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Built site for AMR: 2.0.0.9023@9591688

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2023-05-27 08:53:23 +00:00
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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="">2.0.0.9022</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</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">
@ -89,28 +89,28 @@
</li>
<li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span>
<span class="fa fa-layer-group"></span>
With other pkgs
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span>
<span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse
</a>
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span>
<span class="fa fa-layer-group"></span>
AMR &amp; data.table
</a>
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span>
<span class="fa fa-layer-group"></span>
AMR &amp; tidymodels
</a>
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span>
<span class="fa fa-layer-group"></span>
AMR &amp; base R
</a>
@ -218,30 +218,30 @@
<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 R S I I I R S R S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I I R R I S I I S 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] -0.621059 1.449138 -0.621059 -0.621059 -0.621059 -0.621059 1.449138</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [8] -0.621059 1.449138 -0.621059</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.4743416 -0.4743416 1.8973666 1.8973666 -0.4743416 -0.4743416</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.4743416 -0.4743416 -0.4743416 -0.4743416</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] 0.5 4 1 0.001 32 0.125 0.25 0.125 0.125 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 &gt;=16 0.002 &gt;=16 0.025 &gt;=16 0.002 2 2 2 </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] -0.02261165 0.63329547 0.19602406 -1.98285222 1.28920259 -0.45988306</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.24124735 -0.45988306 -0.45988306 1.50783829</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.6738475 0.8649910 -1.6133339 0.8649910 -0.9168346 0.8649910</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.6133339 0.2915606 0.2915606 0.2915606</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] -0.02261165 0.63329547 0.19602406 -1.98285222 1.28920259 -0.45988306</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.24124735 -0.45988306 -0.45988306 1.50783829</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.6738475 0.8649910 -1.6133339 0.8649910 -0.9168346 0.8649910</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.6133339 0.2915606 0.2915606 0.2915606</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] 12 39 10 7 40 39 30 44 18 39</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 39 15 22 38 19 50 29 46 40 18</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] -1.0909965 0.7733646 -1.2290973 -1.4362486 0.8424150 0.7733646</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.1519109 1.1186167 -0.6766940 0.7733646</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5869812 -1.3167417 -0.7614892 0.5076595 -0.9994545 1.4595209</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.2062367 1.1422338 0.6663030 -1.0787763</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>
@ -252,21 +252,21 @@
<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 27 1 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B I 28 2 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C S 28 &gt;=4 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D S 18 &gt;=4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 19 &gt;=4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F S 30 &gt;=4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 28 1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H S 26 2 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I R 21 &gt;=4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 18 2 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A I 17 8 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B S 31 2 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C R 19 16 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D S 18 8 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 19 16 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F I 31 16 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 24 &lt;=1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H S 24 &lt;=1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I R 22 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 20 2 0.5</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",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.7116852 0.2836947 0.5873608 -0.3661781 -0.1004357 0.2669030</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.2329571 0.1781812 0.3850192 -0.2899029</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.06628516 0.31654289 0.46727798 -0.49122694 -0.05027119 0.77969806</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.42081207 -0.65798290 0.54387830 -0.42081897</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
@ -283,16 +283,16 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and "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 28 &gt;=4 &gt;=4 0.5873608 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 I R 21 &gt;=4 1 0.3850192 0.2023416</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 B I 28 2 &gt;=4 0.2836947 0.3036661</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 F S 30 &gt;=4 1 0.2669030 0.3204579</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 H S 26 2 &gt;=4 0.1781812 0.4091796</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 E S 19 &gt;=4 2 -0.1004357 0.6877965</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 28 1 2 -0.2329571 0.8203179</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 J R 18 2 0.5 -0.2899029 0.8772637</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 D S 18 &gt;=4 1 -0.3661781 0.9535390</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 A S 27 1 0.5 -0.7116852 1.2990461</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C R 19 16 2 0.46727798 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 I R 22 4 4 0.54387830 0.07660032</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 B S 31 2 4 0.31654289 0.15073509</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 F I 31 16 4 0.77969806 0.31242008</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 19 16 2 -0.05027119 0.51754917</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 A I 17 8 4 -0.06628516 0.53356314</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 24 &lt;=1 2 -0.42081207 0.88809005</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 J R 20 2 0.5 -0.42081897 0.88809695</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 D S 18 8 1 -0.49122694 0.95850492</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 H S 24 &lt;=1 1 -0.65798290 1.12526088</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>