P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 18:01:50 +02:00
Code Releases Activity

(v1.3.0.9001) website update

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-08-10 12:46:03 +02:00
parent 0d9602a6a9
commit 7d16bec21f
79 changed files with 2221 additions and 1974 deletions
Download Patch File Download Diff File Expand all files Collapse all files

32
docs/reference/guess_ab_col.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">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@ -235,7 +235,7 @@
<p>This tries to find a column name in a data set based on information from the <a href='antibiotics.html'>antibiotics</a> data set. Also supports WHONET abbreviations.</p>
</div>
<pre class="usage"><span class='fu'>guess_ab_col</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>search_string</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
<pre class="usage"><span class='fu'>guess_ab_col</span>(x = <span class='kw'>NULL</span>, search_string = <span class='kw'>NULL</span>, verbose = <span class='fl'>FALSE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -273,32 +273,32 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>amox</span> <span class='kw'>=</span> <span class='st'>"S"</span>,
<span class='kw'>tetr</span> <span class='kw'>=</span> <span class='st'>"R"</span>)
<pre class="examples"><span class='kw'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(amox = <span class='st'>"S"</span>,
tetr = <span class='st'>"R"</span>)
<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='st'>"amoxicillin"</span>)
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"amoxicillin"</span>)
<span class='co'># [1] "amox"</span>
<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='st'>"J01AA07"</span>) <span class='co'># ATC code of tetracycline</span>
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"J01AA07"</span>) <span class='co'># ATC code of tetracycline</span>
<span class='co'># [1] "tetr"</span>
<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='st'>"J01AA07"</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"J01AA07"</span>, verbose = <span class='fl'>TRUE</span>)
<span class='co'># NOTE: Using column `tetr` as input for `J01AA07` (tetracycline).</span>
<span class='co'># [1] "tetr"</span>
<span class='co'># WHONET codes</span>
<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>AMP_ND10</span> <span class='kw'>=</span> <span class='st'>"R"</span>,
<span class='kw'>AMC_ED20</span> <span class='kw'>=</span> <span class='st'>"S"</span>)
<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='st'>"ampicillin"</span>)
<span class='kw'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(AMP_ND10 = <span class='st'>"R"</span>,
AMC_ED20 = <span class='st'>"S"</span>)
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"ampicillin"</span>)
<span class='co'># [1] "AMP_ND10"</span>
<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='st'>"J01CR02"</span>)
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"J01CR02"</span>)
<span class='co'># [1] "AMC_ED20"</span>
<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='fu'><a href='as.ab.html'>as.ab</a></span>(<span class='st'>"augmentin"</span>))
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='fu'><a href='as.ab.html'>as.ab</a></span>(<span class='st'>"augmentin"</span>))
<span class='co'># [1] "AMC_ED20"</span>
<span class='co'># Longer names take precendence:</span>
<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>AMP_ED2</span> <span class='kw'>=</span> <span class='st'>"S"</span>,
<span class='kw'>AMP_ED20</span> <span class='kw'>=</span> <span class='st'>"S"</span>)
<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='st'>"ampicillin"</span>)
<span class='kw'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(AMP_ED2 = <span class='st'>"S"</span>,
AMP_ED20 = <span class='st'>"S"</span>)
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"ampicillin"</span>)
<span class='co'># [1] "AMP_ED20"</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@ -315,7 +315,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>