.rsi.html
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@ -334,7 +334,7 @@ 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" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://docs.ropensci.org/skimr/" class="external-link">"skimr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span>
<span class="co"># class &lt;rsi&gt; supported in skim() too:</span>
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/skim.html" class="external-link">skim</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
<span class="fu">skim</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
<span class="op">}</span>
<span class="co"># }</span>
<span class="co"># For INTERPRETING disk diffusion and MIC values -----------------------</span>
@ -423,13 +423,11 @@ 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>

6
docs/reference/atc_online.html
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@ -257,13 +257,11 @@ 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>

6
docs/reference/availability.html
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@ -216,13 +216,11 @@ 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>

6
docs/reference/bug_drug_combinations.html
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@ -265,13 +265,11 @@ 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>

4
docs/reference/catalogue_of_life.html
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@ -17,7 +17,11 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span>
</div>

4
docs/reference/catalogue_of_life_version.html
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@ -17,7 +17,11 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span>
</div>

6
docs/reference/count.html
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@ -358,13 +358,11 @@ 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>

6
docs/reference/custom_eucast_rules.html
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@ -301,13 +301,11 @@ 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>

8
docs/reference/dosage.html
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@ -17,7 +17,11 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span>
</div>
@ -207,8 +211,12 @@ Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<<<<<<< HEAD
<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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</div>
</footer></div>

6
docs/reference/eucast_rules.html
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@ -334,13 +334,11 @@ 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>

8
docs/reference/example_isolates.html
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@ -17,7 +17,11 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span>
</div>
@ -204,8 +208,12 @@ Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<<<<<<< HEAD
<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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
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@ -17,7 +17,11 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span>
</div>
@ -199,8 +203,12 @@ Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<<<<<<< HEAD
<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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</div>
</footer></div>

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@ -371,13 +371,11 @@ 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>
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@ -17,7 +17,11 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
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=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span>
</div>

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@ -278,13 +278,11 @@ 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>
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</div>
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@ -304,13 +304,11 @@ 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>
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@ -395,13 +395,11 @@ 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>
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6
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@ -243,13 +243,11 @@ 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>
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@ -157,10 +157,7 @@
<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>
@ -176,9 +173,7 @@ codes.</p>
<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>
@ -198,13 +193,7 @@ from clinical text records, using <code><a href="../reference/ab_from_text.html"
<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>
@ -228,14 +217,7 @@ rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a>
<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>
@ -287,9 +269,7 @@ microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).
<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>
@ -353,9 +333,7 @@ information about how to work with functions in this package.</p>
<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>
@ -403,8 +381,7 @@ be useful: <code>if (x %like% y) {...}</code>.</p>
<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>
@ -420,9 +397,7 @@ added to this package for convenience.</p>
<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>
@ -437,13 +412,11 @@ version.</p>
<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>
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@ -17,7 +17,11 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span>
</div>
@ -215,8 +219,12 @@ Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<<<<<<< HEAD
<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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</div>
</footer></div>

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@ -221,13 +221,11 @@ 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>
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@ -242,13 +242,11 @@ 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>
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@ -308,13 +308,11 @@ 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>
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@ -210,13 +210,11 @@ 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>
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@ -211,13 +211,11 @@ 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>
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@ -260,13 +260,11 @@ 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>
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6
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@ -352,13 +352,11 @@ 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>
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@ -17,7 +17,11 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span>
</div>

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@ -17,7 +17,11 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span>
</div>

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</button>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
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@ -231,13 +231,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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@ -433,13 +433,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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@ -267,13 +267,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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@ -266,13 +266,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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@ -332,13 +332,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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@ -381,13 +381,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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docs/reference/random.html
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@ -232,13 +232,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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@ -358,13 +358,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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@ -17,7 +17,11 @@
</button>
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=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span>
</div>
@ -213,8 +217,12 @@ Erwin E. A. Hassing.</p>
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<div class="pkgdown">
<<<<<<< HEAD
<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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</div>
</footer></div>

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@ -210,13 +210,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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@ -237,13 +237,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
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