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@@ -12,8 +12,8 @@
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@@ -33,7 +33,7 @@
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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="">3.0.1.9057</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9061</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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@@ -85,8 +85,8 @@
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<ul>
|
||||
<li>Provides an <strong>all-in-one solution</strong> for antimicrobial resistance (AMR) data analysis in a One Health approach</li>
|
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<li>Peer-reviewed, used in over 175 countries, available in 28 languages</li>
|
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<li>Generates <strong>antibiograms</strong> - traditional, combined, syndromic, and even WISCA</li>
|
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<li>Provides the <strong>full microbiological taxonomy</strong> of ~79 000 distinct species and extensive info of ~620 antimicrobial drugs</li>
|
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<li>Generates <strong>antibiograms</strong> - WISCA for empiric coverage estimates, or traditional/syndromic for AMR surveillance</li>
|
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<li>Provides the <strong>full microbiological taxonomy</strong> of ~97 000 distinct species and extensive info of ~620 antimicrobial drugs</li>
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<li>Applies <strong>CLSI 2011-2026</strong> and <strong>EUCAST 2011-2026</strong> clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation</li>
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<li>Corrects for duplicate isolates, <strong>calculates</strong> and <strong>predicts</strong> AMR per antimicrobial class</li>
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<li>Integrates with <strong>WHONET</strong>, ATC, <strong>EARS-Net</strong>, PubChem, <strong>LOINC</strong>, <strong>SNOMED CT</strong>, and <strong>NCBI</strong>
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@@ -112,7 +112,7 @@
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</h2>
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<p>The <code>AMR</code> package is a peer-reviewed, <a href="#copyright">free and open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero dependencies</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. We are a team of <a href="./authors.html">many different researchers</a> from around the globe to make this a successful and durable project!</p>
|
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<p>This work was published in the Journal of Statistical Software (Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">DOI 10.18637/jss.v104.i03</a>) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>).</p>
|
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<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~79 000 distinct microbial species</strong></a> (updated June 2024) and all <a href="./reference/antimicrobials.html"><strong>~620 antimicrobial and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
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<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~97 000 distinct microbial species</strong></a> (updated June 2024) and all <a href="./reference/antimicrobials.html"><strong>~620 antimicrobial and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
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<div class="section level3">
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||||
<h3 id="used-in-over-175-countries-available-in-28-languages">Used in over 175 countries, available in 28 languages<a class="anchor" aria-label="anchor" href="#used-in-over-175-countries-available-in-28-languages"></a>
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</h3>
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@@ -145,26 +145,24 @@
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<span><span class="co">#> ℹ Using column mo as input for `mo_fullname()`</span></span>
|
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<span><span class="co">#> ℹ Using column mo as input for `mo_is_gram_negative()`</span></span>
|
||||
<span><span class="co">#> ℹ Using column mo as input for `mo_is_intrinsic_resistant()`</span></span>
|
||||
<span><span class="co">#> ℹ Determining intrinsic resistance based on 'EUCAST Expected</span></span>
|
||||
<span><span class="co">#> Resistant Phenotypes' v1.2 (2023). This note will be shown</span></span>
|
||||
<span><span class="co">#> once per session.</span></span>
|
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<span><span class="co">#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB</span></span>
|
||||
<span><span class="co">#> (tobramycin), AMK (amikacin), and KAN (kanamycin)</span></span>
|
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<span><span class="co">#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM</span></span>
|
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<span><span class="co">#> (meropenem)</span></span>
|
||||
<span><span class="co">#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant</span></span>
|
||||
<span><span class="co">#> Phenotypes' v1.2 (2023). This note will be shown once per session.</span></span>
|
||||
<span><span class="co">#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK</span></span>
|
||||
<span><span class="co">#> (amikacin), and KAN (kanamycin)</span></span>
|
||||
<span><span class="co">#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)</span></span>
|
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<span><span class="co">#> # A tibble: 35 × 7</span></span>
|
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<span><span class="co">#> bacteria GEN TOB AMK KAN IPM MEM </span></span>
|
||||
<span><span class="co">#> <chr> <sir> <sir> <sir> <sir> <sir> <sir></span></span>
|
||||
<span><span class="co">#> 1 Pseudomonas aer… I S NA R S NA </span></span>
|
||||
<span><span class="co">#> 2 Pseudomonas aer… I S NA R S NA </span></span>
|
||||
<span><span class="co">#> 3 Pseudomonas aer… I S NA R S NA </span></span>
|
||||
<span><span class="co">#> 4 Pseudomonas aer… S S S R NA S </span></span>
|
||||
<span><span class="co">#> 5 Pseudomonas aer… S S S R S S </span></span>
|
||||
<span><span class="co">#> 6 Pseudomonas aer… S S S R S S </span></span>
|
||||
<span><span class="co">#> 7 Stenotrophomona… R R R R R R </span></span>
|
||||
<span><span class="co">#> 8 Pseudomonas aer… S S S R NA S </span></span>
|
||||
<span><span class="co">#> 9 Pseudomonas aer… S S S R NA S </span></span>
|
||||
<span><span class="co">#> 10 Pseudomonas aer… S S S R S S </span></span>
|
||||
<span><span class="co">#> bacteria GEN TOB AMK KAN IPM MEM </span></span>
|
||||
<span><span class="co">#> <chr> <sir> <sir> <sir> <sir> <sir> <sir></span></span>
|
||||
<span><span class="co">#> 1 Pseudomonas aeruginosa I S NA R S NA </span></span>
|
||||
<span><span class="co">#> 2 Pseudomonas aeruginosa I S NA R S NA </span></span>
|
||||
<span><span class="co">#> 3 Pseudomonas aeruginosa I S NA R S NA </span></span>
|
||||
<span><span class="co">#> 4 Pseudomonas aeruginosa S S S R NA S </span></span>
|
||||
<span><span class="co">#> 5 Pseudomonas aeruginosa S S S R S S </span></span>
|
||||
<span><span class="co">#> 6 Pseudomonas aeruginosa S S S R S S </span></span>
|
||||
<span><span class="co">#> 7 Stenotrophomonas maltophilia R R R R R R </span></span>
|
||||
<span><span class="co">#> 8 Pseudomonas aeruginosa S S S R NA S </span></span>
|
||||
<span><span class="co">#> 9 Pseudomonas aeruginosa S S S R NA S </span></span>
|
||||
<span><span class="co">#> 10 Pseudomonas aeruginosa S S S R S S </span></span>
|
||||
<span><span class="co">#> # 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>
|
||||
@@ -176,18 +174,17 @@
|
||||
<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">#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB</span></span>
|
||||
<span><span class="co">#> (tobramycin), AMK (amikacin), and KAN (kanamycin)</span></span>
|
||||
<span><span class="co">#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM</span></span>
|
||||
<span><span class="co">#> (meropenem)</span></span></code></pre></div>
|
||||
<table class="table">
|
||||
<span><span class="co">#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK</span></span>
|
||||
<span><span class="co">#> (amikacin), and KAN (kanamycin)</span></span>
|
||||
<span><span class="co">#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)</span></span></code></pre></div>
|
||||
<table style="width:100%;" class="table">
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<colgroup>
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<col width="12%">
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<col width="15%">
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<col width="14%">
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<col width="15%">
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<col width="11%">
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<col width="15%">
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<col width="14%">
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<col width="14%">
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<col width="14%">
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<col width="14%">
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<col width="14%">
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<col width="14%">
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</colgroup>
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<thead><tr>
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@@ -299,10 +296,10 @@
|
||||
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></code></pre></div>
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<table class="table">
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<colgroup>
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<col width="12%">
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<col width="21%">
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<col width="32%">
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<col width="32%">
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<col width="25%">
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<col width="25%">
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<col width="25%">
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<col width="25%">
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</colgroup>
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<thead><tr>
|
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<th align="left">Pathogen</th>
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||||
@@ -407,18 +404,16 @@
|
||||
<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">#> ℹ `resistance()` assumes the EUCAST guideline and thus</span></span>
|
||||
<span><span class="co">#> considers the 'I' category susceptible. Set the `guideline`</span></span>
|
||||
<span><span class="co">#> argument or the `AMR_guideline` option to either "CLSI" or</span></span>
|
||||
<span><span class="co">#> "EUCAST", see `?AMR-options`.</span></span>
|
||||
<span><span class="co">#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span>
|
||||
<span><span class="co">#> category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span>
|
||||
<span><span class="co">#> option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span>
|
||||
<span><span class="co">#> ℹ This message will be shown once per session.</span></span>
|
||||
<span><span class="co">#> # A tibble: 3 × 5</span></span>
|
||||
<span><span class="co">#> ward GEN_total_R GEN_conf_int TOB_total_R</span></span>
|
||||
<span><span class="co">#> <chr> <dbl> <chr> <dbl></span></span>
|
||||
<span><span class="co">#> 1 Clinical 0.229 0.205-0.254 0.315</span></span>
|
||||
<span><span class="co">#> 2 ICU 0.290 0.253-0.33 0.400</span></span>
|
||||
<span><span class="co">#> 3 Outpatient 0.2 0.131-0.285 0.368</span></span>
|
||||
<span><span class="co">#> # ℹ 1 more variable: TOB_conf_int <chr></span></span></code></pre></div>
|
||||
<span><span class="co">#> ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int</span></span>
|
||||
<span><span class="co">#> <chr> <dbl> <chr> <dbl> <chr> </span></span>
|
||||
<span><span class="co">#> 1 Clinical 0.229 0.205-0.254 0.315 0.284-0.347 </span></span>
|
||||
<span><span class="co">#> 2 ICU 0.290 0.253-0.33 0.400 0.353-0.449 </span></span>
|
||||
<span><span class="co">#> 3 Outpatient 0.2 0.131-0.285 0.368 0.254-0.493</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>
|
||||
@@ -430,16 +425,15 @@
|
||||
<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">#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB</span></span>
|
||||
<span><span class="co">#> (tobramycin), AMK (amikacin), and KAN (kanamycin)</span></span>
|
||||
<span><span class="co">#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK</span></span>
|
||||
<span><span class="co">#> (amikacin), and KAN (kanamycin)</span></span>
|
||||
<span><span class="co">#> ℹ For `polymyxins()` using column COL (colistin)</span></span>
|
||||
<span><span class="co">#> Warning: There was 1 warning in `summarise()`.</span></span>
|
||||
<span><span class="co">#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()),</span></span>
|
||||
<span><span class="co">#> resistance)`.</span></span>
|
||||
<span><span class="co">#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.</span></span>
|
||||
<span><span class="co">#> ℹ In group 3: `ward = "Outpatient"`.</span></span>
|
||||
<span><span class="co">#> Caused by warning:</span></span>
|
||||
<span><span class="co">#> ! Introducing NA: only 23 results available for KAN in group:</span></span>
|
||||
<span><span class="co">#> ward = "Outpatient" (whilst `minimum = 30`).</span></span>
|
||||
<span><span class="co">#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient"</span></span>
|
||||
<span><span class="co">#> (whilst `minimum = 30`).</span></span>
|
||||
<span><span class="va">out</span></span>
|
||||
<span><span class="co">#> # A tibble: 3 × 6</span></span>
|
||||
<span><span class="co">#> ward GEN TOB AMK KAN COL</span></span>
|
||||
@@ -451,12 +445,11 @@
|
||||
<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">%>%</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">#> # A tibble: 3 × 6</span></span>
|
||||
<span><span class="co">#> ward gentamicin tobramycin amikacin kanamycin</span></span>
|
||||
<span><span class="co">#> <chr> <dbl> <dbl> <dbl> <dbl></span></span>
|
||||
<span><span class="co">#> 1 Clinical 0.229 0.315 0.626 1</span></span>
|
||||
<span><span class="co">#> 2 ICU 0.290 0.400 0.662 1</span></span>
|
||||
<span><span class="co">#> 3 Outpatient 0.2 0.368 0.605 NA</span></span>
|
||||
<span><span class="co">#> # ℹ 1 more variable: colistin <dbl></span></span></code></pre></div>
|
||||
<span><span class="co">#> ward gentamicin tobramycin amikacin kanamycin colistin</span></span>
|
||||
<span><span class="co">#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl></span></span>
|
||||
<span><span class="co">#> 1 Clinical 0.229 0.315 0.626 1 0.780</span></span>
|
||||
<span><span class="co">#> 2 ICU 0.290 0.400 0.662 1 0.857</span></span>
|
||||
<span><span class="co">#> 3 Outpatient 0.2 0.368 0.605 NA 0.889</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">%>%</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>
|
||||
|
||||
Reference in New Issue
Block a user