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@@ -29,7 +29,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9081</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">
@@ -95,7 +95,7 @@
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 24 September 2024.</p>
generated on 29 September 2024.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@@ -151,21 +151,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2024-09-24</td>
<td align="center">2024-09-29</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2024-09-24</td>
<td align="center">2024-09-29</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2024-09-24</td>
<td align="center">2024-09-29</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@@ -279,37 +279,35 @@ taxonomic codes. Let’s check this:</p>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
<span><span class="co">#&gt; "E. coli" -&gt; Escherichia coli (B_ESCHR_COLI, 0.688)</span></span>
<span><span class="co">#&gt; Also matched: Escherichia coli coli (0.643), Escherichia coli</span></span>
<span><span class="co">#&gt; expressing (0.611), Enterobacter cowanii (0.600), Eubacterium combesii</span></span>
<span><span class="co">#&gt; (0.600), Eggerthia catenaformis (0.591), Eubacterium callanderi</span></span>
<span><span class="co">#&gt; (0.591), Enterocloster citroniae (0.587), Eubacterium cylindroides</span></span>
<span><span class="co">#&gt; (0.583), Enterococcus casseliflavus (0.577), and Enterobacter cloacae</span></span>
<span><span class="co">#&gt; cloacae (0.571)</span></span>
<span><span class="co">#&gt; Also matched: Enterococcus crotali (0.650), Escherichia coli coli</span></span>
<span><span class="co">#&gt; (0.643), Escherichia coli expressing (0.611), Erwinia coffeiphila</span></span>
<span><span class="co">#&gt; (0.605), Eubacterium coprostanoligenes (0.603), Enterobacter cowanii</span></span>
<span><span class="co">#&gt; (0.600), Eubacterium combesii (0.600), Enterococcus columbae (0.595),</span></span>
<span><span class="co">#&gt; Eggerthia catenaformis (0.591), and Enterococcus camelliae (0.591)</span></span>
<span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
<span><span class="co">#&gt; "K. pneumoniae" -&gt; Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786)</span></span>
<span><span class="co">#&gt; Also matched: Klebsiella pneumoniae ozaenae (0.707), Klebsiella</span></span>
<span><span class="co">#&gt; pneumoniae pneumoniae (0.688), Klebsiella pneumoniae rhinoscleromatis</span></span>
<span><span class="co">#&gt; (0.658), Klebsiella pasteurii (0.500), Klebsiella planticola (0.500),</span></span>
<span><span class="co">#&gt; Kingella potus (0.400), Kluyveromyces pseudotropicale (0.386),</span></span>
<span><span class="co">#&gt; Kluyveromyces pseudotropicalis (0.363), Kosakonia pseudosacchari</span></span>
<span><span class="co">#&gt; (0.361), and Kluyveromyces pseudotropicalis pseudotropicalis (0.361)</span></span>
<span><span class="co">#&gt; (0.658), Kosakonia pseudosacchari (0.542), Kaistella palustris (0.500),</span></span>
<span><span class="co">#&gt; Kaistella polysaccharea (0.500), Kingella potus (0.500), Kingella</span></span>
<span><span class="co">#&gt; pumchi (0.500), Klebsiella pasteurii (0.500), and Klebsiella planticola</span></span>
<span><span class="co">#&gt; (0.500)</span></span>
<span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
<span><span class="co">#&gt; "S. aureus" -&gt; Staphylococcus aureus (B_STPHY_AURS, 0.690)</span></span>
<span><span class="co">#&gt; Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus</span></span>
<span><span class="co">#&gt; argenteus (0.625), Staphylococcus aureus anaerobius (0.625), Salmonella</span></span>
<span><span class="co">#&gt; Aurelianis (0.595), Salmonella Aarhus (0.588), Salmonella Amounderness</span></span>
<span><span class="co">#&gt; (0.587), Selenomonas artemidis (0.571), Salmonella choleraesuis</span></span>
<span><span class="co">#&gt; arizonae (0.562), Streptococcus anginosus anginosus (0.561), and</span></span>
<span><span class="co">#&gt; Salmonella Abaetetuba (0.548)</span></span>
<span><span class="co">#&gt; "S. aureus" -&gt; Streptomyces aureus (B_SMYCS_AURS, 0.711)</span></span>
<span><span class="co">#&gt; Also matched: Streptomyces azureus (0.700), Staphylococcus aureus</span></span>
<span><span class="co">#&gt; (0.690), Streptomyces aureorectus (0.667), Streptomyces albipurpureus</span></span>
<span><span class="co">#&gt; (0.654), Streptomyces auratus (0.650), Staphylococcus aureus aureus</span></span>
<span><span class="co">#&gt; (0.643), Streptomyces aurantiogriseus (0.643), Streptomyces</span></span>
<span><span class="co">#&gt; aureocirculatus (0.643), Streptomyces aureoverticillatus (0.629), and</span></span>
<span><span class="co">#&gt; Staphylococcus argenteus (0.625)</span></span>
<span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
<span><span class="co">#&gt; "S. pneumoniae" -&gt; Streptococcus pneumoniae (B_STRPT_PNMN, 0.750)</span></span>
<span><span class="co">#&gt; Also matched: Streptococcus pseudopneumoniae (0.700), Serratia</span></span>
<span><span class="co">#&gt; proteamaculans quinovora (0.545), Streptococcus pseudoporcinus (0.536),</span></span>
<span><span class="co">#&gt; Staphylococcus pseudintermedius (0.532), Serratia proteamaculans</span></span>
<span><span class="co">#&gt; proteamaculans (0.526), Salmonella Portanigra (0.524), Sphingomonas</span></span>
<span><span class="co">#&gt; paucimobilis (0.520), Streptococcus pluranimalium (0.519),</span></span>
<span><span class="co">#&gt; Streptococcus constellatus pharyngis (0.514), and Salmonella Pakistan</span></span>
<span><span class="co">#&gt; (0.500)</span></span>
<span><span class="co">#&gt; Also matched: Streptococcus pseudopneumoniae (0.700), Sphingomonas</span></span>
<span><span class="co">#&gt; piscinae (0.619), Sphingomonas paeninsulae (0.604), Streptomyces</span></span>
<span><span class="co">#&gt; pseudovenezuelae (0.603), Sphingomonas panaciterrae (0.600),</span></span>
<span><span class="co">#&gt; Sphingobacterium pakistanense (0.586), Shewanella pneumatophori</span></span>
<span><span class="co">#&gt; (0.583), Sphingobacterium pakistanensis (0.583), Sphingomonas palmae</span></span>
<span><span class="co">#&gt; (0.579), and Sphingomonas pseudosanguinis (0.571)</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; Only the first 10 other matches of each record are shown. Run</span></span>
<span><span class="co">#&gt; print(mo_uncertainties(), n = ...) to view more entries, or save</span></span>
@@ -348,11 +346,11 @@ dplyr:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> P3 A 2014-09-19 B_ESCHR_COLI R S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> P10 A 2015-12-10 B_ESCHR_COLI S I S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B7 A 2015-03-02 B_ESCHR_COLI S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> W3 A 2018-03-31 B_STPHY_AURS R S R S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> W3 A 2018-03-31 B_SMYCS_AURS R S R S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> J8 A 2016-06-14 B_ESCHR_COLI R S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> M3 A 2015-10-25 B_ESCHR_COLI R S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> J3 A 2019-06-19 B_ESCHR_COLI S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> G6 A 2015-04-27 B_STPHY_AURS S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> G6 A 2015-04-27 B_SMYCS_AURS S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,990 more rows</span></span></span></code></pre></div>
<p>This is basically it for the cleaning, time to start the data
inclusion.</p>
@@ -406,9 +404,9 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
<span><span class="co">#&gt; ℹ Using column 'patient_id' as input for col_patient_id.</span></span>
<span><span class="co">#&gt; ℹ Basing inclusion on all antimicrobial results, using a points threshold</span></span>
<span><span class="co">#&gt; of 2</span></span>
<span><span class="co">#&gt; =&gt; Found 2,712 'phenotype-based' first isolates (90.4% of total where a</span></span>
<span><span class="co">#&gt; =&gt; Found 2,724 'phenotype-based' first isolates (90.8% of total where a</span></span>
<span><span class="co">#&gt; microbial ID was available)</span></span></code></pre></div>
<p>So only 90% is suitable for resistance analysis! We can now filter on
<p>So only 91% 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>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@@ -418,24 +416,24 @@ 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">&lt;-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</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 2 712 isolates for analysis. Now our data looks
<p>So we end up with 2 724 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">#&gt; <span style="color: #949494;"># A tibble: 2,712 × 9</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 9</span></span></span>
<span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> J3 A 2012-11-21 B_ESCHR_COLI R I S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> R7 A 2018-04-03 B_KLBSL_PNMN R I S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> P10 A 2015-12-10 B_ESCHR_COLI S I S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> B7 A 2015-03-02 B_ESCHR_COLI S S S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> W3 A 2018-03-31 B_STPHY_AURS R S R S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> W3 A 2018-03-31 B_SMYCS_AURS R S R S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> M3 A 2015-10-25 B_ESCHR_COLI R S S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> J3 A 2019-06-19 B_ESCHR_COLI S S S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> G6 A 2015-04-27 B_STPHY_AURS S S S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> G6 A 2015-04-27 B_SMYCS_AURS S S S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> P4 A 2011-06-21 B_ESCHR_COLI S S S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> Z1 A 2014-09-05 B_ESCHR_COLI S S S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,702 more rows</span></span></span></code></pre></div>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span></code></pre></div>
<p>Time for the analysis.</p>
</div>
</div>
@@ -448,29 +446,29 @@ 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">#&gt; patient_id hospital date </span></span>
<span><span class="co">#&gt; Length:2712 Length:2712 Min. :2011-01-01 </span></span>
<span><span class="co">#&gt; Class :character Class :character 1st Qu.:2013-05-03 </span></span>
<span><span class="co">#&gt; Mode :character Mode :character Median :2015-06-16 </span></span>
<span><span class="co">#&gt; Mean :2015-06-21 </span></span>
<span><span class="co">#&gt; 3rd Qu.:2017-08-24 </span></span>
<span><span class="co">#&gt; Length:2724 Length:2724 Min. :2011-01-01 </span></span>
<span><span class="co">#&gt; Class :character Class :character 1st Qu.:2013-04-26 </span></span>
<span><span class="co">#&gt; Mode :character Mode :character Median :2015-06-14 </span></span>
<span><span class="co">#&gt; Mean :2015-06-18 </span></span>
<span><span class="co">#&gt; 3rd Qu.:2017-08-21 </span></span>
<span><span class="co">#&gt; Max. :2019-12-27 </span></span>
<span><span class="co">#&gt; bacteria AMX AMC </span></span>
<span><span class="co">#&gt; Class :mo Class:sir Class:sir </span></span>
<span><span class="co">#&gt; &lt;NA&gt; :0 %S :41.0% (n=1112) %S :52.0% (n=1409) </span></span>
<span><span class="co">#&gt; Unique:4 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; #1 :B_ESCHR_COLI %I :16.1% (n=437) %I :12.0% (n=325) </span></span>
<span><span class="co">#&gt; #2 :B_STPHY_AURS %R :42.9% (n=1163) %R :36.1% (n=978) </span></span>
<span><span class="co">#&gt; &lt;NA&gt; :0 %S :41.4% (n=1127) %S :52.2% (n=1421) </span></span>
<span><span class="co">#&gt; Unique:5 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; #1 :B_ESCHR_COLI %I :16.1% (n=438) %I :12.1% (n=329) </span></span>
<span><span class="co">#&gt; #2 :B_STPHY_AURS %R :42.5% (n=1159) %R :35.8% (n=974) </span></span>
<span><span class="co">#&gt; #3 :B_STRPT_PNMN %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; CIP GEN first </span></span>
<span><span class="co">#&gt; Class:sir Class:sir Mode:logical </span></span>
<span><span class="co">#&gt; %S :51.5% (n=1396) %S :59.6% (n=1616) TRUE:2712 </span></span>
<span><span class="co">#&gt; %S :51.7% (n=1407) %S :59.9% (n=1632) TRUE:2724 </span></span>
<span><span class="co">#&gt; %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; %I : 6.6% (n=178) %I : 3.1% (n=85) </span></span>
<span><span class="co">#&gt; %R :42.0% (n=1138) %R :37.3% (n=1011) </span></span>
<span><span class="co">#&gt; %I : 6.5% (n=178) %I : 3.1% (n=85) </span></span>
<span><span class="co">#&gt; %R :41.8% (n=1139) %R :37.0% (n=1007) </span></span>
<span><span class="co">#&gt; %NI : 0.0% (n=0) %NI : 0.0% (n=0)</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">#&gt; Rows: 2,712</span></span>
<span><span class="co">#&gt; Rows: 2,724</span></span>
<span><span class="co">#&gt; Columns: 9</span></span>
<span><span class="co">#&gt; $ patient_id <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> "J3", "R7", "P10", "B7", "W3", "M3", "J3", "G6", "P4", "Z1"…</span></span>
<span><span class="co">#&gt; $ hospital <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A",…</span></span>
@@ -485,7 +483,7 @@ 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">#&gt; patient_id hospital date bacteria AMX AMC CIP </span></span>
<span><span class="co">#&gt; 260 3 1852 4 3 3 3 </span></span>
<span><span class="co">#&gt; 260 3 1853 5 3 3 3 </span></span>
<span><span class="co">#&gt; GEN first </span></span>
<span><span class="co">#&gt; 3 1</span></span></code></pre></div>
<div class="section level3">
@@ -497,23 +495,25 @@ 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">%&gt;%</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">#&gt; <span style="color: #949494;"># A tibble: 4 × 2</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 5 × 2</span></span></span>
<span><span class="co">#&gt; `mo_name(bacteria)` n</span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> Escherichia coli <span style="text-decoration: underline;">1</span>518</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 730</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 483</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae 426</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 326</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">5</span> Streptomyces aureus 247</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">%&gt;%</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">#&gt; <span style="color: #949494;"># A tibble: 4 × 2</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 5 × 2</span></span></span>
<span><span class="co">#&gt; `mo_name(bacteria)` n</span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> Escherichia coli <span style="text-decoration: underline;">1</span>319</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 676</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 456</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae 400</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 317</span></span></code></pre></div>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 317</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">5</span> Streptomyces aureus 232</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>
@@ -525,7 +525,7 @@ 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">%&gt;%</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">#&gt; ℹ For aminoglycosides() using column 'GEN' (gentamicin)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,712 × 2</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 2</span></span></span>
<span><span class="co">#&gt; date GEN </span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> 2012-11-21 S </span></span>
@@ -538,100 +538,100 @@ in:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> 2015-04-27 S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> 2011-06-21 S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> 2014-09-05 S </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,702 more rows</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,714 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">%&gt;%</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">#&gt; ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC'</span></span>
<span><span class="co">#&gt; (amoxicillin/clavulanic acid)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,712 × 3</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 3</span></span></span>
<span><span class="co">#&gt; bacteria AMX AMC </span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> B_ESCHR_COLI R I </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> B_KLBSL_PNMN R I </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> B_ESCHR_COLI S I </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> B_ESCHR_COLI S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B_STPHY_AURS R S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B_SMYCS_AURS R S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> B_ESCHR_COLI R S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> B_ESCHR_COLI S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> B_STPHY_AURS S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> B_SMYCS_AURS S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> B_ESCHR_COLI S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> B_ESCHR_COLI S S </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,702 more rows</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,714 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">%&gt;%</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">#&gt; <span style="color: #949494;"># A tibble: 2,712 × 5</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 5</span></span></span>
<span><span class="co">#&gt; bacteria AMX AMC CIP GEN </span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> B_ESCHR_COLI R I S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> B_KLBSL_PNMN R I S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> B_ESCHR_COLI S I S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> B_ESCHR_COLI S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B_STPHY_AURS R S R S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B_SMYCS_AURS R S R S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> B_ESCHR_COLI R S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> B_ESCHR_COLI S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> B_STPHY_AURS S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> B_SMYCS_AURS S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> B_ESCHR_COLI S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> B_ESCHR_COLI S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,702 more rows</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,714 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">%&gt;%</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">#&gt; ℹ For aminoglycosides() using column 'GEN' (gentamicin)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 1,011 × 9</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 1,007 × 9</span></span></span>
<span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span></span>
<span><span class="co">#&gt; <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">#&gt; <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">#&gt; <span style="color: #BCBCBC;"> 2</span> X1 A 2017-07-04 B_SMYCS_AURS R S S R TRUE </span></span>
<span><span class="co">#&gt; <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">#&gt; <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">#&gt; <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">#&gt; <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">#&gt; <span style="color: #BCBCBC;"> 6</span> R1 A 2018-06-10 B_SMYCS_AURS S S S R TRUE </span></span>
<span><span class="co">#&gt; <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">#&gt; <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">#&gt; <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">#&gt; <span style="color: #BCBCBC;"> 8</span> P5 A 2019-03-09 B_SMYCS_AURS S S S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> Q8 A 2019-08-10 B_SMYCS_AURS S S S R TRUE </span></span>
<span><span class="co">#&gt; <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">#&gt; <span style="color: #949494;"># ℹ 1,001 more rows</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 997 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">%&gt;%</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>
<span><span class="co">#&gt; ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC'</span></span>
<span><span class="co">#&gt; (amoxicillin/clavulanic acid)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 483 × 9</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 479 × 9</span></span></span>
<span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span></span>
<span><span class="co">#&gt; <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">#&gt; <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">#&gt; <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">#&gt; <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">#&gt; <span style="color: #BCBCBC;"> 2</span> R10 A 2013-12-20 B_SMYCS_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> R7 A 2015-10-25 B_SMYCS_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> R8 A 2019-10-25 B_SMYCS_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B6 A 2016-11-20 B_ESCHR_COLI R R R R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> I7 A 2015-08-19 B_ESCHR_COLI R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> N3 A 2014-12-29 B_STRPT_PNMN R R R S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> V1 A 2018-08-07 B_STPHY_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 473 more rows</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> C5 A 2015-08-30 B_KLBSL_PNMN R R S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 469 more rows</span></span></span>
<span></span>
<span><span class="co"># even works in base R (since R 3.0):</span></span>
<span><span class="va">our_data_1st</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>
<span><span class="co">#&gt; ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC'</span></span>
<span><span class="co">#&gt; (amoxicillin/clavulanic acid)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 483 × 9</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 479 × 9</span></span></span>
<span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span></span>
<span><span class="co">#&gt; <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">#&gt; <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">#&gt; <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">#&gt; <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">#&gt; <span style="color: #BCBCBC;"> 2</span> R10 A 2013-12-20 B_SMYCS_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> R7 A 2015-10-25 B_SMYCS_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> R8 A 2019-10-25 B_SMYCS_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B6 A 2016-11-20 B_ESCHR_COLI R R R R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> I7 A 2015-08-19 B_ESCHR_COLI R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> N3 A 2014-12-29 B_STRPT_PNMN R R R S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> V1 A 2018-08-07 B_STPHY_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 473 more rows</span></span></span></code></pre></div>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> C5 A 2015-08-30 B_KLBSL_PNMN R R S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 469 more rows</span></span></span></code></pre></div>
</div>
<div class="section level3">
<h3 id="generate-antibiograms">Generate antibiograms<a class="anchor" aria-label="anchor" href="#generate-antibiograms"></a>
@@ -1230,7 +1230,7 @@ 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">%&gt;%</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">#&gt; [1] 0.4288348</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 0.4254772</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">
@@ -1240,9 +1240,9 @@ own:</p>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 3 × 2</span></span></span>
<span><span class="co">#&gt; hospital amoxicillin</span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> A 0.342</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> A 0.336</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> B 0.564</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> C 0.372</span></span></code></pre></div>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> C 0.370</span></span></code></pre></div>
<hr>
<p><em>Author: Dr. Matthijs Berends, 26th Feb 2023</em></p>
</div>
articles/EUCAST.html
+1 -1
View File
@@ -29,7 +29,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9081</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">
articles/MDR.html
+1 -1
View File
@@ -29,7 +29,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9081</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">
articles/PCA.html
+1 -1
View File
@@ -29,7 +29,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9081</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">
articles/WHONET.html
+1 -1
View File
@@ -29,7 +29,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9081</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">
articles/datasets.html
+52 -77
View File
@@ -29,7 +29,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9081</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">
@@ -84,7 +84,7 @@
<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 September 2024</h4>
<h4 data-toc-skip class="date">29 September 2024</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
@@ -96,16 +96,16 @@
interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are
reliable, up-to-date and freely available. We continually export our
data sets to formats for use in R, MS Excel, Apache Feather, Apache
Parquet, SPSS, SAS, and Stata. We also provide tab-separated text files
that are machine-readable and suitable for input in any software
program, such as laboratory information systems.</p>
Parquet, SPSS, and Stata. We also provide tab-separated text files that
are machine-readable and suitable for input in any software program,
such as laboratory information systems.</p>
<p>On this page, we explain how to download them and how the structure
of the data sets look like.</p>
<div class="section level2">
<h2 id="microorganisms-full-microbial-taxonomy">
<code>microorganisms</code>: Full Microbial Taxonomy<a class="anchor" aria-label="anchor" href="#microorganisms-full-microbial-taxonomy"></a>
</h2>
<p>A data set with 70 547 rows and 26 columns, containing the following
<p>A data set with 78 678 rows and 26 columns, containing the following
column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>,
<em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>,
<em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>,
@@ -116,36 +116,33 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
<em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 17 July 2024 12:29:55 UTC. Find more info
<p>It was last updated on 29 September 2024 20:17:56 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">original
R Data Structure (RDS) file</a> (1.6 MB)<br>
R Data Structure (RDS) file</a> (1.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">tab-separated
text file</a> (16 MB)<br>
text file</a> (17.7 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Microsoft
Excel workbook</a> (7.8 MB)<br>
Excel workbook</a> (8.7 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.feather" class="external-link">Apache
Feather file</a> (19 MB)<br>
Feather file</a> (8.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.parquet" class="external-link">Apache
Parquet file</a> (0 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xpt" class="external-link">SAS
transport (XPT) file</a> (69.5 MB)<br>
Parquet file</a> (3.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">IBM
SPSS Statistics data file</a> (24.5 MB)<br>
SPSS Statistics data file</a> (28.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata
DTA file</a> (69.5 MB)</li>
DTA file</a> (92.5 MB)</li>
</ul>
<p><strong>NOTE: The exported files for SAS, SPSS and Stata contain only
the first 50 SNOMED codes per record, as their file size would otherwise
<p><strong>NOTE: The exported files for SPSS and Stata contain only the
first 50 SNOMED codes per record, as their file size would otherwise
exceed 100 MB; the file size limit of GitHub.</strong> Their file
structures and compression techniques are very inefficient. Advice? Use
R instead. It’s free and much better in many ways.</p>
@@ -193,23 +190,23 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
</tr>
<tr class="even">
<td align="center">Animalia</td>
<td align="center">1 713</td>
<td align="center">1 628</td>
</tr>
<tr class="odd">
<td align="center">Archaea</td>
<td align="center">1 418</td>
<td align="center">1 419</td>
</tr>
<tr class="even">
<td align="center">Bacteria</td>
<td align="center">39 238</td>
<td align="center">39 248</td>
</tr>
<tr class="odd">
<td align="center">Chromista</td>
<td align="center">164</td>
<td align="center">178</td>
</tr>
<tr class="even">
<td align="center">Fungi</td>
<td align="center">19 878</td>
<td align="center">28 137</td>
</tr>
</tbody>
</table>
@@ -297,7 +294,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<td align="center"></td>
<td align="center">11158430</td>
<td align="center"></td>
<td align="center">1.0</td>
<td align="center">1</td>
<td align="center">407310004, 407251000, 407281008, …</td>
</tr>
<tr class="even">
@@ -325,7 +322,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">1.0</td>
<td align="center">1</td>
<td align="center"></td>
</tr>
<tr class="odd">
@@ -353,7 +350,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<td align="center">5427575</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">1.0</td>
<td align="center">1</td>
<td align="center">419388003</td>
</tr>
<tr class="even">
@@ -381,7 +378,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">1.5</td>
<td align="center">1</td>
<td align="center"></td>
</tr>
<tr class="odd">
@@ -409,7 +406,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<td align="center">11286021</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">1.0</td>
<td align="center">1</td>
<td align="center">1095001000112106, 715307006, 737528008, …</td>
</tr>
<tr class="even">
@@ -437,7 +434,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<td align="center">12233256</td>
<td align="center">11286021</td>
<td align="center"></td>
<td align="center">1.0</td>
<td align="center">1</td>
<td align="center"></td>
</tr>
</tbody>
@@ -455,7 +452,7 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
<em>iv_ddd</em>, <em>iv_units</em>, and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 19 September 2024 09:44:56 UTC. Find more info
<p>It was last updated on 29 September 2024 20:17:56 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@@ -474,18 +471,15 @@ Feather file</a> (0.1 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.parquet" class="external-link">Apache
Parquet file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xpt" class="external-link">SAS
transport (XPT) file</a> (1.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">IBM
SPSS Statistics data file</a> (0.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata
DTA file</a> (0.5 MB)</li>
</ul>
<p>The tab-separated text file and Microsoft Excel workbook, and SAS,
SPSS and Stata files all contain the ATC codes, common abbreviations,
trade names and LOINC codes as comma separated values.</p>
<p>The tab-separated text, Microsoft Excel, SPSS, and Stata files all
contain the ATC codes, common abbreviations, trade names and LOINC codes
as comma separated values.</p>
<div class="section level3">
<h3 id="source-1">Source<a class="anchor" aria-label="anchor" href="#source-1"></a>
</h3>
@@ -674,18 +668,14 @@ Feather file</a> (16 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.parquet" class="external-link">Apache
Parquet file</a> (13 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xpt" class="external-link">SAS
transport (XPT) file</a> (73 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">IBM
SPSS Statistics data file</a> (32 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata
DTA file</a> (78 kB)</li>
</ul>
<p>The tab-separated text file and Microsoft Excel workbook, and SAS,
SPSS and Stata files all contain the trade names and LOINC codes as
comma separated values.</p>
<p>The tab-separated text, Microsoft Excel, SPSS, and Stata files all
contain the trade names and LOINC codes as comma separated values.</p>
<div class="section level3">
<h3 id="source-2">Source<a class="anchor" aria-label="anchor" href="#source-2"></a>
</h3>
@@ -834,7 +824,7 @@ column names:<br><em>guideline</em>, <em>type</em>, <em>host</em>, <em>method</e
<em>breakpoint_R</em>, <em>uti</em>, and <em>is_SDD</em>.</p>
<p>This data set is in R available as <code>clinical_breakpoints</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 16 July 2024 12:51:57 UTC. Find more info
<p>It was last updated on 29 September 2024 20:17:56 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/clinical_breakpoints.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@@ -848,13 +838,10 @@ text file</a> (3.1 MB)<br>
Excel workbook</a> (2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.feather" class="external-link">Apache
Feather file</a> (4.9 MB)<br>
Feather file</a> (1.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.parquet" class="external-link">Apache
Parquet file</a> (0 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xpt" class="external-link">SAS
transport (XPT) file</a> (9.6 MB)<br>
Parquet file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.sav" class="external-link">IBM
SPSS Statistics data file</a> (5.6 MB)<br>
@@ -1047,11 +1034,11 @@ use.</p>
<code>intrinsic_resistant</code>: Intrinsic Bacterial
Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intrinsic-bacterial-resistance"></a>
</h2>
<p>A data set with 340 804 rows and 2 columns, containing the following
<p>A data set with 301 583 rows and 2 columns, containing the following
column names:<br><em>mo</em> and <em>ab</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 16 July 2024 12:51:57 UTC. Find more info
<p>It was last updated on 29 September 2024 20:17:56 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@@ -1059,25 +1046,22 @@ about the structure of this data set <a href="https://msberends.github.io/AMR/re
R Data Structure (RDS) file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">tab-separated
text file</a> (12.4 MB)<br>
text file</a> (10.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Microsoft
Excel workbook</a> (3.4 MB)<br>
Excel workbook</a> (3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.feather" class="external-link">Apache
Feather file</a> (13.1 MB)<br>
Feather file</a> (2.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.parquet" class="external-link">Apache
Parquet file</a> (0 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xpt" class="external-link">SAS
transport (XPT) file</a> (28.3 MB)<br>
Parquet file</a> (0.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">IBM
SPSS Statistics data file</a> (18.4 MB)<br>
SPSS Statistics data file</a> (16.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata
DTA file</a> (28.3 MB)</li>
DTA file</a> (25 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
@@ -1358,9 +1342,6 @@ Feather file</a> (21 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.parquet" class="external-link">Apache
Parquet file</a> (9 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xpt" class="external-link">SAS
transport (XPT) file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">IBM
SPSS Statistics data file</a> (64 kB)<br>
</li>
@@ -2011,18 +1992,18 @@ column names:<br><em>mo_group</em>, <em>mo</em>, <em>mo_group_name</em>, and
<p>This data set is in R available as
<code>microorganisms.groups</code>, after you load the <code>AMR</code>
package.</p>
<p>It was last updated on 14 July 2023 08:49:06 UTC. Find more info
<p>It was last updated on 29 September 2024 20:17:56 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.groups.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.rds" class="external-link">original
R Data Structure (RDS) file</a> (6 kB)<br>
R Data Structure (RDS) file</a> (5 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.txt" class="external-link">tab-separated
text file</a> (49 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.xlsx" class="external-link">Microsoft
Excel workbook</a> (20 kB)<br>
Excel workbook</a> (19 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.feather" class="external-link">Apache
Feather file</a> (19 kB)<br>
@@ -2030,11 +2011,8 @@ Feather file</a> (19 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.parquet" class="external-link">Apache
Parquet file</a> (13 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.xpt" class="external-link">SAS
transport (XPT) file</a> (0 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.sav" class="external-link">IBM
SPSS Statistics data file</a> (64 kB)<br>
SPSS Statistics data file</a> (63 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.dta" class="external-link">Stata
DTA file</a> (81 kB)</li>
@@ -2076,7 +2054,7 @@ which are used in the <code>clinical_breakpoints</code> data set.</p>
</tr>
<tr class="odd">
<td align="center">B_ACNTB_BMNN-C</td>
<td align="center">B_ACNTB_DJKS</td>
<td align="center">B_ACNTB_LCTC</td>
<td align="center">Acinetobacter baumannii complex</td>
<td align="center">Acinetobacter dijkshoorniae</td>
</tr>
@@ -2110,7 +2088,7 @@ which are used in the <code>clinical_breakpoints</code> data set.</p>
column names:<br><em>code</em> and <em>mo</em>.</p>
<p>This data set is in R available as <code>microorganisms.codes</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 16 July 2024 12:51:57 UTC. Find more info
<p>It was last updated on 29 September 2024 20:17:56 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.codes.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@@ -2124,13 +2102,10 @@ text file</a> (0.1 MB)<br>
Excel workbook</a> (82 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.feather" class="external-link">Apache
Feather file</a> (0.1 MB)<br>
Feather file</a> (85 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.parquet" class="external-link">Apache
Parquet file</a> (0 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.xpt" class="external-link">SAS
transport (XPT) file</a> (0 kB)<br>
Parquet file</a> (56 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.sav" class="external-link">IBM
SPSS Statistics data file</a> (0.1 MB)<br>
articles/index.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9081</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">
articles/other_pkg.html
+1 -1
View File
@@ -29,7 +29,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9081</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">
articles/resistance_predict.html
+1 -1
View File
@@ -29,7 +29,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9081</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">
articles/welcome_to_AMR.html
+4 -4
View File
@@ -29,7 +29,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9081</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">
@@ -112,7 +112,7 @@ this a successful and durable project!</p>
10.18637/jss.v104.i03</a>) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI
10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI
10.33612/diss.192486375</a>).</p>
<p>After installing this package, R knows ~71 000 distinct microbial
<p>After installing this package, R knows ~79 000 distinct microbial
species and all ~600 antibiotic, antimycotic and antiviral drugs by name
and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED
CT), and knows all about valid SIR and MIC values. The integral
@@ -166,8 +166,8 @@ translate MIC values and disk diffusion diameters to SIR</li>
<p>All reference data sets (about microorganisms, antibiotics, SIR
interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are
publicly and freely available. We continually export our data sets to
formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat
files that are machine-readable and suitable for input in any software
formats for use in R, SPSS, Stata and Excel. We also supply flat files
that are machine-readable and suitable for input in any software
program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all
download links on our website</a>, which is automatically updated with
every code change.</p>