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big website update, licence txt update

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dr. M.S. (Matthijs) Berends
2019-01-02 23:24:07 +01:00
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@ -49,7 +49,7 @@
<meta property="og:description" content="Convenient wrapper around grep to match a pattern: a %like% b. It always returns a logical vector and is always case-insensitive. Also, pattern (b) can be as long as x (a) to compare items of each index in both vectors." />
<meta property="og:image" content="https://msberends.gitlab.io/logo.png" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
@ -80,7 +80,7 @@
</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="Released version">0.5.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9009</span>
</span>
</div>
@ -93,12 +93,65 @@
Home
</a>
</li>
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-question-circle"></span>
Get Started
How to
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/Predict.html">
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../articles/mo_property.html">
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../articles/ab_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/freq.html">
<span class="fa fa-sort-amount-down"></span>
Create frequency tables
</a>
</li>
<li>
<a href="../articles/G_test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
</ul>
</li>
<li>
<a href="../reference/">
@ -121,17 +174,17 @@
Changelog
</a>
</li>
<li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
Source Code
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
@ -204,44 +257,40 @@
<p>Using RStudio? This function can also be inserted from the Addins menu and can have its own Keyboard Shortcut like Ctrl+Shift+L or Cmd+Shift+L (see Tools &gt; Modify Keyboard Shortcuts...).</p>
<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>
<p><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
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 omprehensive tutorial</a> about how to conduct AMR analysis and find <a href='https://msberends.gitlab.io/AMR/reference'>the complete documentation of all functions</a>, which reads a lot easier than in R.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='https://www.rdocumentation.org/packages/base/topics/grep'>grep</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># simple test</span>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># simple test</span>
<span class='no'>a</span> <span class='kw'>&lt;-</span> <span class='st'>"This is a test"</span>
<span class='no'>b</span> <span class='kw'>&lt;-</span> <span class='st'>"TEST"</span>
<span class='no'>a</span> <span class='kw'>%like%</span> <span class='no'>b</span></div><div class='output co'>#&gt; [1] TRUE</div><div class='input'><span class='co'>#&gt; TRUE</span>
<span class='no'>b</span> <span class='kw'>%like%</span> <span class='no'>a</span></div><div class='output co'>#&gt; [1] FALSE</div><div class='input'><span class='co'>#&gt; FALSE</span>
<span class='no'>a</span> <span class='kw'>%like%</span> <span class='no'>b</span>
<span class='co'>#&gt; TRUE</span>
<span class='no'>b</span> <span class='kw'>%like%</span> <span class='no'>a</span>
<span class='co'>#&gt; FALSE</span>
<span class='co'># also supports multiple patterns, length must be equal to x</span>
<span class='no'>a</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Test case"</span>, <span class='st'>"Something different"</span>, <span class='st'>"Yet another thing"</span>)
<span class='no'>b</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"case"</span>, <span class='st'>"diff"</span>, <span class='st'>"yet"</span>)
<span class='no'>a</span> <span class='kw'>%like%</span> <span class='no'>b</span></div><div class='output co'>#&gt; [1] TRUE TRUE TRUE</div><div class='input'><span class='co'>#&gt; TRUE TRUE TRUE</span>
<span class='no'>a</span> <span class='kw'>%like%</span> <span class='no'>b</span>
<span class='co'>#&gt; TRUE TRUE TRUE</span>
<span class='co'># get frequencies of bacteria whose name start with 'Ent' or 'ent'</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='join.html'>left_join_microorganisms</a></span>() <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>genus</span> <span class='kw'>%like%</span> <span class='st'>'^ent'</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>)</div><div class='output co'>#&gt; <span class='message'>Joining, by = "mo"</span></div><div class='output co'>#&gt;
#&gt;
#&gt; **Frequency table of `genus` and `species`**
#&gt;
#&gt;
#&gt; | |Item | Count| Percent| Cum. Count| Cum. Percent|
#&gt; |:--|:--------------------------|-----:|-------:|----------:|------------:|
#&gt; |1 |Enterococcus faecalis | 39| 35.8%| 39| 35.8%|
#&gt; |2 |Enterobacter cloacae | 23| 21.1%| 62| 56.9%|
#&gt; |3 |Enterococcus faecium | 21| 19.3%| 83| 76.1%|
#&gt; |4 |Enterococcus species | 20| 18.3%| 103| 94.5%|
#&gt; |5 |Enterobacter aerogenes | 3| 2.8%| 106| 97.2%|
#&gt; |6 |Enterococcus avium | 2| 1.8%| 108| 99.1%|
#&gt; |7 |Enterococcus casseliflavus | 1| 0.9%| 109| 100.0%|
#&gt;
#&gt; </div></pre>
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>genus</span> <span class='kw'>%like%</span> <span class='st'>'^ent'</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>)
<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@ -254,6 +303,8 @@
<li><a href="#details">Details</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>