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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9147@4416394
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="">1.8.2.9146</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9147</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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@ -32,11 +32,6 @@
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How to
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</a>
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<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
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<a class="dropdown-item" href="../reference/AMR-options.html">
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<span class="fa fa-gear"></span>
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User- Or Team-specific Package Settings
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</a>
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<a class="dropdown-item" href="../articles/AMR.html">
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<span class="fa fa-directions"></span>
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@ -55,7 +50,12 @@
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<a class="dropdown-item" href="../articles/datasets.html">
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<span class="fa fa-database"></span>
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Data Sets for Download / Own Use
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Download Data Sets for Own Use
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</a>
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<a class="dropdown-item" href="../reference/AMR-options.html">
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<span class="fa fa-gear"></span>
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Set User- Or Team-specific Package Settings
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</a>
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<a class="dropdown-item" href="../articles/PCA.html">
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<span class="fa fa-compress"></span>
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@ -201,30 +201,30 @@
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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 R I S S R S I I S</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S S I S R I I S S S</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] -0.4743416 1.8973666 -0.4743416 -0.4743416 -0.4743416 1.8973666</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4743416 -0.4743416 -0.4743416 -0.4743416</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.3162278 -0.3162278 -0.3162278 -0.3162278 2.8460499 -0.3162278</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.3162278 -0.3162278 -0.3162278 -0.3162278</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] 0.25 64 64 0.01 0.025 128 256 4 128 256 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.01 8 0.25 64 0.025 128 1 0.01 128 128 </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] -0.8840919 0.5294878 0.5294878 -1.7046495 -1.4710682 0.7061853</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.8828827 -0.1773020 0.7061853 0.8828827</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.3051841 0.3547377 -0.5058733 0.8711043 -1.0776509 1.0432265</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.1616289 -1.3051841 1.0432265 1.0432265</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] -0.8840919 0.5294878 0.5294878 -1.7046495 -1.4710682 0.7061853</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.8828827 -0.1773020 0.7061853 0.8828827</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.3051841 0.3547377 -0.5058733 0.8711043 -1.0776509 1.0432265</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.1616289 -1.3051841 1.0432265 1.0432265</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] 13 36 18 50 14 40 38 15 45 48</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 17 43 40 10 41 48 32 39 42 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] -1.2438749 0.2860247 -0.9112880 1.2172680 -1.1773575 0.5520942</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.4190595 -1.1108402 0.8846811 1.0842332</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.3988539 0.7280585 0.4826455 -1.9714842 0.5644498 1.1370801</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.1717891 0.4008412 0.6462542 -0.4172021</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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@ -234,22 +234,22 @@
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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 17 <=1 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 20 <=1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 28 >=16 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 22 >=16 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 24 >=16 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 30 >=16 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 17 >=16 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 23 2 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 27 8 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 19 8 0.5</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 17 2 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 23 1 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 18 8 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 25 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 30 8 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 25 1 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 22 0.5 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 18 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 19 4 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 22 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">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",</span>
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<span class="r-msg co"><span class="r-pr">#></span> and "tobr"</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.29633203 -0.33470083 0.68999803 0.04843526 0.30058957 0.64264079</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.40191868 -0.19451042 -0.15234167 -0.10569739</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.30902553 0.37446780 0.09125296 0.28702431 0.82880923 0.01327092</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.34052588 -0.50251321 -0.01669175 -0.42606885</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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@ -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",</span>
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<span class="r-msg co"><span class="r-pr">#></span> and "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 28 >=16 1 0.68999803 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 F R 30 >=16 0.5 0.64264079 0.04735723</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 G R 17 >=16 >=4 0.40191868 0.28807934</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 E I 24 >=16 >=4 0.30058957 0.38940845</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 D R 22 >=16 <=0.25 0.04843526 0.64156276</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 J R 19 8 0.5 -0.10569739 0.79569542</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 I I 27 8 0.5 -0.15234167 0.84233970</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 23 2 >=4 -0.19451042 0.88450845</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 B R 20 <=1 1 -0.33470083 1.02469886</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 A I 17 <=1 <=0.25 -1.29633203 1.98633005</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 18 8 >=8 0.09125296 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 F S 25 1 >=8 0.01327092 0.07798204</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 I S 19 4 >=8 -0.01669175 0.10794471</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 25 2 2 0.28702431 0.19577135</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 B R 23 1 >=8 0.37446780 0.28321484</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 A S 17 2 >=8 -0.30902553 0.40027849</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 22 0.5 >=8 -0.34052588 0.43177884</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 J R 22 0.5 1 -0.42606885 0.51732181</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 H R 18 1 1 -0.50251321 0.59376617</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 E S 30 8 >=8 0.82880923 0.73755627</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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Reference in New Issue
Block a user