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Built site for AMR: 1.8.2.9111@aa48c6b
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@@ -10,7 +10,7 @@
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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="">1.8.2.9103</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</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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@@ -42,6 +42,11 @@
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Conduct AMR Analysis
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</a>
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<a class="dropdown-item" href="../reference/antibiogram.html">
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<span class="fa fa-file-prescription"></span>
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Generate Antibiogram (Trad./Syndromic/WISCA)
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</a>
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<a class="dropdown-item" href="../articles/resistance_predict.html">
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<span class="fa fa-dice"></span>
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@@ -155,7 +160,7 @@
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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> 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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@@ -167,7 +172,7 @@
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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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<dd><p>column name of the names or codes 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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@@ -227,18 +232,31 @@
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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="co">#' # example_isolates is a data set available in the AMR package.</span></span></span>
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<span class="r-in"><span><span class="co"># run ?example_isolates for more info.</span></span></span>
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<span class="r-in"><span><span class="va">example_isolates</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
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<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></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;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows, and 36 more variables: AMC <sir>, AMP <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TZP <sir>, CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CAZ <sir>, CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TMP <sir>, SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MFX <sir>, VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ERY <sir>, CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CHL <sir>, COL <sir>, MUP <sir>, RIF <sir></span></span>
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<span class="r-in"><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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@@ -262,20 +280,20 @@
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<span class="r-in"><span><span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
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<span class="r-in"><span> FUN <span class="op">=</span> <span class="va">mo_gramstain</span></span></span>
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<span class="r-in"><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: 80 × 6</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 120 × 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: #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>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Gram-negative PEN 8 0 717 725</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Gram-negative OXA 6 0 0 6</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Gram-negative FLC 6 0 0 6</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Gram-negative AMC 463 89 174 726</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Gram-negative AMK 251 0 5 256</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Gram-negative AMP 226 0 405 631</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Gram-negative AMX 226 0 405 631</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Gram-negative AMC 463 89 174 726</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Gram-negative AMP 226 0 405 631</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Gram-negative TZP 554 11 76 641</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Gram-negative CZO 94 2 110 206</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Gram-negative FEP 470 1 14 485</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Gram-negative CXM 539 22 142 703</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 70 more rows</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Gram-negative AZM 1 2 696 699</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Gram-negative CAZ 607 0 27 634</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Gram-negative CHL 1 0 30 31</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Gram-negative CIP 610 11 63 684</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Gram-negative CLI 18 1 709 728</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Gram-negative COL 309 0 78 387</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 110 more rows</span></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></span>
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<span class="r-in"><span><span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
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@@ -289,16 +307,16 @@
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 80 × 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: #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>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> E. coli PEN 0 0 467 467</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> E. coli OXA 0 0 0 0</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> E. coli FLC 0 0 0 0</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> E. coli AMC 332 74 61 467</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> E. coli AMK 171 0 0 171</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> E. coli AMP 196 0 196 392</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> E. coli AMX 196 0 196 392</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> E. coli AMC 332 74 61 467</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> E. coli AMP 196 0 196 392</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> E. coli TZP 388 5 23 416</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> E. coli CZO 79 1 2 82</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> E. coli FEP 308 0 9 317</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> E. coli CXM 425 15 25 465</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> E. coli AZM 0 0 467 467</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> E. coli CAZ 449 0 11 460</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> E. coli CHL 0 0 0 0</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> E. coli CIP 398 1 57 456</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> E. coli CLI 0 0 467 467</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> E. coli COL 240 0 0 240</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 70 more rows</span></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="co"># }</span></span></span>
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