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<!DOCTYPE html>
<!-- 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>User-Defined Reference Data Set for Microorganisms — mo_source • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><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-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/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="User-Defined Reference Data Set for Microorganisms — mo_source"><meta name="description" content="These functions can be used to predefine your own reference to be used in as.mo() and consequently all mo_* functions (such as mo_genus() and mo_gramstain()).
<!-- 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>User-Defined Reference Data Set for Microorganisms — mo_source • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><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-5.3.8/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.8/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/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="User-Defined Reference Data Set for Microorganisms — mo_source"><meta name="description" content="These functions can be used to predefine your own reference to be used in as.mo() and consequently all mo_* functions (such as mo_genus() and mo_gramstain()).
This is the fastest way to have your organisation (or analysis) specific codes picked up and translated by this package, since you don't have to bother about it again after setting it up once."><meta property="og:description" content="These functions can be used to predefine your own reference to be used in as.mo() and consequently all mo_* functions (such as mo_genus() and mo_gramstain()).
This is the fastest way to have your organisation (or analysis) specific codes picked up and translated by this package, since you don't have to bother about it again after setting it up once."><meta property="og:image" content="https://amr-for-r.org/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>
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@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<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="">3.0.1.9057</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9061</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">
@@ -58,8 +58,10 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">set_mo_source</span><span class="op">(</span><span class="va">path</span>, destination <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_mo_source"</span>,</span>
<span> <span class="st">"~/mo_source.rds"</span><span class="op">)</span><span class="op">)</span></span>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">set_mo_source</span><span class="op">(</span></span>
<span> <span class="va">path</span>,</span>
<span> destination <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_mo_source"</span>, <span class="st">"~/mo_source.rds"</span><span class="op">)</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">get_mo_source</span><span class="op">(</span>destination <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_mo_source"</span>, <span class="st">"~/mo_source.rds"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
</div>