(v1.7.1.9022) rely on vctrs for ab selectors

2025-07-23 21:43:15 +02:00 · 2021-07-23 21:42:11 +02:00
parent 0ec81cc12e
commit 4e1efd902c
130 changed files with 3785 additions and 2960 deletions
--- a/docs/reference/mo_source.html
+++ b/docs/reference/mo_source.html
@ -56,6 +56,8 @@ This is the fastest way to have your organisation (or analysis) specific codes p



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@ -67,9 +69,15 @@ This is the fastest way to have your organisation (or analysis) specific codes p



+  
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+    
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@ -83,7 +91,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
      </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">1.7.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
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@ -91,14 +99,14 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@ -107,77 +115,77 @@ This is the fastest way to have your organisation (or analysis) specific codes p
  <ul class="dropdown-menu" role="menu">
    <li>
      <a href="../articles/AMR.html">
-        <span class="fas fa-directions"></span>
+        <span class="fa fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="../articles/resistance_predict.html">
-        <span class="fas fa-dice"></span>
+        <span class="fa fa-dice"></span>
         
        Predict antimicrobial resistance
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-        <span class="fas fa-database"></span>
+        <span class="fa fa-database"></span>
         
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      <a href="../articles/PCA.html">
-        <span class="fas fa-compress"></span>
+        <span class="fa fa-compress"></span>
         
        Conduct principal component analysis for AMR
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    <li>
      <a href="../articles/MDR.html">
-        <span class="fas fa-skull-crossbones"></span>
+        <span class="fa fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
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+        <span class="fa fa-globe-americas"></span>
         
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+        <span class="fa fa-exchange-alt"></span>
         
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-        <span class="fas fa-bug"></span>
+        <span class="fa fa-bug"></span>
         
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-        <span class="fas fa-capsules"></span>
+        <span class="fa fa-capsules"></span>
         
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+        <span class="fa fa-shipping-fast"></span>
         
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@ -186,14 +194,14 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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-    <span class="fas fa-book-open"></span>
+    <span class="fa fa-book-open"></span>
     
    Manual
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-    <span class="fas fa-users"></span>
+    <span class="fa fa-users"></span>
     
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@ -216,7 +224,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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+    <span class="fa fa-clipboard-list"></span>
     
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@ -244,12 +252,12 @@ This is the fastest way to have your organisation (or analysis) specific codes p
 <p>This is <strong>the fastest way</strong> to have your organisation (or analysis) specific codes picked up and translated by this package, since you don't have to bother about it again after setting it up once.</p>
    </div>

-    <pre class="usage"><span class='fu'>set_mo_source</span><span class='op'>(</span>
+    <div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>set_mo_source</span><span class='op'>(</span>
  <span class='va'>path</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>

-<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>
+<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></code></pre></div>

    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
    <table class="ref-arguments">
@ -276,22 +284,22 @@ This is the fastest way to have your organisation (or analysis) specific codes p
    


-<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      |
+<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><code>  |         A          |       B      |
 --|--------------------|--------------|
 1 | Organisation XYZ   | mo           |
 2 | lab_mo_ecoli       | B_ESCHR_COLI |
 3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
 4 |                    |              |
-</pre>
+</code></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='op'>(</span><span class='st'>"home/me/ourcodes.xlsx"</span><span class='op'>)</span>
+<p>We save it as <code>"home/me/ourcodes.xlsx"</code>. Now we have to set it as a source:</p><pre class='sourceCode r'><code><span class='fu'>set_mo_source</span><span class='op'>(</span><span class='st'>"home/me/ourcodes.xlsx"</span><span class='op'>)</span>
 <span class='co'>#&gt; NOTE: Created mo_source file '/Users/me/mo_source.rds' (0.3 kB) from</span>
 <span class='co'>#&gt;       '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns </span>
 <span class='co'>#&gt;       "Organisation XYZ" and "mo"</span>
-</pre>
+</code></pre>

 <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='op'>(</span><span class='st'>"lab_mo_ecoli"</span><span class='op'>)</span>
+<p>And now we can use it in our functions:</p><pre class='sourceCode r'><code><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>
 <span class='co'>#&gt; Class &lt;mo&gt;</span>
 <span class='co'>#&gt; [1] B_ESCHR_COLI</span>

@ -304,18 +312,18 @@ This is the fastest way to have your organisation (or analysis) specific codes p
 <span class='co'>#&gt;       Use mo_uncertainties() to review it.</span>
 <span class='co'>#&gt; Class &lt;mo&gt;</span>
 <span class='co'>#&gt; [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI</span>
-</pre>
+</code></pre>

-<p>If we edit the Excel file by, let's say, 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><code>  |         A          |       B      |
 --|--------------------|--------------|
 1 | Organisation XYZ   | mo           |
 2 | lab_mo_ecoli       | B_ESCHR_COLI |
 3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
 4 | lab_Staph_aureus   | B_STPHY_AURS |
 5 |                    |              |
-</pre>
+</code></pre>

-<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>
+<p>...any new usage of an MO function in this package will update your data file:</p><pre class='sourceCode r'><code><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>
 <span class='co'>#&gt; NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from </span>
 <span class='co'>#&gt;       '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns</span>
 <span class='co'>#&gt;        "Organisation XYZ" and "mo"</span>
@ -324,11 +332,11 @@ This is the fastest way to have your organisation (or analysis) specific codes p

 <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>
 <span class='co'>#&gt; [1] "Staphylococcus"</span>
-</pre>
+</code></pre>

-<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>
+<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 class='sourceCode r'><code><span class='fu'>set_mo_source</span><span class='op'>(</span><span class='cn'>NULL</span><span class='op'>)</span>
 <span class='co'>#&gt; Removed mo_source file '/Users/me/mo_source.rds'</span>
-</pre>
+</code></pre>

 <p>If the original file (in the previous case an Excel file) is moved or deleted, the <code>mo_source.rds</code> file will be removed upon the next use of <code><a href='as.mo.html'>as.mo()</a></code> or any <code><a href='mo_property.html'>mo_*</a></code> function.</p>
    <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
@ -355,11 +363,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s

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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/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
+  <p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
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@ -368,6 +376,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
  


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