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(v1.4.0.9041) updates based on review
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@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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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="Latest development version">1.4.0.9032</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9041</span>
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@ -91,14 +91,14 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@ -107,77 +107,77 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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<a href="../articles/AMR.html">
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Conduct principal component analysis for AMR
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Other: benchmarks
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@ -186,21 +186,21 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@ -209,14 +209,14 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@ -244,9 +244,12 @@ This is the fastest way to have your organisation (or analysis) specific codes 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='op'>(</span><span class='va'>path</span><span class='op'>)</span>
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<pre class="usage"><span class='fu'>set_mo_source</span><span class='op'>(</span>
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<span class='va'>path</span>,
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destination <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>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>
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<span class='op'>)</span>
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<span class='fu'>get_mo_source</span><span class='op'>(</span><span class='op'>)</span></pre>
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<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'>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></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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@ -255,14 +258,18 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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<th>path</th>
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<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>
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</tr>
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<tr>
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<th>destination</th>
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<td><p>destination of the compressed data file, default to the user's home directory.</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 separated 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 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'>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 R 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.</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 of the original file will be saved as an R 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>
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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'>readRDS()</a></code>. If the original file has changed (by checking the aforementioned options <code>mo_source</code> and <code>mo_source_datetime</code>), 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><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'>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 R 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> parameter 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>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'>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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<h2 class="hasAnchor" id="how-to-setup"><a class="anchor" href="#how-to-setup"></a>How to setup</h2>
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@ -278,12 +285,14 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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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><span class='fu'>set_mo_source</span><span class='op'>(</span><span class='st'>"home/me/ourcodes.xlsx"</span><span class='op'>)</span>
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<span class='co'>#> NOTE: Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'</span>
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<span class='co'>#> (columns "Organisation XYZ" and "mo")</span>
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<span class='co'>#> NOTE: Created mo_source file '/Users/me/mo_source.rds' (0.3 kB) from</span>
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<span class='co'>#> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns </span>
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<span class='co'>#> "Organisation XYZ" and "mo"</span>
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</pre>
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<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>
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<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>
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<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='op'>(</span><span class='st'>"lab_mo_ecoli"</span><span class='op'>)</span>
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<span class='co'>#> Class <mo></span>
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<span class='co'>#> [1] B_ESCHR_COLI</span>
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<span class='fu'><a href='mo_property.html'>mo_genus</a></span><span class='op'>(</span><span class='st'>"lab_mo_kpneumoniae"</span><span class='op'>)</span>
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@ -291,6 +300,9 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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<span class='co'># other input values still work too</span>
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<span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"Escherichia coli"</span>, <span class='st'>"E. coli"</span>, <span class='st'>"lab_mo_ecoli"</span><span class='op'>)</span><span class='op'>)</span>
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<span class='co'>#> NOTE: Translation to one microorganism was guessed with uncertainty.</span>
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<span class='co'>#> Use mo_uncertainties() to review it.</span>
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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>
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</pre>
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@ -304,8 +316,10 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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</pre>
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<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='op'>(</span><span class='st'>"lab_mo_ecoli"</span><span class='op'>)</span>
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<span class='co'>#> NOTE: Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'</span>
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<span class='co'>#> (columns "Organisation XYZ" and "mo")</span>
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<span class='co'>#> NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from </span>
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<span class='co'>#> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns</span>
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<span class='co'>#> "Organisation XYZ" and "mo"</span>
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<span class='co'>#> Class <mo></span>
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<span class='co'>#> [1] B_ESCHR_COLI</span>
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<span class='fu'><a href='mo_property.html'>mo_genus</a></span><span class='op'>(</span><span class='st'>"lab_Staph_aureus"</span><span class='op'>)</span>
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@ -313,10 +327,10 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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</pre>
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<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='op'>(</span><span class='cn'>NULL</span><span class='op'>)</span>
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<span class='co'># Removed mo_source file '~/.mo_source.rds'.</span>
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<span class='co'>#> Removed mo_source file '/Users/me/mo_source.rds'</span>
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</pre>
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<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>
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<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>.</p>
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<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
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