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set_mo_source

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dr. M.S. (Matthijs) Berends
2019-01-21 15:53:01 +01:00
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docs/LICENSE-text.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
</span>
</div>
@ -178,7 +178,7 @@
<h1>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">17 January 2019</h4>
<h4 class="date">21 January 2019</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
</span>
</div>

2
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
</span>
</div>

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/* class for footer */
.university {
background-image: url(logo_rug.png);
height: 40px;
background-size: 160px;
background-repeat: no-repeat;
background-image: url(logo_rug.png);
background-size: 200px;
background-repeat: no-repeat;
background-position: center right;
}
/* Supports icons for brand using font-awesome */
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font-family: "Font Awesome 5 Brands" !important;
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}
/* Remove the 'Read more on our website!' part from the manual pages */
#read-more-on-our-website-,
#read-more-on-our-website- + p,
li a[href="#read-more-on-our-website-"] {
display: none;
display: none;
}
/* make colour darker and better readable for links */
@ -60,21 +60,33 @@ a pre[href], a pre[href]:hover, a pre[href]:focus {
/* syntax font */
pre, code {
font-family: 'Courier New', monospace;
font-size: 100% !important;
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font-size: 100% !important;
font-weight: bold;
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pre {
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margin: 2px;
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blockquote {
font-size: 98%;
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/* 2nd list in navigation should be smaller */
@ -91,11 +103,11 @@ help {
/* replace 'Developers' with 'Authors' */
.developers h2 {
display: none;
display: none;
}
.developers:before {
content: 'Authors';
font-size: 1.5em;
content: 'Authors';
font-size: 1.5em;
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@ -105,11 +117,11 @@ help {
/* Date of vignettes */
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content: 'Last updated: ';
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font-size: 14px;
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padding-top: 40px;
}
/* more space between icon and text in top menu */
@ -134,15 +146,21 @@ help {
padding: 4px !important;
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thead {
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border-bottom: 2px solid black;
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border-bottom: 2px solid black;
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border-bottom: 2px solid black;
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table a:not(.btn), .table a:not(.btn) {
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@ -29,11 +29,19 @@ $('head').append('<!-- Updated Font Awesome library --><link rel="stylesheet" hr
// Edit footer
$( document ).ready(function() {
// redirect to GitLab
var url_old = window.location.href;
var url_new = url_old.replace("github", "gitlab");
if (url_old != url_new) {
window.location.replace(url);
}
$('footer').html('<p>' +
$('footer .copyright p').html().replace("Developed by",
"<code>AMR</code> (for R). Developed at the University of Groningen.<br>Authors:") +
'<code>AMR</code> (for R). Developed at the <a href="https://www.rug.nl" target="_blank">University of Groningen</a>.<br>Authors:') +
'</p>');
//$('footer').prepend("<div class='university'/>");
$('footer').addClass("university");
// Edit title of manual
$('.template-reference-index h1').text('Manual');

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docs/index.html
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@ -42,7 +42,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
</span>
</div>
@ -191,6 +191,7 @@
<li>Research Microbiologists</li>
<li>Biomedical Researchers</li>
<li>Research Pharmacologists</li>
<li>Data Scientists / Data Analysts</li>
</ul>
<p>Veterinary Microbiology:</p>
<ul>
@ -203,14 +204,6 @@
<li>Extremophile Researchers</li>
<li>Astrobiologists</li>
</ul>
<p>Other specialists in any of the above fields:</p>
<ul>
<li>Data Scientists/Data Analysts</li>
<li>Biotechnologists</li>
<li>Biochemists</li>
<li>Geneticists</li>
<li>Molecular Biologists/Microbiologists</li>
</ul>
<p>Developers:</p>
<ul>
<li>Package developers for R</li>
@ -222,7 +215,7 @@
<a href="#get-this-package" class="anchor"></a>Get this package</h3>
<p>This package is available on the official R network (CRAN), which has a peer-reviewed submission process. Install this package in R with:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"AMR"</span>)</a></code></pre></div>
<p>It will be downloaded and installed automatically. For RStudio, click on menu <em>Tools</em> &gt; <em>Install Packages…</em>, then type in “AMR” and press <kbd>Install</kbd>.</p>
<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
</div>
<div id="get-started" class="section level3">
<h3 class="hasAnchor">

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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
</span>
</div>
@ -235,6 +235,7 @@
<li>Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis</li>
</ul>
</li>
<li>New functions <code><a href="../reference/mo_source.html">set_mo_source()</a></code> and <code><a href="../reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as input for <code><a href="../reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions</li>
<li>Support for the upcoming <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li>
<li>New function <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code> to find an antibiotic column in a table</li>
<li>New function <code><a href="../reference/mo_failures.html">mo_failures()</a></code> to review values that could not be coerced to a valid MO code, using <code><a href="../reference/as.mo.html">as.mo()</a></code>. This latter function will now only show a maximum of 25 uncoerced values.</li>
@ -297,6 +298,8 @@
</ul>
</li>
<li>A note to the manual pages of the <code>portion</code> functions, that low counts can influence the outcome and that the <code>portion</code> functions may camouflage this, since they only return the portion (albeit being dependent on the <code>minimum</code> parameter)</li>
<li>Merged data sets <code>microorganisms.certe</code> and <code>microorganisms.umcg</code> into <code>microorganisms.codes</code>
</li>
<li>Function <code><a href="../reference/mo_property.html">mo_taxonomy()</a></code> now contains the kingdom too</li>
<li>Reduce false positives for <code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code>
</li>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
</span>
</div>
@ -228,7 +228,7 @@
</div>
<pre class="usage"><span class='fu'>as.mo</span>(<span class='no'>x</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>allow_uncertain</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>reference_df</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
<span class='kw'>reference_df</span> <span class='kw'>=</span> <span class='fu'><a href='mo_source.html'>get_mo_source</a></span>())
<span class='fu'>is.mo</span>(<span class='no'>x</span>)</pre>
@ -255,7 +255,7 @@
</tr>
<tr>
<th>reference_df</th>
<td><p>a <code>data.frame</code> to use for extra reference when translating <code>x</code> to a valid <code>mo</code>. The first column can be any microbial name, code or ID (used in your analysis or organisation), the second column must be a valid <code>mo</code> as found in the <code><a href='microorganisms.html'>microorganisms</a></code> data set.</p></td>
<td><p>a <code>data.frame</code> to use for extra reference when translating <code>x</code> to a valid <code>mo</code>. See <code><a href='mo_source.html'>set_mo_source</a></code> and <code><a href='mo_source.html'>get_mo_source</a></code> to automate the usage of your own codes (e.g. used in your analysis or organisation).</p></td>
</tr>
</table>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
</span>
</div>
@ -278,6 +278,12 @@
<td><p>Class 'rsi'</p></td>
</tr><tr>
<td>
<p><code><a href="mo_source.html">set_mo_source()</a></code> <code><a href="mo_source.html">get_mo_source()</a></code> </p>
</td>
<td><p>Use predefined reference data set</p></td>
</tr><tr>
<td>
<p><code><a href="eucast_rules.html">eucast_rules()</a></code> <code><a href="eucast_rules.html">EUCAST_rules()</a></code> <code><a href="eucast_rules.html">interpretive_reading()</a></code> </p>
</td>
@ -299,7 +305,7 @@
<tr>
<th colspan="2">
<h2 id="section-adding-variables-to-your-data" class="hasAnchor"><a href="#section-adding-variables-to-your-data" class="anchor"></a>Adding variables to your data</h2>
<p class="section-desc"><p>Functions to add new data to existing data, like the determination of first isolates,</p></p>
<p class="section-desc"><p>Functions to add new data to existing data, like the determination of first isolates, multi-drug resistant microorganisms (MDRO), getting properties of microorganisms or antibiotics and determining the age of patients or divide ages into age groups.</p></p>
</th>
</tr>
<tr>
@ -373,7 +379,7 @@
<tr>
<th colspan="2">
<h2 id="section-analysing-your-data" class="hasAnchor"><a href="#section-analysing-your-data" class="anchor"></a>Analysing your data</h2>
<p class="section-desc"><p>Functions for conducting AMR analysis</p></p>
<p class="section-desc"><p>Functions for conducting AMR analysis, like counting isolates, calculating resistance or susceptibility, creating frequency tables or make plots.</p></p>
</th>
</tr>
<tr>
@ -459,9 +465,9 @@
</tr><tr>
<td>
<p><code><a href="microorganisms.certe.html">microorganisms.certe</a></code> </p>
<p><code><a href="microorganisms.codes.html">microorganisms.codes</a></code> </p>
</td>
<td><p>Translation table for Certe</p></td>
<td><p>Translation table for microorganism codes</p></td>
</tr><tr>
<td>
@ -470,12 +476,6 @@
<td><p>Data set with old taxonomic data from ITIS</p></td>
</tr><tr>
<td>
<p><code><a href="microorganisms.umcg.html">microorganisms.umcg</a></code> </p>
</td>
<td><p>Translation table for UMCG</p></td>
</tr><tr>
<td>
<p><code><a href="supplementary_data.html">microorganismsDT</a></code> <code><a href="supplementary_data.html">microorganisms.prevDT</a></code> <code><a href="supplementary_data.html">microorganisms.unprevDT</a></code> <code><a href="supplementary_data.html">microorganisms.oldDT</a></code> </p>
</td>

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<h1>Translation table for microorganism codes</h1>
<div class="hidden name"><code>microorganisms.codes.Rd</code></div>
</div>
<div class="ref-description">
<p>A data set containing commonly used codes for microorganisms. Define your own with <code><a href='mo_source.html'>set_mo_source</a></code>.</p>
</div>
<pre class="usage"><span class='no'>microorganisms.codes</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 3,303 observations and 2 variables:</p><dl class='dl-horizontal'>
<dt><code>certe</code></dt><dd><p>Commonly used code of a microorganism</p></dd>
<dt><code>mo</code></dt><dd><p>Code of microorganism in <code><a href='microorganisms.html'>microorganisms</a></code></p></dd>
</dl>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a omprehensive tutorial</a> about how to conduct AMR analysis and find <a href='https://msberends.gitlab.io/AMR/reference'>the complete documentation of all functions</a>, which reads a lot easier than in R.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='as.mo.html'>as.mo</a></code> <code><a href='microorganisms.html'>microorganisms</a></code></p></div>
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<li><a href="#format">Format</a></li>
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<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='as.mo.html'>as.mo</a></code> <code><a href='mo_property.html'>mo_property</a></code> <code><a href='microorganisms.umcg.html'>microorganisms.umcg</a></code></p></div>
<div class='dont-index'><p><code><a href='as.mo.html'>as.mo</a></code> <code><a href='mo_property.html'>mo_property</a></code> <code><a href='microorganisms.codes.html'>microorganisms.codes</a></code></p></div>
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<h1>Use predefined reference data set</h1>
<div class="hidden name"><code>mo_source.Rd</code></div>
</div>
<div class="ref-description">
<p>These functions can be used to predefine your own reference to be used in <code><a href='as.mo.html'>as.mo</a></code> and consequently all <code>mo_*</code> functions like <code><a href='mo_property.html'>mo_genus</a></code> and <code><a href='mo_property.html'>mo_gramstain</a></code>.</p>
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<pre class="usage"><span class='fu'>set_mo_source</span>(<span class='no'>path</span>)
<span class='fu'>get_mo_source</span>()</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>path</th>
<td><p>location of your reference file, see Details</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The reference file can be a text file seperated with commas (CSV) or pipes, an Excel file (old 'xls' format or new 'xlsx' format) or an R object file (extension '.rds'). To use an Excel file, you need to have the <code>readxl</code> package installed.</p>
<p><code>set_mo_source</code> will check the file for validity: it must be a <code>data.frame</code>, must have a column named <code>"mo"</code> which contains values from <code>microorganisms$mo</code> and must have a reference column with your own defined values. If all tests pass, <code>set_mo_source</code> will read the file into R and export it to <code>"~/.mo_source.rds"</code>. This compressed data file will then be used at default for MO determination (function <code><a href='as.mo.html'>as.mo</a></code> and consequently all <code>mo_*</code> functions like <code><a href='mo_property.html'>mo_genus</a></code> and <code><a href='mo_property.html'>mo_gramstain</a></code>). The location of the original file will be saved as option with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>options</a>(mo_source = path)</code>. Its timestamp will be saved with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>options</a>(mo_source_datetime = ...)</code>.</p>
<p><code>get_mo_source</code> will return the data set by reading <code>"~/.mo_source.rds"</code> with <code><a href='https://www.rdocumentation.org/packages/base/topics/readRDS'>readRDS</a></code>. If the original file has changed (the file defined with <code>path</code>), it will call <code>set_mo_source</code> to update the data file automatically.</p>
<p>Reading an Excel file (<code>.xlsx</code>) with only one row has a size of 8-9 kB. The compressed file will have a size of 0.1 kB and can be read by <code>get_mo_source</code> in only a couple of microseconds (a millionth of a second).</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a omprehensive tutorial</a> about how to conduct AMR analysis and find <a href='https://msberends.gitlab.io/AMR/reference'>the complete documentation of all functions</a>, which reads a lot easier than in R.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"># NOT RUN {
# imagine this Excel file (mo codes looked up in `microorganisms` data set):
# A B
# 1 our code mo
# 2 lab_mo_ecoli B_ESCHR_COL
# 3 lab_mo_kpneumoniae B_KLBSL_PNE
# 1. We save it as 'home/me/ourcodes.xlsx'
# 2. We use it for input:
set_mo_source("C:\path\ourcodes.xlsx")
#> Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
# 3. And use it in our functions:
as.mo("lab_mo_ecoli")
#> B_ESCHR_COL
mo_genus("lab_mo_kpneumoniae")
#> "Klebsiella"
# 4. It will look for changes itself:
# (add new row to the Excel file and save it)
mo_genus("lab_mo_kpneumoniae")
#> Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
#> "Klebsiella"
# }
</pre>
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@ -102,6 +99,9 @@
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