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@ -36,7 +36,7 @@
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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9019</small>
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AMR & base R
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@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9019</small>
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AMR & base R
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@ -38,7 +38,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9019</small>
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With other pkgs
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AMR & data.table
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AMR & base R
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</a>
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@ -204,7 +204,7 @@
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website update since they are based on randomly created values and the
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page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
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Markdown</a>. However, the methodology remains unchanged. This page was
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generated on 24 May 2023.</p>
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generated on 26 May 2023.</p>
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<div class="section level2">
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<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
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</h2>
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@ -260,21 +260,21 @@ make the structure of your data generally look like this:</p>
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</tr></thead>
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<tbody>
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<tr class="odd">
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<td align="center">2023-05-24</td>
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<td align="center">2023-05-26</td>
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<td align="center">abcd</td>
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<td align="center">Escherichia coli</td>
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<td align="center">S</td>
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<td align="center">S</td>
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</tr>
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<tr class="even">
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<td align="center">2023-05-24</td>
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<td align="center">2023-05-26</td>
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<td align="center">abcd</td>
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<td align="center">Escherichia coli</td>
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<td align="center">S</td>
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<td align="center">R</td>
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</tr>
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<tr class="odd">
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<td align="center">2023-05-24</td>
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<td align="center">2023-05-26</td>
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<td align="center">efgh</td>
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<td align="center">Escherichia coli</td>
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<td align="center">R</td>
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@ -347,7 +347,7 @@ supports all kinds of input:</p>
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<span><span class="co">#> [1] B_KLBSL_PNMN</span></span>
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<span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"KLPN"</span><span class="op">)</span></span>
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<span><span class="co">#> Class 'mo'</span></span>
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<span><span class="co">#> [1] B_BCLLS_THRN_KRST</span></span></code></pre></div>
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<span><span class="co">#> [1] B_KLBSL_PNMN</span></span></code></pre></div>
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<p>The first character in above codes denote their taxonomic kingdom,
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such as Bacteria (B), Fungi (F), and Protozoa (P).</p>
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<p>The <code>AMR</code> package also contain functions to directly
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@ -388,37 +388,35 @@ taxonomic codes. Let’s check this:</p>
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<span><span class="co">#> </span></span>
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<span><span class="co">#> --------------------------------------------------------------------------------</span></span>
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<span><span class="co">#> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688)</span></span>
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<span><span class="co">#> Also matched: Enterobacter cowanii (0.600), Eubacterium combesii</span></span>
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<span><span class="co">#> (0.600), Eggerthia catenaformis (0.591), Eubacterium callanderi</span></span>
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<span><span class="co">#> (0.591), Enterocloster citroniae (0.587), Eubacterium cylindroides</span></span>
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<span><span class="co">#> (0.583), Enterococcus casseliflavus (0.577), Enterobacter cloacae</span></span>
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<span><span class="co">#> cloacae (0.571), Ehrlichia canis (0.567), and Enterobacter cloacae</span></span>
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<span><span class="co">#> dissolvens (0.565)</span></span>
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<span><span class="co">#> Also matched: Eubacterium alactolyticum (0.620), Erwinia herbicola</span></span>
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<span><span class="co">#> (0.618), Campylobacter coli (0.611), Enterobacter cowanii (0.600),</span></span>
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<span><span class="co">#> Eubacterium combesii (0.600), Enterococcus faecalis (0.595), Eggerthia</span></span>
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<span><span class="co">#> catenaformis (0.591), Enterocloster aldensis (0.591), Eubacterium</span></span>
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<span><span class="co">#> callanderi (0.591), and Rhodococcus corallinus (0.591)</span></span>
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<span><span class="co">#> --------------------------------------------------------------------------------</span></span>
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<span><span class="co">#> "K. pneumoniae" -> Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786)</span></span>
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<span><span class="co">#> Also matched: Klebsiella pneumoniae ozaenae (0.707), Klebsiella</span></span>
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<span><span class="co">#> pneumoniae pneumoniae (0.688), Klebsiella pneumoniae rhinoscleromatis</span></span>
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<span><span class="co">#> (0.658), Klebsiella pasteurii (0.500), Klebsiella planticola (0.500),</span></span>
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<span><span class="co">#> Kingella potus (0.400), Kosakonia pseudosacchari (0.361), Kaistella</span></span>
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<span><span class="co">#> palustris (0.333), Kocuria palustris (0.333), and Kocuria pelophila</span></span>
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<span><span class="co">#> (0.333)</span></span>
|
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<span><span class="co">#> Also matched: Nocardia pneumoniae (0.763), Chlamydia pneumoniae</span></span>
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<span><span class="co">#> (0.750), Mycoplasma pneumoniae (0.738), Klebsiella quasipneumoniae</span></span>
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<span><span class="co">#> (0.731), Chlamydophila pneumoniae (0.708), Streptococcus pneumoniae</span></span>
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<span><span class="co">#> (0.708), Klebsiella pneumoniae ozaenae (0.707), Mycoplasmoides</span></span>
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<span><span class="co">#> pneumoniae (0.700), Klebsiella pneumoniae pneumoniae (0.688), and</span></span>
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<span><span class="co">#> Haemophilus pleuropneumoniae (0.679)</span></span>
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<span><span class="co">#> --------------------------------------------------------------------------------</span></span>
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<span><span class="co">#> "S. aureus" -> Staphylococcus aureus (B_STPHY_AURS, 0.690)</span></span>
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<span><span class="co">#> Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus</span></span>
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<span><span class="co">#> argenteus (0.625), Staphylococcus aureus anaerobius (0.625),</span></span>
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<span><span class="co">#> Streptomyces argenteolus (0.483), Streptomyces aureus (0.474),</span></span>
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<span><span class="co">#> Streptomyces azureus (0.467), Streptomyces aureorectus (0.444),</span></span>
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<span><span class="co">#> Streptomyces auratus (0.433), Streptomyces aurantiogriseus (0.429), and</span></span>
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<span><span class="co">#> Streptomyces aureocirculatus (0.429)</span></span>
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<span><span class="co">#> Staphylococcus capitis urealyticus (0.618), Staphylococcus capitis</span></span>
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<span><span class="co">#> ureolyticus (0.618), Staphylococcus intermedius (0.615), Salmonella</span></span>
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<span><span class="co">#> choleraesuis choleraesuis (0.611), Staphylococcus sciuri lentus</span></span>
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<span><span class="co">#> (0.607), Salmonella Reubeuss (0.605), and Schaalia turicensis (0.605)</span></span>
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<span><span class="co">#> --------------------------------------------------------------------------------</span></span>
|
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<span><span class="co">#> "S. pneumoniae" -> Streptococcus pneumoniae (B_STRPT_PNMN, 0.750)</span></span>
|
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<span><span class="co">#> Also matched: Streptococcus pseudopneumoniae (0.700), Serratia</span></span>
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<span><span class="co">#> proteamaculans quinovora (0.545), Streptococcus pseudoporcinus (0.536),</span></span>
|
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<span><span class="co">#> Staphylococcus pseudintermedius (0.532), Serratia proteamaculans</span></span>
|
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<span><span class="co">#> proteamaculans (0.526), Salmonella Portanigra (0.524), Sphingomonas</span></span>
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<span><span class="co">#> paucimobilis (0.520), Streptococcus pluranimalium (0.519),</span></span>
|
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<span><span class="co">#> Streptococcus constellatus pharyngis (0.514), and Salmonella Pakistan</span></span>
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<span><span class="co">#> (0.500)</span></span>
|
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<span><span class="co">#> "S. pneumoniae" -> Nocardia pneumoniae (B_NOCRD_PNMN, 0.763)</span></span>
|
||||
<span><span class="co">#> Also matched: Chlamydia pneumoniae (0.750), Streptococcus pneumoniae</span></span>
|
||||
<span><span class="co">#> (0.750), Klebsiella pneumoniae (0.738), Mycoplasma pneumoniae (0.738),</span></span>
|
||||
<span><span class="co">#> Chlamydophila pneumoniae (0.708), Mycoplasmoides pneumoniae (0.700),</span></span>
|
||||
<span><span class="co">#> Streptococcus pseudopneumoniae (0.700), Haemophilus pleuropneumoniae</span></span>
|
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<span><span class="co">#> (0.679), Klebsiella pneumoniae ozaenae (0.672), and Actinobacillus</span></span>
|
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<span><span class="co">#> pleuropneumoniae (0.661)</span></span>
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<span><span class="co">#> </span></span>
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<span><span class="co">#> Only the first 10 other matches of each record are shown. Run</span></span>
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<span><span class="co">#> print(mo_uncertainties(), n = ...) to view more entries, or save</span></span>
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@ -515,8 +513,8 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
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<span><span class="co">#> ℹ Using column 'patient_id' as input for col_patient_id.</span></span>
|
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<span><span class="co">#> ℹ Basing inclusion on all antimicrobial results, using a points threshold</span></span>
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<span><span class="co">#> of 2</span></span>
|
||||
<span><span class="co">#> => Found 2,626 'phenotype-based' first isolates (87.6% within scope and</span></span>
|
||||
<span><span class="co">#> 87.5% of total where a microbial ID was available)</span></span></code></pre></div>
|
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<span><span class="co">#> => Found 2,637 'phenotype-based' first isolates (87.9% of total where a</span></span>
|
||||
<span><span class="co">#> microbial ID was available)</span></span></code></pre></div>
|
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<p>So only 88% is suitable for resistance analysis! We can now filter on
|
||||
it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
|
||||
<code>dplyr</code> package:</p>
|
||||
|
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@ -527,11 +525,11 @@ it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" cl
|
|||
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
|
||||
<p>So we end up with 2 626 isolates for analysis. Now our data looks
|
||||
<p>So we end up with 2 637 isolates for analysis. Now our data looks
|
||||
like:</p>
|
||||
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">our_data_1st</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,626 × 9</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,637 × 9</span></span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
|
||||
<span><span class="co">#> <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;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><lgl></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> J3 A 2012-11-21 B_ESCHR_COLI R I S S TRUE </span></span>
|
||||
|
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@ -544,7 +542,7 @@ like:</p>
|
|||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> J3 A 2019-06-19 B_ESCHR_COLI S S S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> G6 A 2015-04-27 B_STPHY_AURS S S S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> P4 A 2011-06-21 B_ESCHR_COLI S S S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,616 more rows</span></span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,627 more rows</span></span></span></code></pre></div>
|
||||
<p>Time for the analysis.</p>
|
||||
</div>
|
||||
</div>
|
||||
|
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@ -557,29 +555,29 @@ impression, as it comes with support for the new <code>mo</code> and
|
|||
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">our_data_1st</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> patient_id hospital date </span></span>
|
||||
<span><span class="co">#> Length:2626 Length:2626 Min. :2011-01-01 </span></span>
|
||||
<span><span class="co">#> Class :character Class :character 1st Qu.:2013-04-14 </span></span>
|
||||
<span><span class="co">#> Mode :character Mode :character Median :2015-06-05 </span></span>
|
||||
<span><span class="co">#> Mean :2015-06-15 </span></span>
|
||||
<span><span class="co">#> Length:2637 Length:2637 Min. :2011-01-01 </span></span>
|
||||
<span><span class="co">#> Class :character Class :character 1st Qu.:2013-04-13 </span></span>
|
||||
<span><span class="co">#> Mode :character Mode :character Median :2015-06-04 </span></span>
|
||||
<span><span class="co">#> Mean :2015-06-14 </span></span>
|
||||
<span><span class="co">#> 3rd Qu.:2017-08-23 </span></span>
|
||||
<span><span class="co">#> Max. :2020-01-01 </span></span>
|
||||
<span><span class="co">#> bacteria AMX AMC </span></span>
|
||||
<span><span class="co">#> Class :mo Class:sir Class:sir </span></span>
|
||||
<span><span class="co">#> <NA> :0 %R :43.2% (n=1134) %R :36.1% (n=947) </span></span>
|
||||
<span><span class="co">#> Unique:4 %SI :56.8% (n=1492) %SI :63.9% (n=1679) </span></span>
|
||||
<span><span class="co">#> #1 :B_ESCHR_COLI - %S :41.1% (n=1080) - %S :52.7% (n=1383) </span></span>
|
||||
<span><span class="co">#> #2 :B_STPHY_AURS - %I :15.7% (n=412) - %I :11.3% (n=296) </span></span>
|
||||
<span><span class="co">#> #3 :B_STRPT_PNMN </span></span>
|
||||
<span><span class="co">#> <NA> :0 %R :43.2% (n=1140) %R :35.9% (n=948) </span></span>
|
||||
<span><span class="co">#> Unique:5 %SI :56.8% (n=1497) %SI :64.1% (n=1689) </span></span>
|
||||
<span><span class="co">#> #1 :B_ESCHR_COLI - %S :41.1% (n=1085) - %S :52.7% (n=1391) </span></span>
|
||||
<span><span class="co">#> #2 :B_STPHY_AURS - %I :15.6% (n=412) - %I :11.3% (n=298) </span></span>
|
||||
<span><span class="co">#> #3 :B_KLBSL_PNMN </span></span>
|
||||
<span><span class="co">#> CIP GEN first </span></span>
|
||||
<span><span class="co">#> Class:sir Class:sir Mode:logical </span></span>
|
||||
<span><span class="co">#> %R :42.0% (n=1102) %R :37.0% (n=971) TRUE:2626 </span></span>
|
||||
<span><span class="co">#> %SI :58.0% (n=1524) %SI :63.0% (n=1655) </span></span>
|
||||
<span><span class="co">#> - %S :51.9% (n=1362) - %S :59.9% (n=1574) </span></span>
|
||||
<span><span class="co">#> - %I : 6.2% (n=162) - %I : 3.1% (n=81) </span></span>
|
||||
<span><span class="co">#> %R :41.9% (n=1105) %R :36.9% (n=972) TRUE:2637 </span></span>
|
||||
<span><span class="co">#> %SI :58.1% (n=1532) %SI :63.1% (n=1665) </span></span>
|
||||
<span><span class="co">#> - %S :52.0% (n=1370) - %S :60.1% (n=1584) </span></span>
|
||||
<span><span class="co">#> - %I : 6.1% (n=162) - %I : 3.1% (n=81) </span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span></span>
|
||||
<span><span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">our_data_1st</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> Rows: 2,626</span></span>
|
||||
<span><span class="co">#> Rows: 2,637</span></span>
|
||||
<span><span class="co">#> Columns: 9</span></span>
|
||||
<span><span class="co">#> $ patient_id <span style="color: #949494; font-style: italic;"><chr></span> "J3", "R7", "P10", "B7", "W3", "J8", "M3", "J3", "G6", "P4"…</span></span>
|
||||
<span><span class="co">#> $ hospital <span style="color: #949494; font-style: italic;"><chr></span> "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A",…</span></span>
|
||||
|
|
@ -594,7 +592,7 @@ impression, as it comes with support for the new <code>mo</code> and
|
|||
<span><span class="co"># number of unique values per column:</span></span>
|
||||
<span><span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">our_data_1st</span>, <span class="va">n_distinct</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP </span></span>
|
||||
<span><span class="co">#> 260 3 1808 4 3 3 3 </span></span>
|
||||
<span><span class="co">#> 260 3 1814 5 3 3 3 </span></span>
|
||||
<span><span class="co">#> GEN first </span></span>
|
||||
<span><span class="co">#> 3 1</span></span></code></pre></div>
|
||||
<div class="section level3">
|
||||
|
|
@ -606,23 +604,25 @@ microorganisms:</p>
|
|||
<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="../reference/count.html">count</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">bacteria</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 4 × 2</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 5 × 2</span></span></span>
|
||||
<span><span class="co">#> `mo_name(bacteria)` n</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">1</span> Escherichia coli <span style="text-decoration: underline;">1</span>518</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 730</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae 426</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 326</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> Klebsiella pneumoniae 326</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">4</span> Streptococcus pneumoniae 275</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">5</span> Nocardia pneumoniae 151</span></span>
|
||||
<span></span>
|
||||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="../reference/count.html">count</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">bacteria</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 4 × 2</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 5 × 2</span></span></span>
|
||||
<span><span class="co">#> `mo_name(bacteria)` n</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">1</span> Escherichia coli <span style="text-decoration: underline;">1</span>250</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 661</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae 399</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 316</span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> Klebsiella pneumoniae 316</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">4</span> Streptococcus pneumoniae 267</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">5</span> Nocardia pneumoniae 143</span></span></code></pre></div>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="select-and-filter-with-antibiotic-selectors">Select and filter with antibiotic selectors<a class="anchor" aria-label="anchor" href="#select-and-filter-with-antibiotic-selectors"></a>
|
||||
|
|
@ -634,7 +634,7 @@ in:</p>
|
|||
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">date</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> ℹ For aminoglycosides() using column 'GEN' (gentamicin)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,626 × 2</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,637 × 2</span></span></span>
|
||||
<span><span class="co">#> date GEN </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><sir></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> 2012-11-21 S </span></span>
|
||||
|
|
@ -647,13 +647,13 @@ in:</p>
|
|||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> 2019-06-19 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> 2015-04-27 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> 2011-06-21 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,616 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,627 more rows</span></span></span>
|
||||
<span></span>
|
||||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC'</span></span>
|
||||
<span><span class="co">#> (amoxicillin/clavulanic acid)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,626 × 3</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,637 × 3</span></span></span>
|
||||
<span><span class="co">#> bacteria AMX AMC </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> B_ESCHR_COLI R I </span></span>
|
||||
|
|
@ -666,11 +666,11 @@ in:</p>
|
|||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> B_ESCHR_COLI S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> B_STPHY_AURS S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> B_ESCHR_COLI S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,616 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,627 more rows</span></span></span>
|
||||
<span></span>
|
||||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,626 × 5</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,637 × 5</span></span></span>
|
||||
<span><span class="co">#> bacteria AMX AMC CIP GEN </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> B_ESCHR_COLI R I S S </span></span>
|
||||
|
|
@ -683,26 +683,26 @@ in:</p>
|
|||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> B_ESCHR_COLI S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> B_STPHY_AURS S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> B_ESCHR_COLI S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,616 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,627 more rows</span></span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># filtering using AB selectors is also possible:</span></span>
|
||||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> ℹ For aminoglycosides() using column 'GEN' (gentamicin)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 971 × 9</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 972 × 9</span></span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
|
||||
<span><span class="co">#> <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;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><lgl></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> J5 A 2017-12-25 B_STRPT_PNMN R S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> J5 A 2017-12-25 B_NOCRD_PNMN R S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> X1 A 2017-07-04 B_STPHY_AURS R S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> B3 A 2016-07-24 B_ESCHR_COLI S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> V7 A 2012-04-03 B_ESCHR_COLI S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> C9 A 2017-03-23 B_ESCHR_COLI S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> R1 A 2018-06-10 B_STPHY_AURS S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> S2 A 2013-07-19 B_STRPT_PNMN S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> S2 A 2013-07-19 B_NOCRD_PNMN S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> P5 A 2019-03-09 B_STPHY_AURS S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> Q8 A 2019-08-10 B_STPHY_AURS S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> K5 A 2013-03-15 B_STRPT_PNMN S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 961 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> K5 A 2013-03-15 B_NOCRD_PNMN S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 962 more rows</span></span></span>
|
||||
<span></span>
|
||||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span>
|
||||
|
|
@ -711,12 +711,12 @@ in:</p>
|
|||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 471 × 9</span></span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
|
||||
<span><span class="co">#> <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;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><lgl></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> M7 A 2013-07-22 B_STRPT_PNMN R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> M7 A 2013-07-22 B_NOCRD_PNMN R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> R10 A 2013-12-20 B_STPHY_AURS R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> R7 A 2015-10-25 B_STPHY_AURS R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> R8 A 2019-10-25 B_STPHY_AURS R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> I7 A 2015-08-19 B_ESCHR_COLI R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> N3 A 2014-12-29 B_STRPT_PNMN R R R S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> N3 A 2014-12-29 B_NOCRD_PNMN R R R S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> C5 A 2015-08-30 B_KLBSL_PNMN R R S R TRUE </span></span>
|
||||
|
|
@ -730,12 +730,12 @@ in:</p>
|
|||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 471 × 9</span></span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
|
||||
<span><span class="co">#> <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;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><lgl></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> M7 A 2013-07-22 B_STRPT_PNMN R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> M7 A 2013-07-22 B_NOCRD_PNMN R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> R10 A 2013-12-20 B_STPHY_AURS R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> R7 A 2015-10-25 B_STPHY_AURS R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> R8 A 2019-10-25 B_STPHY_AURS R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> I7 A 2015-08-19 B_ESCHR_COLI R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> N3 A 2014-12-29 B_STRPT_PNMN R R R S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> N3 A 2014-12-29 B_NOCRD_PNMN R R R S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> C5 A 2015-08-30 B_KLBSL_PNMN R R S R TRUE </span></span>
|
||||
|
|
@ -1352,7 +1352,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
|
|||
own:</p>
|
||||
<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> [1] 0.4318355</span></span></code></pre></div>
|
||||
<span><span class="co">#> [1] 0.4323094</span></span></code></pre></div>
|
||||
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
|
||||
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
|
||||
|
|
@ -1364,7 +1364,7 @@ own:</p>
|
|||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">1</span> A 0.343</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">2</span> B 0.569</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> C 0.375</span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> C 0.378</span></span></code></pre></div>
|
||||
<hr>
|
||||
<p><em>Author: Dr. Matthijs Berends, 26th Feb 2023</em></p>
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -38,7 +38,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -118,28 +118,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -38,7 +38,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -118,28 +118,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
@ -402,19 +402,19 @@ names or codes, this would have worked exactly the same way:</p>
|
|||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
|
||||
<span><span class="co">#> 1 S I S S I R</span></span>
|
||||
<span><span class="co">#> 2 R S S I I I</span></span>
|
||||
<span><span class="co">#> 3 R S S S S S</span></span>
|
||||
<span><span class="co">#> 4 R I I S S R</span></span>
|
||||
<span><span class="co">#> 5 R R R R I I</span></span>
|
||||
<span><span class="co">#> 6 S R S I R R</span></span>
|
||||
<span><span class="co">#> 1 R R S S R R</span></span>
|
||||
<span><span class="co">#> 2 R I S I I R</span></span>
|
||||
<span><span class="co">#> 3 I S R S R S</span></span>
|
||||
<span><span class="co">#> 4 I S R R R R</span></span>
|
||||
<span><span class="co">#> 5 R I I R I R</span></span>
|
||||
<span><span class="co">#> 6 I S R R R R</span></span>
|
||||
<span><span class="co">#> kanamycin</span></span>
|
||||
<span><span class="co">#> 1 S</span></span>
|
||||
<span><span class="co">#> 2 S</span></span>
|
||||
<span><span class="co">#> 3 S</span></span>
|
||||
<span><span class="co">#> 4 I</span></span>
|
||||
<span><span class="co">#> 5 R</span></span>
|
||||
<span><span class="co">#> 6 I</span></span></code></pre></div>
|
||||
<span><span class="co">#> 2 I</span></span>
|
||||
<span><span class="co">#> 3 I</span></span>
|
||||
<span><span class="co">#> 4 S</span></span>
|
||||
<span><span class="co">#> 5 I</span></span>
|
||||
<span><span class="co">#> 6 S</span></span></code></pre></div>
|
||||
<p>We can now add the interpretation of MDR-TB to our data set. You can
|
||||
use:</p>
|
||||
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
|
||||
|
|
@ -455,40 +455,40 @@ Unique: 5</p>
|
|||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Mono-resistant</td>
|
||||
<td align="right">3243</td>
|
||||
<td align="right">64.86%</td>
|
||||
<td align="right">3243</td>
|
||||
<td align="right">64.86%</td>
|
||||
<td align="right">3231</td>
|
||||
<td align="right">64.62%</td>
|
||||
<td align="right">3231</td>
|
||||
<td align="right">64.62%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">971</td>
|
||||
<td align="right">19.42%</td>
|
||||
<td align="right">4214</td>
|
||||
<td align="right">84.28%</td>
|
||||
<td align="right">993</td>
|
||||
<td align="right">19.86%</td>
|
||||
<td align="right">4224</td>
|
||||
<td align="right">84.48%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Multi-drug-resistant</td>
|
||||
<td align="right">450</td>
|
||||
<td align="right">9.00%</td>
|
||||
<td align="right">4664</td>
|
||||
<td align="right">93.28%</td>
|
||||
<td align="right">415</td>
|
||||
<td align="right">8.30%</td>
|
||||
<td align="right">4639</td>
|
||||
<td align="right">92.78%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Poly-resistant</td>
|
||||
<td align="right">230</td>
|
||||
<td align="right">4.60%</td>
|
||||
<td align="right">4894</td>
|
||||
<td align="right">97.88%</td>
|
||||
<td align="right">264</td>
|
||||
<td align="right">5.28%</td>
|
||||
<td align="right">4903</td>
|
||||
<td align="right">98.06%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="left">Extensively drug-resistant</td>
|
||||
<td align="right">106</td>
|
||||
<td align="right">2.12%</td>
|
||||
<td align="right">97</td>
|
||||
<td align="right">1.94%</td>
|
||||
<td align="right">5000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
|
|
|
|||
|
|
@ -38,7 +38,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -118,28 +118,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -38,7 +38,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -118,28 +118,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -38,7 +38,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -118,28 +118,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
@ -193,7 +193,7 @@
|
|||
<main id="main" class="col-md-9"><div class="page-header">
|
||||
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
|
||||
|
||||
<h4 data-toc-skip class="date">24 May 2023</h4>
|
||||
<h4 data-toc-skip class="date">26 May 2023</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
|
||||
<div class="d-none name"><code>datasets.Rmd</code></div>
|
||||
|
|
@ -272,9 +272,9 @@ and the Global Biodiversity Information Facility (GBIF):</p>
|
|||
<li>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names
|
||||
with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong>
|
||||
International Journal of Systematic and Evolutionary Microbiology, 70,
|
||||
5607-5612; . Accessed from <a href="https://lpsn.dsmz.de" class="external-link uri">https://lpsn.dsmz.de</a> on 11 December, 2022.</li>
|
||||
5607-5612; . Accessed from <a href="https://lpsn.dsmz.de" class="external-link uri">https://lpsn.dsmz.de</a> on December 11th, 2022.</li>
|
||||
<li>GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset .
|
||||
Accessed from <a href="https://www.gbif.org" class="external-link uri">https://www.gbif.org</a> on 11 December, 2022.</li>
|
||||
Accessed from <a href="https://www.gbif.org" class="external-link uri">https://www.gbif.org</a> on December 11th, 2022.</li>
|
||||
<li>Public Health Information Network Vocabulary Access and Distribution
|
||||
System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value
|
||||
Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link uri">https://phinvads.cdc.gov</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -38,7 +38,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -118,28 +118,28 @@
|
|||
</li>
|
||||
<li class="active nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -38,7 +38,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -118,28 +118,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -38,7 +38,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -118,28 +118,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
12
authors.html
12
authors.html
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
12
index.html
12
index.html
|
|
@ -42,7 +42,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -122,28 +122,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
@ -159,12 +159,12 @@
|
|||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
<h2 class="pkg-version" data-toc-text="2.0.0.9019" id="amr-2009019">AMR 2.0.0.9019<a class="anchor" aria-label="anchor" href="#amr-2009019"></a></h2>
|
||||
<h2 class="pkg-version" data-toc-text="2.0.0.9020" id="amr-2009020">AMR 2.0.0.9020<a class="anchor" aria-label="anchor" href="#amr-2009020"></a></h2>
|
||||
<div class="section level3">
|
||||
<h3 id="changed-2-0-0-9019">Changed<a class="anchor" aria-label="anchor" href="#changed-2-0-0-9019"></a></h3>
|
||||
<ul><li>Added oxygen tolerance to over 25,000 bacteria in the <code>microorganisms</code> data set
|
||||
<h3 id="changed-2-0-0-9020">Changed<a class="anchor" aria-label="anchor" href="#changed-2-0-0-9020"></a></h3>
|
||||
<ul><li>Added oxygen tolerance from BacDive to over 25,000 bacteria in the <code>microorganisms</code> data set
|
||||
<ul><li>Added <code><a href="../reference/mo_property.html">mo_oxygen_tolerance()</a></code> to retrieve the values</li>
|
||||
<li>Added <code><a href="../reference/mo_property.html">mo_is_anaerobic()</a></code> to determine which species are obligate anaerobic bacteria</li>
|
||||
<li>Added <code><a href="../reference/mo_property.html">mo_is_anaerobic()</a></code> to determine which genera/species are obligate anaerobic bacteria</li>
|
||||
</ul></li>
|
||||
<li>Added LPSN and GBIF identifiers, and oxygen tolerance to <code><a href="../reference/mo_property.html">mo_info()</a></code>
|
||||
</li>
|
||||
|
|
@ -180,6 +180,8 @@
|
|||
<li>Fixed usage of <code>icu_exclude</code> in <code>first_isolates()</code>
|
||||
</li>
|
||||
<li>Improved <code><a href="../reference/as.mo.html">as.mo()</a></code> algorithm for searching on only species names</li>
|
||||
<li>Updated the code table in <code>microorganisms.codes</code>
|
||||
</li>
|
||||
</ul></div>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
|
|
|
|||
|
|
@ -11,7 +11,7 @@ articles:
|
|||
other_pkg: other_pkg.html
|
||||
resistance_predict: resistance_predict.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
last_built: 2023-05-24T14:00Z
|
||||
last_built: 2023-05-26T14:13Z
|
||||
urls:
|
||||
reference: https://msberends.github.io/AMR/reference
|
||||
article: https://msberends.github.io/AMR/articles
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -24,7 +24,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -103,28 +103,28 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
Binary file not shown.
|
Before Width: | Height: | Size: 13 KiB After Width: | Height: | Size: 13 KiB |
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|
Before Width: | Height: | Size: 13 KiB After Width: | Height: | Size: 13 KiB |
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|
Before Width: | Height: | Size: 14 KiB After Width: | Height: | Size: 13 KiB |
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|
Before Width: | Height: | Size: 19 KiB After Width: | Height: | Size: 18 KiB |
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|
Before Width: | Height: | Size: 8.4 KiB After Width: | Height: | Size: 8.3 KiB |
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
@ -206,7 +206,7 @@
|
|||
<span class="r-in"><span><span class="co"># a combination of species is not formal taxonomy, so</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># this will result in only "Enterobacter asburiae":</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Enterobacter asburiae/cloacae"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Enterobacter asburiae"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Enterobacter cloacae cloacae"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># now add a custom entry - it will be considered by as.mo() and</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># all mo_*() functions</span></span></span>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
@ -222,16 +222,16 @@
|
|||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> birth_date age age_exact age_at_y2k</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1943-12-07 79 79.46027 56</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1973-04-06 50 50.13151 26</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1998-12-22 24 24.41918 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1938-09-05 84 84.71507 61</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1994-09-17 28 28.68219 5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1938-01-09 85 85.36986 61</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1993-08-21 29 29.75616 6</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1937-05-15 86 86.02466 62</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1981-07-29 41 41.81918 18</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1947-06-12 75 75.94795 52</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1951-05-01 72 72.06849 48</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1987-07-08 35 35.88219 12</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1981-03-24 42 42.17260 18</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1955-01-22 68 68.33973 44</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1971-12-06 51 51.46849 28</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1935-05-02 88 88.06575 64</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1934-03-23 89 89.17534 65</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1984-02-27 39 39.24110 15</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1936-10-03 86 86.64384 63</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1990-03-21 33 33.18082 9</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -12,7 +12,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -91,28 +91,28 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
@ -627,10 +627,10 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
|
|||
<span class="r-out co"><span class="r-pr">#></span> kefzol</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><sir></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> I </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> I </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> I </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> R </span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># get AMR for all aminoglycosides e.g., per ward:</span></span></span>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
@ -214,7 +214,7 @@
|
|||
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
|
||||
|
||||
<ul><li><p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <a href="https://www.whocc.no/atc_ddd_index/" class="external-link">https://www.whocc.no/atc_ddd_index/</a></p></li>
|
||||
<li><p>Logical Observation Identifiers Names and Codes (LOINC), Version 2.73 (8 August, 2022). Accessed from <a href="https://loinc.org" class="external-link">https://loinc.org</a> on 30 October, 2022.</p></li>
|
||||
<li><p>Logical Observation Identifiers Names and Codes (LOINC), Version 2.73 (8 August, 2022). Accessed from <a href="https://loinc.org" class="external-link">https://loinc.org</a> on October 30th, 2022.</p></li>
|
||||
<li><p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a></p></li>
|
||||
</ul></div>
|
||||
<div class="section level2">
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
@ -299,12 +299,13 @@
|
|||
<li><p>Lancefield RC (1933). <strong>A serological differentiation of human and other groups of hemolytic streptococci.</strong> <em>J Exp Med.</em> 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>Berends MS <em>et al.</em> (2022). <strong>Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019/</strong> <em>Micro.rganisms</em> 10(9), 1801; <a href="https://doi.org/10.3390/microorganisms10091801" class="external-link">doi:10.3390/microorganisms10091801</a></p></li>
|
||||
<li><p>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong> International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a>
|
||||
. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on 11 December, 2022.</p></li>
|
||||
. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on December 11th, 2022.</p></li>
|
||||
<li><p>GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset <a href="https://doi.org/10.15468/39omei" class="external-link">doi:10.15468/39omei</a>
|
||||
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on 11 December, 2022.</p></li>
|
||||
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on December 11th, 2022.</p></li>
|
||||
<li><p>Reimer, LC <em>et al.</em> (2022). <strong><em>BacDive</em> in 2022: the knowledge base for standardized bacterial and archaeal data.</strong> Nucleic Acids Res., 50(D1):D741-D74; <a href="https://doi.org/10.1093/nar/gkab961" class="external-link">doi:10.1093/nar/gkab961</a>
|
||||
. Accessed from <a href="https://bacdive.dsmz.de" class="external-link">https://bacdive.dsmz.de</a> on May 12th, 2023.</p></li>
|
||||
<li><p>Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link">https://phinvads.cdc.gov</a></p></li>
|
||||
<li><p>Bartlett A <em>et al.</em> (2022). <strong>A comprehensive list of bacterial pathogens infecting humans</strong> <em>Microbiology</em> 168:001269; <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a></p></li>
|
||||
<li><p>Reimer <em>et al.</em> (2022). <strong><em>BacDive</em> in 2022: the knowledge base for standardized bacterial and archaeal data.</strong> <em>Nucleic Acids Res.</em> 2022 Jan 7;50(D1):D741-D746; <a href="https://doi.org/10.1093/nar/gkab961" class="external-link">doi:10.1093/nar/gkab961</a></p></li>
|
||||
</ol></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>
|
||||
|
|
@ -360,9 +361,9 @@
|
|||
<span class="r-in"><span> <span class="fl">115329001</span> <span class="co"># SNOMED CT code</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</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_STPHY_AURS B_ROTHI B_ACHRMB_MRPL B_STPHY_AURS B_STPHY_AURS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [6] B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] B_STPHY_AURS B_STPHY_AURS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [6] B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] B_STPHY_AURS B_STPHY_AURS</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># Dyslexia is no problem - these all work:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.mo</span><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></span>
|
||||
|
|
@ -396,7 +397,7 @@
|
|||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_genus</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> [1] "Escherichia"</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"ESCO"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Gram-positive"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Gram-negative"</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"ESCCOL"</span>, ab <span class="op">=</span> <span class="st">"vanco"</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Determining intrinsic resistance based on 'EUCAST Expert Rules' and</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3 (2021). This note</span>
|
||||
|
|
|
|||
|
|
@ -12,7 +12,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -91,28 +91,28 @@ All breakpoints used for interpretation are publicly available in the clinical_b
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
@ -551,16 +551,16 @@ 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: 50 × 12</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> datetime index ab_input ab_guideline mo_input mo_guideline </span>
|
||||
<span class="r-out co"><span class="r-pr">#></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;"><ab></span> <span style="color: #949494; font-style: italic;"><chr></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> 2023-05-24 <span style="color: #949494;">14:00:50</span> 1 TOB TOB Escherichia… B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2023-05-24 <span style="color: #949494;">14:00:49</span> 1 GEN GEN Escherichia… B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2023-05-24 <span style="color: #949494;">14:00:49</span> 1 CIP CIP Escherichia… B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2023-05-24 <span style="color: #949494;">14:00:49</span> 1 AMP AMP Escherichia… B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2023-05-24 <span style="color: #949494;">14:00:43</span> 1 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2023-05-24 <span style="color: #949494;">14:00:43</span> 2 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2023-05-24 <span style="color: #949494;">14:00:43</span> 3 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2023-05-24 <span style="color: #949494;">14:00:43</span> 4 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2023-05-24 <span style="color: #949494;">14:00:43</span> 5 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2023-05-24 <span style="color: #949494;">14:00:43</span> 6 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2023-05-26 <span style="color: #949494;">14:15:02</span> 1 TOB TOB Escherichia… B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2023-05-26 <span style="color: #949494;">14:15:02</span> 1 GEN GEN Escherichia… B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2023-05-26 <span style="color: #949494;">14:15:01</span> 1 CIP CIP Escherichia… B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2023-05-26 <span style="color: #949494;">14:15:01</span> 1 AMP AMP Escherichia… B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2023-05-26 <span style="color: #949494;">14:14:52</span> 1 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2023-05-26 <span style="color: #949494;">14:14:52</span> 2 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2023-05-26 <span style="color: #949494;">14:14:52</span> 3 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2023-05-26 <span style="color: #949494;">14:14:52</span> 4 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2023-05-26 <span style="color: #949494;">14:14:52</span> 5 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2023-05-26 <span style="color: #949494;">14:14:52</span> 6 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 40 more rows</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 6 more variables: guideline <chr>, ref_table <chr>, method <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># input <dbl>, outcome <sir>, breakpoint_S_R <chr></span></span>
|
||||
|
|
@ -575,10 +575,10 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
|||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Note:</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for ampicillin (AMP) in Streptococcus</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> pneumoniae - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • (Some) PK/PD breakpoints were applied - use include_PKPD = FALSE to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> prevent this</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> x <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">18</span><span class="op">)</span>,</span></span>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -91,28 +91,28 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -91,28 +91,28 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
@ -261,7 +261,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
|
|||
<div class="section level2">
|
||||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||||
<p><strong>Note:</strong> This function does not translate MIC values to SIR values. Use <code><a href="as.sir.html">as.sir()</a></code> for that. <br><strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. <br></p>
|
||||
<p>The file containing all EUCAST rules is located here: <a href="https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv</a>. <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The <code>AMR</code> package contains the full microbial taxonomy updated until 11 December, 2022, see <a href="microorganisms.html">microorganisms</a>.</p><div class="section">
|
||||
<p>The file containing all EUCAST rules is located here: <a href="https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv</a>. <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The <code>AMR</code> package contains the full microbial taxonomy updated until December 11th, 2022, see <a href="microorganisms.html">microorganisms</a>.</p><div class="section">
|
||||
<h3 id="custom-rules">Custom Rules<a class="anchor" aria-label="anchor" href="#custom-rules"></a></h3>
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -12,7 +12,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -91,28 +91,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
@ -263,35 +263,33 @@
|
|||
<span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 42 35 39 44 44 10 48 22 28 31 30 37 30 45 28 2 17 33 36 13 43 41 22 23 50</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [26] 17 23 22 46 15 44 24 37 48 9 14 9 32 12 19 31 11 35 18 51 2 47 7 27 20</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [51] 39 47 14 1 41 36 7 46 30 21 27 3 38 2 16 34 3 18 24 11 4 24 8 51 3</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [76] 29 28 50 33 24 24 19 25 8 6 17 9 51 48 26 10 12 5 40 16 22 49 30 23 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 48 39 6 18 52 8 12 53 48 6 33 42 23 1 4 5 7 18 32 45 23 10 49 2 7</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [26] 1 33 20 31 22 3 43 24 13 38 41 11 38 30 9 46 39 2 10 48 12 25 6 46 40</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [51] 36 48 16 35 17 29 11 35 15 47 51 8 42 26 9 16 9 21 13 45 12 34 6 17 29</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [76] 19 22 50 44 28 9 44 18 27 24 50 16 37 5 49 52 31 7 2 4 40 51 14 46 52</span>
|
||||
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] FALSE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] TRUE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] FALSE TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE FALSE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] FALSE TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE FALSE TRUE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] FALSE TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE FALSE FALSE TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></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;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-07-23 F35553 51 M ICU B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-08-28 390178 57 M Clinical B_STRPT_SLVR S NA NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2002-08-31 149442 80 F ICU B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, RIF <sir></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX AMC </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></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;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2003-04-21 6BC362 62 M ICU B_ENTRC NA NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 35 more variables: AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, CXM <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, TOB <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, FOS <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, TCY <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, IPM <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, RIF <sir></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># the functions also work for less than a day, e.g. to include one per hour:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span></span></span>
|
||||
|
|
@ -319,19 +317,19 @@
|
|||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">condition</span>, <span class="va">date</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> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, condition [96]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, condition [100]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient date condition new_episode</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 058917 2002-11-14 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 074321 2015-09-20 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 082413 2002-06-04 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 0DBB93 2009-05-08 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 0E2483 2007-05-29 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 0F9638 2014-09-22 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 149442 2002-08-31 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 156730 2012-04-12 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 173401 2011-06-06 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 175532 2010-04-10 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 000090 2003-10-08 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 023456 2009-11-02 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 05B00F 2004-05-11 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 05C73F 2006-01-12 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 066601 2013-10-30 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 067927 2002-01-13 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 067927 2002-01-07 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 069276 2015-06-18 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 078381 2014-06-28 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 080086 2010-08-08 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
|
|
@ -345,19 +343,19 @@
|
|||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">ward</span>, <span class="va">date</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> <span style="color: #949494;"># A tibble: 100 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [94]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [97]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward date patient new_index new_logical</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> ICU 2002-11-14 058917 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> ICU 2015-09-20 074321 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> ICU 2002-06-04 082413 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> ICU 2009-05-08 0DBB93 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2007-05-29 0E2483 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Clinical 2014-09-22 0F9638 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> ICU 2002-08-31 149442 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Clinical 2012-04-12 156730 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> ICU 2011-06-06 173401 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> ICU 2010-04-10 175532 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> ICU 2003-10-08 000090 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical 2009-11-02 023456 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> ICU 2004-05-11 05B00F 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical 2006-01-12 05C73F 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2013-10-30 066601 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> ICU 2002-01-07 067927 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> ICU 2002-01-13 067927 1 FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Clinical 2015-06-18 069276 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> ICU 2014-06-28 078381 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Clinical 2010-08-08 080086 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
|
|
@ -373,9 +371,9 @@
|
|||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 54 13 39 43</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 33 11 26 31</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 7 4 5 6</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 56 12 38 47</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 33 10 25 29</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 8 5 7 7</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># results as first_isolate() when using 'episode-based':</span></span></span>
|
||||
|
|
@ -405,18 +403,18 @@
|
|||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, mo, ward [98]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient mo ward flag_episode</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 715822 B_STPHY_EPDR Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 156730 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 992282 B_STRPT_GRPA Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> C54153 B_STPHY_EPDR Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 074321 B_STPHY_HMLY ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> E56935 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> BF4515 B_STPHY_EPDR Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> D08605 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> EC9741 B_ESCHR_COLI Outpatient TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> F54287 B_KLBSL_OXYT Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient mo ward flag_episode</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> A79917 B_PSDMN_AERG Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 600967 B_SERRT_MRCS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 118928 B_STPHY_AURS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 650870 B_ENTRBC_CLOC ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> BF4515 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> F35553 B_STPHY_AURS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 6B8C75 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> F50400 B_STPHY_HMNS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 784436 B_STPHY_HMNS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> C36883 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
@ -413,7 +413,7 @@
|
|||
|
||||
<code><a href="microorganisms.codes.html">microorganisms.codes</a></code>
|
||||
</dt>
|
||||
<dd>Data Set with 5 754 Common Microorganism Codes</dd>
|
||||
<dd>Data Set with 4 909 Common Microorganism Codes</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
@ -199,9 +199,9 @@
|
|||
<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">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 2.954493</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 3.071168</span>
|
||||
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.02115676</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.02596136</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
@ -218,30 +218,30 @@
|
|||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">sir</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] I I I I R R S S R R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] I I S I S I I R S R</span>
|
||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.7745967 -0.7745967 -0.7745967 -0.7745967 1.1618950 1.1618950</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.7745967 -0.7745967 1.1618950 1.1618950</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.4743416 -0.4743416 -0.4743416 -0.4743416 -0.4743416 -0.4743416</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.4743416 1.8973666 -0.4743416 1.8973666</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">mic</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">mic</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.0625 0.005 128 128 32 1 >=256 128 8 0.125 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] >=256 1 0.125 0.001 0.002 16 16 2 8 8 </span>
|
||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.1210573 -1.7761606 0.8565554 0.8565554 0.4969895 -0.4019254</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 1.0363384 0.8565554 0.1374235 -0.9412743</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1.35903204 -0.01839609 -0.53493164 -1.73429005 -1.56211153 0.67031797</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.67031797 0.15378242 0.49813946 0.49813946</span>
|
||||
<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
|
||||
<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.1210573 -1.7761606 0.8565554 0.8565554 0.4969895 -0.4019254</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 1.0363384 0.8565554 0.1374235 -0.9412743</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1.35903204 -0.01839609 -0.53493164 -1.73429005 -1.56211153 0.67031797</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.67031797 0.15378242 0.49813946 0.49813946</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">disk</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">disk</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 48 32 44 24 22 48 50 41 43 36</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 50 49 49 14 39 45 24 24 8 41</span>
|
||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.9202045 -0.6801512 0.5201156 -1.4803290 -1.6803735 0.9202045</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 1.1202490 0.2200489 0.4200934 -0.2800622</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1.0096747 0.9453642 0.9453642 -1.3055030 0.3022593 0.6881223</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.6623981 -0.6623981 -1.6913659 0.4308803</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">y</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
|
||||
|
|
@ -251,22 +251,22 @@
|
|||
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">y</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A S 21 8 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B R 25 0.5 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C R 25 >=16 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D I 25 8 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E S 21 0.5 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F I 29 4 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G S 17 4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H I 20 2 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I S 17 0.5 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J I 29 4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A R 17 4 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B S 19 <=0.5 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C S 27 4 >=4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D I 30 >=8 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E S 22 >=8 >=4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F S 30 1 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G R 25 1 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H S 17 <=0.5 >=4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I R 20 >=8 >=4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J S 20 4 <=1</span>
|
||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> and "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.22695748 0.32206771 1.00220170 0.54530143 -0.77106467 0.09331917</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.04702882 -0.55604901 -0.99921640 0.63742636</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.19666410 -0.75540530 0.42065543 0.40679865 0.32292908 -0.05152683</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.21552084 -0.53867305 0.74027765 -0.56391237</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
|
|
@ -282,17 +282,17 @@
|
|||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> and "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C R 25 >=16 2 1.00220170 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 J I 29 4 4 0.63742636 0.3647753</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 D I 25 8 4 0.54530143 0.4569003</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 B R 25 0.5 2 0.32206771 0.6801340</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 F I 29 4 1 0.09331917 0.9088825</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 G S 17 4 4 -0.04702882 1.0492305</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 A S 21 8 1 -0.22695748 1.2291592</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H I 20 2 1 -0.55604901 1.5582507</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 E S 21 0.5 1 -0.77106467 1.7732664</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 I S 17 0.5 1 -0.99921640 2.0014181</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C S 27 4 >=4 0.42065543 0.00000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 D I 30 >=8 2 0.40679865 0.01385678</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 E S 22 >=8 >=4 0.32292908 0.09772635</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 G R 25 1 2 0.21552084 0.20513459</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 I R 20 >=8 >=4 0.74027765 0.31962222</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F S 30 1 2 -0.05152683 0.47218226</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 A R 17 4 <=1 -0.19666410 0.61731953</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H S 17 <=0.5 >=4 -0.53867305 0.95932848</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 J S 20 4 <=1 -0.56391237 0.98456780</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 B S 19 <=0.5 2 -0.75540530 1.17606073</span>
|
||||
<span class="r-in"><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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
<!DOCTYPE html>
|
||||
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions."><title>Data Set with 5 754 Common Microorganism Codes — microorganisms.codes • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.6/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 5 754 Common Microorganism Codes — microorganisms.codes"><meta property="og:description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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||||
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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 5 754 Common Microorganism Codes</h1>
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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 4 909 Common Microorganism Codes</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
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<div class="d-none name"><code>microorganisms.codes.Rd</code></div>
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</div>
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@ -170,7 +170,7 @@
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<div class="section level2">
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<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
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<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 5 754 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism</p></li>
|
||||
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 4 909 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism</p></li>
|
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<li><p><code>mo</code><br> ID of the microorganism in the <a href="microorganisms.html">microorganisms</a> data set</p></li>
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</ul></div>
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<div class="section level2">
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@ -185,20 +185,20 @@
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">microorganisms.codes</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 5,754 × 2</span></span>
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<span class="r-out co"><span class="r-pr">#></span> code mo </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> _FAM_A- B_GRAMN </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> _FAM_A+ B_GRAMP </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> _FAM_AC B_GRAMP </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> _FAM_AE B_GRAMN </span>
|
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> _FAM_AN B_GRAMN </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> _FAM_AO B_GRAMP </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> _FAM_AP UNKNOWN</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> _FAM_AS F_FUNGUS </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> _FAM_AT UNKNOWN</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> _FAM_AV UNKNOWN</span>
|
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 5,744 more rows</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 4,909 × 2</span></span>
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<span class="r-out co"><span class="r-pr">#></span> code mo </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></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> 1011 B_GRAMP </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 1012 B_GRAMP </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 1013 B_GRAMN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 1014 B_GRAMN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 1015 F_YEAST </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 103 B_ESCHR_COLI</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 104 B_SLMNL_HMRM</span>
|
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 1100 B_STRPT </span>
|
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 1101 B_STRPT_VIRI</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 1102 B_STRPT_HAEM</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 4,899 more rows</span></span>
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</code></pre></div>
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</div>
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</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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@ -1,5 +1,5 @@
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<div class="ref-description section level2">
|
||||
<p>A data set containing the full microbial taxonomy (<strong>last updated: 11 December, 2022</strong>) of five kingdoms from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF). This data set is the backbone of this <code>AMR</code> package. MO codes can be looked up using <code><a href="as.mo.html">as.mo()</a></code>.</p>
|
||||
<p>A data set containing the full microbial taxonomy (<strong>last updated: December 11th, 2022</strong>) of five kingdoms from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF). This data set is the backbone of this <code>AMR</code> package. MO codes can be looked up using <code><a href="as.mo.html">as.mo()</a></code>.</p>
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</div>
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<div class="section level2">
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<li><p><code>source</code><br> Either "GBIF", "LPSN", or "manually added" (see <em>Source</em>)</p></li>
|
||||
<li><p><code>prevalence</code><br> Prevalence of the microorganism according to 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>
|
||||
), see <code><a href="mo_matching_score.html">mo_matching_score()</a></code> for the full explanation</p></li>
|
||||
<li><p><code>snomed</code><br> Systematized Nomenclature of Medicine (SNOMED) code of the microorganism, version of 1 July, 2021 (see <em>Source</em>). Use <code><a href="mo_property.html">mo_snomed()</a></code> to retrieve it quickly, see <code><a href="mo_property.html">mo_property()</a></code>.</p></li>
|
||||
<li><p><code>snomed</code><br> Systematized Nomenclature of Medicine (SNOMED) code of the microorganism, version of July 1st, 2021 (see <em>Source</em>). Use <code><a href="mo_property.html">mo_snomed()</a></code> to retrieve it quickly, see <code><a href="mo_property.html">mo_property()</a></code>.</p></li>
|
||||
</ul></div>
|
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<div class="section level2">
|
||||
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
|
||||
|
||||
<ul><li><p>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong> International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a>
|
||||
. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on 11 December, 2022.</p></li>
|
||||
. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on December 11th, 2022.</p></li>
|
||||
<li><p>GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset <a href="https://doi.org/10.15468/39omei" class="external-link">doi:10.15468/39omei</a>
|
||||
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on 11 December, 2022.</p></li>
|
||||
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on December 11th, 2022.</p></li>
|
||||
<li><p>Reimer, LC <em>et al.</em> (2022). <strong><em>BacDive</em> in 2022: the knowledge base for standardized bacterial and archaeal data.</strong> Nucleic Acids Res., 50(D1):D741-D74; <a href="https://doi.org/10.1093/nar/gkab961" class="external-link">doi:10.1093/nar/gkab961</a>
|
||||
. Accessed from <a href="https://bacdive.dsmz.de" class="external-link">https://bacdive.dsmz.de</a> on May 12th, 2023.</p></li>
|
||||
<li><p>Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link">https://phinvads.cdc.gov</a></p></li>
|
||||
<li><p>Grimont <em>et al.</em> (2007). Antigenic Formulae of the Salmonella Serovars, 9th Edition. WHO Collaborating Centre for Reference and Research on <em>Salmonella</em> (WHOCC-SALM).</p></li>
|
||||
<li><p>Bartlett <em>et al.</em> (2022). <strong>A comprehensive list of bacterial pathogens infecting humans</strong> <em>Microbiology</em> 168:001269; <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a></p></li>
|
||||
<li><p>Reimer <em>et al.</em> (2022). <strong><em>BacDive</em> in 2022: the knowledge base for standardized bacterial and archaeal data.</strong> <em>Nucleic Acids Res.</em> 2022 Jan 7;50(D1):D741-D746; <a href="https://doi.org/10.1093/nar/gkab961" class="external-link">doi:10.1093/nar/gkab961</a></p></li>
|
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</ul></div>
|
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<div class="section level2">
|
||||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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@ -233,12 +233,11 @@
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<span class="r-out co"><span class="r-pr">#></span> </span>
|
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<span class="r-out co"><span class="r-pr">#></span> --------------------------------------------------------------------------------</span>
|
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<span class="r-out co"><span class="r-pr">#></span> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688)</span>
|
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<span class="r-out co"><span class="r-pr">#></span> Also matched: Enterobacter cowanii (0.600), Eubacterium combesii</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.600), Eggerthia catenaformis (0.591), Eubacterium callanderi</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.591), Enterocloster citroniae (0.587), Eubacterium cylindroides</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.583), Enterococcus casseliflavus (0.577), Enterobacter cloacae</span>
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<span class="r-out co"><span class="r-pr">#></span> cloacae (0.571), Ehrlichia canis (0.567), and Enterobacter cloacae</span>
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<span class="r-out co"><span class="r-pr">#></span> dissolvens (0.565)</span>
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<span class="r-out co"><span class="r-pr">#></span> Also matched: Eubacterium alactolyticum (0.620), Erwinia herbicola</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.618), Campylobacter coli (0.611), Enterobacter cowanii (0.600),</span>
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<span class="r-out co"><span class="r-pr">#></span> Eubacterium combesii (0.600), Enterococcus faecalis (0.595), Eggerthia</span>
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<span class="r-out co"><span class="r-pr">#></span> catenaformis (0.591), Enterocloster aldensis (0.591), Eubacterium</span>
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<span class="r-out co"><span class="r-pr">#></span> callanderi (0.591), and Rhodococcus corallinus (0.591)</span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> Only the first 10 other matches of each record are shown. Run</span>
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<span class="r-out co"><span class="r-pr">#></span> print(mo_uncertainties(), n = ...) to view more entries, or save</span>
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@ -464,7 +464,7 @@
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<p>Determination of intrinsic resistance (<code>mo_is_intrinsic_resistant()</code>) will be based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, which is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes/" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3</a> (2021). The <code>mo_is_intrinsic_resistant()</code> function can be vectorised over both argument <code>x</code> (input for microorganisms) and <code>ab</code> (input for antibiotics).</p>
|
||||
<p>Determination of bacterial oxygen tolerance (<code>mo_oxygen_tolerance()</code>) will be based on BacDive, see <em>Source</em>. The function <code>mo_is_anaerobic()</code> only returns <code>TRUE</code> if the oxygen tolerance is <code>"anaerobe"</code>, indicting an obligate anaerobic species or genus. It always returns <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
|
||||
<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
|
||||
<p>SNOMED codes (<code>mo_snomed()</code>) are from the version of 1 July, 2021. See <em>Source</em> and the <a href="microorganisms.html">microorganisms</a> data set for more info.</p>
|
||||
<p>SNOMED codes (<code>mo_snomed()</code>) are from the version of July 1st, 2021. See <em>Source</em> and the <a href="microorganisms.html">microorganisms</a> data set for more info.</p>
|
||||
<p>Old taxonomic names (so-called 'synonyms') can be retrieved with <code>mo_synonyms()</code> (which will have the scientific reference as <a href="https://rdrr.io/r/base/names.html" class="external-link">name</a>), the current taxonomic name can be retrieved with <code>mo_current()</code>. Both functions return full names.</p>
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<p>All output <a href="translate.html">will be translated</a> where possible.</p>
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</div>
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|
|||
<li><p>Lancefield RC (1933). <strong>A serological differentiation of human and other groups of hemolytic streptococci.</strong> <em>J Exp Med.</em> 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>Berends MS <em>et al.</em> (2022). <strong>Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019/</strong> <em>Micro.rganisms</em> 10(9), 1801; <a href="https://doi.org/10.3390/microorganisms10091801" class="external-link">doi:10.3390/microorganisms10091801</a></p></li>
|
||||
<li><p>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong> International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a>
|
||||
. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on 11 December, 2022.</p></li>
|
||||
. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on December 11th, 2022.</p></li>
|
||||
<li><p>GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset <a href="https://doi.org/10.15468/39omei" class="external-link">doi:10.15468/39omei</a>
|
||||
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on 11 December, 2022.</p></li>
|
||||
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on December 11th, 2022.</p></li>
|
||||
<li><p>Reimer, LC <em>et al.</em> (2022). <strong><em>BacDive</em> in 2022: the knowledge base for standardized bacterial and archaeal data.</strong> Nucleic Acids Res., 50(D1):D741-D74; <a href="https://doi.org/10.1093/nar/gkab961" class="external-link">doi:10.1093/nar/gkab961</a>
|
||||
. Accessed from <a href="https://bacdive.dsmz.de" class="external-link">https://bacdive.dsmz.de</a> on May 12th, 2023.</p></li>
|
||||
<li><p>Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link">https://phinvads.cdc.gov</a></p></li>
|
||||
<li><p>Bartlett A <em>et al.</em> (2022). <strong>A comprehensive list of bacterial pathogens infecting humans</strong> <em>Microbiology</em> 168:001269; <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a></p></li>
|
||||
<li><p>Reimer <em>et al.</em> (2022). <strong><em>BacDive</em> in 2022: the knowledge base for standardized bacterial and archaeal data.</strong> <em>Nucleic Acids Res.</em> 2022 Jan 7;50(D1):D741-D746; <a href="https://doi.org/10.1093/nar/gkab961" class="external-link">doi:10.1093/nar/gkab961</a></p></li>
|
||||
</ol></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>
|
||||
|
|
|
|||
|
|
@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -91,28 +91,28 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
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|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</small>
|
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|
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|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -91,28 +91,28 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
@ -210,43 +210,42 @@
|
|||
<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">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 64 8 4 0.01 0.25 <=0.001 2 0.5 0.125 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 4 0.005 1 32 64 0.01 >=128 0.25 0.0625 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] 0.025 4 0.125 64 0.005 0.5 0.0625 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 4 0.005 0.025 64 1 2 0.005 64 0.002 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 0.0625 <=0.001 0.25 0.025 16 16 32 0.125 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] 0.125 <=0.001 0.005 0.002 8 2 64 </span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 41 41 50 42 9 18 6 13 38 13 35 13 26 24 22 49 42 10 49 49 35 24 42 41 41</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 46 9 26 16 29 29 48 9 13 22 33 6 22 8 37 44 45 49 21 37 10 42 41 33 44</span>
|
||||
<span class="r-in"><span><span class="fu">random_sir</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R S S R R R I S R S R R S S R R I I S R I I S R I</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S S S S R I S S R S S S I I S R S R R S I R S I I</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] <=0.001 0.002 <=0.001 0.125 0.005 32 0.025 32 64 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 0.0625 8 0.125 64 0.025 1 1 0.025 0.002 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] <=0.001 0.005 0.125 0.002 <=0.001 32 0.125 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.25 256 0.0625 0.025 16 0.5 0.125 128 0.01 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 1 2 1 0.005 8 256 4 0.5 0.005 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] 256 0.0625 8 <=0.001 0.5 128 0.025 </span>
|
||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] <=1 <=1 4 <=1 16 4 16 64 32 2 2 64 32 2 64 16 <=1 16 64 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [20] 4 2 4 4 8 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 32 32 32 0.25 8 2 >=64 16 4 >=64 >=64 0.5 1 >=64 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [16] 32 0.25 2 0.25 8 4 8 8 0.25 0.25</span>
|
||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 16 16 16 16 <=0.0625 8 8 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [9] 8 <=0.0625 1 0.5 2 0.5 8 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [17] 0.125 8 2 0.125 <=0.0625 0.125 0.25 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] 0.25 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 4 0.25 2 1 0.0625 4 2 1 4 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] 4 4 0.25 1 0.5 1 4 0.125 8 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] 1 0.5 0.125 0.125 4 </span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 40 32 46 40 24 29 50 24 47 40 31 11 48 41 38 9 48 42 39 14 9 48 39 29 24</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 49 10 26 27 49 50 31 18 15 47 43 44 22 22 33 39 43 32 10 22 32 31 41 47 16</span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 16 16 17 13 15 11 15 17 17 11 12 16 12 13 14 11 14 13 16 12 11 13 12 11 13</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 15 12 16 11 15 16 14 16 17 16 13 13 16 15 13 15 13 12 12 14 15 16 11 17 15</span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 18 16 21 23 18 19 27 19 27 16 23 15 16 27 17 15 26 21 27 20 24 26 24 24 19</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 23 17 19 23 16 27 22 26 15 26 23 19 27 21 21 16 22 19 24 18 15 15 21 25 15</span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
|
|
@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -91,28 +91,28 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
@ -198,7 +198,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
|||
<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">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.02767595</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.08407527</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
|
||||
<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="">2.0.0.9019</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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">
|
||||
|
|
@ -89,28 +89,28 @@
|
|||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-circles-overlap"></span>
|
||||
<span class="fa fa-layer-plus"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
|
|
|
|||
File diff suppressed because one or more lines are too long
Loading…
Reference in New Issue