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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9063</small>
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articles/AMR.html
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articles/resistance_predict.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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authors.html
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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index.html
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@ -35,7 +35,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9063</small>
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news/index.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9063</small>
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@ -53,18 +53,18 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9063" id="amr-2119063">AMR 2.1.1.9063<a class="anchor" aria-label="anchor" href="#amr-2119063"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9066" id="amr-2119066">AMR 2.1.1.9066<a class="anchor" aria-label="anchor" href="#amr-2119066"></a></h2>
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p>
<div class="section level5">
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9063">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9063"></a></h5>
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9066">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9066"></a></h5>
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
</div>
<div class="section level3">
<h3 id="breaking-2-1-1-9063">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9063"></a></h3>
<h3 id="breaking-2-1-1-9066">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9066"></a></h3>
<ul><li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over a year ago</li>
</ul></div>
<div class="section level3">
<h3 id="new-2-1-1-9063">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9063"></a></h3>
<h3 id="new-2-1-1-9066">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9066"></a></h3>
<ul><li>One Health implementation
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for animal breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
<li>The <code>clinical_breakpoints</code> data set contains all these breakpoints, and can be downloaded on our <a href="https://msberends.github.io/AMR/articles/datasets.html">download page</a>.</li>
@ -97,7 +97,7 @@
</ul></li>
</ul></div>
<div class="section level3">
<h3 id="changed-2-1-1-9063">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9063"></a></h3>
<h3 id="changed-2-1-1-9066">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9066"></a></h3>
<ul><li>SIR interpretation
<ul><li>It is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
<li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
@ -137,7 +137,7 @@
<li>Fixed a bug for when <code><a href="../reference/antibiogram.html">antibiogram()</a></code> returns an empty data set</li>
</ul></div>
<div class="section level3">
<h3 id="other-2-1-1-9063">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9063"></a></h3>
<h3 id="other-2-1-1-9066">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9066"></a></h3>
<ul><li>Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
</ul></div>
</div>

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pkgdown.yml
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resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
WHONET: WHONET.html
last_built: 2024-07-16T12:57Z
last_built: 2024-07-16T14:13Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

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reference/AMR-options.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9063</small>
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reference/AMR.html
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@ -21,7 +21,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
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reference/WHOCC.html
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reference/WHONET.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/ab_from_text.html
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reference/ab_property.html
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reference/add_custom_antimicrobials.html
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reference/add_custom_microorganisms.html
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reference/age.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/age_groups.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/antibiogram.html
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reference/antibiotic_class_selectors.html
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@ -9,7 +9,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
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reference/antibiotics.html
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@ -7,7 +7,7 @@
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reference/as.ab.html
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@ -7,7 +7,7 @@
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reference/as.av.html
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@ -7,7 +7,7 @@
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reference/as.disk.html
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reference/as.mic.html
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reference/as.mo.html
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@ -7,7 +7,7 @@
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@ -158,7 +158,7 @@
<p>Values that cannot be coerced will be considered 'unknown' and will be returned as the MO code <code>UNKNOWN</code> with a warning.</p>
<p>Use the <code><a href="mo_property.html">mo_*</a></code> functions to get properties based on the returned code, see <em>Examples</em>.</p>
<p>The <code>as.mo()</code> function uses a novel <a href="mo_matching_score.html">matching score algorithm</a> (see <em>Matching Score for Microorganisms</em> below) to match input against the <a href="microorganisms.html">available microbial taxonomy</a> in this package. This will lead to the effect that e.g. <code>"E. coli"</code> (a microorganism highly prevalent in humans) will return the microbial ID of <em>Escherichia coli</em> and not <em>Entamoeba coli</em> (a microorganism less prevalent in humans), although the latter would alphabetically come first.</p>
<p>With <code>Becker = TRUE</code>, the following 85 staphylococci will be converted to the <strong>coagulase-negative group</strong>: <em>S. argensis</em>, <em>S. arlettae</em>, <em>S. auricularis</em>, <em>S. borealis</em>, <em>S. caeli</em>, <em>S. caledonicus</em>, <em>S. canis</em>, <em>S. capitis</em>, <em>S. capitis capitis</em>, <em>S. capitis urealyticus</em>, <em>S. capitis ureolyticus</em>, <em>S. caprae</em>, <em>S. carnosus</em>, <em>S. carnosus carnosus</em>, <em>S. carnosus utilis</em>, <em>S. casei</em>, <em>S. caseolyticus</em>, <em>S. chromogenes</em>, <em>S. cohnii</em>, <em>S. cohnii cohnii</em>, <em>S. cohnii urealyticum</em>, <em>S. cohnii urealyticus</em>, <em>S. condimenti</em>, <em>S. croceilyticus</em>, <em>S. debuckii</em>, <em>S. devriesei</em>, <em>S. durrellii</em>, <em>S. edaphicus</em>, <em>S. epidermidis</em>, <em>S. equorum</em>, <em>S. equorum equorum</em>, <em>S. equorum linens</em>, <em>S. felis</em>, <em>S. fleurettii</em>, <em>S. gallinarum</em>, <em>S. haemolyticus</em>, <em>S. hominis</em>, <em>S. hominis hominis</em>, <em>S. hominis novobiosepticus</em>, <em>S. jettensis</em>, <em>S. kloosii</em>, <em>S. lentus</em>, <em>S. lloydii</em>, <em>S. lugdunensis</em>, <em>S. massiliensis</em>, <em>S. microti</em>, <em>S. muscae</em>, <em>S. nepalensis</em>, <em>S. pasteuri</em>, <em>S. petrasii</em>, <em>S. petrasii croceilyticus</em>, <em>S. petrasii jettensis</em>, <em>S. petrasii petrasii</em>, <em>S. petrasii pragensis</em>, <em>S. pettenkoferi</em>, <em>S. piscifermentans</em>, <em>S. pragensis</em>, <em>S. pseudoxylosus</em>, <em>S. pulvereri</em>, <em>S. ratti</em>, <em>S. rostri</em>, <em>S. saccharolyticus</em>, <em>S. saprophyticus</em>, <em>S. saprophyticus bovis</em>, <em>S. saprophyticus saprophyticus</em>, <em>S. schleiferi</em>, <em>S. schleiferi schleiferi</em>, <em>S. sciuri</em>, <em>S. sciuri carnaticus</em>, <em>S. sciuri lentus</em>, <em>S. sciuri rodentium</em>, <em>S. sciuri sciuri</em>, <em>S. simulans</em>, <em>S. stepanovicii</em>, <em>S. succinus</em>, <em>S. succinus casei</em>, <em>S. succinus succinus</em>, <em>S. taiwanensis</em>, <em>S. urealyticus</em>, <em>S. ureilyticus</em>, <em>S. veratri</em>, <em>S. vitulinus</em>, <em>S. vitulus</em>, <em>S. warneri</em>, and <em>S. xylosus</em>.<br> The following 16 staphylococci will be converted to the <strong>coagulase-positive group</strong>: <em>S. agnetis</em>, <em>S. argenteus</em>, <em>S. coagulans</em>, <em>S. cornubiensis</em>, <em>S. delphini</em>, <em>S. hyicus</em>, <em>S. hyicus chromogenes</em>, <em>S. hyicus hyicus</em>, <em>S. intermedius</em>, <em>S. lutrae</em>, <em>S. pseudintermedius</em>, <em>S. roterodami</em>, <em>S. schleiferi coagulans</em>, <em>S. schweitzeri</em>, <em>S. simiae</em>, and <em>S. singaporensis</em>.</p>
<p>With <code>Becker = TRUE</code>, the following 89 staphylococci will be converted to the <strong>coagulase-negative group</strong>: <em>S. americanisciuri</em>, <em>S. argensis</em>, <em>S. arlettae</em>, <em>S. auricularis</em>, <em>S. borealis</em>, <em>S. brunensis</em>, <em>S. caeli</em>, <em>S. caledonicus</em>, <em>S. canis</em>, <em>S. capitis</em>, <em>S. capitis capitis</em>, <em>S. capitis urealyticus</em>, <em>S. capitis ureolyticus</em>, <em>S. caprae</em>, <em>S. carnosus</em>, <em>S. carnosus carnosus</em>, <em>S. carnosus utilis</em>, <em>S. casei</em>, <em>S. caseolyticus</em>, <em>S. chromogenes</em>, <em>S. cohnii</em>, <em>S. cohnii cohnii</em>, <em>S. cohnii urealyticum</em>, <em>S. cohnii urealyticus</em>, <em>S. condimenti</em>, <em>S. croceilyticus</em>, <em>S. debuckii</em>, <em>S. devriesei</em>, <em>S. durrellii</em>, <em>S. edaphicus</em>, <em>S. epidermidis</em>, <em>S. equorum</em>, <em>S. equorum equorum</em>, <em>S. equorum linens</em>, <em>S. felis</em>, <em>S. fleurettii</em>, <em>S. gallinarum</em>, <em>S. haemolyticus</em>, <em>S. hominis</em>, <em>S. hominis hominis</em>, <em>S. hominis novobiosepticus</em>, <em>S. jettensis</em>, <em>S. kloosii</em>, <em>S. lentus</em>, <em>S. lloydii</em>, <em>S. lugdunensis</em>, <em>S. marylandisciuri</em>, <em>S. massiliensis</em>, <em>S. microti</em>, <em>S. muscae</em>, <em>S. nepalensis</em>, <em>S. pasteuri</em>, <em>S. petrasii</em>, <em>S. petrasii croceilyticus</em>, <em>S. petrasii jettensis</em>, <em>S. petrasii petrasii</em>, <em>S. petrasii pragensis</em>, <em>S. pettenkoferi</em>, <em>S. piscifermentans</em>, <em>S. pragensis</em>, <em>S. pseudoxylosus</em>, <em>S. pulvereri</em>, <em>S. ratti</em>, <em>S. rostri</em>, <em>S. saccharolyticus</em>, <em>S. saprophyticus</em>, <em>S. saprophyticus bovis</em>, <em>S. saprophyticus saprophyticus</em>, <em>S. schleiferi</em>, <em>S. schleiferi schleiferi</em>, <em>S. sciuri</em>, <em>S. sciuri carnaticus</em>, <em>S. sciuri lentus</em>, <em>S. sciuri rodentium</em>, <em>S. sciuri sciuri</em>, <em>S. shinii</em>, <em>S. simulans</em>, <em>S. stepanovicii</em>, <em>S. succinus</em>, <em>S. succinus casei</em>, <em>S. succinus succinus</em>, <em>S. taiwanensis</em>, <em>S. urealyticus</em>, <em>S. ureilyticus</em>, <em>S. veratri</em>, <em>S. vitulinus</em>, <em>S. vitulus</em>, <em>S. warneri</em>, and <em>S. xylosus</em>.<br> The following 16 staphylococci will be converted to the <strong>coagulase-positive group</strong>: <em>S. agnetis</em>, <em>S. argenteus</em>, <em>S. coagulans</em>, <em>S. cornubiensis</em>, <em>S. delphini</em>, <em>S. hyicus</em>, <em>S. hyicus chromogenes</em>, <em>S. hyicus hyicus</em>, <em>S. intermedius</em>, <em>S. lutrae</em>, <em>S. pseudintermedius</em>, <em>S. roterodami</em>, <em>S. schleiferi coagulans</em>, <em>S. schweitzeri</em>, <em>S. simiae</em>, and <em>S. singaporensis</em>.</p>
<p>With <code>Lancefield = TRUE</code>, the following streptococci will be converted to their corresponding Lancefield group: <em>S. agalactiae</em> (Group B), <em>S. anginosus anginosus</em> (Group F), <em>S. anginosus whileyi</em> (Group F), <em>S. anginosus</em> (Group F), <em>S. canis</em> (Group G), <em>S. dysgalactiae dysgalactiae</em> (Group C), <em>S. dysgalactiae equisimilis</em> (Group C), <em>S. dysgalactiae</em> (Group C), <em>S. equi equi</em> (Group C), <em>S. equi ruminatorum</em> (Group C), <em>S. equi zooepidemicus</em> (Group C), <em>S. equi</em> (Group C), <em>S. pyogenes</em> (Group A), <em>S. salivarius salivarius</em> (Group K), <em>S. salivarius thermophilus</em> (Group K), <em>S. salivarius</em> (Group K), and <em>S. sanguinis</em> (Group H).</p><div class="section">
<h3 id="coping-with-uncertain-results">Coping with Uncertain Results<a class="anchor" aria-label="anchor" href="#coping-with-uncertain-results"></a></h3>

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reference/as.sir.html
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@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
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@ -760,16 +760,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 59 × 16</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_given mo_given host_given ab mo </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-07-16 <span style="color: #949494;">12:58:17</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-07-16 <span style="color: #949494;">12:58:23</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-07-16 <span style="color: #949494;">12:58:24</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-07-16 <span style="color: #949494;">12:58:24</span> 4 genta Escheri… cattle GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-07-16 <span style="color: #949494;">12:58:25</span> 4 genta Escheri… cattle GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-07-16 <span style="color: #949494;">12:58:17</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-07-16 <span style="color: #949494;">12:58:23</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-07-16 <span style="color: #949494;">12:58:24</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-07-16 <span style="color: #949494;">12:58:24</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-07-16 <span style="color: #949494;">12:58:25</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-07-16 <span style="color: #949494;">14:14:03</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-07-16 <span style="color: #949494;">14:14:04</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-07-16 <span style="color: #949494;">14:14:04</span> 4 genta Escheri… cattle GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-07-16 <span style="color: #949494;">14:14:05</span> 4 genta Escheri… cattle GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-07-16 <span style="color: #949494;">14:14:03</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-07-16 <span style="color: #949494;">14:14:04</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-07-16 <span style="color: #949494;">14:14:04</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-07-16 <span style="color: #949494;">14:14:05</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-07-16 <span style="color: #949494;">14:14:03</span> 2 cipro Escheri… human CIP B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-07-16 <span style="color: #949494;">14:14:04</span> 2 cipro Escheri… human CIP B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 49 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 9 more variables: host &lt;chr&gt;, method &lt;chr&gt;, input &lt;dbl&gt;, outcome &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>

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reference/atc_online.html
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@ -7,7 +7,7 @@
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reference/av_property.html
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reference/availability.html
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reference/bug_drug_combinations.html
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@ -7,7 +7,7 @@
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reference/clinical_breakpoints.html
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@ -13,7 +13,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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reference/example_isolates_unclean.html
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@ -7,7 +7,7 @@
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reference/export_ncbi_biosample.html
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@ -7,7 +7,7 @@
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reference/first_isolate.html
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@ -9,7 +9,7 @@
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reference/g.test.html
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@ -7,7 +7,7 @@
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reference/get_episode.html
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@ -7,7 +7,7 @@
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reference/ggplot_pca.html
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@ -7,7 +7,7 @@
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reference/ggplot_sir.html
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@ -7,7 +7,7 @@
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reference/guess_ab_col.html
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@ -7,7 +7,7 @@
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reference/index.html
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@ -7,7 +7,7 @@
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reference/intrinsic_resistant.html
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@ -7,7 +7,7 @@
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reference/italicise_taxonomy.html
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@ -7,7 +7,7 @@
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reference/join.html
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@ -7,7 +7,7 @@
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reference/key_antimicrobials.html
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@ -7,7 +7,7 @@
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reference/kurtosis.html
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@ -7,7 +7,7 @@
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reference/like.html
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@ -7,7 +7,7 @@
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reference/mdro.html
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@ -7,7 +7,7 @@
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reference/mean_amr_distance.html
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@ -7,7 +7,7 @@
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reference/microorganisms.codes.html
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@ -7,7 +7,7 @@
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reference/microorganisms.groups.html
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@ -7,7 +7,7 @@
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reference/microorganisms.html
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@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
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reference/mo_matching_score.html
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@ -7,7 +7,7 @@
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reference/mo_property.html
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@ -7,7 +7,7 @@
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reference/mo_source.html
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@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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reference/pca.html
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@ -7,7 +7,7 @@
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reference/plot.html
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@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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reference/proportion.html
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@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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reference/random.html
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@ -7,7 +7,7 @@
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reference/resistance_predict.html
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@ -7,7 +7,7 @@
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reference/skewness.html
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@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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reference/translate.html
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search.json
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