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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9083@4801a60
This commit is contained in:
github-actions
@ -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="">1.8.2.9082</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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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@ -191,30 +191,30 @@
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">rsi</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_rsi</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">rsi</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'rsi'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I I I R R I I S R S</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S R I R I R I S R 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">rsi</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.621059 -0.621059 -0.621059 1.449138 1.449138 -0.621059 -0.621059</span>
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<span class="r-out co"><span class="r-pr">#></span> [8] -0.621059 1.449138 -0.621059</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.7745967 1.1618950 -0.7745967 1.1618950 -0.7745967 1.1618950</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.7745967 -0.7745967 1.1618950 -0.7745967</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 'mic'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 64 2 0.25 0.002 0.125 256 8 16 32 0.005</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1 0.025 128 128 0.025 0.125 32 0.01 128 0.0625</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] 0.94601143 0.07985353 -0.43984121 -1.64653502 -0.61307279 1.29247458</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.42631669 0.59954827 0.77277985 -1.41753533</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.02978237 -0.95544246 1.18775017 1.18775017 -0.95544246 -0.55158203</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.83988373 -1.18536967 1.18775017 -0.72551525</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] 0.94601143 0.07985353 -0.43984121 -1.64653502 -0.61307279 1.29247458</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.42631669 0.59954827 0.77277985 -1.41753533</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.02978237 -0.95544246 1.18775017 1.18775017 -0.95544246 -0.55158203</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.83988373 -1.18536967 1.18775017 -0.72551525</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 'disk'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 14 12 9 45 44 22 42 31 47 34</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 45 44 9 49 49 8 6 35 47 46</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] -1.08531752 -1.22098221 -1.42447924 1.01748517 0.94965283 -0.54265876</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.81398814 0.06783234 1.15314986 0.27132938</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.60645473 0.55230698 -1.34286403 0.82304570 0.82304570 -1.39701178</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.50530726 0.06497729 0.71475021 0.66060247</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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@ -224,36 +224,36 @@
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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 S 27 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 26 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 29 16 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 31 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 29 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 23 8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 25 <=0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 23 8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 25 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 25 1 <=1</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 25 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 19 2 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 27 >=8 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 21 2 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 26 >=8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 21 2 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 27 <=1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 25 <=1 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 18 <=1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 27 >=8 8</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" 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> [1] -0.15307753 0.07017847 0.57030268 0.53856269 0.20198126 -0.04314696</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.84354651 0.47440221 -0.34043122 -0.47522509</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.3442580 -0.2743798 0.6961282 0.4613073 0.2926426 -0.1316197</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4012318 -0.7100447 -0.7115465 1.1230024</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "gent" and "tobr"</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</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> 10 J R 25 1 <=1 -1.43145922</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 25 <=0.5 2 -1.13300373</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A S 27 4 2 -0.12677314</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 25 4 2 -0.12677314</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 29 16 <=1 -0.08981844</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 29 8 2 0.20863706</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 26 4 4 0.50709255</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 31 4 4 0.50709255</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 23 8 4 0.84250275</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 23 8 4 0.84250275</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> 8 H S 25 <=1 <=1 -1.3827826</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 27 <=1 2 -1.0506770</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A I 25 2 2 -0.6512093</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 18 <=1 8 -0.3864658</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 19 2 >=16 0.3451075</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 21 2 >=16 0.3451075</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 21 2 >=16 0.3451075</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 26 >=8 4 0.4798318</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 27 >=8 8 0.8119374</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 27 >=8 >=16 1.1440430</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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@ -265,17 +265,17 @@
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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> 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 R 29 16 <=1 0.57030268 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 D I 31 4 4 0.53856269 0.03173999</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 H R 23 8 4 0.47440221 0.09590047</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 E I 29 8 2 0.20198126 0.36832142</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 B I 26 4 4 0.07017847 0.50012421</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 23 8 4 -0.04314696 0.61344964</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 A S 27 4 2 -0.15307753 0.72338021</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 I S 25 4 2 -0.34043122 0.91073389</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 J R 25 1 <=1 -0.47522509 1.04552777</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 G I 25 <=0.5 2 -0.84354651 1.41384919</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 S 27 >=8 >=16 0.6961282 0.0000000</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 2 D R 21 2 >=16 0.4613073 0.2348209</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 3 E S 26 >=8 4 0.2926426 0.4034856</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 4 J R 27 >=8 8 1.1230024 0.4268743</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 5 F I 21 2 >=16 -0.1316197 0.8277479</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 B S 19 2 >=16 -0.2743798 0.9705080</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 A I 25 2 2 -0.3442580 1.0403862</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 8 G I 27 <=1 2 -0.4012318 1.0973600</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 9 H S 25 <=1 <=1 -0.7100447 1.4061728</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 10 I I 18 <=1 8 -0.7115465 1.4076747</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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