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2023-05-24 14:03:18 +00:00
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reference/mean_amr_distance.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9019</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -18,14 +18,7 @@
</button>
<div id="navbar" class="collapse navbar-collapse ms-3">
<ul class="navbar-nav me-auto"><li class="nav-item">
<a class="nav-link" href="../index.html">
<span class="fa fa-home"></span>
Home
</a>
</li>
<li class="nav-item dropdown">
<ul class="navbar-nav me-auto"><li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--how-to">
<span class="fa fa-question-circle"></span>
@ -72,11 +65,6 @@
Work with WHONET Data
</a>
<a class="dropdown-item" href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
Import Data From SPSS/SAS/Stata
</a>
<a class="dropdown-item" href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
@ -99,6 +87,35 @@
</a>
</div>
</li>
<li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-circles-overlap"></span>
With other pkgs
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-circles-overlap"></span>
AMR &amp; dplyr/tidyverse
</a>
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-circles-overlap"></span>
AMR &amp; data.table
</a>
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-circles-overlap"></span>
AMR &amp; tidymodels
</a>
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-circles-overlap"></span>
AMR &amp; base R
</a>
</div>
</li>
<li class="active nav-item">
<a class="nav-link" href="../reference/index.html">
<span class="fa fa-book-open"></span>
@ -113,17 +130,17 @@
Authors
</a>
</li>
<li class="nav-item">
</ul><form class="form-inline my-2 my-lg-0" role="search">
<input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
<ul class="navbar-nav"><li class="nav-item">
<a class="nav-link" href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
</a>
</li>
</ul><form class="form-inline my-2 my-lg-0" role="search">
<input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
<ul class="navbar-nav"><li class="nav-item">
<li class="nav-item">
<a class="external-link nav-link" href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
@ -201,30 +218,30 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op">&lt;-</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>
<span class="r-in"><span><span class="va">sir</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I R R I R I R R R S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I I I I R R S S R R</span>
<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>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.1618950 0.7745967 0.7745967 -1.1618950 0.7745967 -1.1618950</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.7745967 0.7745967 0.7745967 -1.1618950</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.7745967 -0.7745967 -0.7745967 -0.7745967 1.1618950 1.1618950</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.7745967 -0.7745967 1.1618950 1.1618950</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">mic</span> <span class="op">&lt;-</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>
<span class="r-in"><span><span class="va">mic</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.0625 4 128 0.0625 0.002 0.001 8 0.001 4 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.0625 0.005 128 128 32 1 &gt;=256 128 8 0.125 </span>
<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>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.3120147 0.6680004 1.4846796 -0.3120147 -1.1231053 -1.2864411</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.8313362 -1.2864411 0.6680004 0.6680004</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.1210573 -1.7761606 0.8565554 0.8565554 0.4969895 -0.4019254</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 1.0363384 0.8565554 0.1374235 -0.9412743</span>
<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
<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>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.3120147 0.6680004 1.4846796 -0.3120147 -1.1231053 -1.2864411</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.8313362 -1.2864411 0.6680004 0.6680004</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.1210573 -1.7761606 0.8565554 0.8565554 0.4969895 -0.4019254</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 1.0363384 0.8565554 0.1374235 -0.9412743</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">disk</span> <span class="op">&lt;-</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>
<span class="r-in"><span><span class="va">disk</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 10 15 33 50 37 6 50 7 27 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 48 32 44 24 22 48 50 41 43 36</span>
<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>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.02416943 -0.73485604 0.30667220 1.29033776 0.53812292 -1.25562015</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 1.29033776 -1.19775747 -0.04050388 0.82743632</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.9202045 -0.6801512 0.5201156 -1.4803290 -1.6803735 0.9202045</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 1.1202490 0.2200489 0.4200934 -0.2800622</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</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>
<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>
@ -235,21 +252,21 @@
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A R 22 1 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B R 27 0.5 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C I 27 8 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D R 30 8 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 18 0.5 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F I 19 8 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G S 27 2 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H R 21 8 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I S 30 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J S 19 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A S 21 8 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B R 25 0.5 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C R 25 &gt;=16 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D I 25 8 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 21 0.5 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F I 29 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G S 17 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H I 20 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I S 17 0.5 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J I 29 4 4</span>
<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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.16915536 -0.32319888 0.10243586 1.05012543 -0.67969116 -0.02029945</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.10305622 0.26675770 -0.19285261 -0.47548846</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.22695748 0.32206771 1.00220170 0.54530143 -0.77106467 0.09331917</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.04702882 -0.55604901 -0.99921640 0.63742636</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
@ -265,17 +282,17 @@
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C I 27 8 2 0.10243586 0.0000000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 G S 27 2 &gt;=4 0.10305622 0.0006203605</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 A R 22 1 &gt;=4 0.16915536 0.0667195016</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 F I 19 8 &gt;=4 -0.02029945 0.1227353089</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 H R 21 8 2 0.26675770 0.1643218437</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 I S 30 4 1 -0.19285261 0.2952884682</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 B R 27 0.5 1 -0.32319888 0.4256347323</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 J S 19 4 2 -0.47548846 0.5779243144</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 E S 18 0.5 &gt;=4 -0.67969116 0.7821270147</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 D R 30 8 &gt;=4 1.05012543 0.9476895794</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C R 25 &gt;=16 2 1.00220170 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 J I 29 4 4 0.63742636 0.3647753</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 D I 25 8 4 0.54530143 0.4569003</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 B R 25 0.5 2 0.32206771 0.6801340</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 F I 29 4 1 0.09331917 0.9088825</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 G S 17 4 4 -0.04702882 1.0492305</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 A S 21 8 1 -0.22695748 1.2291592</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H I 20 2 1 -0.55604901 1.5582507</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 E S 21 0.5 1 -0.77106467 1.7732664</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 I S 17 0.5 1 -0.99921640 2.0014181</span>
<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>
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
<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">%&gt;%</a></span></span></span>