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<h1>Use predefined reference data set</h1>
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<div class="hidden name"><code>mo_source.Rd</code></div>
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<div class="ref-description">
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<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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<p>This is <strong>the fastest way</strong> to have your organisation (or analysis) specific codes picked up and translated by this package.</p>
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</div>
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<pre class="usage"><span class='fu'>set_mo_source</span>(<span class='no'>path</span>)
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<span class='fu'>get_mo_source</span>()</pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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<colgroup><col class="name" /><col class="desc" /></colgroup>
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<tr>
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<th>path</th>
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<td><p>location of your reference file, see Details</p></td>
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</tr>
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</table>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p>The reference file can be a text file seperated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or '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>
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<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>
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<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>
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<p>Reading an Excel file (<code>.xlsx</code>) with only one row has a size of 8-9 kB. The compressed file used by this package 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>
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<h2 class="hasAnchor" id="how-it-works"><a class="anchor" href="#how-it-works"></a>How it works</h2>
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<p>Imagine this data on a sheet of an Excel file (mo codes were looked up in the `microorganisms` data set). The first column contains the organisation specific codes, the second column contains an MO code from this package:</p><pre>
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| A | B |
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--|--------------------|-------------|
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1 | Organisation XYZ | mo |
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2 | lab_mo_ecoli | B_ESCHR_COL |
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3 | lab_mo_kpneumoniae | B_KLBSL_PNE |
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4 | | |
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</pre>
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<p>We save it as <code>'home/me/ourcodes.xlsx'</code>. Now we have to set it as a source:</p><pre>
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set_mo_source("home/me/ourcodes.xlsx")
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# Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
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</pre>
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<p>It has now created a file "~/.mo_source.rds" with the contents of our Excel file, but only the first column with foreign values and the 'mo' column will be kept.</p>
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<p>And now we can use it in our functions:</p><pre>
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as.mo("lab_mo_ecoli")
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[1] B_ESCHR_COL
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mo_genus("lab_mo_kpneumoniae")
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[1] "Klebsiella"
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# other input values still work too
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as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli"))
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[1] B_ESCHR_COL B_ESCHR_COL B_ESCHR_COL
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</pre>
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<p>If we edit the Excel file to, let's say, this:</p><pre>
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| A | B |
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--|--------------------|-------------|
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1 | Organisation XYZ | mo |
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2 | lab_mo_ecoli | B_ESCHR_COL |
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3 | lab_mo_kpneumoniae | B_KLBSL_PNE |
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4 | lab_Staph_aureus | B_STPHY_AUR |
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5 | | |
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</pre>
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<p>...any new usage of an MO function in this package will update your data:</p><pre>
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as.mo("lab_mo_ecoli")
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# Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
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[1] B_ESCHR_COL
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mo_genus("lab_Staph_aureus")
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[1] "Staphylococcus"
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</pre>
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<p>To remove the reference completely, just use any of these:</p><pre>
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set_mo_source("")
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set_mo_source(NULL)
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# Removed mo_source file '~/.mo_source.rds'.
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</pre>
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<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>
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<p>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 comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
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<h2>Contents</h2>
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<li><a href="#arguments">Arguments</a></li>
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<li><a href="#details">Details</a></li>
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<li><a href="#how-it-works">How it works</a></li>
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<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
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