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Built site for AMR@3.0.1.9065: 39b6a25
This commit is contained in:
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@@ -7,7 +7,7 @@
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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="">3.0.1.9063</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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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@@ -110,31 +110,31 @@
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op"><-</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>
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<span class="r-in"><span><span class="va">sir</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class <span style="color: #0000BB;"><sir></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S S I S I S I S I R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S R I R R R R I I I</span>
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<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>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.3162278 -0.3162278 -0.3162278 -0.3162278 -0.3162278 -0.3162278</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.3162278 -0.3162278 -0.3162278 2.8460499</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.9486833 0.9486833 -0.9486833 0.9486833 0.9486833 0.9486833</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.9486833 -0.9486833 -0.9486833 -0.9486833</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="va">mic</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">mic</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class <span style="color: #0000BB;"><mic></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] <=0.0001 0.0002 0.5 0.0005 0.004 0.001 0.016 0.0002 </span>
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<span class="r-out co"><span class="r-pr">#></span> [9] 0.032 1 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.032 0.064 0.125 0.5 0.016 0.008 <=0.0005 0.032 </span>
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<span class="r-out co"><span class="r-pr">#></span> [9] 0.5 1 </span>
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<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>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.13933320 -0.92906618 1.44436742 -0.65110831 -0.02030726 -0.44084129</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.40022677 -0.92906618 0.61049379 1.65463443</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.20876566 0.09541835 0.38919449 0.99756251 -0.51294967 -0.81713368</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -2.03386972 -0.20876566 0.99756251 1.30174652</span>
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<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
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<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>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.13933320 -0.92906618 1.44436742 -0.65110831 -0.02030726 -0.44084129</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.40022677 -0.92906618 0.61049379 1.65463443</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.20876566 0.09541835 0.38919449 0.99756251 -0.51294967 -0.81713368</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -2.03386972 -0.20876566 0.99756251 1.30174652</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="va">disk</span> <span class="op"><-</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>
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<span class="r-in"><span><span class="va">disk</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class <span style="color: #0000BB;"><disk></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 49 30 42 50 16 27 12 13 28 32</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 48 45 48 40 44 9 39 49 39 29</span>
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<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>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.37726856 0.00721083 0.87251045 1.44937686 -1.00230539 -0.20911407</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.29073860 -1.21863029 -0.13700577 0.15142743</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.74202711 0.49468474 0.74202711 0.08244746 0.41223728 -2.47342369</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.00000000 0.82447456 0.00000000 -0.82447456</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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@@ -145,35 +145,35 @@
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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 I 32 4 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 32 4 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 30 8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 16 4 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 33 4 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 32 4 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 29 8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 31 8 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 30 4 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 20 8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A R 26 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 28 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 31 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 30 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 32 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 28 32 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 33 <=2 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 24 <=2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 20 <=2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 19 16 2</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> <span style="color: #00BBBB;">ℹ</span> Calculating mean AMR distance based on columns <span style="color: #0000BB;">"amox"</span>, <span style="color: #0000BB;">"cipr"</span>, <span style="color: #0000BB;">"gent"</span>, and</span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">"tobr"</span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.351732344 0.165816825 0.045278388 -1.048629829 0.209372918</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] 0.165816825 0.001722296 0.606383651 0.078704640 0.127266630</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.31430391 0.09942875 0.25436185 0.26948082 0.08306514 0.24576214</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.26823618 -0.44796371 -1.15734233 0.07066724</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="as.mic.html">is.mic</a></span><span class="op">(</span><span class="va">y</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Calculating mean AMR distance based on columns <span style="color: #0000BB;">"gent"</span> and <span style="color: #0000BB;">"tobr"</span></span>
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<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</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> 1 A I 32 4 8 -0.6978278</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 32 4 8 -0.6978278</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 16 4 8 -0.6978278</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 32 4 8 -0.6978278</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 30 8 8 0.2704180</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 29 8 8 0.2704180</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 20 8 8 0.2704180</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 33 4 16 0.3372705</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 30 4 16 0.3372705</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 31 8 16 1.3055163</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 20 <=2 1 -1.1069930</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 28 8 1 -0.3684440</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 31 8 1 -0.3684440</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 30 4 2 -0.2349174</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 24 <=2 4 -0.1013907</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 32 8 2 0.1343571</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A R 26 4 4 0.2678838</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 33 <=2 >=8 0.4014105</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 19 16 2 0.5036316</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 28 32 2 0.8729061</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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@@ -185,17 +185,17 @@
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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> <span style="color: #00BBBB;">ℹ</span> Calculating mean AMR distance based on columns <span style="color: #0000BB;">"amox"</span>, <span style="color: #0000BB;">"cipr"</span>, <span style="color: #0000BB;">"gent"</span>, and</span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">"tobr"</span></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 I 30 8 8 0.045278388 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 I I 30 4 16 0.078704640 0.03342625</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 G I 29 8 8 0.001722296 0.04355609</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 J R 20 8 8 0.127266630 0.08198824</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 B R 32 4 8 0.165816825 0.12053844</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 32 4 8 0.165816825 0.12053844</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 E S 33 4 16 0.209372918 0.16409453</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 A I 32 4 8 -0.351732344 0.39701073</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 9 H I 31 8 16 0.606383651 0.56110526</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 10 D S 16 4 8 -1.048629829 1.09390822</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 R 31 8 1 0.25436185 0.000000000</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 2 F S 28 32 2 0.24576214 0.008599711</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 3 G S 33 <=2 >=8 0.26823618 0.013874329</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D R 30 4 2 0.26948082 0.015118966</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 A R 26 4 4 0.31430391 0.059942062</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 6 B R 28 8 1 0.09942875 0.154933106</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 7 E I 32 8 2 0.08306514 0.171296709</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 8 J R 19 16 2 0.07066724 0.183694618</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 H I 24 <=2 4 -0.44796371 0.702325561</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 I S 20 <=2 1 -1.15734233 1.411704178</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>
|
||||
<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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@@ -231,7 +231,7 @@
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<footer><div class="pkgdown-footer-left">
|
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
|
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</div>
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<div class="pkgdown-footer-right">
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