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(v1.8.1.9003) set_mo_source() fix
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@ -18,7 +18,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9003</span>
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@ -31,7 +31,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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</a>
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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How to
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@ -175,15 +175,15 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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<div id="arguments">
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<h2>Arguments</h2>
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<dl><dt>path</dt>
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<dd><p>location of your reference file, see <em>Details</em>. Can be <code>""</code>, <code>NULL</code> or <code>FALSE</code> to delete the reference file.</p></dd>
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<dd><p>location of your reference file, this can be any text file (comma-, tab- or pipe-separated) or an Excel file (see <em>Details</em>). Can also be <code>""</code>, <code>NULL</code> or <code>FALSE</code> to delete the reference file.</p></dd>
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<dt>destination</dt>
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<dd><p>destination of the compressed data file, default to the user's home directory.</p></dd>
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</dl></div>
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<div id="details">
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<h2>Details</h2>
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<p>The reference file can be a text file separated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an <span style="R">R</span> object file (extension '.rds'). To use an Excel file, you will 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 <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, must have a column named <code>"mo"</code> which contains values from <code><a href="microorganisms.html">microorganisms$mo</a></code> and must have a reference column with your own defined values. If all tests pass, <code>set_mo_source()</code> will read the file into <span style="R">R</span> and will ask to export it to <code>"~/mo_source.rds"</code>. The CRAN policy disallows packages to write to the file system, although '<em>exceptions may be allowed in interactive sessions if the package obtains confirmation from the user</em>'. For this reason, this function only works in interactive sessions so that the user can <strong>specifically confirm and allow</strong> that this file will be created. The destination of this file can be set with the <code>destination</code> argument and defaults to the user's home directory. It can also be set as an <span style="R">R</span> option, using <code>options(AMR_mo_source = "my/location/file.rds")</code>.</p>
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<p>The created compressed data file <code>"mo_source.rds"</code> will be used at default for MO determination (function <code><a href="as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions like <code><a href="mo_property.html">mo_genus()</a></code> and <code><a href="mo_property.html">mo_gramstain()</a></code>). The location and timestamp of the original file will be saved as an attribute to the compressed data file.</p>
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<p><code>set_mo_source()</code> will check the file for validity: it must be a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, must have a column named <code>"mo"</code> which contains values from <code><a href="microorganisms.html">microorganisms$mo</a></code> or <code><a href="microorganisms.html">microorganisms$fullname</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 <span style="R">R</span> and will ask to export it to <code>"~/mo_source.rds"</code>. The CRAN policy disallows packages to write to the file system, although '<em>exceptions may be allowed in interactive sessions if the package obtains confirmation from the user</em>'. For this reason, this function only works in interactive sessions so that the user can <strong>specifically confirm and allow</strong> that this file will be created. The destination of this file can be set with the <code>destination</code> argument and defaults to the user's home directory. It can also be set as an <span style="R">R</span> option, using <code>options(AMR_mo_source = "my/location/file.rds")</code>.</p>
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<p>The created compressed data file <code>"mo_source.rds"</code> will 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 and timestamp of the original file will be saved as an <a href="https://rdrr.io/r/base/attributes.html" class="external-link">attribute</a> to the compressed data file.</p>
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<p>The function <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" class="external-link">readRDS()</a></code>. If the original file has changed (by checking the location and timestamp of the original file), it will call <code>set_mo_source()</code> to update the data file automatically if used in an interactive session.</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 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>
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</div>
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@ -192,12 +192,12 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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<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><div class="sourceCode"><pre><code> | A | B |
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--|--------------------|--------------|
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1 | Organisation XYZ | mo |
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2 | lab_mo_ecoli | B_ESCHR_COLI |
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3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
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4 | | |
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<p>Imagine this data on a sheet of an Excel file. The first column contains the organisation specific codes, the second column contains valid taxonomic names:</p><div class="sourceCode"><pre><code> | A | B |
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--|--------------------|-----------------------|
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1 | Organisation XYZ | mo |
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2 | lab_mo_ecoli | Escherichia coli |
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3 | lab_mo_kpneumoniae | Klebsiella pneumoniae |
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4 | | |
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</code></pre></div>
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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><div class="sourceCode"><pre><code><span class="fu"><a href="../reference/mo_source.html">set_mo_source</a></span><span class="op">(</span><span class="st">"home/me/ourcodes.xlsx"</span><span class="op">)</span>
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@ -220,13 +220,13 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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<span class="co">#> Class <mo></span>
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<span class="co">#> [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI</span></code></pre></div>
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<p>If we edit the Excel file by, let's say, adding row 4 like this:</p><div class="sourceCode"><pre><code> | A | B |
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--|--------------------|--------------|
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1 | Organisation XYZ | mo |
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2 | lab_mo_ecoli | B_ESCHR_COLI |
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3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
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4 | lab_Staph_aureus | B_STPHY_AURS |
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5 | | |
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<p>If we edit the Excel file by, let's say, adding row 4 like this:</p><div class="sourceCode"><pre><code> | A | B |
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--|--------------------|-----------------------|
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1 | Organisation XYZ | mo |
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2 | lab_mo_ecoli | Escherichia coli |
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3 | lab_mo_kpneumoniae | Klebsiella pneumoniae |
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4 | lab_Staph_aureus | Staphylococcus aureus |
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5 | | |
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</code></pre></div>
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<p>...any new usage of an MO function in this package will update your data file:</p><div class="sourceCode"><pre><code><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"lab_mo_ecoli"</span><span class="op">)</span>
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@ -271,7 +271,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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</div>
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<div class="pkgdown">
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<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
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