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@@ -31,7 +31,7 @@
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<a class="navbar-brand me-2" href="https://amr-for-r.org/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="">3.0.1.9003</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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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+1
-1
@@ -7,7 +7,7 @@
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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="">3.0.1.9003</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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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+39
-39
@@ -30,7 +30,7 @@
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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="">3.0.1.9003</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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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@@ -91,7 +91,7 @@
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website update since they are based on randomly created values and the
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page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
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Markdown</a>. However, the methodology remains unchanged. This page was
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generated on 24 November 2025.</p>
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generated on 15 December 2025.</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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@@ -147,21 +147,21 @@ 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">2025-11-24</td>
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<td align="center">2025-12-15</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">2025-11-24</td>
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<td align="center">2025-12-15</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">2025-11-24</td>
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<td align="center">2025-12-15</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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@@ -405,7 +405,7 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
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<span><span class="co">#> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">patient_id</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #444444;">`col_patient_id`</span><span style="color: #0000BB;">.</span></span></span>
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<span><span class="co">#> <span style="color: #BB0000;">ℹ Basing inclusion on all antimicrobial results, using a points threshold</span></span></span>
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<span><span class="co"><span style="color: #BB0000;">#> of 2</span></span></span>
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<span><span class="co">#> <span style="color: #BBBBBB;">=> Found </span><span style="color: #BBBBBB; font-weight: bold;">2,724 'phenotype-based' first isolates</span><span style="color: #BBBBBB;"> (90.8% of total where a</span></span></span>
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<span><span class="co">#> <span style="color: #BBBBBB;">=> Found </span><span style="color: #BBBBBB; font-weight: bold;">2,730 'phenotype-based' first isolates</span><span style="color: #BBBBBB;"> (91.0% of total where a</span></span></span>
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<span><span class="co"><span style="color: #BBBBBB;">#> microbial ID was available)</span></span></span></code></pre></div>
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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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@@ -417,11 +417,11 @@ 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 2 724 isolates for analysis. Now our data looks
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<p>So we end up with 2 730 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: 2,724 × 9</span></span></span>
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<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,730 × 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 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
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@@ -434,7 +434,7 @@ like:</p>
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||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> J3 A 2019-06-19 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> G6 A 2015-04-27 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> P4 A 2011-06-21 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span></code></pre></div>
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||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,720 more rows</span></span></span></code></pre></div>
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||||
<p>Time for the analysis.</p>
|
||||
</div>
|
||||
</div>
|
||||
@@ -447,29 +447,29 @@ 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>
|
||||
<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">#> Length:2730 Length:2730 Min. :2011-01-01 </span></span>
|
||||
<span><span class="co">#> Class :character Class :character 1st Qu.:2013-04-06 </span></span>
|
||||
<span><span class="co">#> Mode :character Mode :character Median :2015-06-04 </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">#> 3rd Qu.:2017-08-14 </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 :41.6% (n=1133) %S :52.6% (n=1432) </span></span>
|
||||
<span><span class="co">#> <NA> :0 %S :40.1% (n=1071) %S :51.1% (n=1354) </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">#> #1 :B_ESCHR_COLI %I :17.0% (n=453) %I :12.7% (n=335) </span></span>
|
||||
<span><span class="co">#> #2 :B_STPHY_AURS %R :42.9% (n=1147) %R :36.2% (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 :52.5% (n=1431) %S :61.0% (n=1661) TRUE:2724 </span></span>
|
||||
<span><span class="co">#> %S :52.2% (n=1426) %S :60.7% (n=1656) TRUE:2730 </span></span>
|
||||
<span><span class="co">#> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </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">#> %I : 6.5% (n=178) %I : 3.0% (n=83) </span></span>
|
||||
<span><span class="co">#> %R :41.2% (n=1126) %R :36.3% (n=991) </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: 2,724</span></span>
|
||||
<span><span class="co">#> Rows: 2,730</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"<span style="color: #949494;">, </span>"R7"<span style="color: #949494;">, </span>"P3"<span style="color: #949494;">, </span>"P10"<span style="color: #949494;">, </span>"B7"<span style="color: #949494;">, </span>"W3"<span style="color: #949494;">, </span>"M3"<span style="color: #949494;">, </span>"J3"<span style="color: #949494;">, </span>"G6"<span style="color: #949494;">, </span>"P4"…</span></span>
|
||||
<span><span class="co">#> $ hospital <span style="color: #949494; font-style: italic;"><chr></span> "A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">,</span>…</span></span>
|
||||
@@ -484,7 +484,7 @@ impression, as it comes with support for the new <code>mo</code> and
|
||||
<span><span class="co"># number of unique values per column:</span></span>
|
||||
<span><span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">our_data_1st</span>, <span class="va">n_distinct</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP </span></span>
|
||||
<span><span class="co">#> 260 3 1854 4 3 3 3 </span></span>
|
||||
<span><span class="co">#> 260 3 1854 4 4 4 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">
|
||||
@@ -509,9 +509,9 @@ microorganisms:</p>
|
||||
<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>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> Streptococcus pneumoniae 402</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">1</span> Escherichia coli <span style="text-decoration: underline;">1</span>326</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 684</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae 401</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">
|
||||
@@ -524,7 +524,7 @@ in:</p>
|
||||
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">date</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`aminoglycosides()`</span><span style="color: #0000BB;"> using column '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin)</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,724 × 2</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,730 × 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 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||||
@@ -537,13 +537,13 @@ in:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> 2019-06-19 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> 2015-04-27 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> 2011-06-21 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,720 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/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`betalactams()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin) and '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> (amoxicillin/clavulanic acid)</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,724 × 3</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,730 × 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> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FFD787;"> I </span></span></span>
|
||||
@@ -556,11 +556,11 @@ in:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,720 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: 2,724 × 5</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,730 × 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> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||||
@@ -573,13 +573,13 @@ in:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,720 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/antimicrobial_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">#> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`aminoglycosides()`</span><span style="color: #0000BB;"> using column '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin)</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 981 × 9</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 991 × 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 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
|
||||
@@ -592,13 +592,13 @@ in:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> P5 A 2019-03-09 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> Q8 A 2019-08-10 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> K5 A 2013-03-15 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 971 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 981 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/antimicrobial_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">#> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`betalactams()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin) and '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> (amoxicillin/clavulanic acid)</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 462 × 9</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 461 × 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 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||||
@@ -611,13 +611,13 @@ in:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> Q2 A 2019-09-22 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> X7 A 2011-03-20 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> V1 A 2018-08-07 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 452 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 451 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/antimicrobial_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">#> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`betalactams()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin) and '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> (amoxicillin/clavulanic acid)</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 462 × 9</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 461 × 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 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||||
@@ -630,7 +630,7 @@ in:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> Q2 A 2019-09-22 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> X7 A 2011-03-20 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> V1 A 2018-08-07 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 452 more rows</span></span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 451 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>
|
||||
@@ -1283,7 +1283,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
|
||||
own:</p>
|
||||
<div class="sourceCode" id="cb23"><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] 0.4203377</span></span></code></pre></div>
|
||||
<span><span class="co">#> [1] 0.4294272</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="cb24"><pre class="downlit sourceCode r">
|
||||
@@ -1293,8 +1293,8 @@ 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 0.340</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;">1</span> A 0.341</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">2</span> B 0.586</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> C 0.370</span></span></code></pre></div>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
|
||||
+38
-38
@@ -3,7 +3,7 @@
|
||||
**Note:** values on this page will change with every website update
|
||||
since they are based on randomly created values and the page was written
|
||||
in [R Markdown](https://rmarkdown.rstudio.com/). However, the
|
||||
methodology remains unchanged. This page was generated on 24 November
|
||||
methodology remains unchanged. This page was generated on 15 December
|
||||
2025.
|
||||
|
||||
## Introduction
|
||||
@@ -52,9 +52,9 @@ structure of your data generally look like this:
|
||||
|
||||
| date | patient_id | mo | AMX | CIP |
|
||||
|:----------:|:----------:|:----------------:|:---:|:---:|
|
||||
| 2025-11-24 | abcd | Escherichia coli | S | S |
|
||||
| 2025-11-24 | abcd | Escherichia coli | S | R |
|
||||
| 2025-11-24 | efgh | Escherichia coli | R | S |
|
||||
| 2025-12-15 | abcd | Escherichia coli | S | S |
|
||||
| 2025-12-15 | abcd | Escherichia coli | S | R |
|
||||
| 2025-12-15 | efgh | Escherichia coli | R | S |
|
||||
|
||||
### Needed R packages
|
||||
|
||||
@@ -322,7 +322,7 @@ our_data <- our_data %>%
|
||||
#> ℹ Using column 'patient_id' as input for `col_patient_id`.
|
||||
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold
|
||||
#> of 2
|
||||
#> => Found 2,724 'phenotype-based' first isolates (90.8% of total where a
|
||||
#> => Found 2,730 'phenotype-based' first isolates (91.0% of total where a
|
||||
#> microbial ID was available)
|
||||
```
|
||||
|
||||
@@ -342,11 +342,11 @@ our_data_1st <- our_data %>%
|
||||
filter_first_isolate()
|
||||
```
|
||||
|
||||
So we end up with 2 724 isolates for analysis. Now our data looks like:
|
||||
So we end up with 2 730 isolates for analysis. Now our data looks like:
|
||||
|
||||
``` r
|
||||
our_data_1st
|
||||
#> # A tibble: 2,724 × 9
|
||||
#> # A tibble: 2,730 × 9
|
||||
#> patient_id hospital date bacteria AMX AMC CIP GEN first
|
||||
#> <chr> <chr> <date> <mo> <sir> <sir> <sir> <sir> <lgl>
|
||||
#> 1 J3 A 2012-11-21 B_ESCHR_COLI R I S S TRUE
|
||||
@@ -359,7 +359,7 @@ our_data_1st
|
||||
#> 8 J3 A 2019-06-19 B_ESCHR_COLI S S S S TRUE
|
||||
#> 9 G6 A 2015-04-27 B_STPHY_AURS S S S S TRUE
|
||||
#> 10 P4 A 2011-06-21 B_ESCHR_COLI S S S S TRUE
|
||||
#> # ℹ 2,714 more rows
|
||||
#> # ℹ 2,720 more rows
|
||||
```
|
||||
|
||||
Time for the analysis.
|
||||
@@ -373,29 +373,29 @@ and `sir` classes that we now have in our data set:
|
||||
``` r
|
||||
summary(our_data_1st)
|
||||
#> patient_id hospital date
|
||||
#> Length:2724 Length:2724 Min. :2011-01-01
|
||||
#> Class :character Class :character 1st Qu.:2013-04-07
|
||||
#> Mode :character Mode :character Median :2015-06-03
|
||||
#> Length:2730 Length:2730 Min. :2011-01-01
|
||||
#> Class :character Class :character 1st Qu.:2013-04-06
|
||||
#> Mode :character Mode :character Median :2015-06-04
|
||||
#> Mean :2015-06-09
|
||||
#> 3rd Qu.:2017-08-11
|
||||
#> 3rd Qu.:2017-08-14
|
||||
#> Max. :2019-12-27
|
||||
#> bacteria AMX AMC
|
||||
#> Class :mo Class:sir Class:sir
|
||||
#> <NA> :0 %S :41.6% (n=1133) %S :52.6% (n=1432)
|
||||
#> <NA> :0 %S :40.1% (n=1071) %S :51.1% (n=1354)
|
||||
#> Unique:4 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0)
|
||||
#> #1 :B_ESCHR_COLI %I :16.4% (n=446) %I :12.2% (n=333)
|
||||
#> #2 :B_STPHY_AURS %R :42.0% (n=1145) %R :35.2% (n=959)
|
||||
#> #1 :B_ESCHR_COLI %I :17.0% (n=453) %I :12.7% (n=335)
|
||||
#> #2 :B_STPHY_AURS %R :42.9% (n=1147) %R :36.2% (n=959)
|
||||
#> #3 :B_STRPT_PNMN %NI : 0.0% (n=0) %NI : 0.0% (n=0)
|
||||
#> CIP GEN first
|
||||
#> Class:sir Class:sir Mode:logical
|
||||
#> %S :52.5% (n=1431) %S :61.0% (n=1661) TRUE:2724
|
||||
#> %S :52.2% (n=1426) %S :60.7% (n=1656) TRUE:2730
|
||||
#> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0)
|
||||
#> %I : 6.5% (n=176) %I : 3.0% (n=82)
|
||||
#> %R :41.0% (n=1117) %R :36.0% (n=981)
|
||||
#> %I : 6.5% (n=178) %I : 3.0% (n=83)
|
||||
#> %R :41.2% (n=1126) %R :36.3% (n=991)
|
||||
#> %NI : 0.0% (n=0) %NI : 0.0% (n=0)
|
||||
|
||||
glimpse(our_data_1st)
|
||||
#> Rows: 2,724
|
||||
#> Rows: 2,730
|
||||
#> Columns: 9
|
||||
#> $ patient_id <chr> "J3", "R7", "P3", "P10", "B7", "W3", "M3", "J3", "G6", "P4"…
|
||||
#> $ hospital <chr> "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A",…
|
||||
@@ -410,7 +410,7 @@ glimpse(our_data_1st)
|
||||
# number of unique values per column:
|
||||
sapply(our_data_1st, n_distinct)
|
||||
#> patient_id hospital date bacteria AMX AMC CIP
|
||||
#> 260 3 1854 4 3 3 3
|
||||
#> 260 3 1854 4 4 4 3
|
||||
#> GEN first
|
||||
#> 3 1
|
||||
```
|
||||
@@ -437,9 +437,9 @@ our_data_1st %>%
|
||||
#> # A tibble: 4 × 2
|
||||
#> `mo_name(bacteria)` n
|
||||
#> <chr> <int>
|
||||
#> 1 Escherichia coli 1321
|
||||
#> 2 Staphylococcus aureus 682
|
||||
#> 3 Streptococcus pneumoniae 402
|
||||
#> 1 Escherichia coli 1326
|
||||
#> 2 Staphylococcus aureus 684
|
||||
#> 3 Streptococcus pneumoniae 401
|
||||
#> 4 Klebsiella pneumoniae 319
|
||||
```
|
||||
|
||||
@@ -453,7 +453,7 @@ in:
|
||||
our_data_1st %>%
|
||||
select(date, aminoglycosides())
|
||||
#> ℹ For `aminoglycosides()` using column 'GEN' (gentamicin)
|
||||
#> # A tibble: 2,724 × 2
|
||||
#> # A tibble: 2,730 × 2
|
||||
#> date GEN
|
||||
#> <date> <sir>
|
||||
#> 1 2012-11-21 S
|
||||
@@ -466,13 +466,13 @@ our_data_1st %>%
|
||||
#> 8 2019-06-19 S
|
||||
#> 9 2015-04-27 S
|
||||
#> 10 2011-06-21 S
|
||||
#> # ℹ 2,714 more rows
|
||||
#> # ℹ 2,720 more rows
|
||||
|
||||
our_data_1st %>%
|
||||
select(bacteria, betalactams())
|
||||
#> ℹ For `betalactams()` using columns 'AMX' (amoxicillin) and 'AMC'
|
||||
#> (amoxicillin/clavulanic acid)
|
||||
#> # A tibble: 2,724 × 3
|
||||
#> # A tibble: 2,730 × 3
|
||||
#> bacteria AMX AMC
|
||||
#> <mo> <sir> <sir>
|
||||
#> 1 B_ESCHR_COLI R I
|
||||
@@ -485,11 +485,11 @@ our_data_1st %>%
|
||||
#> 8 B_ESCHR_COLI S S
|
||||
#> 9 B_STPHY_AURS S S
|
||||
#> 10 B_ESCHR_COLI S S
|
||||
#> # ℹ 2,714 more rows
|
||||
#> # ℹ 2,720 more rows
|
||||
|
||||
our_data_1st %>%
|
||||
select(bacteria, where(is.sir))
|
||||
#> # A tibble: 2,724 × 5
|
||||
#> # A tibble: 2,730 × 5
|
||||
#> bacteria AMX AMC CIP GEN
|
||||
#> <mo> <sir> <sir> <sir> <sir>
|
||||
#> 1 B_ESCHR_COLI R I S S
|
||||
@@ -502,13 +502,13 @@ our_data_1st %>%
|
||||
#> 8 B_ESCHR_COLI S S S S
|
||||
#> 9 B_STPHY_AURS S S S S
|
||||
#> 10 B_ESCHR_COLI S S S S
|
||||
#> # ℹ 2,714 more rows
|
||||
#> # ℹ 2,720 more rows
|
||||
|
||||
# filtering using AB selectors is also possible:
|
||||
our_data_1st %>%
|
||||
filter(any(aminoglycosides() == "R"))
|
||||
#> ℹ For `aminoglycosides()` using column 'GEN' (gentamicin)
|
||||
#> # A tibble: 981 × 9
|
||||
#> # A tibble: 991 × 9
|
||||
#> patient_id hospital date bacteria AMX AMC CIP GEN first
|
||||
#> <chr> <chr> <date> <mo> <sir> <sir> <sir> <sir> <lgl>
|
||||
#> 1 J5 A 2017-12-25 B_STRPT_PNMN R S S R TRUE
|
||||
@@ -521,13 +521,13 @@ our_data_1st %>%
|
||||
#> 8 P5 A 2019-03-09 B_STPHY_AURS S S S R TRUE
|
||||
#> 9 Q8 A 2019-08-10 B_STPHY_AURS S S S R TRUE
|
||||
#> 10 K5 A 2013-03-15 B_STRPT_PNMN S S S R TRUE
|
||||
#> # ℹ 971 more rows
|
||||
#> # ℹ 981 more rows
|
||||
|
||||
our_data_1st %>%
|
||||
filter(all(betalactams() == "R"))
|
||||
#> ℹ For `betalactams()` using columns 'AMX' (amoxicillin) and 'AMC'
|
||||
#> (amoxicillin/clavulanic acid)
|
||||
#> # A tibble: 462 × 9
|
||||
#> # A tibble: 461 × 9
|
||||
#> patient_id hospital date bacteria AMX AMC CIP GEN first
|
||||
#> <chr> <chr> <date> <mo> <sir> <sir> <sir> <sir> <lgl>
|
||||
#> 1 M7 A 2013-07-22 B_STRPT_PNMN R R S S TRUE
|
||||
@@ -540,13 +540,13 @@ our_data_1st %>%
|
||||
#> 8 Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE
|
||||
#> 9 X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE
|
||||
#> 10 V1 A 2018-08-07 B_STPHY_AURS R R S S TRUE
|
||||
#> # ℹ 452 more rows
|
||||
#> # ℹ 451 more rows
|
||||
|
||||
# even works in base R (since R 3.0):
|
||||
our_data_1st[all(betalactams() == "R"), ]
|
||||
#> ℹ For `betalactams()` using columns 'AMX' (amoxicillin) and 'AMC'
|
||||
#> (amoxicillin/clavulanic acid)
|
||||
#> # A tibble: 462 × 9
|
||||
#> # A tibble: 461 × 9
|
||||
#> patient_id hospital date bacteria AMX AMC CIP GEN first
|
||||
#> <chr> <chr> <date> <mo> <sir> <sir> <sir> <sir> <lgl>
|
||||
#> 1 M7 A 2013-07-22 B_STRPT_PNMN R R S S TRUE
|
||||
@@ -559,7 +559,7 @@ our_data_1st[all(betalactams() == "R"), ]
|
||||
#> 8 Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE
|
||||
#> 9 X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE
|
||||
#> 10 V1 A 2018-08-07 B_STPHY_AURS R R S S TRUE
|
||||
#> # ℹ 452 more rows
|
||||
#> # ℹ 451 more rows
|
||||
```
|
||||
|
||||
### Generate antibiograms
|
||||
@@ -843,7 +843,7 @@ These functions can be used on their own:
|
||||
|
||||
``` r
|
||||
our_data_1st %>% resistance(AMX)
|
||||
#> [1] 0.4203377
|
||||
#> [1] 0.4294272
|
||||
```
|
||||
|
||||
Or can be used in conjunction with
|
||||
@@ -858,8 +858,8 @@ our_data_1st %>%
|
||||
#> # A tibble: 3 × 2
|
||||
#> hospital amoxicillin
|
||||
#> <chr> <dbl>
|
||||
#> 1 A 0.340
|
||||
#> 2 B 0.551
|
||||
#> 1 A 0.341
|
||||
#> 2 B 0.586
|
||||
#> 3 C 0.370
|
||||
```
|
||||
|
||||
|
||||
@@ -30,7 +30,7 @@
|
||||
|
||||
<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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -30,7 +30,7 @@
|
||||
|
||||
<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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -30,7 +30,7 @@
|
||||
|
||||
<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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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
@@ -30,7 +30,7 @@
|
||||
|
||||
<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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -30,7 +30,7 @@
|
||||
|
||||
<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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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
@@ -30,7 +30,7 @@
|
||||
|
||||
<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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -30,7 +30,7 @@
|
||||
|
||||
<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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
@@ -80,7 +80,7 @@
|
||||
<main id="main" class="col-md-9"><div class="page-header">
|
||||
<img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
|
||||
|
||||
<h4 data-toc-skip class="date">24 November 2025</h4>
|
||||
<h4 data-toc-skip class="date">15 December 2025</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>
|
||||
|
||||
+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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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
@@ -33,7 +33,7 @@
|
||||
|
||||
<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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
+12
-3
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
@@ -49,11 +49,20 @@
|
||||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
<h2 class="pkg-version" data-toc-text="3.0.1.9003" id="amr-3019003">AMR 3.0.1.9003<a class="anchor" aria-label="anchor" href="#amr-3019003"></a></h2>
|
||||
<h2 class="pkg-version" data-toc-text="3.0.1.9004" id="amr-3019004">AMR 3.0.1.9004<a class="anchor" aria-label="anchor" href="#amr-3019004"></a></h2>
|
||||
<div class="section level4">
|
||||
<h4 id="changed-3-0-1-9003">Changed<a class="anchor" aria-label="anchor" href="#changed-3-0-1-9003"></a></h4>
|
||||
<h4 id="changed-3-0-1-9004">Changed<a class="anchor" aria-label="anchor" href="#changed-3-0-1-9004"></a></h4>
|
||||
<ul><li>Fixed a bug in <code><a href="../reference/antibiogram.html">antibiogram()</a></code> for when no antimicrobials are set</li>
|
||||
<li>Added taniborbactam (<code>TAN</code>) and cefepime/taniborbactam (<code>FTA</code>) to the <code>antimicrobials</code> data set</li>
|
||||
<li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where for numeric input the arguments <code>S</code>, <code>i</code>, and <code>R</code> would not be considered (<a href="https://github.com/msberends/AMR/issues/244" class="external-link">#244</a>)</li>
|
||||
<li>Added explaining message to <code><a href="../reference/as.sir.html">as.sir()</a></code> when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) (<a href="https://github.com/msberends/AMR/issues/244" class="external-link">#244</a>)</li>
|
||||
<li>Updated handling of capped MIC values (<code><</code>, <code><=</code>, <code>></code>, <code>>=</code>) in <code><a href="../reference/as.sir.html">as.sir()</a></code> in the argument <code>capped_mic_handling</code>: (<a href="https://github.com/msberends/AMR/issues/243" class="external-link">#243</a>)
|
||||
<ul><li>Introduced four clearly defined options: <code>"none"</code>, <code>"conservative"</code> (default), <code>"standard"</code>, and <code>"lenient"</code>
|
||||
</li>
|
||||
<li>Interpretation of capped MIC values now consistently returns <code>"NI"</code> (non-interpretable) when the true MIC could be at either side of a breakpoint, depending on the selected handling mode</li>
|
||||
<li>This results in more reliable behaviour compared to previous versions for capped MIC values</li>
|
||||
<li>Removed the <code>"inverse"</code> option, which has now become redundant</li>
|
||||
</ul></li>
|
||||
</ul></div>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
|
||||
+20
-1
@@ -1,6 +1,6 @@
|
||||
# Changelog
|
||||
|
||||
## AMR 3.0.1.9003
|
||||
## AMR 3.0.1.9004
|
||||
|
||||
#### Changed
|
||||
|
||||
@@ -9,6 +9,25 @@
|
||||
when no antimicrobials are set
|
||||
- Added taniborbactam (`TAN`) and cefepime/taniborbactam (`FTA`) to the
|
||||
`antimicrobials` data set
|
||||
- Fixed a bug in [`as.sir()`](https://amr-for-r.org/reference/as.sir.md)
|
||||
where for numeric input the arguments `S`, `i`, and `R` would not be
|
||||
considered ([\#244](https://github.com/msberends/AMR/issues/244))
|
||||
- Added explaining message to
|
||||
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md) when
|
||||
interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R)
|
||||
([\#244](https://github.com/msberends/AMR/issues/244))
|
||||
- Updated handling of capped MIC values (`<`, `<=`, `>`, `>=`) in
|
||||
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md) in the
|
||||
argument `capped_mic_handling`:
|
||||
([\#243](https://github.com/msberends/AMR/issues/243))
|
||||
- Introduced four clearly defined options: `"none"`, `"conservative"`
|
||||
(default), `"standard"`, and `"lenient"`
|
||||
- Interpretation of capped MIC values now consistently returns `"NI"`
|
||||
(non-interpretable) when the true MIC could be at either side of a
|
||||
breakpoint, depending on the selected handling mode
|
||||
- This results in more reliable behaviour compared to previous
|
||||
versions for capped MIC values
|
||||
- Removed the `"inverse"` option, which has now become redundant
|
||||
|
||||
## AMR 3.0.1
|
||||
|
||||
|
||||
+1
-1
@@ -10,7 +10,7 @@ articles:
|
||||
PCA: PCA.html
|
||||
WHONET: WHONET.html
|
||||
WISCA: WISCA.html
|
||||
last_built: 2025-11-24T10:38Z
|
||||
last_built: 2025-12-15T12:28Z
|
||||
urls:
|
||||
reference: https://amr-for-r.org/reference
|
||||
article: https://amr-for-r.org/articles
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
@@ -60,7 +60,7 @@
|
||||
|
||||
<ul><li><p><code>AMR_antibiogram_formatting_type</code> <br> A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> (1-22) to use in <code><a href="antibiogram.html">antibiogram()</a></code>, to indicate which formatting type to use.</p></li>
|
||||
<li><p><code>AMR_breakpoint_type</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate which breakpoint type to use. This must be either "ECOFF", "animal", or "human".</p></li>
|
||||
<li><p><code>AMR_capped_mic_handling</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate how capped MIC values (<code><</code>, <code><=</code>, <code>></code>, <code>>=</code>) should be interpreted. Must be one of <code>"standard"</code>, <code>"strict"</code>, <code>"relaxed"</code>, or <code>"inverse"</code> - the default is <code>"standard"</code>.</p></li>
|
||||
<li><p><code>AMR_capped_mic_handling</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate how capped MIC values (<code><</code>, <code><=</code>, <code>></code>, <code>>=</code>) should be interpreted. Must be one of <code>"none"</code>, <code>"conservative"</code>, <code>"standard"</code>, or <code>"lenient"</code> - the default is <code>"conservative"</code>.</p></li>
|
||||
<li><p><code>AMR_cleaning_regex</code> <br> A <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> (case-insensitive) to use in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions, to clean the user input. The default is the outcome of <code><a href="as.mo.html">mo_cleaning_regex()</a></code>, which removes texts between brackets and texts such as "species" and "serovar".</p></li>
|
||||
<li><p><code>AMR_custom_ab</code> <br> A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in <code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code>.</p></li>
|
||||
<li><p><code>AMR_custom_mo</code> <br> A file location to an RDS file, to use custom microorganisms with this package. This is explained in <code><a href="add_custom_microorganisms.html">add_custom_microorganisms()</a></code>.</p></li>
|
||||
|
||||
@@ -21,8 +21,8 @@ This is an overview of all the package-specific
|
||||
A [character](https://rdrr.io/r/base/character.html) to use in
|
||||
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md), to indicate
|
||||
how capped MIC values (`<`, `<=`, `>`, `>=`) should be interpreted.
|
||||
Must be one of `"standard"`, `"strict"`, `"relaxed"`, or `"inverse"` -
|
||||
the default is `"standard"`.
|
||||
Must be one of `"none"`, `"conservative"`, `"standard"`, or
|
||||
`"lenient"` - the default is `"conservative"`.
|
||||
|
||||
- `AMR_cleaning_regex`
|
||||
A [regular expression](https://rdrr.io/r/base/regex.html)
|
||||
|
||||
+1
-1
@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
|
||||
|
||||
<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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
+11
-11
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
@@ -112,16 +112,16 @@
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> birth_date age age_exact age_at_y2k</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1980-02-27 45 45.73973 19</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1953-07-26 72 72.33151 46</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1949-09-02 76 76.22740 50</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1986-08-03 39 39.30959 13</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1932-11-19 93 93.01370 67</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1949-03-30 76 76.65479 50</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1996-06-23 29 29.42192 3</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1963-09-16 62 62.18904 36</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1952-05-16 73 73.52603 47</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1952-11-14 73 73.02740 47</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1980-02-27 45 45.79726 19</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1953-07-26 72 72.38904 46</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1949-09-02 76 76.28493 50</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1986-08-03 39 39.36712 13</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1932-11-19 93 93.07123 67</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1949-03-30 76 76.71233 50</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1996-06-23 29 29.47945 3</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1963-09-16 62 62.24658 36</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1952-05-16 73 73.58356 47</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1952-11-14 73 73.08493 47</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||||
|
||||
+10
-10
@@ -81,14 +81,14 @@ df$age_at_y2k <- age(df$birth_date, "2000-01-01")
|
||||
|
||||
df
|
||||
#> birth_date age age_exact age_at_y2k
|
||||
#> 1 1980-02-27 45 45.73973 19
|
||||
#> 2 1953-07-26 72 72.33151 46
|
||||
#> 3 1949-09-02 76 76.22740 50
|
||||
#> 4 1986-08-03 39 39.30959 13
|
||||
#> 5 1932-11-19 93 93.01370 67
|
||||
#> 6 1949-03-30 76 76.65479 50
|
||||
#> 7 1996-06-23 29 29.42192 3
|
||||
#> 8 1963-09-16 62 62.18904 36
|
||||
#> 9 1952-05-16 73 73.52603 47
|
||||
#> 10 1952-11-14 73 73.02740 47
|
||||
#> 1 1980-02-27 45 45.79726 19
|
||||
#> 2 1953-07-26 72 72.38904 46
|
||||
#> 3 1949-09-02 76 76.28493 50
|
||||
#> 4 1986-08-03 39 39.36712 13
|
||||
#> 5 1932-11-19 93 93.07123 67
|
||||
#> 6 1949-03-30 76 76.71233 50
|
||||
#> 7 1996-06-23 29 29.47945 3
|
||||
#> 8 1963-09-16 62 62.24658 36
|
||||
#> 9 1952-05-16 73 73.58356 47
|
||||
#> 10 1952-11-14 73 73.08493 47
|
||||
```
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
|
||||
|
||||
<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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&gt;%
|
||||
|
||||
<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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
+32
-19
@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
|
||||
<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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
@@ -67,8 +67,9 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
<span><span class="fu">is_sir_eligible</span><span class="op">(</span><span class="va">x</span>, threshold <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># Default S3 method</span></span>
|
||||
<span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, S <span class="op">=</span> <span class="st">"^(S|U)+$"</span>, I <span class="op">=</span> <span class="st">"^(I)+$"</span>, R <span class="op">=</span> <span class="st">"^(R)+$"</span>,</span>
|
||||
<span> NI <span class="op">=</span> <span class="st">"^(N|NI|V)+$"</span>, SDD <span class="op">=</span> <span class="st">"^(SDD|D|H)+$"</span>, info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, S <span class="op">=</span> <span class="st">"^(S|U|1)+$"</span>, I <span class="op">=</span> <span class="st">"^(I|2)+$"</span>,</span>
|
||||
<span> R <span class="op">=</span> <span class="st">"^(R|3)+$"</span>, NI <span class="op">=</span> <span class="st">"^(N|NI|V|4)+$"</span>, SDD <span class="op">=</span> <span class="st">"^(SDD|D|H|5)+$"</span>,</span>
|
||||
<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># S3 method for class 'mic'</span></span>
|
||||
<span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span>
|
||||
@@ -128,7 +129,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
|
||||
|
||||
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
|
||||
<dd><p>For using on a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: selection of columns to apply <code>as.sir()</code> to. Supports <a href="https://tidyselect.r-lib.org/reference/starts_with.html" class="external-link">tidyselect language</a> such as <code>where(is.mic)</code>, <code>starts_with(...)</code>, or <code>column1:column4</code>, and can thus also be <a href="antimicrobial_selectors.html">antimicrobial selectors</a> such as <code>as.sir(df, penicillins())</code>.</p>
|
||||
<dd><p>For using on a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: selection of columns to apply <code>as.sir()</code> to. Supports <a href="https://tidyselect.r-lib.org/reference/starts_with.html" class="external-link">tidyselect language</a> such as <code>where(is.mic)</code>, <code>starts_with(...)</code>, or <code>column1:column4</code>, and can thus also be <a href="antimicrobial_selectors.html">antimicrobial selectors</a>, e.g. <code>as.sir(df, penicillins())</code>.</p>
|
||||
<p>Otherwise: arguments passed on to methods.</p></dd>
|
||||
|
||||
|
||||
@@ -162,15 +163,15 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
|
||||
<dt id="arg-capped-mic-handling">capped_mic_handling<a class="anchor" aria-label="anchor" href="#arg-capped-mic-handling"></a></dt>
|
||||
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> string that controls how MIC values with a cap (i.e., starting with <code><</code>, <code><=</code>, <code>></code>, or <code>>=</code>) are interpreted. Supports the following options:</p>
|
||||
<p><code>"none"</code></p><ul><li><p><code><=</code> and <code>>=</code> are treated as-is.</p></li>
|
||||
<li><p><code><</code> and <code>></code> are treated as-is.</p></li>
|
||||
</ul><p><code>"conservative"</code></p><ul><li><p><code><=</code> and <code>>=</code> return <code>"NI"</code> (non-interpretable) if the MIC is within the breakpoint guideline range.</p></li>
|
||||
<li><p><code><</code> always returns <code>"S"</code>, and <code>></code> always returns <code>"R"</code>.</p></li>
|
||||
</ul><p><code>"standard"</code> (default)</p><ul><li><p><code><=</code> and <code>>=</code> return <code>"NI"</code> (non-interpretable) if the MIC is within the breakpoint guideline range.</p></li>
|
||||
<li><p><code><</code> and <code>></code> are treated as-is.</p></li>
|
||||
</ul><p><code>"inverse"</code></p><ul><li><p><code><=</code> and <code>>=</code> are treated as-is.</p></li>
|
||||
<li><p><code><</code> always returns <code>"S"</code>, and <code>></code> always returns <code>"R"</code>.</p></li>
|
||||
</ul><p>The default <code>"standard"</code> setting ensures cautious handling of uncertain values while preserving interpretability. This option can also be set with the package option <code><a href="AMR-options.html">AMR_capped_mic_handling</a></code>.</p></dd>
|
||||
<p><code>"none"</code></p><ul><li><p><code><=</code>, <code><</code>, <code>></code> and <code>>=</code> are ignored.</p></li>
|
||||
</ul><p><code>"conservative"</code> (default)</p><ul><li><p><code><=</code>, <code><</code>, <code>></code> and <code>>=</code> return <code>"NI"</code> (non-interpretable) if the <em>true</em> MIC could be at either side of the breakpoint.</p></li>
|
||||
<li><p>This is the only mode that preserves uncertainty for ECOFFs.</p></li>
|
||||
</ul><p><code>"standard"</code></p><ul><li><p><code><=</code> and <code>>=</code> return <code>"NI"</code> (non-interpretable) if the <em>true</em> MIC could be at either side of the breakpoint.</p></li>
|
||||
<li><p><code><</code> always returns <code>"S"</code>, regardless of the breakpoint.</p></li>
|
||||
<li><p><code>></code> always returns <code>"R"</code>, regardless of the breakpoint.</p></li>
|
||||
</ul><p><code>"lenient"</code></p><ul><li><p><code><=</code> and <code><</code> always return <code>"S"</code>, regardless of the breakpoint.</p></li>
|
||||
<li><p><code>>=</code> and <code>></code> always return <code>"R"</code>, regardless of the breakpoint.</p></li>
|
||||
</ul><p>The default <code>"conservative"</code> setting ensures cautious handling of uncertain values while preserving interpretability. This option can also be set with the package option <code><a href="AMR-options.html">AMR_capped_mic_handling</a></code>.</p></dd>
|
||||
|
||||
|
||||
<dt id="arg-add-intrinsic-resistance">add_intrinsic_resistance<a class="anchor" aria-label="anchor" href="#arg-add-intrinsic-resistance"></a></dt>
|
||||
@@ -251,7 +252,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
<span></span>
|
||||
<span><span class="co"># fast processing with parallel computing:</span></span>
|
||||
<span><span class="fu"><a href="../reference/as.sir.html">as.sir</a></span><span class="op">(</span><span class="va">your_data</span>, <span class="va">...</span>, parallel <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre><p></p></div></li>
|
||||
<li><p>Operators like "<=" will be stripped before interpretation. When using <code>capped_mic_handling = "conservative"</code>, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (<code>capped_mic_handling = "standard"</code>) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".</p></li>
|
||||
<li><p>Operators like "<=" will be considered according to the <code>capped_mic_handling</code> setting. At default, an MIC value of e.g. ">2" will return "NI" (non-interpretable) if the breakpoint is 4-8; the <em>true</em> MIC could be at either side of the breakpoint. This is to prevent that capped values from raw laboratory data would not be treated conservatively.</p></li>
|
||||
<li><p><strong>Note:</strong> When using CLSI as the guideline, MIC values must be log2-based doubling dilutions. Values not in this format, will be automatically rounded up to the nearest log2 level as CLSI instructs, and a warning will be thrown.</p></li>
|
||||
</ul></li>
|
||||
<li><p>For <strong>interpreting disk diffusion diameters</strong> according to EUCAST or CLSI. You must clean your disk zones first using <code><a href="as.disk.html">as.disk()</a></code>, that also gives your columns the new data class <code><a href="as.disk.html">disk</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul><li><p>Example to apply using <code>dplyr</code>:</p>
|
||||
@@ -415,10 +416,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> datetime index method ab_given mo_given host_given input_given</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2025-11-24 <span style="color: #949494;">10:38:56</span> 1 MIC amoxicillin Escherich… human 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2025-11-24 <span style="color: #949494;">10:38:56</span> 1 MIC cipro Escherich… human 0.256 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2025-11-24 <span style="color: #949494;">10:38:56</span> 1 DISK tobra Escherich… human 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2025-11-24 <span style="color: #949494;">10:38:56</span> 1 DISK genta Escherich… human 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2025-12-15 <span style="color: #949494;">12:29:02</span> 1 MIC amoxicillin Escherich… human 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2025-12-15 <span style="color: #949494;">12:29:02</span> 1 MIC cipro Escherich… human 0.256 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2025-12-15 <span style="color: #949494;">12:29:02</span> 1 DISK tobra Escherich… human 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2025-12-15 <span style="color: #949494;">12:29:03</span> 1 DISK genta Escherich… human 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># breakpoint_S_R <chr>, site <chr></span></span>
|
||||
@@ -624,8 +625,20 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S SDD I R NI <NA> <NA> <NA></span>
|
||||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="st">"<= 0.002; S"</span><span class="op">)</span> <span class="co"># will return "S"</span></span></span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in <span style="background-color: #444444;">`as.sir()`</span>: 1 result in index '20' truncated (100%) that were invalid</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> antimicrobial interpretations: "<= 0.002; S"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] <NA></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ in </span><span style="color: #0000BB; background-color: #444444;">`as.sir()`</span><span style="color: #0000BB;">: Interpreting input value 1 as "S", 2 as "I", and 3 as "R"</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S I R</span>
|
||||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span>, S <span class="op">=</span> <span class="fl">3</span>, I <span class="op">=</span> <span class="fl">2</span>, R <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ in </span><span style="color: #0000BB; background-color: #444444;">`as.sir()`</span><span style="color: #0000BB;">: Interpreting input value 1 as "R", 2 as "I", and 3 as "S"</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R I S</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">sir_data</span> <span class="op"><-</span> <span class="fu">as.sir</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="fl">474</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"I"</span>, <span class="fl">36</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"R"</span>, <span class="fl">370</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">is.sir</span><span class="op">(</span><span class="va">sir_data</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE</span>
|
||||
|
||||
+42
-31
@@ -24,8 +24,9 @@ is.sir(x)
|
||||
is_sir_eligible(x, threshold = 0.05)
|
||||
|
||||
# Default S3 method
|
||||
as.sir(x, S = "^(S|U)+$", I = "^(I)+$", R = "^(R)+$",
|
||||
NI = "^(N|NI|V)+$", SDD = "^(SDD|D|H)+$", info = interactive(), ...)
|
||||
as.sir(x, S = "^(S|U|1)+$", I = "^(I|2)+$",
|
||||
R = "^(R|3)+$", NI = "^(N|NI|V|4)+$", SDD = "^(SDD|D|H|5)+$",
|
||||
info = interactive(), ...)
|
||||
|
||||
# S3 method for class 'mic'
|
||||
as.sir(x, mo = NULL, ab = deparse(substitute(x)),
|
||||
@@ -115,8 +116,8 @@ disk diffusion diameters:
|
||||
language](https://tidyselect.r-lib.org/reference/starts_with.html)
|
||||
such as `where(is.mic)`, `starts_with(...)`, or `column1:column4`, and
|
||||
can thus also be [antimicrobial
|
||||
selectors](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
such as `as.sir(df, penicillins())`.
|
||||
selectors](https://amr-for-r.org/reference/antimicrobial_selectors.md),
|
||||
e.g. `as.sir(df, penicillins())`.
|
||||
|
||||
Otherwise: arguments passed on to methods.
|
||||
|
||||
@@ -187,31 +188,31 @@ disk diffusion diameters:
|
||||
|
||||
`"none"`
|
||||
|
||||
- `<=` and `>=` are treated as-is.
|
||||
- `<=`, `<`, `>` and `>=` are ignored.
|
||||
|
||||
- `<` and `>` are treated as-is.
|
||||
`"conservative"` (default)
|
||||
|
||||
`"conservative"`
|
||||
- `<=`, `<`, `>` and `>=` return `"NI"` (non-interpretable) if the
|
||||
*true* MIC could be at either side of the breakpoint.
|
||||
|
||||
- `<=` and `>=` return `"NI"` (non-interpretable) if the MIC is within
|
||||
the breakpoint guideline range.
|
||||
- This is the only mode that preserves uncertainty for ECOFFs.
|
||||
|
||||
- `<` always returns `"S"`, and `>` always returns `"R"`.
|
||||
`"standard"`
|
||||
|
||||
`"standard"` (default)
|
||||
- `<=` and `>=` return `"NI"` (non-interpretable) if the *true* MIC
|
||||
could be at either side of the breakpoint.
|
||||
|
||||
- `<=` and `>=` return `"NI"` (non-interpretable) if the MIC is within
|
||||
the breakpoint guideline range.
|
||||
- `<` always returns `"S"`, regardless of the breakpoint.
|
||||
|
||||
- `<` and `>` are treated as-is.
|
||||
- `>` always returns `"R"`, regardless of the breakpoint.
|
||||
|
||||
`"inverse"`
|
||||
`"lenient"`
|
||||
|
||||
- `<=` and `>=` are treated as-is.
|
||||
- `<=` and `<` always return `"S"`, regardless of the breakpoint.
|
||||
|
||||
- `<` always returns `"S"`, and `>` always returns `"R"`.
|
||||
- `>=` and `>` always return `"R"`, regardless of the breakpoint.
|
||||
|
||||
The default `"standard"` setting ensures cautious handling of
|
||||
The default `"conservative"` setting ensures cautious handling of
|
||||
uncertain values while preserving interpretability. This option can
|
||||
also be set with the package option
|
||||
[`AMR_capped_mic_handling`](https://amr-for-r.org/reference/AMR-options.md).
|
||||
@@ -397,14 +398,12 @@ The `as.sir()` function can work in four ways:
|
||||
# fast processing with parallel computing:
|
||||
as.sir(your_data, ..., parallel = TRUE)
|
||||
|
||||
- Operators like "\<=" will be stripped before interpretation. When
|
||||
using `capped_mic_handling = "conservative"`, an MIC value of e.g.
|
||||
"\>2" will always return "R", even if the breakpoint according to
|
||||
the chosen guideline is "\>=4". This is to prevent that capped
|
||||
values from raw laboratory data would not be treated
|
||||
conservatively. The default behaviour
|
||||
(`capped_mic_handling = "standard"`) considers "\>2" to be lower
|
||||
than "\>=4" and might in this case return "S" or "I".
|
||||
- Operators like "\<=" will be considered according to the
|
||||
`capped_mic_handling` setting. At default, an MIC value of e.g.
|
||||
"\>2" will return "NI" (non-interpretable) if the breakpoint is
|
||||
4-8; the *true* MIC could be at either side of the breakpoint.
|
||||
This is to prevent that capped values from raw laboratory data
|
||||
would not be treated conservatively.
|
||||
|
||||
- **Note:** When using CLSI as the guideline, MIC values must be
|
||||
log2-based doubling dilutions. Values not in this format, will be
|
||||
@@ -649,10 +648,10 @@ sir_interpretation_history()
|
||||
#> # A tibble: 4 × 18
|
||||
#> datetime index method ab_given mo_given host_given input_given
|
||||
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
|
||||
#> 1 2025-11-24 10:38:56 1 MIC amoxicillin Escherich… human 8
|
||||
#> 2 2025-11-24 10:38:56 1 MIC cipro Escherich… human 0.256
|
||||
#> 3 2025-11-24 10:38:56 1 DISK tobra Escherich… human 16
|
||||
#> 4 2025-11-24 10:38:56 1 DISK genta Escherich… human 18
|
||||
#> 1 2025-12-15 12:29:02 1 MIC amoxicillin Escherich… human 8
|
||||
#> 2 2025-12-15 12:29:02 1 MIC cipro Escherich… human 0.256
|
||||
#> 3 2025-12-15 12:29:02 1 DISK tobra Escherich… human 16
|
||||
#> 4 2025-12-15 12:29:03 1 DISK genta Escherich… human 18
|
||||
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
|
||||
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
|
||||
#> # breakpoint_S_R <chr>, site <chr>
|
||||
@@ -858,8 +857,20 @@ as.sir(c("S", "SDD", "I", "R", "NI", "A", "B", "C"))
|
||||
#> Class 'sir'
|
||||
#> [1] S SDD I R NI <NA> <NA> <NA>
|
||||
as.sir("<= 0.002; S") # will return "S"
|
||||
#> Warning: in `as.sir()`: 1 result in index '20' truncated (100%) that were invalid
|
||||
#> antimicrobial interpretations: "<= 0.002; S"
|
||||
#> Class 'sir'
|
||||
#> [1] S
|
||||
#> [1] <NA>
|
||||
|
||||
as.sir(c(1, 2, 3))
|
||||
#> ℹ in `as.sir()`: Interpreting input value 1 as "S", 2 as "I", and 3 as "R"
|
||||
#> Class 'sir'
|
||||
#> [1] S I R
|
||||
as.sir(c(1, 2, 3), S = 3, I = 2, R = 1)
|
||||
#> ℹ in `as.sir()`: Interpreting input value 1 as "R", 2 as "I", and 3 as "S"
|
||||
#> Class 'sir'
|
||||
#> [1] R I S
|
||||
|
||||
sir_data <- as.sir(c(rep("S", 474), rep("I", 36), rep("R", 370)))
|
||||
is.sir(sir_data)
|
||||
#> [1] TRUE
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
|
||||
|
||||
<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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -9,7 +9,7 @@
|
||||
|
||||
<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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -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="">3.0.1.9003</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
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[{"path":"https://amr-for-r.org/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) reliable data thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations SIR values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://amr-for-r.org/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"Conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://amr-for-r.org/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"Conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables. AMR package contains data set example_isolates_unclean, might look data users extracted laboratory systems: AMR data analysis, like microorganism column contain valid, --date taxonomy, antibiotic columns cleaned SIR values well.","code":"library(dplyr) library(ggplot2) library(AMR) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\")) example_isolates_unclean #> # A tibble: 3,000 × 8 #> patient_id hospital date bacteria AMX AMC CIP GEN #> <chr> <chr> <date> <chr> <chr> <chr> <chr> <chr> #> 1 J3 A 2012-11-21 E. coli R I S S #> 2 R7 A 2018-04-03 K. pneumoniae R I S S #> 3 P3 A 2014-09-19 E. coli R S S S #> 4 P10 A 2015-12-10 E. coli S I S S #> 5 B7 A 2015-03-02 E. coli S S S S #> 6 W3 A 2018-03-31 S. aureus R S R S #> 7 J8 A 2016-06-14 E. coli R S S S #> 8 M3 A 2015-10-25 E. coli R S S S #> 9 J3 A 2019-06-19 E. coli S S S S #> 10 G6 A 2015-04-27 S. aureus S S S S #> # ℹ 2,990 more rows # we will use 'our_data' as the data set name for this tutorial our_data <- example_isolates_unclean"},{"path":"https://amr-for-r.org/articles/AMR.html","id":"taxonomy-of-microorganisms","dir":"Articles","previous_headings":"Preparation","what":"Taxonomy of microorganisms","title":"Conduct AMR data analysis","text":".mo(), users can transform arbitrary microorganism names codes current taxonomy. AMR package contains --date taxonomic data. specific, currently included data retrieved 24 Jun 2024. codes AMR packages come .mo() short, still human readable. importantly, .mo() supports kinds input: first character codes denote taxonomic kingdom, Bacteria (B), Fungi (F), Protozoa (P). AMR package also contain functions directly retrieve taxonomic properties, name, genus, species, family, order, even Gram-stain. start mo_ use .mo() internally, still arbitrary user input can used: Now can thus clean data: Apparently, uncertainty translation taxonomic codes. Let’s check : ’s good.","code":"as.mo(\"Klebsiella pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"K. pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"KLEPNE\") #> Class 'mo' #> [1] Line truncated
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[{"path":"https://amr-for-r.org/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) reliable data thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations SIR values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://amr-for-r.org/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"Conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://amr-for-r.org/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"Conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables. AMR package contains data set example_isolates_unclean, might look data users extracted laboratory systems: AMR data analysis, like microorganism column contain valid, --date taxonomy, antibiotic columns cleaned SIR values well.","code":"library(dplyr) library(ggplot2) library(AMR) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\")) example_isolates_unclean #> # A tibble: 3,000 × 8 #> patient_id hospital date bacteria AMX AMC CIP GEN #> <chr> <chr> <date> <chr> <chr> <chr> <chr> <chr> #> 1 J3 A 2012-11-21 E. coli R I S S #> 2 R7 A 2018-04-03 K. pneumoniae R I S S #> 3 P3 A 2014-09-19 E. coli R S S S #> 4 P10 A 2015-12-10 E. coli S I S S #> 5 B7 A 2015-03-02 E. coli S S S S #> 6 W3 A 2018-03-31 S. aureus R S R S #> 7 J8 A 2016-06-14 E. coli R S S S #> 8 M3 A 2015-10-25 E. coli R S S S #> 9 J3 A 2019-06-19 E. coli S S S S #> 10 G6 A 2015-04-27 S. aureus S S S S #> # ℹ 2,990 more rows # we will use 'our_data' as the data set name for this tutorial our_data <- example_isolates_unclean"},{"path":"https://amr-for-r.org/articles/AMR.html","id":"taxonomy-of-microorganisms","dir":"Articles","previous_headings":"Preparation","what":"Taxonomy of microorganisms","title":"Conduct AMR data analysis","text":".mo(), users can transform arbitrary microorganism names codes current taxonomy. AMR package contains --date taxonomic data. specific, currently included data retrieved 24 Jun 2024. codes AMR packages come .mo() short, still human readable. importantly, .mo() supports kinds input: first character codes denote taxonomic kingdom, Bacteria (B), Fungi (F), Protozoa (P). AMR package also contain functions directly retrieve taxonomic properties, name, genus, species, family, order, even Gram-stain. start mo_ use .mo() internally, still arbitrary user input can used: Now can thus clean data: Apparently, uncertainty translation taxonomic codes. Let’s check : ’s good.","code":"as.mo(\"Klebsiella pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"K. pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"KLEPNE\") #> Class 'mo' #> [1] Line truncated
|
||||
Reference in new issue
Block a user