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@@ -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="">3.0.1.9018</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</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">
@@ -127,7 +127,7 @@
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<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", "SDD", "I", "R", and "total".</p>
<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", "SDD", "I", "R", "WT, "NWT", and "total".</p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -163,30 +163,30 @@
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
<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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 6 × 8</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab S SDD I R NI total</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> (unknown species) AMC 15 0 0 0 0 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> (unknown species) AMK 0 0 0 0 0 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> (unknown species) AMP 15 0 0 1 0 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> (unknown species) AMX 15 0 0 1 0 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> (unknown species) AZM 3 0 0 3 0 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> (unknown species) CAZ 0 0 0 0 0 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 6 × 11</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab S SDD I R NI WT NWT NS total</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> (unknown species) AMC 15 0 0 0 0 0 0 0 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> (unknown species) AMK 0 0 0 0 0 0 0 0 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> (unknown species) AMP 15 0 0 1 0 0 0 0 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> (unknown species) AMX 15 0 0 1 0 0 0 0 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> (unknown species) AZM 3 0 0 3 0 0 0 0 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> (unknown species) CAZ 0 0 0 0 0 0 0 0 0</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Use 'format()' on this result to get a publishable/printable format.</span></span>
<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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 39 × 12</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Group Drug CoNS `E. coli` `E. faecalis` `K. pneumoniae` `P. aeruginosa`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</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% (39/… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</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% (39/… <span style="color: #949494;">"</span> 10.3% (6/58)<span style="color: #949494;">"</span> <span style="color: #949494;">"</span> 0.0% (0/30)<span style="color: #949494;">"</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">""</span> Gent… <span style="color: #949494;">"</span> 16… <span style="color: #949494;">"</span> 2.0% … <span style="color: #949494;">"</span>100.0% (39/… <span style="color: #949494;">"</span> 10.3% (6/58)<span style="color: #949494;">"</span> <span style="color: #949494;">"</span> 10.0% (3/30)<span style="color: #949494;">"</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</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% (39/… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0% (30/30…</span>
<span class="r-out co"><span class="r-pr">#&gt;</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% (39/… <span style="color: #949494;">"</span> 10.3% (6/58)<span style="color: #949494;">"</span> <span style="color: #949494;">"</span> 0.0% (0/30)<span style="color: #949494;">"</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">"</span>Aminope… 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% (58/58… <span style="color: #949494;">"</span>100.0% (30/30…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</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% (6/58)<span style="color: #949494;">"</span> <span style="color: #949494;">"</span>100.0% (30/30…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">""</span> Amox… <span style="color: #949494;">"</span> 42… <span style="color: #949494;">"</span> 28.9% … <span style="color: #949494;">""</span> <span style="color: #949494;">"</span> 15.5% (9/58)<span style="color: #949494;">"</span> <span style="color: #949494;">"</span>100.0% (30/30…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</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% (58/58… <span style="color: #949494;">"</span>100.0% (30/30…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">"</span>Carbape… Imip… <span style="color: #949494;">"</span> 47… <span style="color: #949494;">"</span> 0.0% … <span style="color: #949494;">"</span> 0.0% (0/3… <span style="color: #949494;">"</span> 0.0% (0/51)<span style="color: #949494;">"</span> <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">""</span> Mero… <span style="color: #949494;">"</span> 47… <span style="color: #949494;">"</span> 0.0% … <span style="color: #949494;">""</span> <span style="color: #949494;">"</span> 0.0% (0/53)<span style="color: #949494;">"</span> <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">"</span>Cephalo… Cefa… <span style="color: #949494;">"</span> 47… <span style="color: #949494;">"</span> 2.4% … <span style="color: #949494;">"</span>100.0% (39/… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0% (30/30…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">"</span>Cephalo… Cefa… <span style="color: #949494;">"</span> 47… <span style="color: #949494;">"</span> 3.7% … <span style="color: #949494;">"</span>100.0% (39/… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0% (30/30…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 29 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 5 more variables: `P. mirabilis` &lt;chr&gt;, `S. aureus` &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># `S. epidermidis` &lt;chr&gt;, `S. hominis` &lt;chr&gt;, `S. pneumoniae` &lt;chr&gt;</span></span>
@@ -195,19 +195,19 @@
<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">#&gt;</span> <span style="color: #949494;"># A tibble: 80 × 8</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab S SDD I R NI total</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Gram-negative AMC 463 0 89 174 0 726</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Gram-negative AMK 251 0 0 5 0 256</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Gram-negative AMP 226 0 0 405 0 631</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Gram-negative AMX 226 0 0 405 0 631</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Gram-negative AZM 1 0 2 696 0 699</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Gram-negative CAZ 607 0 0 27 0 634</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Gram-negative CHL 1 0 0 30 0 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Gram-negative CIP 610 0 11 63 0 684</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Gram-negative CLI 18 0 1 709 0 728</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Gram-negative COL 309 0 0 78 0 387</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 80 × 11</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab S SDD I R NI WT NWT NS total</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Gram-negative AMC 463 0 89 174 0 0 0 0 726</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Gram-negative AMK 251 0 0 5 0 0 0 0 256</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Gram-negative AMP 226 0 0 405 0 0 0 0 631</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Gram-negative AMX 226 0 0 405 0 0 0 0 631</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Gram-negative AZM 1 0 2 696 0 0 0 0 699</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Gram-negative CAZ 607 0 0 27 0 0 0 0 634</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Gram-negative CHL 1 0 0 30 0 0 0 0 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Gram-negative CIP 610 0 11 63 0 0 0 0 684</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Gram-negative CLI 18 0 1 709 0 0 0 0 728</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Gram-negative COL 309 0 0 78 0 0 0 0 387</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 70 more rows</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Use 'format()' on this result to get a publishable/printable format.</span></span>
<span class="r-in"><span></span></span>
@@ -219,19 +219,19 @@
<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">#&gt;</span> <span style="color: #949494;"># A tibble: 80 × 8</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab S SDD I R NI total</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> E. coli AMC 332 0 74 61 0 467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> E. coli AMK 171 0 0 0 0 171</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E. coli AMP 196 0 0 196 0 392</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> E. coli AMX 196 0 0 196 0 392</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> E. coli AZM 0 0 0 467 0 467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> E. coli CAZ 449 0 0 11 0 460</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> E. coli CHL 0 0 0 0 0 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> E. coli CIP 398 0 1 57 0 456</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> E. coli CLI 0 0 0 467 0 467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> E. coli COL 240 0 0 0 0 240</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 80 × 11</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab S SDD I R NI WT NWT NS total</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> E. coli AMC 332 0 74 61 0 0 0 0 467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> E. coli AMK 171 0 0 0 0 0 0 0 171</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E. coli AMP 196 0 0 196 0 0 0 0 392</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> E. coli AMX 196 0 0 196 0 0 0 0 392</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> E. coli AZM 0 0 0 467 0 0 0 0 467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> E. coli CAZ 449 0 0 11 0 0 0 0 460</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> E. coli CHL 0 0 0 0 0 0 0 0 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> E. coli CIP 398 0 1 57 0 0 0 0 456</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> E. coli CLI 0 0 0 467 0 0 0 0 467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> E. coli COL 240 0 0 0 0 0 0 0 240</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 70 more rows</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Use 'format()' on this result to get a publishable/printable format.</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>