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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate the Mean AMR Distance — mean_amr_distance • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Calculate the Mean AMR Distance — mean_amr_distance"><meta name="description" content="Calculates a normalised mean for antimicrobial resistance between multiple observations, to help to identify similar isolates without comparing antibiograms by hand."><meta property="og:description" content="Calculates a normalised mean for antimicrobial resistance between multiple observations, to help to identify similar isolates without comparing antibiograms by hand."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"></head><body>
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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate the Mean AMR Distance — mean_amr_distance • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Calculate the Mean AMR Distance — mean_amr_distance"><meta name="description" content="Calculates a normalised mean for antimicrobial resistance between multiple observations, to help to identify similar isolates without comparing antibiograms by hand."><meta property="og:description" content="Calculates a normalised mean for antimicrobial resistance between multiple observations, to help to identify similar isolates without comparing antibiograms by hand."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
|
||||
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
|
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|
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@ -109,31 +109,31 @@
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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>
|
||||
<span class="r-in"><span><span class="va">sir</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S I S I I I R R I R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S S I I S R S R S 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">#></span> [1] -0.621059 -0.621059 -0.621059 -0.621059 -0.621059 -0.621059 1.449138</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.621059 -0.621059 -0.621059 -0.621059 -0.621059 1.449138 -0.621059</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [8] 1.449138 -0.621059 1.449138</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<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>
|
||||
<span class="r-in"><span><span class="va">mic</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 64 16 8 64 256 0.5 128 128 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] <=0.002</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.005 <=0.002 <=0.002 >=128 64 0.01 0.0625 0.125 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 0.025 </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">#></span> [1] 0.54295251 0.15465479 -0.03949407 0.54295251 0.93125022 -0.81608950</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.73710137 0.73710137 -0.42779178 -2.36263742</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.79195592 -1.01052933 -1.01052933 1.62932373 1.46397933 -0.62661152</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.18946469 -0.02412029 0.96794612 -0.40803811</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">#></span> [1] 0.54295251 0.15465479 -0.03949407 0.54295251 0.93125022 -0.81608950</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.73710137 0.73710137 -0.42779178 -2.36263742</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.79195592 -1.01052933 -1.01052933 1.62932373 1.46397933 -0.62661152</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.18946469 -0.02412029 0.96794612 -0.40803811</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<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>
|
||||
<span class="r-in"><span><span class="va">disk</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 28 27 30 48 9 45 12 26 42 25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 37 13 9 50 9 10 12 46 11 49</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">#></span> [1] -0.09277857 -0.17009405 0.06185238 1.45353101 -1.56177268 1.22158457</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -1.32982624 -0.24740953 0.98963813 -0.32472501</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.6757607 -0.6321633 -0.8501506 1.3842196 -0.8501506 -0.7956538</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.6866601 1.1662323 -0.7411569 1.3297228</span>
|
||||
<span class="r-in"><span></span></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/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>
|
||||
@ -143,22 +143,22 @@
|
||||
<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>
|
||||
<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">#></span> id amox cipr gent tobr</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A I 28 2 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B R 29 1 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C S 23 4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D I 27 4 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E S 19 1 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F S 22 0.5 <=0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 26 1 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H R 17 2 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I S 19 1 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J I 30 2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A I 26 >=8 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B R 19 4 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C R 26 >=8 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D S 23 4 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E R 30 >=8 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F R 24 1 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G R 25 >=8 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H S 25 <=0.5 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I S 17 2 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J S 19 2 2</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">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> and "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.06537260 0.82078512 0.42232605 0.47166071 -0.31061057 -1.07205573</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.06631747 -0.06476102 -0.64271615 0.37442671</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.28451298 -0.01875836 0.27473171 0.08104917 0.68750659 -0.05708302</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.85737880 -0.96761082 -0.47233937 -0.66938769</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
@ -174,17 +174,17 @@
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> and "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C S 23 4 4 0.42232605 0.00000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 J I 30 2 2 0.37442671 0.04789934</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 D I 27 4 2 0.47166071 0.04933466</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 G I 26 1 4 0.06631747 0.35600858</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 B R 29 1 4 0.82078512 0.39845906</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 H R 17 2 0.5 -0.06476102 0.48708707</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 A I 28 2 0.5 -0.06537260 0.48769865</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 E S 19 1 4 -0.31061057 0.73293662</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I S 19 1 1 -0.64271615 1.06504220</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 F S 22 0.5 <=0.25 -1.07205573 1.49438178</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C R 26 >=8 0.5 0.27473171 0.000000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 A I 26 >=8 4 0.28451298 0.009781269</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 D S 23 4 8 0.08104917 0.193682539</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 B R 19 4 2 -0.01875836 0.293490073</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 F R 24 1 2 -0.05708302 0.331814730</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 E R 30 >=8 1 0.68750659 0.412774877</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G R 25 >=8 8 0.85737880 0.582647082</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 I S 17 2 8 -0.47233937 0.747071081</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 J S 19 2 2 -0.66938769 0.944119407</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 H S 25 <=0.5 0.5 -0.96761082 1.242342534</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">%>%</a></span></span></span>
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Reference in New Issue
Block a user