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(v1.1.0.9019) mo_source fix

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dr. M.S. (Matthijs) Berends
2020-05-25 01:01:14 +02:00
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9019</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9019</span>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>All output will be <a href='translate.html'>translate</a>d where possible.</p>
<p>The function <code>ab_url()</code> will return the direct URL to the official WHO website. A warning will be returned if the reauired ATC code is not available.</p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
<p>The function <code>ab_url()</code> will return the direct URL to the official WHO website. A warning will be returned if the required ATC code is not available.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>

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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
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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="Latest development version">1.1.0.9018</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9019</span>
</span>
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<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>
<td><p>User-defined reference data set for microorganisms</p></td>
</tr>
</tbody><tbody>
<tr>

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<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="Latest development version">1.1.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9019</span>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9019</span>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9019</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9019</span>
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@ -329,6 +329,13 @@
<p>The Gram stain - <code>mo_gramstain()</code> - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>.</p>
<p>All output will be <a href='translate.html'>translate</a>d where possible.</p>
<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>

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<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Use predefined reference data set — mo_source • AMR (for R)</title>
<title>User-defined reference data set for microorganisms — mo_source • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Use predefined reference data set — mo_source" />
<meta property="og:title" content="User-defined reference data set for microorganisms — mo_source" />
<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 like 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." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</button>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9019</span>
</span>
</div>
@ -227,7 +227,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Use predefined reference data set</h1>
<h1>User-defined reference data set for microorganisms</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mo_source.R'><code>R/mo_source.R</code></a></small>
<div class="hidden name"><code>mo_source.Rd</code></div>
</div>
@ -246,7 +246,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>path</th>
<td><p>location of your reference file, see Details</p></td>
<td><p>location of your reference file, see Details. Can be <code>""</code>, <code>NULL</code> or <code>FALSE</code> to delete the reference file.</p></td>
</tr>
</table>
@ -255,10 +255,13 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<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>
<p><code>set_mo_source()</code> will check the file for validity: it must be a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code>, must have a column named <code>"mo"</code> which contains values from <code><a href='microorganisms.html'>microorganisms$mo</a></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://rdrr.io/r/base/options.html'>options(mo_source = path)</a></code>. Its timestamp will be saved with <code><a href='https://rdrr.io/r/base/options.html'>options(mo_source_datetime = ...)</a></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://rdrr.io/r/base/readRDS.html'>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 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><h3>How it works</h3>
<p>Reading an Excel file (<code>.xlsx</code>) with only one row has a size of 8-9 kB. The compressed file created with <code>set_mo_source()</code> will then have a size of 0.1 kB and can be read by <code>get_mo_source()</code> in only a couple of microseconds (millionths of a second).</p>
<h2 class="hasAnchor" id="how-to-setup"><a class="anchor" href="#how-to-setup"></a>How to setup</h2>
<p>Imagine this data on a sheet of an Excel file (mo codes were looked up in the <code>microorganisms</code> data set). The first column contains the organisation specific codes, the second column contains an MO code from this package:</p><pre> | A | B |
<p>Imagine this data on a sheet of an Excel file (mo codes were looked up in the <a href='microorganisms.html'>microorganisms</a> data set). The first column contains the organisation specific codes, the second column contains an MO code from this package:</p><pre> | A | B |
--|--------------------|--------------|
1 | Organisation XYZ | mo |
2 | lab_mo_ecoli | B_ESCHR_COLI |
@ -267,21 +270,21 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</pre>
<p>We save it as <code>"home/me/ourcodes.xlsx"</code>. Now we have to set it as a source:</p><pre><span class='fu'>set_mo_source</span>(<span class='st'>"home/me/ourcodes.xlsx"</span>)
<span class='co'># Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.</span></pre>
<span class='co'>#&amp;gt; NOTE: Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'</span>
<span class='co'>#&amp;gt; (columns "Organisation XYZ" and "mo")</span></pre>
<p>It has now created a file <code>"~/.mo_source.rds"</code> with the contents of our Excel file, but only the first column with foreign values and the 'mo' column will be kept.</p>
<p>And now we can use it in our functions:</p><pre>as.mo("lab_mo_ecoli")
[1] B_ESCHR_COLI
<p>It has now created a file <code>"~/.mo_source.rds"</code> with the contents of our Excel file. Only the first column with foreign values and the 'mo' column will be kept when creating the RDS file.</p>
<p>And now we can use it in our functions:</p><pre><span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"lab_mo_ecoli"</span>)
<span class='co'>#&amp;gt; [1] B_ESCHR_COLI</span>
mo_genus("lab_mo_kpneumoniae")
[1] "Klebsiella"
<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='st'>"lab_mo_kpneumoniae"</span>)
<span class='co'>#&amp;gt; [1] "Klebsiella"</span>
# other input values still work too
as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli"))
[1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI
</pre>
<span class='co'># other input values still work too</span>
<span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Escherichia coli"</span>, <span class='st'>"E. coli"</span>, <span class='st'>"lab_mo_ecoli"</span>))
<span class='co'>#&amp;gt; [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI</span></pre>
<p>If we edit the Excel file to, let's say, by adding row 4 like this:</p><pre> | A | B |
<p>If we edit the Excel file by, let's say, adding row 4 like this:</p><pre> | A | B |
--|--------------------|--------------|
1 | Organisation XYZ | mo |
2 | lab_mo_ecoli | B_ESCHR_COLI |
@ -290,18 +293,18 @@ as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli"))
5 | | |
</pre>
<p>...any new usage of an MO function in this package will update your data file:</p><pre>as.mo("lab_mo_ecoli")
# Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
[1] B_ESCHR_COLI
<p>...any new usage of an MO function in this package will update your data file:</p><pre><span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"lab_mo_ecoli"</span>)
<span class='co'>#&amp;gt; NOTE: Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'</span>
<span class='co'>#&amp;gt; (columns "Organisation XYZ" and "mo")</span>
<span class='co'>#&amp;gt; [1] B_ESCHR_COLI</span>
mo_genus("lab_Staph_aureus")
[1] "Staphylococcus"
</pre>
<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='st'>"lab_Staph_aureus"</span>)
<span class='co'>#&amp;gt; [1] "Staphylococcus"</span></pre>
<p>To remove the reference data file completely, just use <code>""</code> or <code>NULL</code> as input for <code>[set_mo_source()]</code>:</p><pre><span class='fu'>set_mo_source</span>(<span class='kw'>NULL</span>)
<p>To delete the reference data file, just use <code>""</code>, <code>NULL</code> or <code>FALSE</code> as input for <code>set_mo_source()</code>:</p><pre><span class='fu'>set_mo_source</span>(<span class='kw'>NULL</span>)
<span class='co'># Removed mo_source file '~/.mo_source.rds'.</span></pre>
<p>If the original Excel file is moved or deleted, the mo_source file will be removed upon the next use of <code><a href='as.mo.html'>as.mo()</a></code>. If the mo_source file is manually deleted (i.e. without using <code>set_mo_source()</code>), the references to the mo_source file will be removed upon the next use of <code><a href='as.mo.html'>as.mo()</a></code>.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>

2
docs/reference/p_symbol.html
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@ -82,7 +82,7 @@
</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="Latest development version">1.1.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9019</span>
</span>
</div>

2
docs/reference/pca.html
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@ -82,7 +82,7 @@
</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="Latest development version">1.1.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9019</span>
</span>
</div>

2
docs/reference/proportion.html
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@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</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="Latest development version">1.1.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9019</span>
</span>
</div>

2
docs/reference/resistance_predict.html
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@ -82,7 +82,7 @@
</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="Latest development version">1.1.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9019</span>
</span>
</div>

2
docs/reference/skewness.html
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@ -83,7 +83,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</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="Latest development version">1.1.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9019</span>
</span>
</div>

2
docs/reference/translate.html
View File

@ -82,7 +82,7 @@
</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="Latest development version">1.1.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9019</span>
</span>
</div>