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(v1.8.1.9002) fix for table() on MICs

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dr. M.S. (Matthijs) Berends
2022-05-09 17:08:40 +02:00
parent 4754848e96
commit 152db9d1b5
21 changed files with 742 additions and 2179 deletions
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6
docs/reference/antibiotic_class_selectors.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9002</span>
</span>
</div>
@ -30,7 +30,7 @@
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-question-circle"></span>
How to
@ -434,7 +434,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</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> 2.0.3.</p>
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8
docs/reference/as.rsi.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9002</span>
</span>
</div>
@ -30,7 +30,7 @@
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-question-circle"></span>
How to
@ -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">skim</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</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="op">}</span>
<span class="co"># }</span>
<span class="co"># For INTERPRETING disk diffusion and MIC values -----------------------</span>
@ -427,7 +427,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</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> 2.0.3.</p>
</div>
</footer></div>

8
docs/reference/g.test.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9002</span>
</span>
</div>
@ -30,7 +30,7 @@
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-question-circle"></span>
How to
@ -180,7 +180,7 @@
<dd><p>a numeric vector; ignored if <code>x</code> is a matrix. If
<code>x</code> is a factor, <code>y</code> should be a factor of the same length.</p></dd>
<dt>p</dt>
<dd><p>a vector of probabilities of the same length of <code>x</code>.
<dd><p>a vector of probabilities of the same length as <code>x</code>.
An error is given if any entry of <code>p</code> is negative.</p></dd>
<dt>rescale.p</dt>
<dd><p>a logical scalar; if TRUE then <code>p</code> is rescaled
@ -327,7 +327,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>questioni
</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> 2.0.3.</p>
</div>
</footer></div>

6
docs/reference/index.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9002</span>
</span>
</div>
@ -30,7 +30,7 @@
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-question-circle"></span>
How to
@ -416,7 +416,7 @@
</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> 2.0.3.</p>
</div>
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6
docs/reference/intrinsic_resistant.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9002</span>
</span>
</div>
@ -30,7 +30,7 @@
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-question-circle"></span>
How to
@ -214,7 +214,7 @@
</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> 2.0.3.</p>
</div>
</footer></div>

8
docs/reference/mdro.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9002</span>
</span>
</div>
@ -30,7 +30,7 @@
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-question-circle"></span>
How to
@ -247,7 +247,7 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
<li><p><code>guideline = "TB"</code></p>
<p>The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (<a href="https://www.who.int/publications/i/item/9789241548809" class="external-link">link</a>)</p></li>
<li><p><code>guideline = "MRGN"</code></p>
<p>The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7; doi: <a href="https://doi.org/10.1186/s13756-015-0047-6" class="external-link">10.1186/s13756-015-0047-6</a></p></li>
<p>The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7; <a href="https://doi.org/10.1186/s13756-015-0047-6" class="external-link">doi:10.1186/s13756-015-0047-6</a></p></li>
<li><p><code>guideline = "BRMO"</code></p>
<p>The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)" (<a href="https://www.rivm.nl/wip-richtlijn-brmo-bijzonder-resistente-micro-organismen-zkh" class="external-link">link</a>)</p></li>
</ul><p>Please suggest your own (country-specific) guidelines by letting us know: <a href="https://github.com/msberends/AMR/issues/new" class="external-link">https://github.com/msberends/AMR/issues/new</a>.</p>
@ -356,7 +356,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</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> 2.0.3.</p>
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16
docs/reference/mo_property.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9002</span>
</span>
</div>
@ -30,7 +30,7 @@
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-question-circle"></span>
How to
@ -295,12 +295,12 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<h2>Source</h2>
<ol><li><p>Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870-926; doi: <a href="https://doi.org/10.1128/CMR.00109-13" class="external-link">10.1128/CMR.00109-13</a></p></li>
<li><p>Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect; doi: <a href="https://doi.org/10.1016/j.cmi.2019.02.028" class="external-link">10.1016/j.cmi.2019.02.028</a></p></li>
<li><p>Becker K <em>et al.</em> <strong>Emergence of coagulase-negative staphylococci</strong> 2020. Expert Rev Anti Infect Ther. 18(4):349-366; doi: <a href="https://doi.org/10.1080/14787210.2020.1730813" class="external-link">10.1080/14787210.2020.1730813</a></p></li>
<li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571-95; doi: <a href="https://doi.org/10.1084/jem.57.4.571" class="external-link">10.1084/jem.57.4.571</a></p></li>
<ol><li><p>Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870-926; <a href="https://doi.org/10.1128/CMR.00109-13" class="external-link">doi:10.1128/CMR.00109-13</a></p></li>
<li><p>Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect; <a href="https://doi.org/10.1016/j.cmi.2019.02.028" class="external-link">doi:10.1016/j.cmi.2019.02.028</a></p></li>
<li><p>Becker K <em>et al.</em> <strong>Emergence of coagulase-negative staphylococci</strong> 2020. Expert Rev Anti Infect Ther. 18(4):349-366; <a href="https://doi.org/10.1080/14787210.2020.1730813" class="external-link">doi:10.1080/14787210.2020.1730813</a></p></li>
<li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571-95; <a href="https://doi.org/10.1084/jem.57.4.571" class="external-link">doi:10.1084/jem.57.4.571</a></p></li>
<li><p>Catalogue of Life: 2019 Annual Checklist, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a></p></li>
<li><p>List of Prokaryotic names with Standing in Nomenclature (5 October 2021), doi: <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">10.1099/ijsem.0.004332</a></p></li>
<li><p>List of Prokaryotic names with Standing in Nomenclature (5 October 2021), <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a></p></li>
<li><p>US Edition of SNOMED CT from 1 September 2020, retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009</a></p></li>
</ol></div>
<div id="reference-data-publicly-available">
@ -437,7 +437,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</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> 2.0.3.</p>
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