mirror of
https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9111@aa48c6b
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="">1.8.2.9103</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</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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@ -42,6 +42,11 @@
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Conduct AMR Analysis
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</a>
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<a class="dropdown-item" href="../reference/antibiogram.html">
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<span class="fa fa-file-prescription"></span>
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Generate Antibiogram (Trad./Syndromic/WISCA)
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</a>
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<a class="dropdown-item" href="../articles/resistance_predict.html">
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<span class="fa fa-dice"></span>
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@ -196,31 +201,31 @@
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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] S I R I S R R I R S</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] R S R R S R I S I 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] -0.7745967 -0.7745967 1.1618950 -0.7745967 -0.7745967 1.1618950</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.1618950 -0.7745967 1.1618950 -0.7745967</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 'mic'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5 0.005 4 0.005 4 16 8 >=128 <=0.002</span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.125 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] <=0.001 8 2 <=0.001 16 <=0.001 0.25 128 0.125 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] <=0.001</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] 0.004555148 -1.189296722 0.543632982 -1.189296722 0.543632982</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] 0.903018205 0.723325594 1.442096040 -1.426837433 -0.354830075</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.052079574 0.902371938 0.600893605 -1.052079574 1.053111104</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] -1.052079574 0.148676107 1.505328602 -0.002063059 -1.052079574</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] 0.004555148 -1.189296722 0.543632982 -1.189296722 0.543632982</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] 0.903018205 0.723325594 1.442096040 -1.426837433 -0.354830075</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.052079574 0.902371938 0.600893605 -1.052079574 1.053111104</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] -1.052079574 0.148676107 1.505328602 -0.002063059 -1.052079574</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] 8 32 43 15 44 37 16 14 29 29</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 38 7 36 29 48 15 25 50 50 39</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] -1.4621577 0.4144083 1.2745011 -0.9148259 1.3526913 0.8053596</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.8366357 -0.9930162 0.1798376 0.1798376</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.2922699 -1.8147922 0.1563304 -0.3194578 0.9719673 -1.2710342</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.5913368 1.1079068 1.1079068 0.3602396</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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@ -230,36 +235,26 @@
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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 I 25 16 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 30 16 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 28 0.5 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 26 16 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 26 8 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 21 16 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 19 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 27 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 19 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 28 8 4</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 26 <=0.5 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 20 >=16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 22 1 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 25 >=16 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 18 >=16 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 18 <=0.5 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 19 2 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 21 8 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 25 1 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 25 <=0.5 <=0.25</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] -0.19598774 0.12451337 -0.09209741 -0.13188752 -0.14956959 0.06516053</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.63363528 0.05123363 0.05598101 0.90628900</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "gent" and "tobr"</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.08308833 0.31310698 0.30459906 1.01959980 -0.15475222 -0.87382971</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.56840820 -0.02905708 0.38884763 -0.31701792</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">$</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="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>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</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">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 28 0.5 8 -0.27108669</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 19 2 2 -0.20035843</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 26 8 0.5 -0.12963016</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A I 25 16 0.25 -0.09426603</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 30 16 0.25 -0.09426603</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 26 16 0.25 -0.09426603</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 21 16 0.25 -0.09426603</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 27 8 1 0.14377582</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 19 8 1 0.14377582</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 28 8 4 0.69058778</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in order(y$amr_distance):</span> argument 1 is not a vector</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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@ -271,17 +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 I 28 0.5 8 -0.09209741 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 D I 26 16 0.25 -0.13188752 0.03979011</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 E S 26 8 0.5 -0.14956959 0.05747218</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 A I 25 16 0.25 -0.19598774 0.10389034</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 H I 27 8 1 0.05123363 0.14333103</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 I R 19 8 1 0.05598101 0.14807842</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 F R 21 16 0.25 0.06516053 0.15725794</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 B I 30 16 0.25 0.12451337 0.21661078</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 G S 19 2 2 -0.63363528 0.54153787</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 28 8 4 0.90628900 0.99838641</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 22 1 0.5 0.30459906 0.000000000</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 2 B I 20 >=16 2 0.31310698 0.008507921</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 3 I R 25 1 <=0.25 0.38884763 0.084248568</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 4 H S 21 8 0.5 -0.02905708 0.333656139</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 5 A S 26 <=0.5 0.5 -0.08308833 0.387687383</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 6 E I 18 >=16 0.5 -0.15475222 0.459351276</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 7 J S 25 <=0.5 <=0.25 -0.31701792 0.621616981</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 D S 25 >=16 >=8 1.01959980 0.715000742</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 G S 19 2 <=0.25 -0.56840820 0.873007255</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 10 F S 18 <=0.5 <=0.25 -0.87382971 1.178428772</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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