P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-05-31 19:41:51 +02:00
Code Releases Activity

Built site for AMR@3.0.1.9053: 23beebc

Browse Source
This commit is contained in:
github-actions
2026-04-30 08:07:42 +00:00
parent 425f4ad827
commit 3a3027f171
100 changed files with 742 additions and 649 deletions
Download Patch File Download Diff File Expand all files Collapse all files

139
index.html
View File

@@ -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="">3.0.1.9052</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9053</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">
@@ -145,24 +145,26 @@
<span><span class="co">#&gt; ℹ Using column mo as input for `mo_fullname()`</span></span>
<span><span class="co">#&gt; ℹ Using column mo as input for `mo_is_gram_negative()`</span></span>
<span><span class="co">#&gt; ℹ Using column mo as input for `mo_is_intrinsic_resistant()`</span></span>
<span><span class="co">#&gt; ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant</span></span>
<span><span class="co">#&gt; Phenotypes' v1.2 (2023). This note will be shown once per session.</span></span>
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK</span></span>
<span><span class="co">#&gt; (amikacin), and KAN (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)</span></span>
<span><span class="co">#&gt; ℹ Determining intrinsic resistance based on 'EUCAST Expected</span></span>
<span><span class="co">#&gt; Resistant Phenotypes' v1.2 (2023). This note will be shown</span></span>
<span><span class="co">#&gt; once per session.</span></span>
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB</span></span>
<span><span class="co">#&gt; (tobramycin), AMK (amikacin), and KAN (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM</span></span>
<span><span class="co">#&gt; (meropenem)</span></span>
<span><span class="co">#&gt; # A tibble: 35 × 7</span></span>
<span><span class="co">#&gt; bacteria GEN TOB AMK KAN IPM MEM </span></span>
<span><span class="co">#&gt; &lt;chr&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;</span></span>
<span><span class="co">#&gt; 1 Pseudomonas aeruginosa I S NA R S NA </span></span>
<span><span class="co">#&gt; 2 Pseudomonas aeruginosa I S NA R S NA </span></span>
<span><span class="co">#&gt; 3 Pseudomonas aeruginosa I S NA R S NA </span></span>
<span><span class="co">#&gt; 4 Pseudomonas aeruginosa S S S R NA S </span></span>
<span><span class="co">#&gt; 5 Pseudomonas aeruginosa S S S R S S </span></span>
<span><span class="co">#&gt; 6 Pseudomonas aeruginosa S S S R S S </span></span>
<span><span class="co">#&gt; 7 Stenotrophomonas maltophilia R R R R R R </span></span>
<span><span class="co">#&gt; 8 Pseudomonas aeruginosa S S S R NA S </span></span>
<span><span class="co">#&gt; 9 Pseudomonas aeruginosa S S S R NA S </span></span>
<span><span class="co">#&gt; 10 Pseudomonas aeruginosa S S S R S S </span></span>
<span><span class="co">#&gt; bacteria GEN TOB AMK KAN IPM MEM </span></span>
<span><span class="co">#&gt; &lt;chr&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;</span></span>
<span><span class="co">#&gt; 1 Pseudomonas aer… I S NA R S NA </span></span>
<span><span class="co">#&gt; 2 Pseudomonas aer… I S NA R S NA </span></span>
<span><span class="co">#&gt; 3 Pseudomonas aer… I S NA R S NA </span></span>
<span><span class="co">#&gt; 4 Pseudomonas aer… S S S R NA S </span></span>
<span><span class="co">#&gt; 5 Pseudomonas aer… S S S R S S </span></span>
<span><span class="co">#&gt; 6 Pseudomonas aer… S S S R S S </span></span>
<span><span class="co">#&gt; 7 Stenotrophomona… R R R R R R </span></span>
<span><span class="co">#&gt; 8 Pseudomonas aer… S S S R NA S </span></span>
<span><span class="co">#&gt; 9 Pseudomonas aer… S S S R NA S </span></span>
<span><span class="co">#&gt; 10 Pseudomonas aer… S S S R S S </span></span>
<span><span class="co">#&gt; # ℹ 25 more rows</span></span></code></pre></div>
<p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><a href="reference/antimicrobial_selectors.html">aminoglycosides()</a></code> and <code><a href="reference/antimicrobial_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antimicrobials.html">all antimicrobials</a> in the <code>AMR</code> package make sure you get what you meant.</p>
</div>
@@ -174,20 +176,21 @@
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antimicrobials <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="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK</span></span>
<span><span class="co">#&gt; (amikacin), and KAN (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)</span></span></code></pre></div>
<table style="width:100%;" class="table">
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB</span></span>
<span><span class="co">#&gt; (tobramycin), AMK (amikacin), and KAN (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM</span></span>
<span><span class="co">#&gt; (meropenem)</span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="12%">
<col width="15%">
<col width="14%">
<col width="14%">
<col width="14%">
<col width="14%">
<col width="14%">
<col width="14%">
<col width="15%">
<col width="11%">
<col width="15%">
<col width="14%">
</colgroup>
<thead><tr class="header">
<thead><tr>
<th align="left">Pathogen</th>
<th align="left">Amikacin</th>
<th align="left">Gentamicin</th>
@@ -197,7 +200,7 @@
<th align="left">Tobramycin</th>
</tr></thead>
<tbody>
<tr class="odd">
<tr>
<td align="left">CoNS</td>
<td align="left">0% (0-8%,N=43)</td>
<td align="left">86% (82-90%,N=309)</td>
@@ -206,7 +209,7 @@
<td align="left">52% (37-67%,N=48)</td>
<td align="left">22% (12-35%,N=55)</td>
</tr>
<tr class="even">
<tr>
<td align="left"><em>E. coli</em></td>
<td align="left">100% (98-100%,N=171)</td>
<td align="left">98% (96-99%,N=460)</td>
@@ -215,7 +218,7 @@
<td align="left">100% (99-100%,N=418)</td>
<td align="left">97% (96-99%,N=462)</td>
</tr>
<tr class="odd">
<tr>
<td align="left"><em>E. faecalis</em></td>
<td align="left">0% (0-9%,N=39)</td>
<td align="left">0% (0-9%,N=39)</td>
@@ -224,7 +227,7 @@
<td align="left">NA</td>
<td align="left">0% (0-9%,N=39)</td>
</tr>
<tr class="even">
<tr>
<td align="left"><em>K. pneumoniae</em></td>
<td align="left">NA</td>
<td align="left">90% (79-96%,N=58)</td>
@@ -233,7 +236,7 @@
<td align="left">100% (93-100%,N=53)</td>
<td align="left">90% (79-96%,N=58)</td>
</tr>
<tr class="odd">
<tr>
<td align="left"><em>P. aeruginosa</em></td>
<td align="left">NA</td>
<td align="left">100% (88-100%,N=30)</td>
@@ -242,7 +245,7 @@
<td align="left">NA</td>
<td align="left">100% (88-100%,N=30)</td>
</tr>
<tr class="even">
<tr>
<td align="left"><em>P. mirabilis</em></td>
<td align="left">NA</td>
<td align="left">94% (80-99%,N=34)</td>
@@ -251,7 +254,7 @@
<td align="left">NA</td>
<td align="left">94% (80-99%,N=34)</td>
</tr>
<tr class="odd">
<tr>
<td align="left"><em>S. aureus</em></td>
<td align="left">NA</td>
<td align="left">99% (97-100%,N=233)</td>
@@ -260,7 +263,7 @@
<td align="left">NA</td>
<td align="left">98% (92-100%,N=86)</td>
</tr>
<tr class="even">
<tr>
<td align="left"><em>S. epidermidis</em></td>
<td align="left">0% (0-8%,N=44)</td>
<td align="left">79% (71-85%,N=163)</td>
@@ -269,7 +272,7 @@
<td align="left">NA</td>
<td align="left">51% (40-61%,N=89)</td>
</tr>
<tr class="odd">
<tr>
<td align="left"><em>S. hominis</em></td>
<td align="left">NA</td>
<td align="left">92% (84-97%,N=80)</td>
@@ -278,7 +281,7 @@
<td align="left">NA</td>
<td align="left">85% (74-93%,N=62)</td>
</tr>
<tr class="even">
<tr>
<td align="left"><em>S. pneumoniae</em></td>
<td align="left">0% (0-3%,N=117)</td>
<td align="left">0% (0-3%,N=117)</td>
@@ -296,25 +299,25 @@
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="25%">
<col width="25%">
<col width="25%">
<col width="25%">
<col width="12%">
<col width="21%">
<col width="32%">
<col width="32%">
</colgroup>
<thead><tr class="header">
<thead><tr>
<th align="left">Pathogen</th>
<th align="left">Piperacillin/tazobactam</th>
<th align="left">Piperacillin/tazobactam + Gentamicin</th>
<th align="left">Piperacillin/tazobactam + Tobramycin</th>
</tr></thead>
<tbody>
<tr class="odd">
<tr>
<td align="left">Gram-negative</td>
<td align="left">88% (85-91%,N=641)</td>
<td align="left">99% (97-99%,N=691)</td>
<td align="left">98% (97-99%,N=693)</td>
</tr>
<tr class="even">
<tr>
<td align="left">Gram-positive</td>
<td align="left">86% (82-89%,N=345)</td>
<td align="left">98% (96-98%,N=1044)</td>
@@ -336,20 +339,20 @@
<col width="26%">
<col width="26%">
</colgroup>
<thead><tr class="header">
<thead><tr>
<th align="left">Збудник</th>
<th align="left">Гентаміцин</th>
<th align="left">Тобраміцин</th>
<th align="left">Ципрофлоксацин</th>
</tr></thead>
<tbody>
<tr class="odd">
<tr>
<td align="left">Грамнегативні</td>
<td align="left">96% (95-98%,N=684)</td>
<td align="left">96% (94-97%,N=686)</td>
<td align="left">91% (88-93%,N=684)</td>
</tr>
<tr class="even">
<tr>
<td align="left">Грампозитивні</td>
<td align="left">63% (60-66%,N=1170)</td>
<td align="left">34% (31-38%,N=665)</td>
@@ -404,16 +407,18 @@
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></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="va">GEN</span>, <span class="va">TOB</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>total_R <span class="op">=</span> <span class="va">resistance</span>,</span>
<span> conf_int <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="reference/proportion.html">sir_confidence_interval</a></span><span class="op">(</span><span class="va">x</span>, collapse <span class="op">=</span> <span class="st">"-"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span>
<span><span class="co">#&gt; category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span>
<span><span class="co">#&gt; option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span>
<span><span class="co">#&gt; ℹ `resistance()` assumes the EUCAST guideline and thus</span></span>
<span><span class="co">#&gt; considers the 'I' category susceptible. Set the `guideline`</span></span>
<span><span class="co">#&gt; argument or the `AMR_guideline` option to either "CLSI" or</span></span>
<span><span class="co">#&gt; "EUCAST", see `?AMR-options`.</span></span>
<span><span class="co">#&gt; ℹ This message will be shown once per session.</span></span>
<span><span class="co">#&gt; # A tibble: 3 × 5</span></span>
<span><span class="co">#&gt; ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int</span></span>
<span><span class="co">#&gt; &lt;chr&gt; &lt;dbl&gt; &lt;chr&gt; &lt;dbl&gt; &lt;chr&gt; </span></span>
<span><span class="co">#&gt; 1 Clinical 0.229 0.205-0.254 0.315 0.284-0.347 </span></span>
<span><span class="co">#&gt; 2 ICU 0.290 0.253-0.33 0.400 0.353-0.449 </span></span>
<span><span class="co">#&gt; 3 Outpatient 0.2 0.131-0.285 0.368 0.254-0.493</span></span></code></pre></div>
<span><span class="co">#&gt; ward GEN_total_R GEN_conf_int TOB_total_R</span></span>
<span><span class="co">#&gt; &lt;chr&gt; &lt;dbl&gt; &lt;chr&gt; &lt;dbl&gt;</span></span>
<span><span class="co">#&gt; 1 Clinical 0.229 0.205-0.254 0.315</span></span>
<span><span class="co">#&gt; 2 ICU 0.290 0.253-0.33 0.400</span></span>
<span><span class="co">#&gt; 3 Outpatient 0.2 0.131-0.285 0.368</span></span>
<span><span class="co">#&gt; # ℹ 1 more variable: TOB_conf_int &lt;chr&gt;</span></span></code></pre></div>
<p>Or use <a href="https://amr-for-r.org/reference/antimicrobial_selectors.html">antimicrobial selectors</a> to select a series of antibiotic columns:</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
@@ -425,15 +430,16 @@
<span> <span class="co"># calculate AMR using resistance(), over all aminoglycosides and polymyxins:</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></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="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">polymyxins</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
<span> <span class="va">resistance</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK</span></span>
<span><span class="co">#&gt; (amikacin), and KAN (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB</span></span>
<span><span class="co">#&gt; (tobramycin), AMK (amikacin), and KAN (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For `polymyxins()` using column COL (colistin)</span></span>
<span><span class="co">#&gt; Warning: There was 1 warning in `summarise()`.</span></span>
<span><span class="co">#&gt; ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.</span></span>
<span><span class="co">#&gt; ℹ In argument: `across(c(aminoglycosides(), polymyxins()),</span></span>
<span><span class="co">#&gt; resistance)`.</span></span>
<span><span class="co">#&gt; ℹ In group 3: `ward = "Outpatient"`.</span></span>
<span><span class="co">#&gt; Caused by warning:</span></span>
<span><span class="co">#&gt; ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient"</span></span>
<span><span class="co">#&gt; (whilst `minimum = 30`).</span></span>
<span><span class="co">#&gt; ! Introducing NA: only 23 results available for KAN in group:</span></span>
<span><span class="co">#&gt; ward = "Outpatient" (whilst `minimum = 30`).</span></span>
<span><span class="va">out</span></span>
<span><span class="co">#&gt; # A tibble: 3 × 6</span></span>
<span><span class="co">#&gt; ward GEN TOB AMK KAN COL</span></span>
@@ -445,11 +451,12 @@
<code class="sourceCode R"><span><span class="co"># transform the antibiotic columns to names:</span></span>
<span><span class="va">out</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="reference/ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; # A tibble: 3 × 6</span></span>
<span><span class="co">#&gt; ward gentamicin tobramycin amikacin kanamycin colistin</span></span>
<span><span class="co">#&gt; &lt;chr&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;</span></span>
<span><span class="co">#&gt; 1 Clinical 0.229 0.315 0.626 1 0.780</span></span>
<span><span class="co">#&gt; 2 ICU 0.290 0.400 0.662 1 0.857</span></span>
<span><span class="co">#&gt; 3 Outpatient 0.2 0.368 0.605 NA 0.889</span></span></code></pre></div>
<span><span class="co">#&gt; ward gentamicin tobramycin amikacin kanamycin</span></span>
<span><span class="co">#&gt; &lt;chr&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;</span></span>
<span><span class="co">#&gt; 1 Clinical 0.229 0.315 0.626 1</span></span>
<span><span class="co">#&gt; 2 ICU 0.290 0.400 0.662 1</span></span>
<span><span class="co">#&gt; 3 Outpatient 0.2 0.368 0.605 NA</span></span>
<span><span class="co">#&gt; # ℹ 1 more variable: colistin &lt;dbl&gt;</span></span></code></pre></div>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># transform the antibiotic column to ATC codes:</span></span>
<span><span class="va">out</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="reference/ab_property.html">set_ab_names</a></span><span class="op">(</span>property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></span>