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Conduct AMR analysis
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Predict antimicrobial resistance
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<img src="../logo.svg" class="logo" alt=""><h1>Determine Bug-Drug Combinations</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/bug_drug_combinations.R" class="external-link"><code>R/bug_drug_combinations.R</code></a></small>
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<div class="d-none name"><code>bug_drug_combinations.Rd</code></div>
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<div class="ref-description section level2">
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<p>Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use <code><a href="https://rdrr.io/r/base/format.html" class="external-link">format()</a></code> on the result to prettify it to a publishable/printable format, see <em>Examples</em>.</p>
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<div class="section level2">
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">x</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>, FUN <span class="op">=</span> <span class="va">mo_shortname</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="co"># S3 method for bug_drug_combinations</span></span>
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<span><span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span></span>
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<span> <span class="va">x</span>,</span>
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<span> translate_ab <span class="op">=</span> <span class="st">"name (ab, atc)"</span>,</span>
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<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
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<span> minimum <span class="op">=</span> <span class="fl">30</span>,</span>
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<span> combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
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<span> add_ab_group <span class="op">=</span> <span class="cn">TRUE</span>,</span>
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<span> remove_intrinsic_resistant <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span> decimal.mark <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"OutDec"</span><span class="op">)</span>,</span>
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<span> big.mark <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">decimal.mark</span> <span class="op">==</span> <span class="st">","</span>, <span class="st">"."</span>, <span class="st">","</span><span class="op">)</span>,</span>
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<span> <span class="va">...</span></span>
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<span><span class="op">)</span></span></code></pre></div>
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</div>
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<div class="section level2">
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<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
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<dl><dt>x</dt>
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<dd><p>a data set with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></dd>
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<dt>col_mo</dt>
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<dd><p>column name of the IDs of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
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<dt>FUN</dt>
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<dd><p>the function to call on the <code>mo</code> column to transform the microorganism codes, defaults to <code><a href="mo_property.html">mo_shortname()</a></code></p></dd>
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<dt>...</dt>
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<dd><p>arguments passed on to <code>FUN</code></p></dd>
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<dt>translate_ab</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> of length 1 containing column names of the <a href="antibiotics.html">antibiotics</a> data set</p></dd>
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<dt>language</dt>
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<dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with <code>getOption("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
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<dt>minimum</dt>
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<dd><p>the minimum allowed number of available (tested) isolates. Any isolate count lower than <code>minimum</code> will return <code>NA</code> with a warning. The default number of <code>30</code> isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see <em>Source</em>.</p></dd>
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<dt>combine_SI</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether values S and I should be summed, so resistance will be based on only R, defaults to <code>TRUE</code></p></dd>
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<dt>add_ab_group</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate where the group of the antimicrobials must be included as a first column</p></dd>
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<dt>remove_intrinsic_resistant</dt>
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<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that rows and columns with 100% resistance for all tested antimicrobials must be removed from the table</p></dd>
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<dt>decimal.mark</dt>
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<dd><p>the character to be used to indicate the numeric
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decimal point.</p></dd>
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<dt>big.mark</dt>
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<dd><p>character; if not empty used as mark between every
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<code>big.interval</code> decimals <em>before</em> (hence <code>big</code>) the
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decimal point.</p></dd>
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</dl></div>
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<div class="section level2">
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<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
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<p>The function <code>bug_drug_combinations()</code> returns a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with columns "mo", "ab", "S", "I", "R" and "total".</p>
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</div>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<p>The function <code><a href="https://rdrr.io/r/base/format.html" class="external-link">format()</a></code> calculates the resistance per bug-drug combination. Use <code>combine_SI = TRUE</code> (default) to test R vs. S+I and <code>combine_SI = FALSE</code> to test R+I vs. S.</p>
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</div>
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \donttest{</span></span></span>
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<span class="r-in"><span><span class="va">x</span> <span class="op"><-</span> <span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 6 × 6</span></span>
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<span class="r-out co"><span class="r-pr">#></span> mo ab S I R total</span>
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<span class="r-out co"><span class="r-pr">#></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;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> (unknown species) PEN 14 0 1 15</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> (unknown species) OXA 0 0 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> (unknown species) FLC 0 0 0 0</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> (unknown species) AMX 15 0 1 16</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> (unknown species) AMC 15 0 0 15</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">6</span> (unknown species) AMP 15 0 1 16</span>
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<span class="r-msg co"><span class="r-pr">#></span> Use 'format()' on this result to get a publishable/printable format.</span>
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<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span><span class="va">x</span>, translate_ab <span class="op">=</span> <span class="st">"name (atc)"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 39 × 12</span></span>
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<span class="r-out co"><span class="r-pr">#></span> Group Drug CoNS E. co…¹ E. fa…² K. pn…³ P. ae…⁴ P. mi…⁵ S. au…⁶ S. ep…⁷</span>
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<span class="r-out co"><span class="r-pr">#></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 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>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">"</span>Aminogl… Amik… <span style="color: #949494;">"</span>100… <span style="color: #949494;">"</span> 0.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">""</span> Gent… <span style="color: #949494;">"</span> 13… <span style="color: #949494;">"</span> 2.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span> 10.3… <span style="color: #949494;">"</span> 0.0… <span style="color: #949494;">"</span> 5.9… <span style="color: #949494;">"</span> 0.9… <span style="color: #949494;">"</span> 21.5…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">""</span> Kana… <span style="color: #949494;">"</span>100… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;">""</span> Tobr… <span style="color: #949494;">"</span> 78… <span style="color: #949494;">"</span> 2.6… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span> 10.3… <span style="color: #949494;">"</span> 0.0… <span style="color: #949494;">"</span> 5.9… <span style="color: #949494;">"</span> 2.3… <span style="color: #949494;">"</span> 49.4…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">"</span>Ampheni… Chlo… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span> 0.0… <span style="color: #949494;">"</span> 3.1…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">"</span>Antimyc… Rifa… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span> 0.0… <span style="color: #949494;">"</span> 2.7…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;">"</span>Beta-la… Amox… <span style="color: #949494;">"</span> 93… <span style="color: #949494;">"</span> 50.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span> 93.9… <span style="color: #949494;">"</span> 98.9…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">""</span> Amox… <span style="color: #949494;">"</span> 42… <span style="color: #949494;">"</span> 13.1… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span> 10.3… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span> 2.8… <span style="color: #949494;">"</span> 0.4… <span style="color: #949494;">"</span> 54.5…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">""</span> Ampi… <span style="color: #949494;">"</span> 93… <span style="color: #949494;">"</span> 50.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span> 93.9… <span style="color: #949494;">"</span> 98.9…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">""</span> Benz… <span style="color: #949494;">"</span> 77… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span> 80.9… <span style="color: #949494;">"</span> 89.4…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 29 more rows, 2 more variables: `S. hominis` <chr>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `S. pneumoniae` <chr>, and abbreviated variable names ¹`E. coli`,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ²`E. faecalis`, ³`K. pneumoniae`, ⁴`P. aeruginosa`, ⁵`P. mirabilis`,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ⁶`S. aureus`, ⁷`S. epidermidis`</span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># Use FUN to change to transformation of microorganism codes</span></span></span>
|
||
<span class="r-in"><span><span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
|
||
<span class="r-in"><span> FUN <span class="op">=</span> <span class="va">mo_gramstain</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 80 × 6</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> mo ab S I R total</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</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;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Gram-negative PEN 8 0 717 725</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Gram-negative OXA 6 0 0 6</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Gram-negative FLC 6 0 0 6</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Gram-negative AMX 226 0 405 631</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Gram-negative AMC 463 89 174 726</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Gram-negative AMP 226 0 405 631</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Gram-negative TZP 554 11 76 641</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Gram-negative CZO 94 2 110 206</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Gram-negative FEP 470 1 14 485</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Gram-negative CXM 539 22 142 703</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 70 more rows</span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> Use 'format()' on this result to get a publishable/printable format.</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
|
||
<span class="r-in"><span> FUN <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">x</span> <span class="op">==</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> <span class="st">"E. coli"</span>,</span></span>
|
||
<span class="r-in"><span> <span class="st">"Others"</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="op">}</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 80 × 6</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> mo ab S I R total</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</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;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> E. coli PEN 0 0 467 467</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> E. coli OXA 0 0 0 0</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> E. coli FLC 0 0 0 0</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> E. coli AMX 196 0 196 392</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> E. coli AMC 332 74 61 467</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> E. coli AMP 196 0 196 392</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> E. coli TZP 388 5 23 416</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> E. coli CZO 79 1 2 82</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> E. coli FEP 308 0 9 317</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> E. coli CXM 425 15 25 465</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 70 more rows</span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> Use 'format()' on this result to get a publishable/printable format.</span>
|
||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||
</code></pre></div>
|
||
</div>
|
||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||
</nav></aside></div>
|
||
|
||
|
||
<footer><div class="pkgdown-footer-left">
|
||
<p></p><p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
|
||
</div>
|
||
|
||
<div class="pkgdown-footer-right">
|
||
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style="max-width: 150px;"></a></p>
|
||
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|
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|
||
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