mirror of
https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9096@af139a3
This commit is contained in:
github-actions
@ -191,31 +191,31 @@
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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 'sir'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] R I S S I R S R R I</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] R I S S S S S I S R</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] 1.1618950 -0.7745967 -0.7745967 -0.7745967 -0.7745967 1.1618950</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.7745967 1.1618950 1.1618950 -0.7745967</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.8973666 -0.4743416 -0.4743416 -0.4743416 -0.4743416 -0.4743416</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4743416 -0.4743416 -0.4743416 1.8973666</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] 8 4 <=0.0625 256 32 1 <=0.0625 256 </span>
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<span class="r-out co"><span class="r-pr">#></span> [9] 64 0.5 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.005 <=0.002 0.005 0.005 <=0.002 2 64 256 0.025 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 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">mic</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.15561961 -0.06669412 -1.40057649 1.26718825 0.60024707 -0.51132157</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.40057649 1.26718825 0.82256079 -0.73363530</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.7319933 -0.9284550 -0.7319933 -0.7319933 -0.9284550 0.5526353</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.2957230 1.5929580 -0.3869141 0.9984879</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] 0.15561961 -0.06669412 -1.40057649 1.26718825 0.60024707 -0.51132157</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.40057649 1.26718825 0.82256079 -0.73363530</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.7319933 -0.9284550 -0.7319933 -0.7319933 -0.9284550 0.5526353</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.2957230 1.5929580 -0.3869141 0.9984879</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] 47 26 16 48 35 11 26 27 44 49</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 43 18 9 46 21 44 15 7 12 40</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] 1.0232507 -0.5007397 -1.2264494 1.0958217 0.1523990 -1.5893042</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.5007397 -0.4281687 0.8055378 1.1683926</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.1037355 -0.4730295 -1.0406649 1.2929473 -0.2838177 1.1668061</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.6622413 -1.1668061 -0.8514531 0.9145237</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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@ -225,36 +225,36 @@
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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 R 22 2 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 26 1 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 17 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 17 2 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 19 0.5 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 23 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 21 <=0.25 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 26 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 19 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 18 1 >=8</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 R 19 <=1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 19 >=4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 19 2 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 27 >=4 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 24 <=1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 30 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 31 <=1 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 18 2 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 27 <=1 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 22 2 >=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] 0.42479243 0.60367076 -0.35088351 -0.39086870 -0.15337200 -0.05446405</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.41325021 0.41799269 -0.09780504 0.01418764</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.10395052 0.01413264 -0.56431322 0.81427297 0.35886977 0.25802215</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.13868335 -0.61529708 -0.47337526 0.24242087</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> 5 E R 19 0.5 0.5 -0.99015989</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 21 <=0.25 4 -0.61880376</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A R 22 2 <=0.25 -0.27594337</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 23 1 1 -0.19597299</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 17 2 0.5 0.01544239</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 17 1 2 0.09541277</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 26 2 1 0.30682815</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 19 2 1 0.30682815</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 26 1 >=8 0.67818428</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 18 1 >=8 0.67818428</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 I 27 <=1 0.25 -1.0562699</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 31 <=1 0.5 -0.7947569</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 19 2 0.25 -0.4224042</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 18 2 0.25 -0.4224042</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A R 19 <=1 2 -0.2717308</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 24 <=1 2 -0.2717308</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 30 2 1 0.1006218</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 19 >=4 1 0.7344875</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 22 2 >=8 0.8851609</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 27 >=4 >=8 1.5190266</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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@ -266,17 +266,17 @@
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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 S 17 1 2 -0.35088351 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 D I 17 2 0.5 -0.39086870 0.03998519</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 G S 21 <=0.25 4 -0.41325021 0.06236670</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 E R 19 0.5 0.5 -0.15337200 0.19751151</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I I 19 2 1 -0.09780504 0.25307847</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 23 1 1 -0.05446405 0.29641946</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 J S 18 1 >=8 0.01418764 0.36507115</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 26 2 1 0.41799269 0.76887620</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 A R 22 2 <=0.25 0.42479243 0.77567594</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 B S 26 1 >=8 0.60367076 0.95455427</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 19 2 0.25 -0.56431322 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 H I 18 2 0.25 -0.61529708 0.05098385</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 I I 27 <=1 0.25 -0.47337526 0.09093796</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 G I 31 <=1 0.5 -0.13868335 0.42562987</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 5 B S 19 >=4 1 0.01413264 0.57844586</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 A R 19 <=1 2 0.10395052 0.66826374</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 J S 22 2 >=8 0.24242087 0.80673409</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 F S 30 2 1 0.25802215 0.82233538</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 E R 24 <=1 2 0.35886977 0.92318299</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 D I 27 >=4 >=8 0.81427297 1.37858619</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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