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Built site for AMR: 1.8.2.9099@eef0006

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2023-01-23 19:14:37 +00:00
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commit 59c39dc5d1
99 changed files with 1788 additions and 1376 deletions
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reference/mean_amr_distance.html
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@@ -10,7 +10,7 @@
<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="">1.8.2.9098</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9099</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">
@@ -32,60 +32,65 @@
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
Conduct AMR analysis
Conduct AMR Analysis
</a>
<a class="dropdown-item" href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
Predict Antimicrobial Resistance
</a>
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data sets for download / own use
Data Sets for Download / Own Use
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
Conduct Principal Component Analysis for AMR
</a>
<a class="dropdown-item" href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
Determine Multi-Drug Resistance (MDR)
</a>
<a class="dropdown-item" href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
Work with WHONET data
Work with WHONET Data
</a>
<a class="dropdown-item" href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
Import Data From SPSS/SAS/Stata
</a>
<a class="dropdown-item" href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
Apply Eucast Rules
</a>
<a class="dropdown-item" href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
Get taxonomy of a microorganism
Get Taxonomy of a Microorganism
</a>
<a class="dropdown-item" href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antibiotic drug
Get Properties of an Antibiotic Drug
</a>
<a class="dropdown-item" href="../reference/av_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antiviral drug
Get Properties of an Antiviral Drug
</a>
</div>
</li>
@@ -191,31 +196,30 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">sir</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S I S R R R S R R R</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R R R I S S R I R S</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.1618950 -1.1618950 -1.1618950 0.7745967 0.7745967 0.7745967</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.1618950 0.7745967 0.7745967 0.7745967</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.9486833 0.9486833 0.9486833 -0.9486833 -0.9486833 -0.9486833</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.9486833 -0.9486833 0.9486833 -0.9486833</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">mic</span> <span class="op">&lt;-</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>
<span class="r-in"><span><span class="va">mic</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.125 0.0625 0.25 64 0.0625 32 &lt;=0.001 0.01 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &gt;=128 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 8 8 0.25 32 0.25 &lt;=0.01 &gt;=256 128 0.0625</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.3704641 -0.5436561 -0.1972720 1.1882645 -0.5436561 1.0150725</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.5768826 -1.0015510 0.6686883 1.3614566</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.2344009 0.3848258 0.3848258 -0.6472187 0.7976436 -0.6472187</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.6057520 1.4168703 1.2104614 -1.0600365</span>
<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.3704641 -0.5436561 -0.1972720 1.1882645 -0.5436561 1.0150725</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.5768826 -1.0015510 0.6686883 1.3614566</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.2344009 0.3848258 0.3848258 -0.6472187 0.7976436 -0.6472187</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.6057520 1.4168703 1.2104614 -1.0600365</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">disk</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">disk</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 37 48 42 45 41 36 45 11 9 26</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 35 32 25 11 24 50 37 25 45 42</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.2132007 0.9949367 0.5685352 0.7817360 0.4974683 0.1421338</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.7817360 -1.6345388 -1.7766726 -0.5685352</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.20559684 -0.05139921 -0.65105665 -1.85037152 -0.73672199 1.49057706</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.37692753 -0.65105665 1.06225032 0.80525427</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</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>
<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>
@@ -226,35 +230,35 @@
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A S 26 &gt;=8 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B S 17 2 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C S 22 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D I 21 4 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 18 &gt;=8 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F R 26 &lt;=1 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G S 17 2 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H I 31 &lt;=1 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I R 21 2 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 20 &gt;=8 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A S 23 4 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B R 18 8 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C I 23 16 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D R 27 4 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E R 27 8 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F S 29 4 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G R 23 8 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H R 26 1 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I I 26 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 31 2 &lt;=1</span>
<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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.21379008 -0.70858534 0.29772954 -0.27497563 -0.22745796 0.09238219</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.70858534 0.36816222 0.54713702 0.40040322</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.21933074 -0.41717151 0.19830380 0.53628817 0.74510544 0.05006051</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.19790396 -0.50063133 -0.63808424 0.04755593</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "gent" and "tobr"</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F R 26 &lt;=1 &lt;=1 -0.99208370</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B S 17 2 &lt;=1 -0.56611233</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G S 17 2 &lt;=1 -0.56611233</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D I 21 4 &lt;=1 -0.14014095</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H I 31 &lt;=1 4 0.04301464</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A S 26 &gt;=8 &lt;=1 0.28583042</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 18 &gt;=8 &lt;=1 0.28583042</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 20 &gt;=8 &lt;=1 0.28583042</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I R 21 2 4 0.46898601</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C S 22 4 4 0.89495739</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H R 26 1 &lt;=1 -1.4835846</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 31 2 &lt;=1 -1.0659501</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I I 26 2 2 -0.7902446</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B R 18 8 &lt;=1 -0.2306810</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F S 29 4 8 0.1788009</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G R 23 8 4 0.3207300</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A S 23 4 &gt;=16 0.4545064</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D R 27 4 &gt;=16 0.4545064</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E R 27 8 &gt;=16 0.8721410</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C I 23 16 &gt;=16 1.2897755</span>
<span class="r-in"><span></span></span>
<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>
<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">%&gt;%</a></span></span></span>
@@ -266,17 +270,17 @@
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C S 22 4 4 0.29772954 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 H I 31 &lt;=1 4 0.36816222 0.07043268</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 A S 26 &gt;=8 &lt;=1 0.21379008 0.08393946</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 J R 20 &gt;=8 &lt;=1 0.40040322 0.10267368</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 F R 26 &lt;=1 &lt;=1 0.09238219 0.20534735</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 I R 21 2 4 0.54713702 0.24940748</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 E S 18 &gt;=8 &lt;=1 -0.22745796 0.52518750</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 D I 21 4 &lt;=1 -0.27497563 0.57270518</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 B S 17 2 &lt;=1 -0.70858534 1.00631489</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 G S 17 2 &lt;=1 -0.70858534 1.00631489</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C I 23 16 &gt;=16 0.19830380 0.0000000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 G R 23 8 4 0.19790396 0.0003998324</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 F S 29 4 8 0.05006051 0.1482432883</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 J R 31 2 &lt;=1 0.04755593 0.1507478663</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 D R 27 4 &gt;=16 0.53628817 0.3379843756</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 A S 23 4 &gt;=16 -0.21933074 0.4176345348</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 E R 27 8 &gt;=16 0.74510544 0.5468016429</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 B R 18 8 &lt;=1 -0.41717151 0.6154753058</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 H R 26 1 &lt;=1 -0.50063133 0.6989351238</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 I I 26 2 2 -0.63808424 0.8363880331</span>
<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>
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
<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">%&gt;%</a></span></span></span>