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(v0.8.0.9028) examples fix

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dr. M.S. (Matthijs) Berends
2019-11-10 13:17:20 +01:00
parent 59ededa8dc
commit 54b6322056
12 changed files with 19 additions and 19 deletions
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6
docs/reference/first_isolate.html
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@ -85,7 +85,7 @@
</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">0.8.0.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9028</span>
</span>
</div>
@ -395,13 +395,13 @@ To conduct an analysis of antimicrobial resistance, you should only include the
<span class='no'>A</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>GEN</span>), <span class='co'># gentamicin availability</span>
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='AMR-deprecated.html'>portion_IR</a></span>(<span class='no'>GEN</span>)) <span class='co'># gentamicin resistance</span>
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='proportion.html'>resistance</a></span>(<span class='no'>GEN</span>)) <span class='co'># gentamicin resistance</span>
<span class='no'>B</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'>filter_first_weighted_isolate</span>() <span class='kw'>%&gt;%</span> <span class='co'># the 1st isolate filter</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>GEN</span>), <span class='co'># gentamicin availability</span>
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='AMR-deprecated.html'>portion_IR</a></span>(<span class='no'>GEN</span>)) <span class='co'># gentamicin resistance</span>
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='proportion.html'>resistance</a></span>(<span class='no'>GEN</span>)) <span class='co'># gentamicin resistance</span>
<span class='co'># Have a look at A and B.</span>
<span class='co'># B is more reliable because every isolate is only counted once.</span>