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fix warnings

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dr. M.S. (Matthijs) Berends
2019-01-04 09:49:42 +01:00
parent 80ea555663
commit 6652f7d82b
31 changed files with 948 additions and 762 deletions
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docs/reference/key_antibiotics.html
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@ -220,13 +220,17 @@
</div>
<pre class="usage"><span class='fu'>key_antibiotics</span>(<span class='no'>tbl</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>universal_1</span> <span class='kw'>=</span> <span class='st'>"amox"</span>,
<span class='kw'>universal_2</span> <span class='kw'>=</span> <span class='st'>"amcl"</span>, <span class='kw'>universal_3</span> <span class='kw'>=</span> <span class='st'>"cfur"</span>, <span class='kw'>universal_4</span> <span class='kw'>=</span> <span class='st'>"pita"</span>,
<span class='kw'>universal_5</span> <span class='kw'>=</span> <span class='st'>"cipr"</span>, <span class='kw'>universal_6</span> <span class='kw'>=</span> <span class='st'>"trsu"</span>, <span class='kw'>GramPos_1</span> <span class='kw'>=</span> <span class='st'>"vanc"</span>,
<span class='kw'>GramPos_2</span> <span class='kw'>=</span> <span class='st'>"teic"</span>, <span class='kw'>GramPos_3</span> <span class='kw'>=</span> <span class='st'>"tetr"</span>, <span class='kw'>GramPos_4</span> <span class='kw'>=</span> <span class='st'>"eryt"</span>,
<span class='kw'>GramPos_5</span> <span class='kw'>=</span> <span class='st'>"oxac"</span>, <span class='kw'>GramPos_6</span> <span class='kw'>=</span> <span class='st'>"rifa"</span>, <span class='kw'>GramNeg_1</span> <span class='kw'>=</span> <span class='st'>"gent"</span>,
<span class='kw'>GramNeg_2</span> <span class='kw'>=</span> <span class='st'>"tobr"</span>, <span class='kw'>GramNeg_3</span> <span class='kw'>=</span> <span class='st'>"coli"</span>, <span class='kw'>GramNeg_4</span> <span class='kw'>=</span> <span class='st'>"cfot"</span>,
<span class='kw'>GramNeg_5</span> <span class='kw'>=</span> <span class='st'>"cfta"</span>, <span class='kw'>GramNeg_6</span> <span class='kw'>=</span> <span class='st'>"mero"</span>, <span class='kw'>warnings</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
<pre class="usage"><span class='fu'>key_antibiotics</span>(<span class='no'>tbl</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>universal_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
<span class='st'>"amox"</span>), <span class='kw'>universal_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"amcl"</span>),
<span class='kw'>universal_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"cfur"</span>), <span class='kw'>universal_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
<span class='st'>"pita"</span>), <span class='kw'>universal_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"cipr"</span>),
<span class='kw'>universal_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"trsu"</span>), <span class='kw'>GramPos_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
<span class='st'>"vanc"</span>), <span class='kw'>GramPos_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"teic"</span>), <span class='kw'>GramPos_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
<span class='st'>"tetr"</span>), <span class='kw'>GramPos_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"eryt"</span>), <span class='kw'>GramPos_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
<span class='st'>"oxac"</span>), <span class='kw'>GramPos_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"rifa"</span>), <span class='kw'>GramNeg_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
<span class='st'>"gent"</span>), <span class='kw'>GramNeg_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"tobr"</span>), <span class='kw'>GramNeg_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
<span class='st'>"coli"</span>), <span class='kw'>GramNeg_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"cfot"</span>), <span class='kw'>GramNeg_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
<span class='st'>"cfta"</span>), <span class='kw'>GramNeg_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"mero"</span>), <span class='kw'>warnings</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
<span class='fu'>key_antibiotics_equal</span>(<span class='no'>x</span>, <span class='no'>y</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span>),
<span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>points_threshold</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
@ -320,8 +324,8 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='co'># set key antibiotics to a new variable</span>
<span class='no'>my_patients</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(<span class='kw'>keyab</span> <span class='kw'>=</span> <span class='fu'>key_antibiotics</span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>keyab</span> <span class='kw'>=</span> <span class='fu'>key_antibiotics</span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(
<span class='co'># now calculate first isolates</span>
<span class='kw'>first_regular</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>, <span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
<span class='co'># and first WEIGHTED isolates</span>