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Built site for AMR: 2.0.0.9020@c6135d2
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@ -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="">2.0.0.9019</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9020</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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@ -89,28 +89,28 @@
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</li>
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<li class="nav-item dropdown">
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<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
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<span class="fa fa-circles-overlap"></span>
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<span class="fa fa-layer-plus"></span>
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With other pkgs
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</a>
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<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
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<a class="dropdown-item" href="../articles/other_pkg.html">
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<span class="fa fa-circles-overlap"></span>
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<span class="fa fa-layer-plus"></span>
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AMR & dplyr/tidyverse
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</a>
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<a class="dropdown-item" href="../articles/other_pkg.html">
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<span class="fa fa-circles-overlap"></span>
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<span class="fa fa-layer-plus"></span>
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AMR & data.table
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</a>
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<a class="dropdown-item" href="../articles/other_pkg.html">
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<span class="fa fa-circles-overlap"></span>
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<span class="fa fa-layer-plus"></span>
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AMR & tidymodels
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</a>
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<a class="dropdown-item" href="../articles/other_pkg.html">
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<span class="fa fa-circles-overlap"></span>
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<span class="fa fa-layer-plus"></span>
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AMR & base R
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</a>
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@ -218,30 +218,30 @@
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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] I I I I R R S S R R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I I S I S I I R 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] -0.7745967 -0.7745967 -0.7745967 -0.7745967 1.1618950 1.1618950</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.7745967 -0.7745967 1.1618950 1.1618950</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.4743416 -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 1.8973666 -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] 0.0625 0.005 128 128 32 1 >=256 128 8 0.125 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] >=256 1 0.125 0.001 0.002 16 16 2 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">mic</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.1210573 -1.7761606 0.8565554 0.8565554 0.4969895 -0.4019254</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.0363384 0.8565554 0.1374235 -0.9412743</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.35903204 -0.01839609 -0.53493164 -1.73429005 -1.56211153 0.67031797</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.67031797 0.15378242 0.49813946 0.49813946</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] -1.1210573 -1.7761606 0.8565554 0.8565554 0.4969895 -0.4019254</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.0363384 0.8565554 0.1374235 -0.9412743</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.35903204 -0.01839609 -0.53493164 -1.73429005 -1.56211153 0.67031797</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.67031797 0.15378242 0.49813946 0.49813946</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] 48 32 44 24 22 48 50 41 43 36</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 50 49 49 14 39 45 24 24 8 41</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] 0.9202045 -0.6801512 0.5201156 -1.4803290 -1.6803735 0.9202045</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.1202490 0.2200489 0.4200934 -0.2800622</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.0096747 0.9453642 0.9453642 -1.3055030 0.3022593 0.6881223</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.6623981 -0.6623981 -1.6913659 0.4308803</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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@ -251,22 +251,22 @@
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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 S 21 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 25 0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 25 >=16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 25 8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 21 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 29 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 17 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 20 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 17 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 29 4 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 R 17 4 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 19 <=0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 27 4 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 30 >=8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 22 >=8 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 30 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 25 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 17 <=0.5 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 20 >=8 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 20 4 <=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] -0.22695748 0.32206771 1.00220170 0.54530143 -0.77106467 0.09331917</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.04702882 -0.55604901 -0.99921640 0.63742636</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.19666410 -0.75540530 0.42065543 0.40679865 0.32292908 -0.05152683</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.21552084 -0.53867305 0.74027765 -0.56391237</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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@ -282,17 +282,17 @@
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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 25 >=16 2 1.00220170 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 J I 29 4 4 0.63742636 0.3647753</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 D I 25 8 4 0.54530143 0.4569003</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 B R 25 0.5 2 0.32206771 0.6801340</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 F I 29 4 1 0.09331917 0.9088825</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 G S 17 4 4 -0.04702882 1.0492305</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 A S 21 8 1 -0.22695748 1.2291592</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 20 2 1 -0.55604901 1.5582507</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 E S 21 0.5 1 -0.77106467 1.7732664</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 I S 17 0.5 1 -0.99921640 2.0014181</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 4 >=4 0.42065543 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 D I 30 >=8 2 0.40679865 0.01385678</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 E S 22 >=8 >=4 0.32292908 0.09772635</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 G R 25 1 2 0.21552084 0.20513459</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I R 20 >=8 >=4 0.74027765 0.31962222</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 30 1 2 -0.05152683 0.47218226</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 A R 17 4 <=1 -0.19666410 0.61731953</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 17 <=0.5 >=4 -0.53867305 0.95932848</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 J S 20 4 <=1 -0.56391237 0.98456780</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 B S 19 <=0.5 2 -0.75540530 1.17606073</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