mirror of
https://github.com/msberends/AMR.git
synced 2025-09-03 14:39:37 +02:00
Built site for AMR@2.1.1.9083: 8907e8e
This commit is contained in:
github-actions
@@ -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="">2.1.1.9081</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9083</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -76,10 +76,10 @@
|
||||
</dl></div>
|
||||
<div class="section level2">
|
||||
<h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
|
||||
<p>This algorithm was originally described in: Berends MS <em>et al.</em> (2022). <strong>AMR: An R Package for Working with Antimicrobial Resistance Data</strong>. <em>Journal of Statistical Software</em>, 104(3), 1-31; <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">doi:10.18637/jss.v104.i03</a>
|
||||
<p>This algorithm was originally developed in 2018 and subsequently described in: Berends MS <em>et al.</em> (2022). <strong>AMR: An R Package for Working with Antimicrobial Resistance Data</strong>. <em>Journal of Statistical Software</em>, 104(3), 1-31; <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">doi:10.18637/jss.v104.i03</a>
|
||||
.</p>
|
||||
<p>Later, the work of Bartlett A <em>et al.</em> about bacterial pathogens infecting humans (2022, <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a>
|
||||
) was incorporated.</p>
|
||||
) was incorporated, and optimalisations to the algorithm were made.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="matching-score-for-microorganisms">Matching Score for Microorganisms<a class="anchor" aria-label="anchor" href="#matching-score-for-microorganisms"></a></h2>
|
||||
@@ -92,17 +92,18 @@
|
||||
<li><p>\(l_n\) is the length of \(n\);</p></li>
|
||||
<li><p>\(lev\) is the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance" class="external-link">Levenshtein distance function</a> (counting any insertion as 1, and any deletion or substitution as 2) that is needed to change \(x\) into \(n\);</p></li>
|
||||
<li><p>\(p_n\) is the human pathogenic prevalence group of \(n\), as described below;</p></li>
|
||||
<li><p>\(k_n\) is the taxonomic kingdom of \(n\), set as Bacteria = 1, Fungi = 1.25, Protozoa = 1.5, Archaea = 2, others = 3.</p></li>
|
||||
<li><p>\(k_n\) is the taxonomic kingdom of \(n\), set as Bacteria = 1, Fungi = 1.25, Protozoa = 1.5, Chromista = 1.75, Archaea = 2, others = 3.</p></li>
|
||||
</ul><p>The grouping into human pathogenic prevalence \(p\) is based on recent work from Bartlett <em>et al.</em> (2022, <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a>
|
||||
) who extensively studied medical-scientific literature to categorise all bacterial species into these groups:</p><ul><li><p><strong>Established</strong>, if a taxonomic species has infected at least three persons in three or more references. These records have <code>prevalence = 1.0</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
|
||||
) who extensively studied medical-scientific literature to categorise all bacterial species into these groups:</p><ul><li><p><strong>Established</strong>, if a taxonomic species has infected at least three persons in three or more references. These records have <code>prevalence = 1.15</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
|
||||
<li><p><strong>Putative</strong>, if a taxonomic species has fewer than three known cases. These records have <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
|
||||
</ul><p>Furthermore,</p><ul><li><p>Any genus present in the <strong>established</strong> list also has <code>prevalence = 1.0</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
|
||||
</ul><p>Furthermore,</p><ul><li><p>Genera from the World Health Organization's (WHO) Priority Pathogen List have <code>prevalence = 1.0</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
|
||||
<li><p>Any genus present in the <strong>established</strong> list also has <code>prevalence = 1.15</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
|
||||
<li><p>Any other genus present in the <strong>putative</strong> list has <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
|
||||
<li><p>Any other species or subspecies of which the genus is present in the two aforementioned groups, has <code>prevalence = 1.5</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
|
||||
<li><p>Any <em>non-bacterial</em> genus, species or subspecies of which the genus is present in the following list, has <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set: <em>Absidia</em>, <em>Acanthamoeba</em>, <em>Acremonium</em>, <em>Actinomucor</em>, <em>Aedes</em>, <em>Alternaria</em>, <em>Amoeba</em>, <em>Ancylostoma</em>, <em>Angiostrongylus</em>, <em>Anisakis</em>, <em>Anopheles</em>, <em>Apophysomyces</em>, <em>Arthroderma</em>, <em>Aspergillus</em>, <em>Aureobasidium</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Bipolaris</em>, <em>Blastobotrys</em>, <em>Blastocystis</em>, <em>Blastomyces</em>, <em>Candida</em>, <em>Capillaria</em>, <em>Chaetomium</em>, <em>Chilomastix</em>, <em>Chrysonilia</em>, <em>Chrysosporium</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Clavispora</em>, <em>Coccidioides</em>, <em>Cokeromyces</em>, <em>Conidiobolus</em>, <em>Coniochaeta</em>, <em>Contracaecum</em>, <em>Cordylobia</em>, <em>Cryptococcus</em>, <em>Cryptosporidium</em>, <em>Cunninghamella</em>, <em>Curvularia</em>, <em>Cyberlindnera</em>, <em>Debaryozyma</em>, <em>Demodex</em>, <em>Dermatobia</em>, <em>Dientamoeba</em>, <em>Diphyllobothrium</em>, <em>Dirofilaria</em>, <em>Echinostoma</em>, <em>Entamoeba</em>, <em>Enterobius</em>, <em>Epidermophyton</em>, <em>Exidia</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Fasciola</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Geotrichum</em>, <em>Giardia</em>, <em>Graphium</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Hansenula</em>, <em>Hendersonula</em>, <em>Heterophyes</em>, <em>Histomonas</em>, <em>Histoplasma</em>, <em>Hortaea</em>, <em>Hymenolepis</em>, <em>Hypomyces</em>, <em>Hysterothylacium</em>, <em>Kloeckera</em>, <em>Kluyveromyces</em>, <em>Kodamaea</em>, <em>Lacazia</em>, <em>Leishmania</em>, <em>Lichtheimia</em>, <em>Lodderomyces</em>, <em>Lomentospora</em>, <em>Madurella</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Metagonimus</em>, <em>Meyerozyma</em>, <em>Microsporidium</em>, <em>Microsporum</em>, <em>Millerozyma</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Nannizzia</em>, <em>Necator</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oesophagostomum</em>, <em>Oidiodendron</em>, <em>Opisthorchis</em>, <em>Paecilomyces</em>, <em>Paracoccidioides</em>, <em>Pediculus</em>, <em>Penicillium</em>, <em>Phaeoacremonium</em>, <em>Phaeomoniella</em>, <em>Phialophora</em>, <em>Phlebotomus</em>, <em>Phoma</em>, <em>Pichia</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Pneumocystis</em>, <em>Pseudallescheria</em>, <em>Pseudoscopulariopsis</em>, <em>Pseudoterranova</em>, <em>Pulex</em>, <em>Purpureocillium</em>, <em>Quambalaria</em>, <em>Rhinocladiella</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Saccharomyces</em>, <em>Saksenaea</em>, <em>Saprochaete</em>, <em>Sarcoptes</em>, <em>Scedosporium</em>, <em>Schistosoma</em>, <em>Schizosaccharomyces</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Spirometra</em>, <em>Sporobolomyces</em>, <em>Sporopachydermia</em>, <em>Sporothrix</em>, <em>Sporotrichum</em>, <em>Stachybotrys</em>, <em>Strongyloides</em>, <em>Syncephalastrum</em>, <em>Syngamus</em>, <em>Taenia</em>, <em>Talaromyces</em>, <em>Teleomorph</em>, <em>Toxocara</em>, <em>Trichinella</em>, <em>Trichobilharzia</em>, <em>Trichoderma</em>, <em>Trichomonas</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Trichostrongylus</em>, <em>Trichuris</em>, <em>Tritirachium</em>, <em>Trombicula</em>, <em>Trypanosoma</em>, <em>Tunga</em>, <em>Ulocladium</em>, <em>Ustilago</em>, <em>Verticillium</em>, <em>Wallemia</em>, <em>Wangiella</em>, <em>Wickerhamomyces</em>, <em>Wuchereria</em>, <em>Yarrowia</em>, or <em>Zygosaccharomyces</em>;</p></li>
|
||||
<li><p>All other records have <code>prevalence = 2.0</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
|
||||
</ul><p>When calculating the matching score, all characters in \(x\) and \(n\) are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.</p>
|
||||
<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.381\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
|
||||
<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.598\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.381\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
@@ -110,30 +111,26 @@
|
||||
|
||||
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
|
||||
<p>Dr. Matthijs Berends, 2018</p>
|
||||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="as.mo.html">mo_reset_session</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Reset 17 previously matched input values.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Reset 16 previously matched input values.</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mo'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_ENTRC_CRTL</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Matching scores are based on the resemblance between the input and the full</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> taxonomic name, and the pathogenicity in humans. See ?mo_matching_score.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> --------------------------------------------------------------------------------</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Also matched: Enterococcus crotali (0.650), Escherichia coli coli</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> (0.643), Escherichia coli expressing (0.611), Erwinia coffeiphila</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> (0.605), Eubacterium coprostanoligenes (0.603), Enterobacter cowanii</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> (0.600), Eubacterium combesii (0.600), Enterococcus columbae (0.595),</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Eggerthia catenaformis (0.591), and Enterococcus camelliae (0.591)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> "E. coli" -> Enterococcus crotali (B_ENTRC_CRTL, 0.650)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Also matched: Escherichia coli (0.598), Enterococcus columbae (0.595),</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Enterococcus camelliae (0.591), Enterococcus casseliflavus (0.577),</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Escherichia coli coli (0.559), Enterococcus canis (0.556), Enterococcus</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> cecorum (0.550), Enterococcus canintestini (0.540), Escherichia coli</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> expressing (0.531), and Enterobacter cowanii (0.522)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Only the first 10 other matches of each record are shown. Run</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> print(mo_uncertainties(), n = ...) to view more entries, or save</span>
|
||||
@@ -143,7 +140,7 @@
|
||||
<span class="r-in"><span> x <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
|
||||
<span class="r-in"><span> n <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span>, <span class="st">"Entamoeba coli"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.6875000 0.3809524</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.5978261 0.3809524</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||||
|
||||
Reference in New Issue
Block a user