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@@ -29,7 +29,7 @@
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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="">2.1.1.9084</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9086</small>
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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">
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@@ -87,7 +87,7 @@
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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 30 September 2024.</p>
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generated on 02 October 2024.</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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@@ -143,21 +143,21 @@ 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">2024-09-30</td>
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<td align="center">2024-10-02</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">2024-09-30</td>
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<td align="center">2024-10-02</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">2024-09-30</td>
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<td align="center">2024-10-02</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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@@ -270,12 +270,12 @@ taxonomic codes. Let’s check this:</p>
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<span><span class="co">#> taxonomic name, and the pathogenicity in humans. See ?mo_matching_score.</span></span>
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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" -> Enterococcus crotali (B_ENTRC_CRTL, 0.650)</span></span>
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<span><span class="co">#> Also matched: Escherichia coli (0.598), Enterococcus columbae (0.595),</span></span>
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<span><span class="co">#> Enterococcus camelliae (0.591), Enterococcus casseliflavus (0.577),</span></span>
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<span><span class="co">#> Escherichia coli coli (0.559), Enterococcus canis (0.556), Enterococcus</span></span>
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<span><span class="co">#> cecorum (0.550), Enterococcus canintestini (0.540), Escherichia coli</span></span>
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<span><span class="co">#> expressing (0.531), and Enterobacter cowanii (0.522)</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: Enterococcus crotali (0.650), Escherichia coli coli</span></span>
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<span><span class="co">#> (0.643), Escherichia coli expressing (0.611), Enterococcus columbae</span></span>
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<span><span class="co">#> (0.595), Enterococcus camelliae (0.591), Enterococcus casseliflavus</span></span>
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<span><span class="co">#> (0.577), Enterococcus canis (0.556), Enterococcus cecorum (0.550),</span></span>
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<span><span class="co">#> Enterococcus canintestini (0.540), and Enterobacter cowanii (0.522)</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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@@ -333,15 +333,15 @@ dplyr:</p>
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<span><span class="co">#> <span style="color: #949494;"># A tibble: 3,000 × 8</span></span></span>
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<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN </span></span>
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<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></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> J3 A 2012-11-21 B_ENTRC_CRTL R I S S </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> J3 A 2012-11-21 B_ESCHR_COLI R I S S </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> R7 A 2018-04-03 B_KLBSL_PNMN R I S S </span></span>
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||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> P3 A 2014-09-19 B_ENTRC_CRTL R S S S </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> P10 A 2015-12-10 B_ENTRC_CRTL S I S S </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B7 A 2015-03-02 B_ENTRC_CRTL S S S S </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> P3 A 2014-09-19 B_ESCHR_COLI R S S S </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> P10 A 2015-12-10 B_ESCHR_COLI S I S S </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B7 A 2015-03-02 B_ESCHR_COLI S S S S </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> W3 A 2018-03-31 B_STPHY_AURS R S R S </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> J8 A 2016-06-14 B_ENTRC_CRTL R S S S </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> M3 A 2015-10-25 B_ENTRC_CRTL R S S S </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> J3 A 2019-06-19 B_ENTRC_CRTL S S S S </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> J8 A 2016-06-14 B_ESCHR_COLI R S S S </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> M3 A 2015-10-25 B_ESCHR_COLI R S S S </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> J3 A 2019-06-19 B_ESCHR_COLI S S S S </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;">10</span> G6 A 2015-04-27 B_STPHY_AURS S S S S </span></span>
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<span><span class="co">#> <span style="color: #949494;"># ℹ 2,990 more rows</span></span></span></code></pre></div>
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<p>This is basically it for the cleaning, time to start the data
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@@ -396,9 +396,9 @@ 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>
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||||
<span><span class="co">#> => Found 2,764 'phenotype-based' first isolates (92.1% of total where a</span></span>
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||||
<span><span class="co">#> => Found 2,724 'phenotype-based' first isolates (90.8% of total where a</span></span>
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<span><span class="co">#> microbial ID was available)</span></span></code></pre></div>
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<p>So only 92% is suitable for resistance analysis! We can now filter on
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<p>So only 91% is suitable for resistance analysis! We can now filter on
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it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
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<code>dplyr</code> package:</p>
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<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
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@@ -408,24 +408,24 @@ it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" cl
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<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
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<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>
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<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>
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<p>So we end up with 2 764 isolates for analysis. Now our data looks
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<p>So we end up with 2 724 isolates for analysis. Now our data looks
|
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like:</p>
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<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="va">our_data_1st</span></span>
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||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,764 × 9</span></span></span>
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<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,724 × 9</span></span></span>
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<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
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<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>
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||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> J3 A 2012-11-21 B_ENTRC_CRTL R I S S TRUE </span></span>
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||||
<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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||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> R7 A 2018-04-03 B_KLBSL_PNMN R I S S TRUE </span></span>
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||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> P10 A 2015-12-10 B_ENTRC_CRTL S I S S TRUE </span></span>
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||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> B7 A 2015-03-02 B_ENTRC_CRTL S S S S TRUE </span></span>
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||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> W3 A 2018-03-31 B_STPHY_AURS R S R S TRUE </span></span>
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||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> M3 A 2015-10-25 B_ENTRC_CRTL R S S S TRUE </span></span>
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||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> J3 A 2019-06-19 B_ENTRC_CRTL S S S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> G6 A 2015-04-27 B_STPHY_AURS S S S S TRUE </span></span>
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||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> P4 A 2011-06-21 B_ENTRC_CRTL S S S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> Z1 A 2014-09-05 B_ENTRC_CRTL S S S S TRUE </span></span>
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||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,754 more rows</span></span></span></code></pre></div>
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||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> P3 A 2014-09-19 B_ESCHR_COLI R S S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> P10 A 2015-12-10 B_ESCHR_COLI S I S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B7 A 2015-03-02 B_ESCHR_COLI S S S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> W3 A 2018-03-31 B_STPHY_AURS R S R S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> M3 A 2015-10-25 B_ESCHR_COLI R S S S TRUE </span></span>
|
||||
<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>
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<span><span class="co">#> <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span></code></pre></div>
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<p>Time for the analysis.</p>
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</div>
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</div>
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@@ -438,44 +438,44 @@ impression, as it comes with support for the new <code>mo</code> and
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<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>
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<span><span class="co">#> patient_id hospital date </span></span>
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||||
<span><span class="co">#> Length:2764 Length:2764 Min. :2011-01-01 </span></span>
|
||||
<span><span class="co">#> Class :character Class :character 1st Qu.:2013-04-18 </span></span>
|
||||
<span><span class="co">#> Mode :character Mode :character Median :2015-06-07 </span></span>
|
||||
<span><span class="co">#> Mean :2015-06-16 </span></span>
|
||||
<span><span class="co">#> 3rd Qu.:2017-08-23 </span></span>
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||||
<span><span class="co">#> Max. :2020-01-01 </span></span>
|
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<span><span class="co">#> Length:2724 Length:2724 Min. :2011-01-01 </span></span>
|
||||
<span><span class="co">#> Class :character Class :character 1st Qu.:2013-04-07 </span></span>
|
||||
<span><span class="co">#> Mode :character Mode :character Median :2015-06-03 </span></span>
|
||||
<span><span class="co">#> Mean :2015-06-09 </span></span>
|
||||
<span><span class="co">#> 3rd Qu.:2017-08-11 </span></span>
|
||||
<span><span class="co">#> Max. :2019-12-27 </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 %S :42.1% (n=1163) %S :53.0% (n=1464) </span></span>
|
||||
<span><span class="co">#> Unique:5 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
|
||||
<span><span class="co">#> #1 :B_ESCHR_COLI %I :16.2% (n=447) %I :12.2% (n=337) </span></span>
|
||||
<span><span class="co">#> #2 :B_STPHY_AURS %R :41.8% (n=1154) %R :34.8% (n=963) </span></span>
|
||||
<span><span class="co">#> #3 :B_ENTRC_CRTL %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span></span>
|
||||
<span><span class="co">#> <NA> :0 %S :41.6% (n=1133) %S :52.6% (n=1432) </span></span>
|
||||
<span><span class="co">#> Unique:4 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
|
||||
<span><span class="co">#> #1 :B_ESCHR_COLI %I :16.4% (n=446) %I :12.2% (n=333) </span></span>
|
||||
<span><span class="co">#> #2 :B_STPHY_AURS %R :42.0% (n=1145) %R :35.2% (n=959) </span></span>
|
||||
<span><span class="co">#> #3 :B_STRPT_PNMN %NI : 0.0% (n=0) %NI : 0.0% (n=0) </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">#> %S :52.9% (n=1462) %S :61.5% (n=1699) TRUE:2764 </span></span>
|
||||
<span><span class="co">#> %S :52.5% (n=1431) %S :61.0% (n=1661) TRUE:2724 </span></span>
|
||||
<span><span class="co">#> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
|
||||
<span><span class="co">#> %I : 6.3% (n=174) %I : 3.0% (n=82) </span></span>
|
||||
<span><span class="co">#> %R :40.8% (n=1128) %R :35.6% (n=983) </span></span>
|
||||
<span><span class="co">#> %I : 6.5% (n=176) %I : 3.0% (n=82) </span></span>
|
||||
<span><span class="co">#> %R :41.0% (n=1117) %R :36.0% (n=981) </span></span>
|
||||
<span><span class="co">#> %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">#> Rows: 2,764</span></span>
|
||||
<span><span class="co">#> Rows: 2,724</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", "M3", "J3", "G6", "P4", "Z1"…</span></span>
|
||||
<span><span class="co">#> $ patient_id <span style="color: #949494; font-style: italic;"><chr></span> "J3", "R7", "P3", "P10", "B7", "W3", "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>
|
||||
<span><span class="co">#> $ date <span style="color: #949494; font-style: italic;"><date></span> 2012-11-21, 2018-04-03, 2015-12-10, 2015-03-02, 2018-03-31…</span></span>
|
||||
<span><span class="co">#> $ bacteria <span style="color: #949494; font-style: italic;"><mo></span> "B_ENTRC_CRTL", "B_KLBSL_PNMN", "B_ENTRC_CRTL", "B_ENTRC_CRT…</span></span>
|
||||
<span><span class="co">#> $ AMX <span style="color: #949494; font-style: italic;"><sir></span> R, R, S, S, R, R, S, S, S, S, R, S, S, S, R, R, R, R, S, R,…</span></span>
|
||||
<span><span class="co">#> $ AMC <span style="color: #949494; font-style: italic;"><sir></span> I, I, I, S, S, S, S, S, S, S, S, S, I, S, S, S, S, R, S, S,…</span></span>
|
||||
<span><span class="co">#> $ CIP <span style="color: #949494; font-style: italic;"><sir></span> S, S, S, S, R, S, S, S, S, S, S, S, S, S, S, S, S, S, S, S,…</span></span>
|
||||
<span><span class="co">#> $ GEN <span style="color: #949494; font-style: italic;"><sir></span> S, S, S, S, S, S, S, S, S, S, R, S, S, S, S, S, S, S, S, S,…</span></span>
|
||||
<span><span class="co">#> $ date <span style="color: #949494; font-style: italic;"><date></span> 2012-11-21, 2018-04-03, 2014-09-19, 2015-12-10, 2015-03-02…</span></span>
|
||||
<span><span class="co">#> $ bacteria <span style="color: #949494; font-style: italic;"><mo></span> "B_ESCHR_COLI", "B_KLBSL_PNMN", "B_ESCHR_COLI", "B_ESCHR_COL…</span></span>
|
||||
<span><span class="co">#> $ AMX <span style="color: #949494; font-style: italic;"><sir></span> R, R, R, S, S, R, R, S, S, S, S, R, S, S, R, R, R, R, S, R,…</span></span>
|
||||
<span><span class="co">#> $ AMC <span style="color: #949494; font-style: italic;"><sir></span> I, I, S, I, S, S, S, S, S, S, S, S, S, S, S, S, S, R, S, S,…</span></span>
|
||||
<span><span class="co">#> $ CIP <span style="color: #949494; font-style: italic;"><sir></span> S, S, S, S, S, R, S, S, S, S, S, S, S, S, S, S, S, S, S, S,…</span></span>
|
||||
<span><span class="co">#> $ GEN <span style="color: #949494; font-style: italic;"><sir></span> S, S, S, S, S, S, S, S, S, S, S, R, S, S, S, S, S, S, S, S,…</span></span>
|
||||
<span><span class="co">#> $ first <span style="color: #949494; font-style: italic;"><lgl></span> TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,…</span></span>
|
||||
<span></span>
|
||||
<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 1877 5 3 3 3 </span></span>
|
||||
<span><span class="co">#> 260 3 1854 4 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">
|
||||
@@ -487,25 +487,23 @@ 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: 5 × 2</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 4 × 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>024</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> Enterococcus crotali 494</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">4</span> Streptococcus pneumoniae 426</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">5</span> Klebsiella pneumoniae 326</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>
|
||||
<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: 5 × 2</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 4 × 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 919</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">1</span> Escherichia coli <span style="text-decoration: underline;">1</span>321</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 682</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> Enterococcus crotali 442</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">4</span> Streptococcus pneumoniae 402</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">5</span> Klebsiella pneumoniae 319</span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae 402</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 319</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>
|
||||
@@ -517,113 +515,113 @@ 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: 2,764 × 2</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,724 × 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>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> 2018-04-03 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> 2015-12-10 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> 2015-03-02 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> 2018-03-31 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> 2015-10-25 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> 2019-06-19 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> 2015-04-27 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> 2011-06-21 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> 2014-09-05 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,754 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> 2014-09-19 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> 2015-12-10 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> 2015-03-02 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> 2018-03-31 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> 2015-10-25 S </span></span>
|
||||
<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 2,714 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">%>%</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: 2,764 × 3</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,724 × 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_ENTRC_CRTL R I </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> B_ESCHR_COLI R I </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> B_KLBSL_PNMN R I </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> B_ENTRC_CRTL S I </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> B_ENTRC_CRTL S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B_STPHY_AURS R S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> B_ENTRC_CRTL R S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> B_ENTRC_CRTL S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> B_STPHY_AURS S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> B_ENTRC_CRTL S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> B_ENTRC_CRTL S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,754 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> B_ESCHR_COLI R S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> B_ESCHR_COLI S I </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B_ESCHR_COLI S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> B_STPHY_AURS R S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> B_ESCHR_COLI R S </span></span>
|
||||
<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 2,714 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">%>%</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: 2,764 × 5</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,724 × 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_ENTRC_CRTL R I S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> B_ESCHR_COLI R I S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> B_KLBSL_PNMN R I S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> B_ENTRC_CRTL S I S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> B_ENTRC_CRTL S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B_STPHY_AURS R S R S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> B_ENTRC_CRTL R S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> B_ENTRC_CRTL S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> B_STPHY_AURS S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> B_ENTRC_CRTL S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> B_ENTRC_CRTL S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,754 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> B_ESCHR_COLI R S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> B_ESCHR_COLI S I S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B_ESCHR_COLI S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> B_STPHY_AURS R S R S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> B_ESCHR_COLI R S S S </span></span>
|
||||
<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 2,714 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">%>%</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: 983 × 9</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 981 × 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;"> 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_ENTRC_CRTL S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> V7 A 2012-04-03 B_ENTRC_CRTL S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> C9 A 2017-03-23 B_ENTRC_CRTL S 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;"> 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 973 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 971 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>
|
||||
<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: 464 × 9</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 462 × 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;"> 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> B6 A 2016-11-20 B_ENTRC_CRTL R R R R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> I7 A 2015-08-19 B_ENTRC_CRTL R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <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">#> <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">#> <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">#> <span style="color: #BCBCBC;"> 8</span> Q2 A 2019-09-22 B_ENTRC_CRTL R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> X7 A 2011-03-20 B_ENTRC_CRTL R R S R TRUE </span></span>
|
||||
<span><span class="co">#> <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">#> <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">#> <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">#> <span style="color: #949494;"># ℹ 454 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 452 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">#> 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: 464 × 9</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 462 × 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;"> 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> B6 A 2016-11-20 B_ENTRC_CRTL R R R R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> I7 A 2015-08-19 B_ENTRC_CRTL R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <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">#> <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">#> <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">#> <span style="color: #BCBCBC;"> 8</span> Q2 A 2019-09-22 B_ENTRC_CRTL R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> X7 A 2011-03-20 B_ENTRC_CRTL R R S R TRUE </span></span>
|
||||
<span><span class="co">#> <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">#> <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">#> <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">#> <span style="color: #949494;"># ℹ 454 more rows</span></span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 452 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>
|
||||
@@ -1222,7 +1220,7 @@ 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] 0.4175109</span></span></code></pre></div>
|
||||
<span><span class="co">#> [1] 0.4203377</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">
|
||||
@@ -1232,9 +1230,9 @@ own:</p>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 3 × 2</span></span></span>
|
||||
<span><span class="co">#> hospital amoxicillin</span></span>
|
||||
<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 0.342</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">1</span> A 0.340</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">2</span> B 0.551</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> C 0.362</span></span></code></pre></div>
|
||||
<span><span class="co">#> <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>
|
||||
|
||||
@@ -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="">2.1.1.9084</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9086</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">
|
||||
@@ -91,13 +91,14 @@ antimicrobial resistance (AMR) data analysis, providing extensive
|
||||
functionality for working with microbial and antimicrobial properties.
|
||||
But what if you’re working in Python and still want to benefit from the
|
||||
robust features of <code>AMR</code>?</p>
|
||||
<p>Luckily, there is no need to port the package to Python! With the
|
||||
help of <code>rpy2</code>, a powerful Python package, you can easily
|
||||
access R from Python and call functions from the <code>AMR</code>
|
||||
package to process your own data. This post will guide you through
|
||||
<p>The best way is to access R directly from Python with the help of
|
||||
<code>rpy2</code>, a simple yet powerful Python package. You can easily
|
||||
call functions from the <code>AMR</code> package to process your own
|
||||
data in your own Python environment. This post will guide you through
|
||||
setting up <code>rpy2</code> and show you how to use R functions from
|
||||
<code>AMR</code> in Python to supercharge your antimicrobial resistance
|
||||
analysis.</p>
|
||||
<p><a href="https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant" class="external-link"><img src="../AMRforRGPT.svg" style="min-width: 300px; width: 10%;"></a></p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="what-is-rpy2">What is <code>rpy2</code>?<a class="anchor" aria-label="anchor" href="#what-is-rpy2"></a>
|
||||
@@ -127,19 +128,44 @@ environment.</li>
|
||||
<div class="section level3">
|
||||
<h3 id="step-1-install-r">Step 1: Install R<a class="anchor" aria-label="anchor" href="#step-1-install-r"></a>
|
||||
</h3>
|
||||
<p>Ensure that you have R installed on your system. You can download R
|
||||
from <a href="https://cran.r-project.org/" class="external-link">CRAN</a>.</p>
|
||||
<p>Ensure that R is installed on your system. R has minimal dependencies
|
||||
and is very simple to install:</p>
|
||||
<ul>
|
||||
<li>
|
||||
<strong>Linux</strong>
|
||||
<ul>
|
||||
<li>Ubuntu / Debian:<br><code>sudo apt install r-base</code>
|
||||
</li>
|
||||
<li>Fedora:<br><code>sudo dnf install R</code>
|
||||
</li>
|
||||
<li>CentOS/RHEL:<br><code>sudo yum install R</code>
|
||||
</li>
|
||||
<li>Arch Linux:<br><code>sudo pacman -S r</code>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<strong>macOS</strong> (with Homebrew):<br><code>brew install r</code>
|
||||
</li>
|
||||
<li>
|
||||
<strong>Other Systems:</strong><br>
|
||||
Visit the <a href="https://cran.r-project.org" class="external-link">CRAN download
|
||||
page</a>.</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="step-2-install-the-amr-package-in-r">Step 2: Install the <code>AMR</code> package in R<a class="anchor" aria-label="anchor" href="#step-2-install-the-amr-package-in-r"></a>
|
||||
</h3>
|
||||
<p>Once you have R installed, open your R console and install the
|
||||
<code>AMR</code> package:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></span></code></pre></div>
|
||||
<p>You can also install the latest development version of the
|
||||
<code>AMR</code> package if needed:</p>
|
||||
<p>On Linux and macOS, open Terminal and run:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="ex">Rscript</span> <span class="at">-e</span> <span class="st">'install.packages("AMR")'</span></span></code></pre></div>
|
||||
<p>For other systems, open your R console and install the
|
||||
<code>AMR</code> package by running:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></span></code></pre></div>
|
||||
<p>On any system, you can also install the latest development version of
|
||||
the <code>AMR</code> package by setting <code>repos</code> to our beta
|
||||
channel:</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span>, repos <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span></span></code></pre></div>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
@@ -147,58 +173,53 @@ from <a href="https://cran.r-project.org/" class="external-link">CRAN</a>.</p>
|
||||
</h3>
|
||||
<p>To install <code>rpy2</code>, simply run the following command in
|
||||
your terminal:</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="ex">pip</span> install rpy2</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb4"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="ex">pip</span> install rpy2</span></code></pre></div>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="step-4-test-rpy2-installation">Step 4: Test <code>rpy2</code> Installation<a class="anchor" aria-label="anchor" href="#step-4-test-rpy2-installation"></a>
|
||||
</h3>
|
||||
<p>To ensure everything is set up correctly, you can test your
|
||||
installation by running the following Python script:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="im">import</span> rpy2.robjects <span class="im">as</span> ro</span>
|
||||
<span id="cb4-2"><a href="#cb4-2" tabindex="-1"></a></span>
|
||||
<span id="cb4-3"><a href="#cb4-3" tabindex="-1"></a><span class="co"># Test a simple R function from Python</span></span>
|
||||
<span id="cb4-4"><a href="#cb4-4" tabindex="-1"></a>ro.r(<span class="st">'1 + 1'</span>)</span></code></pre></div>
|
||||
installation by running the following Python script, which essentially
|
||||
runs R in the background:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="im">import</span> rpy2.robjects <span class="im">as</span> ro</span>
|
||||
<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a></span>
|
||||
<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a><span class="co"># Test a simple R function from Python</span></span>
|
||||
<span id="cb5-4"><a href="#cb5-4" tabindex="-1"></a>ro.r(<span class="st">'1 + 1'</span>)</span></code></pre></div>
|
||||
<p>If this returns <code>2</code>, you’re good to go!</p>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="working-with-amr-in-python-using-rpy2">Working with AMR in Python using <code>rpy2</code><a class="anchor" aria-label="anchor" href="#working-with-amr-in-python-using-rpy2"></a>
|
||||
<h2 id="working-with-amr-in-python">Working with <code>AMR</code> in Python<a class="anchor" aria-label="anchor" href="#working-with-amr-in-python"></a>
|
||||
</h2>
|
||||
<p>Now that we have <code>rpy2</code> set up, let’s walk through some
|
||||
practical examples of using the <code>AMR</code> package within
|
||||
Python.</p>
|
||||
<div class="section level3">
|
||||
<h3 id="example-1-loading-amr-and-example-data">Example 1: Loading <code>AMR</code> and Example Data<a class="anchor" aria-label="anchor" href="#example-1-loading-amr-and-example-data"></a>
|
||||
<h3 id="example-1-converting-taxonomic-data">Example 1: Converting Taxonomic Data<a class="anchor" aria-label="anchor" href="#example-1-converting-taxonomic-data"></a>
|
||||
</h3>
|
||||
<p>Let’s start by converting taxonomic user input to valid taxonomy
|
||||
using the <code>AMR</code> package, from within Python:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
|
||||
<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a><span class="im">import</span> rpy2.robjects <span class="im">as</span> ro</span>
|
||||
<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a><span class="im">from</span> rpy2.robjects.packages <span class="im">import</span> importr</span>
|
||||
<span id="cb5-4"><a href="#cb5-4" tabindex="-1"></a><span class="im">from</span> rpy2.robjects <span class="im">import</span> pandas2ri</span>
|
||||
<span id="cb5-5"><a href="#cb5-5" tabindex="-1"></a></span>
|
||||
<span id="cb5-6"><a href="#cb5-6" tabindex="-1"></a><span class="co"># Enable conversion between pandas and R data frames</span></span>
|
||||
<span id="cb5-7"><a href="#cb5-7" tabindex="-1"></a>pandas2ri.activate()</span>
|
||||
<span id="cb5-8"><a href="#cb5-8" tabindex="-1"></a></span>
|
||||
<span id="cb5-9"><a href="#cb5-9" tabindex="-1"></a><span class="co"># Load the AMR package from R</span></span>
|
||||
<span id="cb5-10"><a href="#cb5-10" tabindex="-1"></a>amr <span class="op">=</span> importr(<span class="st">'AMR'</span>)</span>
|
||||
<span id="cb5-11"><a href="#cb5-11" tabindex="-1"></a></span>
|
||||
<span id="cb5-12"><a href="#cb5-12" tabindex="-1"></a><span class="co"># Example user dataset in Python</span></span>
|
||||
<span id="cb5-13"><a href="#cb5-13" tabindex="-1"></a>data <span class="op">=</span> pd.DataFrame({</span>
|
||||
<span id="cb5-14"><a href="#cb5-14" tabindex="-1"></a> <span class="st">'microorganism'</span>: [<span class="st">'E. coli'</span>, <span class="st">'S. aureus'</span>, <span class="st">'P. aeruginosa'</span>, <span class="st">'K. pneumoniae'</span>]</span>
|
||||
<span id="cb5-15"><a href="#cb5-15" tabindex="-1"></a>})</span>
|
||||
<span id="cb5-16"><a href="#cb5-16" tabindex="-1"></a></span>
|
||||
<span id="cb5-17"><a href="#cb5-17" tabindex="-1"></a><span class="co"># Convert the Python DataFrame to an R DataFrame</span></span>
|
||||
<span id="cb5-18"><a href="#cb5-18" tabindex="-1"></a>r_data <span class="op">=</span> pandas2ri.py2rpy(data)</span>
|
||||
<span id="cb5-19"><a href="#cb5-19" tabindex="-1"></a></span>
|
||||
<span id="cb5-20"><a href="#cb5-20" tabindex="-1"></a><span class="co"># Apply mo_name() from the AMR package to the 'microorganism' column</span></span>
|
||||
<span id="cb5-21"><a href="#cb5-21" tabindex="-1"></a>ro.globalenv[<span class="st">'r_data'</span>] <span class="op">=</span> r_data</span>
|
||||
<span id="cb5-22"><a href="#cb5-22" tabindex="-1"></a>ro.r(<span class="st">'r_data$mo_name <- mo_name(r_data$microorganism)'</span>)</span>
|
||||
<span id="cb5-23"><a href="#cb5-23" tabindex="-1"></a></span>
|
||||
<span id="cb5-24"><a href="#cb5-24" tabindex="-1"></a><span class="co"># Retrieve and print the modified R DataFrame in Python</span></span>
|
||||
<span id="cb5-25"><a href="#cb5-25" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(r_data)'</span>)</span>
|
||||
<span id="cb5-26"><a href="#cb5-26" tabindex="-1"></a>result <span class="op">=</span> pandas2ri.rpy2py(result)</span>
|
||||
<span id="cb5-27"><a href="#cb5-27" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb6"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
|
||||
<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="im">import</span> rpy2.robjects <span class="im">as</span> ro</span>
|
||||
<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a><span class="im">from</span> rpy2.robjects.packages <span class="im">import</span> importr</span>
|
||||
<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="im">from</span> rpy2.robjects <span class="im">import</span> pandas2ri</span>
|
||||
<span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a></span>
|
||||
<span id="cb6-6"><a href="#cb6-6" tabindex="-1"></a><span class="co"># Load the AMR package from R</span></span>
|
||||
<span id="cb6-7"><a href="#cb6-7" tabindex="-1"></a>amr <span class="op">=</span> importr(<span class="st">'AMR'</span>)</span>
|
||||
<span id="cb6-8"><a href="#cb6-8" tabindex="-1"></a></span>
|
||||
<span id="cb6-9"><a href="#cb6-9" tabindex="-1"></a><span class="co"># Example user dataset in Python</span></span>
|
||||
<span id="cb6-10"><a href="#cb6-10" tabindex="-1"></a>data <span class="op">=</span> pd.DataFrame({</span>
|
||||
<span id="cb6-11"><a href="#cb6-11" tabindex="-1"></a> <span class="st">'microorganism'</span>: [<span class="st">'E. coli'</span>, <span class="st">'S. aureus'</span>, <span class="st">'P. aeruginosa'</span>, <span class="st">'K. pneumoniae'</span>]</span>
|
||||
<span id="cb6-12"><a href="#cb6-12" tabindex="-1"></a>})</span>
|
||||
<span id="cb6-13"><a href="#cb6-13" tabindex="-1"></a></span>
|
||||
<span id="cb6-14"><a href="#cb6-14" tabindex="-1"></a><span class="co"># Apply mo_name() from the AMR package to the 'microorganism' column</span></span>
|
||||
<span id="cb6-15"><a href="#cb6-15" tabindex="-1"></a>ro.globalenv[<span class="st">'r_data'</span>] <span class="op">=</span> data</span>
|
||||
<span id="cb6-16"><a href="#cb6-16" tabindex="-1"></a>ro.r(<span class="st">'r_data$mo_name <- mo_name(r_data$microorganism)'</span>)</span>
|
||||
<span id="cb6-17"><a href="#cb6-17" tabindex="-1"></a></span>
|
||||
<span id="cb6-18"><a href="#cb6-18" tabindex="-1"></a><span class="co"># Retrieve and print the modified R DataFrame in Python</span></span>
|
||||
<span id="cb6-19"><a href="#cb6-19" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'r_data'</span>)</span>
|
||||
<span id="cb6-20"><a href="#cb6-20" tabindex="-1"></a>result <span class="op">=</span> pandas2ri.rpy2py(result)</span>
|
||||
<span id="cb6-21"><a href="#cb6-21" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
|
||||
<p>In this example, a Python dataset with microorganism names like
|
||||
<em>E. coli</em> and <em>S. aureus</em> is passed to the R function
|
||||
<code><a href="../reference/mo_property.html">mo_name()</a></code>. The result is an updated <code>DataFrame</code>
|
||||
@@ -212,12 +233,12 @@ that includes the standardised microorganism names based on the
|
||||
generating an antibiogram, a table that summarises the antimicrobial
|
||||
susceptibility of bacterial isolates. Here’s how you can generate an
|
||||
antibiogram from Python:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="co"># Run an antibiogram in R from Python</span></span>
|
||||
<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a>ro.r(<span class="st">'result <- antibiogram(example_isolates, antibiotics = c(aminoglycosides(), carbapenems()))'</span>)</span>
|
||||
<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a></span>
|
||||
<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="co"># Retrieve the result in Python</span></span>
|
||||
<span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
|
||||
<span id="cb6-6"><a href="#cb6-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb7"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="co"># Run an antibiogram in R from Python</span></span>
|
||||
<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a>ro.r(<span class="st">'result <- antibiogram(example_isolates, antibiotics = c(aminoglycosides(), carbapenems()))'</span>)</span>
|
||||
<span id="cb7-3"><a href="#cb7-3" tabindex="-1"></a></span>
|
||||
<span id="cb7-4"><a href="#cb7-4" tabindex="-1"></a><span class="co"># Retrieve the result in Python</span></span>
|
||||
<span id="cb7-5"><a href="#cb7-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
|
||||
<span id="cb7-6"><a href="#cb7-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
|
||||
<p>In this example, we generate an antibiogram by selecting
|
||||
aminoglycosides and carbapenems, two classes of antibiotics, and then
|
||||
convert the resulting R data frame into a Python-readable format.</p>
|
||||
@@ -227,12 +248,12 @@ convert the resulting R data frame into a Python-readable format.</p>
|
||||
</h3>
|
||||
<p>Let’s say you want to filter the dataset for Gram-negative bacteria
|
||||
and display their resistance to certain antibiotics:</p>
|
||||
<div class="sourceCode" id="cb7"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="co"># Filter for Gram-negative bacteria with intrinsic resistance to cefotaxime</span></span>
|
||||
<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a>ro.r(<span class="st">'result <- example_isolates[which(mo_is_gram_negative() & mo_is_intrinsic_resistant(ab = "cefotax")), c("bacteria", aminoglycosides(), carbapenems())]'</span>)</span>
|
||||
<span id="cb7-3"><a href="#cb7-3" tabindex="-1"></a></span>
|
||||
<span id="cb7-4"><a href="#cb7-4" tabindex="-1"></a><span class="co"># Retrieve the filtered result in Python</span></span>
|
||||
<span id="cb7-5"><a href="#cb7-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
|
||||
<span id="cb7-6"><a href="#cb7-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb8"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a><span class="co"># Filter for Gram-negative bacteria with intrinsic resistance to cefotaxime</span></span>
|
||||
<span id="cb8-2"><a href="#cb8-2" tabindex="-1"></a>ro.r(<span class="st">'result <- example_isolates[which(mo_is_gram_negative() & mo_is_intrinsic_resistant(ab = "cefotax")), c("bacteria", aminoglycosides(), carbapenems())]'</span>)</span>
|
||||
<span id="cb8-3"><a href="#cb8-3" tabindex="-1"></a></span>
|
||||
<span id="cb8-4"><a href="#cb8-4" tabindex="-1"></a><span class="co"># Retrieve the filtered result in Python</span></span>
|
||||
<span id="cb8-5"><a href="#cb8-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
|
||||
<span id="cb8-6"><a href="#cb8-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
|
||||
<p>This example uses the AMR functions
|
||||
<code><a href="../reference/mo_property.html">mo_is_gram_negative()</a></code> and
|
||||
<code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> to filter the dataset and
|
||||
@@ -243,12 +264,12 @@ returns a subset of bacteria with resistance data.</p>
|
||||
</h3>
|
||||
<p>You can easily customise the antibiogram by passing different
|
||||
antibiotics or microorganism transformations, as shown below:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a><span class="co"># Customise the antibiogram with different settings</span></span>
|
||||
<span id="cb8-2"><a href="#cb8-2" tabindex="-1"></a>ro.r(<span class="st">'result <- antibiogram(example_isolates, antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"), mo_transform = "gramstain")'</span>)</span>
|
||||
<span id="cb8-3"><a href="#cb8-3" tabindex="-1"></a></span>
|
||||
<span id="cb8-4"><a href="#cb8-4" tabindex="-1"></a><span class="co"># Retrieve and print the result</span></span>
|
||||
<span id="cb8-5"><a href="#cb8-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
|
||||
<span id="cb8-6"><a href="#cb8-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb9"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a><span class="co"># Customise the antibiogram with different settings</span></span>
|
||||
<span id="cb9-2"><a href="#cb9-2" tabindex="-1"></a>ro.r(<span class="st">'result <- antibiogram(example_isolates, antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"), mo_transform = "gramstain")'</span>)</span>
|
||||
<span id="cb9-3"><a href="#cb9-3" tabindex="-1"></a></span>
|
||||
<span id="cb9-4"><a href="#cb9-4" tabindex="-1"></a><span class="co"># Retrieve and print the result</span></span>
|
||||
<span id="cb9-5"><a href="#cb9-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
|
||||
<span id="cb9-6"><a href="#cb9-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
|
||||
<p>Here, we use piperacillin/tazobactam (TZP) in combination with
|
||||
tobramycin (TOB) and gentamicin (GEN) to see how they perform against
|
||||
various Gram-negative bacteria.</p>
|
||||
|
||||
@@ -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="">2.1.1.9084</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9086</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">
|
||||
|
||||
+1
-1
@@ -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="">2.1.1.9084</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9086</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">
|
||||
|
||||
+1
-1
@@ -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="">2.1.1.9084</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9086</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">
|
||||
|
||||
@@ -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="">2.1.1.9084</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9086</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">
|
||||
|
||||
@@ -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="">2.1.1.9084</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9086</small>
|
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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">
|
||||
@@ -76,7 +76,7 @@
|
||||
<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">30 September 2024</h4>
|
||||
<h4 data-toc-skip class="date">02 October 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>
|
||||
@@ -108,7 +108,7 @@ 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 30 September 2024 16:46:55 UTC. Find more info
|
||||
<p>It was last updated on 2 October 2024 08:20:05 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>
|
||||
@@ -286,7 +286,7 @@ 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">1.15</td>
|
||||
<td align="center">1</td>
|
||||
<td align="center">407310004, 407251000, 407281008, …</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
@@ -314,7 +314,7 @@ 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">1.15</td>
|
||||
<td align="center">1</td>
|
||||
<td align="center"></td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
@@ -342,7 +342,7 @@ 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">1.15</td>
|
||||
<td align="center">1</td>
|
||||
<td align="center">419388003</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
@@ -370,7 +370,7 @@ 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">1.50</td>
|
||||
<td align="center">1</td>
|
||||
<td align="center"></td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
@@ -398,7 +398,7 @@ 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">1.15</td>
|
||||
<td align="center">1</td>
|
||||
<td align="center">1095001000112106, 715307006, 737528008, …</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
@@ -426,7 +426,7 @@ 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">1.15</td>
|
||||
<td align="center">1</td>
|
||||
<td align="center"></td>
|
||||
</tr>
|
||||
</tbody>
|
||||
|
||||
+1
-1
@@ -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="">2.1.1.9084</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9086</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">
|
||||
|
||||
@@ -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="">2.1.1.9084</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9086</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">
|
||||
|
||||
@@ -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="">2.1.1.9084</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9086</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">
|
||||
|
||||
@@ -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="">2.1.1.9084</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9086</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">
|
||||
|
||||
Reference in new issue
Block a user