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Built site for AMR: 1.8.2.9029@faca6d6
This commit is contained in:
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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="">1.8.2.9027</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9029</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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@ -145,12 +145,12 @@
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<span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</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 rsi</span></span>
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<span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
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<span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
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<span></span>
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<span><span class="co"># S3 method for data.frame</span></span>
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<span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">distance_from_row</span><span class="op">(</span><span class="va">mean_distance</span>, <span class="va">row</span><span class="op">)</span></span></code></pre></div>
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<span><span class="fu">amr_distance_from_row</span><span class="op">(</span><span class="va">amr_distance</span>, <span class="va">row</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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@ -167,7 +167,7 @@
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<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S and I must be merged into one, so the input only consists of S+I vs. R (susceptible vs. resistant), defaults to <code>TRUE</code></p></dd>
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<dt>mean_distance</dt>
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<dt>amr_distance</dt>
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<dd><p>the outcome of <code>mean_amr_distance()</code></p></dd>
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@ -181,7 +181,7 @@
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<p>MIC values (see <code><a href="as.mic.html">as.mic()</a></code>) are transformed with <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2()</a></code> first; their distance is calculated as <code>(log2(x) - mean(log2(x))) / sd(log2(x))</code>.</p>
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<p>R/SI values (see <code><a href="as.rsi.html">as.rsi()</a></code>) are transformed using <code>"S"</code> = 1, <code>"I"</code> = 2, and <code>"R"</code> = 3. If <code>combine_SI</code> is <code>TRUE</code> (default), the <code>"I"</code> will be considered to be 1.</p>
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<p>For data sets, the mean AMR distance will be calculated per variable, after which the mean of all columns will returned per row (using <code><a href="https://rdrr.io/r/base/colSums.html" class="external-link">rowMeans()</a></code>), see <em>Examples</em>.</p>
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<p>Use <code>distance_from_row()</code> to subtract distances from the distance of one row, see <em>Examples</em>.</p>
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<p>Use <code>amr_distance_from_row()</code> to subtract distances from the distance of one row, see <em>Examples</em>.</p>
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</div>
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<div class="section level2">
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<h2 id="interpretation">Interpretation<a class="anchor" aria-label="anchor" href="#interpretation"></a></h2>
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@ -195,10 +195,11 @@
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="va">x</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1 8 0.01 16 16 32 0.125 0.002 0.25 4 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 16 >=128 2 0.25 0.005 0.0625 <=0.001 0.002 <=0.001</span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.002 </span>
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<span class="r-in"><span><span class="fu">mean_amr_distance</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> [1] 0.05443514 0.68021258 -1.33142330 0.88880505 0.88880505 1.09739753</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.57134230 -1.81576003 -0.36274982 0.47162010</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.2790614 1.7616837 0.7964392 0.3138170 -0.5941332 -0.0079312</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.9676713 -0.8067972 -0.9676713 -0.8067972</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="va">y</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
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<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
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@ -208,60 +209,60 @@
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<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</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-in"><span><span class="va">y</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 16 2 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B >=64 <=0.125 0.5 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 1 2 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D >=64 1 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 8 0.25 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F >=64 0.5 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G >=64 <=0.125 2 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 32 1 8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 32 0.5 2 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 2 0.25 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 4 >=2 1 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 >=2 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 1 0.5 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D >=16 <=0.025 <=0.5 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 1 2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 2 <=0.025 2 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.0625 4 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 2 <=0.025 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 1 0.0625 2 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J >=16 0.25 <=0.5 >=16</span>
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<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
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<span class="r-msg co"><span class="r-pr">#></span> "id" and "tobr"</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.293688592 -0.841354186 0.001879471 0.529439629 -0.499298613</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] 0.538022217 -0.488778815 0.930958554 -0.266952843 -0.197604006</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.01137355 0.60662547 -0.07897661 -0.51499446 0.63134780 -0.53682141</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.50648345 -0.41657103 -0.58931443 0.40359478</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
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<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B >=64 <=0.125 0.5 <=1 -0.841354186</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 8 0.25 1 2 -0.499298613</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G >=64 <=0.125 2 <=1 -0.488778815</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 32 0.5 2 <=1 -0.266952843</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 2 0.25 8 2 -0.197604006</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 1 2 1 4 0.001879471</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 16 2 2 2 0.293688592</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D >=64 1 4 2 0.529439629</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F >=64 0.5 8 2 0.538022217</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 32 1 8 4 0.930958554</span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 1 0.0625 2 <=0.5 -0.58931443</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 2 <=0.025 2 <=0.5 -0.53682141</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D >=16 <=0.025 <=0.5 <=0.5 -0.51499446</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 2 <=0.025 2 1 -0.41657103</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 1 0.5 1 8 -0.07897661</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 4 >=2 1 <=0.5 -0.01137355</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J >=16 0.25 <=0.5 >=16 0.40359478</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.0625 4 8 0.50648345</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 >=2 2 4 0.60662547</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 1 2 8 0.63134780</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
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<span class="r-in"><span> <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span></span>
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<span class="r-in"><span> amr_distance <span class="op">=</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">.</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> check_id_C <span class="op">=</span> <span class="fu">distance_from_row</span><span class="op">(</span><span class="va">amr_distance</span>, <span class="va">id</span> <span class="op">==</span> <span class="st">"C"</span><span class="op">)</span></span></span>
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<span class="r-in"><span> check_id_C <span class="op">=</span> <span class="fu">amr_distance_from_row</span><span class="op">(</span><span class="va">amr_distance</span>, <span class="va">id</span> <span class="op">==</span> <span class="st">"C"</span><span class="op">)</span></span></span>
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<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">check_id_C</span><span class="op">)</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-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
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<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 C 1 2 1 4 0.001879471 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 J 2 0.25 8 2 -0.197604006 0.1994835</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 I 32 0.5 2 <=1 -0.266952843 0.2688323</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 A 16 2 2 2 0.293688592 0.2918091</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 G >=64 <=0.125 2 <=1 -0.488778815 0.4906583</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 E 8 0.25 1 2 -0.499298613 0.5011781</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D >=64 1 4 2 0.529439629 0.5275602</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 F >=64 0.5 8 2 0.538022217 0.5361427</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 B >=64 <=0.125 0.5 <=1 -0.841354186 0.8432337</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 H 32 1 8 4 0.930958554 0.9290791</span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 C 1 0.5 1 8 -0.07897661 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 A 4 >=2 1 <=0.5 -0.01137355 0.06760306</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 3 H 2 <=0.025 2 1 -0.41657103 0.33759442</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 4 D >=16 <=0.025 <=0.5 <=0.5 -0.51499446 0.43601785</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 5 F 2 <=0.025 2 <=0.5 -0.53682141 0.45784481</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 6 J >=16 0.25 <=0.5 >=16 0.40359478 0.48257139</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 I 1 0.0625 2 <=0.5 -0.58931443 0.51033782</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 G 4 0.0625 4 8 0.50648345 0.58546006</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 B 4 >=2 2 4 0.60662547 0.68560208</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 E 4 1 2 8 0.63134780 0.71032441</span>
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<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
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<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
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<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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