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+45
-45
@@ -61,27 +61,35 @@
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Casper J. Albers</strong>. Thesis advisor. <a href="https://orcid.org/0000-0002-9213-6743" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
<p><strong>Andrew P. Norgan</strong>. Contributor. <a href="https://orcid.org/0000-0002-2955-2066" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Larisse Bolton</strong>. Contributor. <a href="https://orcid.org/0000-0001-7879-2173" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
<p><strong>Anita Williams</strong>. Contributor. <a href="https://orcid.org/0000-0002-5295-8451" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Peter Dutey-Magni</strong>. Contributor. <a href="https://orcid.org/0000-0002-8942-9836" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
<p><strong>Annick Lenglet</strong>. Contributor. <a href="https://orcid.org/0000-0003-2013-8405" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Judith M. Fonville</strong>. Contributor.
|
||||
<p><strong>Anthony Underwood</strong>. Contributor. <a href="https://orcid.org/0000-0002-8547-4277" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Alex W. Friedrich</strong>. Thesis advisor. <a href="https://orcid.org/0000-0003-4881-038X" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
<p><strong>Anton Mymrikov</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Corinna Glasner</strong>. Thesis advisor. <a href="https://orcid.org/0000-0003-1241-1328" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
<p><strong>Bart C. Meijer</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Christian F. Luz</strong>. Contributor. <a href="https://orcid.org/0000-0001-5809-5995" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Dmytro Mykhailenko</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
@@ -93,63 +101,55 @@
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Annick Lenglet</strong>. Contributor. <a href="https://orcid.org/0000-0003-2013-8405" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Christian F. Luz</strong>. Contributor. <a href="https://orcid.org/0000-0001-5809-5995" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Bart C. Meijer</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Dmytro Mykhailenko</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Anton Mymrikov</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Andrew P. Norgan</strong>. Contributor. <a href="https://orcid.org/0000-0002-2955-2066" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Sofia Ny</strong>. Contributor. <a href="https://orcid.org/0000-0002-2017-1363" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Matthew Saab</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Jonas Salm</strong>. Contributor.
|
||||
<p><strong>Jason Stull</strong>. Contributor. <a href="https://orcid.org/0000-0002-9028-8153" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Javier Sanchez</strong>. Contributor. <a href="https://orcid.org/0000-0003-2605-8094" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Jonas Salm</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Judith M. Fonville</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Larisse Bolton</strong>. Contributor. <a href="https://orcid.org/0000-0001-7879-2173" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Matthew Saab</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Peter Dutey-Magni</strong>. Contributor. <a href="https://orcid.org/0000-0002-8942-9836" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Rogier P. Schade</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Sofia Ny</strong>. Contributor. <a href="https://orcid.org/0000-0002-2017-1363" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Alex W. Friedrich</strong>. Thesis advisor. <a href="https://orcid.org/0000-0003-4881-038X" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Bhanu N. M. Sinha</strong>. Thesis advisor. <a href="https://orcid.org/0000-0003-1634-0010" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Jason Stull</strong>. Contributor. <a href="https://orcid.org/0000-0002-9028-8153" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
<p><strong>Casper J. Albers</strong>. Thesis advisor. <a href="https://orcid.org/0000-0002-9213-6743" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Anthony Underwood</strong>. Contributor. <a href="https://orcid.org/0000-0002-8547-4277" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Anita Williams</strong>. Contributor. <a href="https://orcid.org/0000-0002-5295-8451" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
<p><strong>Corinna Glasner</strong>. Thesis advisor. <a href="https://orcid.org/0000-0003-1241-1328" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
</p>
|
||||
</li>
|
||||
</ul></div>
|
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|
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@@ -63,6 +63,41 @@ $(document).ready(function() {
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$('img[src="../logo.svg"]').attr('src', '../logo_python.svg'); /* replace base logo */
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$('img[src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/AMRforRGPT.svg"]').attr('src', 'https://github.com/msberends/AMR/raw/main/pkgdown/assets/AMRforRGPT_python.svg'); /* replace GPT logo */
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}
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||||
// add country flags
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||||
function country_flag(x) {
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if (typeof(x) != "undefined") {
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x = x.replace("Alex", '<img src="lang_de.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Alex');
|
||||
x = x.replace("Andrew", '<img src="lang_us.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Andrew');
|
||||
x = x.replace("Anita", '<img src="lang_au.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Anita');
|
||||
x = x.replace("Annick", '<img src="lang_nl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Annick');
|
||||
x = x.replace("Anthony", '<img src="lang_en.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Anthony');
|
||||
x = x.replace("Anton", '<img src="lang_uk.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Anton');
|
||||
x = x.replace("Bart", '<img src="lang_nl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Bart');
|
||||
x = x.replace("Bhanu", '<img src="lang_nl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Bhanu');
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||||
x = x.replace("Casper", '<img src="lang_nl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Casper');
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||||
x = x.replace("Christian", '<img src="lang_de.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Christian');
|
||||
x = x.replace("Corinna", '<img src="lang_nl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Corinna');
|
||||
x = x.replace("Dennis", '<img src="lang_nl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Dennis');
|
||||
x = x.replace("Dmytro", '<img src="lang_uk.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Dmytro');
|
||||
x = x.replace("Eric", '<img src="lang_nl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Eric');
|
||||
x = x.replace("Erwin", '<img src="lang_nl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Erwin');
|
||||
x = x.replace("Gwen", '<img src="lang_en.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Gwen');
|
||||
x = x.replace("Jason", '<img src="lang_ca.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Jason');
|
||||
x = x.replace("Javier", '<img src="lang_ca.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Javier');
|
||||
x = x.replace("Jonas", '<img src="lang_de.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Jonas');
|
||||
x = x.replace("Judith", '<img src="lang_nl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Judith');
|
||||
x = x.replace("Larisse", '<img src="lang_sa.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Larisse');
|
||||
x = x.replace("Matthew", '<img src="lang_ca.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Matthew');
|
||||
x = x.replace("Matthijs", '<img src="lang_nl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Matthijs');
|
||||
x = x.replace("Peter", '<img src="lang_en.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Peter');
|
||||
x = x.replace("Rogier", '<img src="lang_nl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Rogier');
|
||||
x = x.replace("Sofia", '<img src="lang_sv.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Sofia');
|
||||
}
|
||||
return(x);
|
||||
}
|
||||
$(".template-authors").html(country_flag($(".template-authors").html()));
|
||||
$(".template-citation-authors").html(country_flag($(".template-citation-authors").html()));
|
||||
|
||||
// add doctoral titles to authors
|
||||
function doct_tit(x) {
|
||||
|
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+24
@@ -0,0 +1,24 @@
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||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="1280" height="640" viewBox="0 0 10080 5040">
|
||||
<defs>
|
||||
<clipPath id="c1"><path d="M0,0H6V3H0z"/></clipPath>
|
||||
<clipPath id="c2"><path d="M0,0V1.5H6V3H6zM6,0H3V3H0V3z"/></clipPath>
|
||||
<path id="Star7" d="M0,-360 69.421398,-144.155019 281.459334,-224.456329 155.988466,-35.603349 350.974048,80.107536 125.093037,99.758368 156.198146,324.348792 0,160 -156.198146,324.348792 -125.093037,99.758368 -350.974048,80.107536 -155.988466,-35.603349 -281.459334,-224.456329 -69.421398,-144.155019z"/>
|
||||
<path id="Star5" d="M0,-210 54.859957,-75.508253 199.721868,-64.893569 88.765275,28.841586 123.434903,169.893569 0,93.333333 -123.434903,169.893569 -88.765275,28.841586 -199.721868,-64.893569 -54.859957,-75.508253z"/>
|
||||
</defs>
|
||||
<g transform="scale(840)">
|
||||
<rect width="12" height="6" fill="#012169"/>
|
||||
<path d="M0,0 6,3M6,0 0,3" stroke="#fff" stroke-width="0.6" clip-path="url(#c1)"/>
|
||||
<path d="M0,0 6,3M6,0 0,3" stroke="#e4002b" stroke-width="0.4" clip-path="url(#c2)"/>
|
||||
<path d="M3,0V3M0,1.5H6" stroke="#fff"/>
|
||||
<path d="M3,0V3M0,1.5H6" stroke="#e4002b" stroke-width="0.6"/>
|
||||
</g>
|
||||
<g fill="#fff">
|
||||
<use id="Comwlth" xlink:href="#Star7" transform="translate(2520, 3780) scale(2.1)"/>
|
||||
<use id="αCrucis" xlink:href="#Star7" x="7560" y="4200"/>
|
||||
<use id="βCrucis" xlink:href="#Star7" x="6300" y="2205"/>
|
||||
<use id="γCrucis" xlink:href="#Star7" x="7560" y="840"/>
|
||||
<use id="δCrucis" xlink:href="#Star7" x="8680" y="1869"/>
|
||||
<use id="εCrucis" xlink:href="#Star5" x="8064" y="2730"/>
|
||||
</g>
|
||||
</svg>
|
||||
|
After Width: | Height: | Size: 1.6 KiB |
@@ -0,0 +1,5 @@
|
||||
<svg xmlns="http://www.w3.org/2000/svg" width="1200" height="600" viewBox="0 0 9600 4800">
|
||||
<title>Flag of Canada (Pantone colours)</title>
|
||||
<path fill="#d52b1e" d="m0 0h2400l99 99h4602l99-99h2400v4800h-2400l-99-99h-4602l-99 99H0z"/>
|
||||
<path fill="#fff" d="m2400 0h4800v4800h-4800zm2490 4430-45-863a95 95 0 0 1 111-98l859 151-116-320a65 65 0 0 1 20-73l941-762-212-99a65 65 0 0 1-34-79l186-572-542 115a65 65 0 0 1-73-38l-105-247-423 454a65 65 0 0 1-111-57l204-1052-327 189a65 65 0 0 1-91-27l-332-652-332 652a65 65 0 0 1-91 27l-327-189 204 1052a65 65 0 0 1-111 57l-423-454-105 247a65 65 0 0 1-73 38l-542-115 186 572a65 65 0 0 1-34 79l-212 99 941 762a65 65 0 0 1 20 73l-116 320 859-151a95 95 0 0 1 111 98l-45 863z"/>
|
||||
</svg>
|
||||
|
After Width: | Height: | Size: 720 B |
+18
@@ -0,0 +1,18 @@
|
||||
<svg xmlns="http://www.w3.org/2000/svg" width="900" height="600" viewBox="0 0 90 60">
|
||||
<title>Flag of South Africa</title>
|
||||
<defs>
|
||||
<clipPath id="t">
|
||||
<path d="m0 0 45 30L0 60z"/>
|
||||
</clipPath>
|
||||
<clipPath id="f">
|
||||
<path d="m0 0h90v60H0z"/>
|
||||
</clipPath>
|
||||
</defs>
|
||||
<path fill="#e03c31" d="m0 0h90v30H45z"/>
|
||||
<path fill="#001489" d="m0 60h90V30H45z"/>
|
||||
<g clip-path="url(#f)" fill="none">
|
||||
<path stroke="#fff" stroke-width="20" d="m90 30H45L0 0v60l45-30"/>
|
||||
<path fill="#000" stroke="#ffb81c" stroke-width="20" clip-path="url(#t)" d="m0 0 45 30L0 60"/>
|
||||
<path stroke="#007749" stroke-width="12" d="m0 0 45 30h45M0 60l45-30"/>
|
||||
</g>
|
||||
</svg>
|
||||
|
After Width: | Height: | Size: 646 B |
@@ -0,0 +1 @@
|
||||
<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="1235" height="650" viewBox="0 0 7410 3900"><path d="M0,0h7410v3900H0" fill="#b31942"/><path d="M0,450H7410m0,600H0m0,600H7410m0,600H0m0,600H7410m0,600H0" stroke="#FFF" stroke-width="300"/><path d="M0,0h2964v2100H0" fill="#0a3161"/><g fill="#FFF"><g id="s18"><g id="s9"><g id="s5"><g id="s4"><path id="s" d="M247,90 317.534230,307.082039 132.873218,172.917961H361.126782L176.465770,307.082039z"/><use xlink:href="#s" y="420"/><use xlink:href="#s" y="840"/><use xlink:href="#s" y="1260"/></g><use xlink:href="#s" y="1680"/></g><use xlink:href="#s4" x="247" y="210"/></g><use xlink:href="#s9" x="494"/></g><use xlink:href="#s18" x="988"/><use xlink:href="#s9" x="1976"/><use xlink:href="#s5" x="2470"/></g></svg>
|
||||
|
After Width: | Height: | Size: 799 B |
+1
-1
@@ -11,7 +11,7 @@ articles:
|
||||
resistance_predict: resistance_predict.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
WHONET: WHONET.html
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last_built: 2024-12-09T09:33Z
|
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last_built: 2024-12-09T13:46Z
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urls:
|
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reference: https://msberends.github.io/AMR/reference
|
||||
article: https://msberends.github.io/AMR/articles
|
||||
+10
-10
@@ -785,16 +785,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 57 × 16</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> datetime index ab_given mo_given host_given ab mo </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2024-12-09 <span style="color: #949494;">09:34:39</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2024-12-09 <span style="color: #949494;">09:34:46</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2024-12-09 <span style="color: #949494;">09:34:46</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2024-12-09 <span style="color: #949494;">09:34:47</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2024-12-09 <span style="color: #949494;">09:34:47</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2024-12-09 <span style="color: #949494;">09:34:39</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2024-12-09 <span style="color: #949494;">09:34:46</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2024-12-09 <span style="color: #949494;">09:34:46</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2024-12-09 <span style="color: #949494;">09:34:47</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2024-12-09 <span style="color: #949494;">09:34:47</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2024-12-09 <span style="color: #949494;">13:47:36</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2024-12-09 <span style="color: #949494;">13:47:43</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2024-12-09 <span style="color: #949494;">13:47:43</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2024-12-09 <span style="color: #949494;">13:47:44</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2024-12-09 <span style="color: #949494;">13:47:44</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2024-12-09 <span style="color: #949494;">13:47:36</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2024-12-09 <span style="color: #949494;">13:47:43</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2024-12-09 <span style="color: #949494;">13:47:43</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2024-12-09 <span style="color: #949494;">13:47:44</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2024-12-09 <span style="color: #949494;">13:47:44</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 47 more rows</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 9 more variables: host <chr>, method <chr>, input <dbl>, outcome <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
|
||||
|
||||
+1
-1
@@ -1 +1 @@
|
||||
[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) reliable data thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations SIR values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables. AMR package contains data set example_isolates_unclean, might look data users extracted laboratory systems: AMR data analysis, like microorganism column contain valid, --date taxonomy, antibiotic columns cleaned SIR values well.","code":"library(dplyr) library(ggplot2) library(AMR) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\")) example_isolates_unclean #> # A tibble: 3,000 × 8 #> patient_id hospital date bacteria AMX AMC CIP GEN #> <chr> <chr> <date> <chr> <chr> <chr> <chr> <chr> #> 1 J3 A 2012-11-21 E. coli R I S S #> 2 R7 A 2018-04-03 K. pneumoniae R I S S #> 3 P3 A 2014-09-19 E. coli R S S S #> 4 P10 A 2015-12-10 E. coli S I S S #> 5 B7 A 2015-03-02 E. coli S S S S #> 6 W3 A 2018-03-31 S. aureus R S R S #> 7 J8 A 2016-06-14 E. coli R S S S #> 8 M3 A 2015-10-25 E. coli R S S S #> 9 J3 A 2019-06-19 E. coli S S S S #> 10 G6 A 2015-04-27 S. aureus S S S S #> # ℹ 2,990 more rows # we will use 'our_data' as the data set name for this tutorial our_data <- example_isolates_unclean"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"taxonomy-of-microorganisms","dir":"Articles","previous_headings":"Preparation","what":"Taxonomy of microorganisms","title":"How to conduct AMR data analysis","text":".mo(), users can transform arbitrary microorganism names codes current taxonomy. AMR package contains --date taxonomic data. specific, currently included data retrieved 24 Jun 2024. codes AMR packages come .mo() short, still human readable. importantly, .mo() supports kinds input: first character codes denote taxonomic kingdom, Bacteria (B), Fungi (F), Protozoa (P). AMR package also contain functions directly retrieve taxonomic properties, name, genus, species, family, order, even Gram-stain. start mo_ use .mo() internally, still arbitrary user input can used: Now can thus clean data: Apparently, uncertainty translation taxonomic codes. Let’s check : ’s good.","code":"as.mo(\"Klebsiella pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"K. pneumoniae\") #> ClLine truncated
|
||||
[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) reliable data thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations SIR values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables. AMR package contains data set example_isolates_unclean, might look data users extracted laboratory systems: AMR data analysis, like microorganism column contain valid, --date taxonomy, antibiotic columns cleaned SIR values well.","code":"library(dplyr) library(ggplot2) library(AMR) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\")) example_isolates_unclean #> # A tibble: 3,000 × 8 #> patient_id hospital date bacteria AMX AMC CIP GEN #> <chr> <chr> <date> <chr> <chr> <chr> <chr> <chr> #> 1 J3 A 2012-11-21 E. coli R I S S #> 2 R7 A 2018-04-03 K. pneumoniae R I S S #> 3 P3 A 2014-09-19 E. coli R S S S #> 4 P10 A 2015-12-10 E. coli S I S S #> 5 B7 A 2015-03-02 E. coli S S S S #> 6 W3 A 2018-03-31 S. aureus R S R S #> 7 J8 A 2016-06-14 E. coli R S S S #> 8 M3 A 2015-10-25 E. coli R S S S #> 9 J3 A 2019-06-19 E. coli S S S S #> 10 G6 A 2015-04-27 S. aureus S S S S #> # ℹ 2,990 more rows # we will use 'our_data' as the data set name for this tutorial our_data <- example_isolates_unclean"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"taxonomy-of-microorganisms","dir":"Articles","previous_headings":"Preparation","what":"Taxonomy of microorganisms","title":"How to conduct AMR data analysis","text":".mo(), users can transform arbitrary microorganism names codes current taxonomy. AMR package contains --date taxonomic data. specific, currently included data retrieved 24 Jun 2024. codes AMR packages come .mo() short, still human readable. importantly, .mo() supports kinds input: first character codes denote taxonomic kingdom, Bacteria (B), Fungi (F), Protozoa (P). AMR package also contain functions directly retrieve taxonomic properties, name, genus, species, family, order, even Gram-stain. start mo_ use .mo() internally, still arbitrary user input can used: Now can thus clean data: Apparently, uncertainty translation taxonomic codes. Let’s check : ’s good.","code":"as.mo(\"Klebsiella pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"K. pneumoniae\") #> ClLine truncated
|
||||
Reference in new issue
Block a user