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@ -1,12 +1,12 @@
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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"><meta name="description" content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor.
|
||||
<!-- 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"><meta name="description" content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor containing the levels S, SDD, I, R, N.
|
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These breakpoints are currently implemented:
|
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For clinical microbiology: EUCAST 2011-2023 and CLSI 2011-2023;
|
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For veterinary microbiology: EUCAST 2021-2023 and CLSI 2019-2023;
|
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ECOFFs (Epidemiological cut-off values): EUCAST 2020-2023 and CLSI 2022-2023.
|
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|
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|
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All breakpoints used for interpretation are available in our clinical_breakpoints data set."><title>Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir • 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"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir"><meta property="og:description" content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor.
|
||||
All breakpoints used for interpretation are available in our clinical_breakpoints data set."><title>Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir • 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"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir"><meta property="og:description" content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor containing the levels S, SDD, I, R, N.
|
||||
These breakpoints are currently implemented:
|
||||
For clinical microbiology: EUCAST 2011-2023 and CLSI 2011-2023;
|
||||
For veterinary microbiology: EUCAST 2021-2023 and CLSI 2019-2023;
|
||||
@ -24,7 +24,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
|
||||
|
||||
<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="">2.1.1.9037</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</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">
|
||||
@ -174,7 +174,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
|
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</div>
|
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|
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<div class="ref-description section level2">
|
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<p>Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. <code>as.sir()</code> transforms the input to a new class <code>sir</code>, which is an ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a>.</p>
|
||||
<p>Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. <code>as.sir()</code> transforms the input to a new class <code>sir</code>, which is an ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> containing the levels <code>S</code>, <code>SDD</code>, <code>I</code>, <code>R</code>, <code>N</code>.</p>
|
||||
<p>These breakpoints are currently implemented:</p><ul><li><p>For <strong>clinical microbiology</strong>: EUCAST 2011-2023 and CLSI 2011-2023;</p></li>
|
||||
<li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2023 and CLSI 2019-2023;</p></li>
|
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<li><p>ECOFFs (Epidemiological cut-off values): EUCAST 2020-2023 and CLSI 2022-2023.</p></li>
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@ -195,10 +195,10 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
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<span><span class="fu">as.sir</span><span class="op">(</span></span>
|
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<span> <span class="va">x</span>,</span>
|
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<span> S <span class="op">=</span> <span class="st">"^(S|U)+$"</span>,</span>
|
||||
<span> I <span class="op">=</span> <span class="st">"^(I|H)+$"</span>,</span>
|
||||
<span> I <span class="op">=</span> <span class="st">"^(I)+$"</span>,</span>
|
||||
<span> R <span class="op">=</span> <span class="st">"^(R)+$"</span>,</span>
|
||||
<span> N <span class="op">=</span> <span class="st">"^(N|V)+$"</span>,</span>
|
||||
<span> SDD <span class="op">=</span> <span class="st">"^(SDD|D)+$"</span>,</span>
|
||||
<span> SDD <span class="op">=</span> <span class="st">"^(SDD|D|H)+$"</span>,</span>
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<span> <span class="va">...</span></span>
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||||
<span><span class="op">)</span></span>
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<span></span>
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@ -276,7 +276,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
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<dt>S, I, R, N, SDD</dt>
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||||
<dd><p>a case-independent <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> to translate input to this result. This regular expression will be run <em>after</em> all non-letters are removed from the input.</p></dd>
|
||||
<dd><p>a case-independent <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> to translate input to this result. This regular expression will be run <em>after</em> all non-letters and whitespaces are removed from the input.</p></dd>
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<dt>mo</dt>
|
||||
@ -405,7 +405,8 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
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||||
|
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<p>The function <code>is.sir()</code> detects if the input contains class <code>sir</code>. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, it iterates over all columns and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
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<p>The function <code>is_sir_eligible()</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R and/or N and/or SDD), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> argument. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, it iterates over all columns and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
|
||||
<p>The base R function <code><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double()</a></code> can be used to retrieve quantitative values from a <code>sir</code> object: <code>"S"</code> = 1, <code>"I"</code>/<code>"SDD"</code> = 2, <code>"R"</code> = 3. All other values are rendered <code>NA</code> . <strong>Note:</strong> Do not use <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code>, since that (because of how R works internally) will return the factor level indices, and not these aforementioned quantitative values.</p>
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<p>The function <code>is_sir_eligible()</code> returns <code>TRUE</code> when a column contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R and/or N and/or SDD), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> argument. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, it iterates over all columns and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
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</div>
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<p><code>NA_sir_</code> is a missing value of the new <code>sir</code> class, analogous to e.g. base <span style="R">R</span>'s <code><a href="https://rdrr.io/r/base/NA.html" class="external-link">NA_character_</a></code>.</p>
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@ -467,102 +468,102 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
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<span class="r-out co"><span class="r-pr">#></span> Max. :2017-12-28 Max. :97.00 </span>
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||||
<span class="r-out co"><span class="r-pr">#></span> ward mo PEN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Length:2000 Class :mo Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class :character <NA> :0 %R :73.7% (n=1201) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Mode :character Unique:90 %SI :26.3% (n=428) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> #1 :B_ESCHR_COLI - %S :25.6% (n=417) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> #2 :B_STPHY_CONS - %I : 0.7% (n=11) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> #3 :B_STPHY_AURS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class :character <NA> :0 %S :25.6% (n=417) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Mode :character Unique:90 %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> #1 :B_ESCHR_COLI %I : 0.7% (n=11) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> #2 :B_STPHY_CONS %R :73.7% (n=1201) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> #3 :B_STPHY_AURS %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :68.8% (n=251) %S :70.5% (n=665) %S :40.2% (n=543) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 0.2% (n=3) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :31.2% (n=114) %R :29.5% (n=278) %R :59.6% (n=804) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :68.8% (n=251) %SI :70.5% (n=665) %SI :40.4% (n=546) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :68.8% (n=251) - %S :70.5% (n=665) - %S :40.2% (n=543) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 0.0% (n=0) - %I : 0.2% (n=3) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMC AMP TZP </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :71.4% (n=1342) %S :40.2% (n=543) %S :86.1% (n=862) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 4.8% (n=91) %I : 0.2% (n=3) %I : 1.3% (n=13) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :23.7% (n=446) %R :59.6% (n=804) %R :12.6% (n=126) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :76.3% (n=1433) %SI :40.4% (n=546) %SI :87.4% (n=875) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :71.4% (n=1342) - %S :40.2% (n=543) - %S :86.1% (n=862) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 4.8% (n=91) - %I : 0.2% (n=3) - %I : 1.3% (n=13) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CZO FEP CXM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :54.9% (n=245) %S :85.6% (n=620) %S :72.5% (n=1297) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.4% (n=2) %I : 0.1% (n=1) %I : 1.2% (n=22) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :44.6% (n=199) %R :14.2% (n=103) %R :26.3% (n=470) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :55.4% (n=247) %SI :85.8% (n=621) %SI :73.7% (n=1319) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :54.9% (n=245) - %S :85.6% (n=620) - %S :72.5% (n=1297) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.4% (n=2) - %I : 0.1% (n=1) - %I : 1.2% (n=22) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> FOX CTX CAZ </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :71.6% (n=586) %S :84.4% (n=796) %S :33.5% (n=607) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 1.0% (n=8) %I : 0.1% (n=1) %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :27.4% (n=224) %R :15.5% (n=146) %R :66.5% (n=1204) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :72.6% (n=594) %SI :84.5% (n=797) %SI :33.5% (n=607) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :71.6% (n=586) - %S :84.4% (n=796) - %S :33.5% (n=607) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 1.0% (n=8) - %I : 0.1% (n=1) - %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CRO GEN TOB </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :84.4% (n=796) %S :74.0% (n=1372) %S :65.1% (n=879) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.1% (n=1) %I : 1.5% (n=27) %I : 0.5% (n=7) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :15.5% (n=146) %R :24.6% (n=456) %R :34.4% (n=465) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :84.5% (n=797) %SI :75.4% (n=1399) %SI :65.6% (n=886) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :84.4% (n=796) - %S :74.0% (n=1372) - %S :65.1% (n=879) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.1% (n=1) - %I : 1.5% (n=27) - %I : 0.5% (n=7) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMK KAN TMP </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :36.3% (n=251) %S : 0.0% (n=0) %S :61.2% (n=918) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 0.7% (n=10) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :63.7% (n=441) %R :100.0% (n=471) %R :38.1% (n=571) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :36.3% (n=251) %SI : 0.0% (n=0) %SI :61.9% (n=928) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :36.3% (n=251) - %S : 0.0% (n=0) - %S :61.2% (n=918) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 0.0% (n=0) - %I : 0.7% (n=10) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> SXT NIT FOS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :79.1% (n=1392) %S :76.0% (n=565) %S :57.8% (n=203) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.3% (n=6) %I : 6.9% (n=51) %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :20.5% (n=361) %R :17.1% (n=127) %R :42.2% (n=148) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :79.5% (n=1398) %SI :82.9% (n=616) %SI :57.8% (n=203) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :79.1% (n=1392) - %S :76.0% (n=565) - %S :57.8% (n=203) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.3% (n=6) - %I : 6.9% (n=51) - %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> LNZ CIP MFX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :30.7% (n=314) %S :78.9% (n=1112) %S :64.5% (n=136) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 4.9% (n=69) %I : 1.9% (n=4) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :69.3% (n=709) %R :16.2% (n=228) %R :33.6% (n=71) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :30.7% (n=314) %SI :83.8% (n=1181) %SI :66.4% (n=140) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :30.7% (n=314) - %S :78.9% (n=1112) - %S :64.5% (n=136) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 4.9% (n=69) - %I : 1.9% (n=4) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> VAN TEC TCY </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :61.7% (n=1149) %S :24.3% (n=237) %S :68.3% (n=820) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 1.9% (n=23) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :38.3% (n=712) %R :75.7% (n=739) %R :29.8% (n=357) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :61.7% (n=1149) %SI :24.3% (n=237) %SI :70.3% (n=843) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :61.7% (n=1149) - %S :24.3% (n=237) - %S :68.3% (n=820) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 0.0% (n=0) - %I : 1.9% (n=23) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> TGC DOX ERY </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :87.3% (n=697) %S :71.7% (n=814) %S :42.3% (n=801) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 0.6% (n=7) %I : 0.5% (n=9) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :12.7% (n=101) %R :27.7% (n=315) %R :57.2% (n=1084) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :87.3% (n=697) %SI :72.3% (n=821) %SI :42.8% (n=810) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :87.3% (n=697) - %S :71.7% (n=814) - %S :42.3% (n=801) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 0.6% (n=7) - %I : 0.5% (n=9) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CLI AZM IPM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :38.6% (n=586) %S :42.3% (n=801) %S :92.7% (n=824) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.3% (n=4) %I : 0.5% (n=9) %I : 1.1% (n=10) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :61.2% (n=930) %R :57.2% (n=1084) %R : 6.2% (n=55) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :38.8% (n=590) %SI :42.8% (n=810) %SI :93.8% (n=834) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :38.6% (n=586) - %S :42.3% (n=801) - %S :92.7% (n=824) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.3% (n=4) - %I : 0.5% (n=9) - %I : 1.1% (n=10) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> MEM MTR CHL </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :94.1% (n=780) %S :85.3% (n=29) %S :78.6% (n=121) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R : 5.9% (n=49) %R :14.7% (n=5) %R :21.4% (n=33) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :94.1% (n=780) %SI :85.3% (n=29) %SI :78.6% (n=121) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :94.1% (n=780) - %S :85.3% (n=29) - %S :78.6% (n=121) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 0.0% (n=0) - %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> COL MUP RIF </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :18.8% (n=309) %S :93.0% (n=251) %S :30.2% (n=303) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 1.1% (n=3) %I : 0.2% (n=2) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :81.2% (n=1331) %R : 5.9% (n=16) %R :69.6% (n=698) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :18.8% (n=309) %SI :94.1% (n=254) %SI :30.4% (n=305) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :18.8% (n=309) - %S :93.0% (n=251) - %S :30.2% (n=303) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 1.1% (n=3) - %I : 0.2% (n=2) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># For INTERPRETING disk diffusion and MIC values -----------------------</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
@ -580,17 +581,41 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in as_sir_method(method_short = "mic", method_long = "MIC values", x = x, mo = mo, ab = ab, guideline = guideline, uti = uti, conserve_capped_values = conserve_capped_values, add_intrinsic_resistance = add_intrinsic_resistance, reference_data = reference_data, include_screening = include_screening, include_PKPD = include_PKPD, breakpoint_type = breakpoint_type, host = host, ...):</span> object 'mo_var_found' not found</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column 'AMP' (ampicillin), EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column 'CIP' (ciprofloxacin), EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: column 'GEN' (gentamicin), EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: column 'TOB' (tobramycin), EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Assigning class 'sir' to already clean column 'ERY' (erythromycin)...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> microorganism AMP CIP GEN TOB ERY</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli S I S S R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># return a 'logbook' about the results:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">sir_interpretation_history</span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 4 × 14</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> datetime index ab_user mo_user ab mo input</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2024-05-31 <span style="color: #949494;">19:28:05</span> 1 AMX B_STRPT_PNMN AMX B_STRPT_PNMN 0.01</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2024-05-31 <span style="color: #949494;">19:28:05</span> 2 AMX B_STRPT_PNMN AMX B_STRPT_PNMN 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2024-05-31 <span style="color: #949494;">19:28:05</span> 3 AMX B_STRPT_PNMN AMX B_STRPT_PNMN 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2024-05-31 <span style="color: #949494;">19:28:05</span> 4 AMX B_STRPT_PNMN AMX B_STRPT_PNMN 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 13 × 14</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> datetime index ab_user mo_user ab mo input</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2024-06-10 <span style="color: #949494;">08:38:18</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2024-06-10 <span style="color: #949494;">08:38:18</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2024-06-10 <span style="color: #949494;">08:38:17</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR 0.256</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2024-06-10 <span style="color: #949494;">08:38:17</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2024-06-10 <span style="color: #949494;">08:38:13</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 0.01 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2024-06-10 <span style="color: #949494;">08:38:13</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2024-06-10 <span style="color: #949494;">08:38:13</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2024-06-10 <span style="color: #949494;">08:38:13</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2024-06-10 <span style="color: #949494;">08:38:13</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2024-06-10 <span style="color: #949494;">08:38:13</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> 2024-06-10 <span style="color: #949494;">08:38:13</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> 2024-06-10 <span style="color: #949494;">08:38:12</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 20 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">13</span> 2024-06-10 <span style="color: #949494;">08:38:12</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 7 more variables: outcome <sir>, method <chr>, breakpoint_S_R <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># guideline <chr>, host <chr>, ref_table <chr>, uti <lgl></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
@ -605,7 +630,12 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in as_sir_method(method_short = "mic", method_long = "MIC values", x = x, mo = mo, ab = ab, guideline = guideline, uti = uti, conserve_capped_values = conserve_capped_values, add_intrinsic_resistance = add_intrinsic_resistance, reference_data = reference_data, include_screening = include_screening, include_PKPD = include_PKPD, breakpoint_type = breakpoint_type, host = host, ...):</span> object 'mo_var_found' not found</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for ampicillin (AMP) in Streptococcus</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> pneumoniae - assuming body site 'Non-meningitis'.</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] R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> x <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">18</span><span class="op">)</span>,</span></span>
|
||||
@ -617,7 +647,10 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in as_sir_method(method_short = "disk", method_long = "disk diffusion zones", x = x, mo = mo, ab = ab, guideline = guideline, uti = uti, conserve_capped_values = FALSE, add_intrinsic_resistance = add_intrinsic_resistance, reference_data = reference_data, include_screening = include_screening, include_PKPD = include_PKPD, breakpoint_type = breakpoint_type, host = NULL, ...):</span> object 'mo_var_found' not found</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'ampicillin' (AMP), EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </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] R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># the dplyr way</span></span></span>
|
||||
@ -661,12 +694,6 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There were 2 warnings in `mutate()`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> The first warning was:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `AMP = (function (x, ...) ...`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> invalid microorganism code, NA generated</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
@ -685,12 +712,6 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There were 4 warnings in `mutate()`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> The first warning was:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `AMP = (function (x, ...) ...`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> invalid microorganism code, NA generated</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
@ -703,12 +724,6 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There were 2 warnings in `mutate()`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> The first warning was:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(where(is.mic), as.sir)`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> invalid microorganism code, NA generated</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
@ -727,12 +742,6 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There were 4 warnings in `mutate()`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> The first warning was:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `AMP = (function (x, ...) ...`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> invalid microorganism code, NA generated</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
@ -751,12 +760,6 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There were 4 warnings in `mutate()`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> The first warning was:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(AMP:TOB, as.sir)`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> invalid microorganism code, NA generated</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
@ -775,17 +778,41 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There were 4 warnings in `mutate()`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> The first warning was:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `AMP = (function (x, ...) ...`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> invalid microorganism code, NA generated</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in as_sir_method(method_short = "mic", method_long = "MIC values", x = x, mo = mo, ab = ab, guideline = guideline, uti = uti, conserve_capped_values = conserve_capped_values, add_intrinsic_resistance = add_intrinsic_resistance, reference_data = reference_data, include_screening = include_screening, include_PKPD = include_PKPD, breakpoint_type = breakpoint_type, host = host, ...):</span> object 'mo_var_found' not found</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column for NIT, EUCAST 2023...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.sir(): interpretation of nitrofurantoin (NIT) is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms,</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> thus assuming uti = TRUE. See ?as.sir.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Assuming value "urine" in column 'specimen' reflects a urinary tract</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> infection.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Use as.sir(uti = FALSE) to prevent this.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column for NIT, EUCAST 2023...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.sir(): interpretation of nitrofurantoin (NIT) is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms,</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> thus assuming uti = TRUE. See ?as.sir.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'CIP' (ciprofloxacin), EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'GEN' (gentamicin), EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'TOB' (tobramycin), EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> microorganism AMP CIP GEN TOB ERY</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli S <NA> S S R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># For CLEANING existing SIR values ------------------------------------</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
@ -805,6 +832,13 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/barplot.html" class="external-link">barplot</a></span><span class="op">(</span><span class="va">sir_data</span><span class="op">)</span> <span class="co"># for frequencies</span></span></span>
|
||||
<span class="r-plt img"><img src="as.sir-2.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># as common in R, you can use as.integer() to return factor indices:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer</a></span><span class="op">(</span><span class="fu">as.sir</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"N"</span>, <span class="cn">NA</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1 2 3 4 5 NA</span>
|
||||
<span class="r-in"><span><span class="co"># but for computational use, as.double() will return 1 for S, 2 for I/SDD, and 3 for R:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double</a></span><span class="op">(</span><span class="fu">as.sir</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"N"</span>, <span class="cn">NA</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1 2 2 3 NA NA</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># the dplyr way</span></span></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="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
|
||||
Reference in New Issue
Block a user