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WHONET/EARS-Net support

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dr. M.S. (Matthijs) Berends
2019-01-29 00:06:50 +01:00
parent f6336fdd89
commit 6aae206320
83 changed files with 1428 additions and 633 deletions
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docs/reference/freq.html
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@ -81,7 +81,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
</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">0.5.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
</span>
</div>
@ -117,6 +117,13 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
@ -385,8 +392,8 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># you could also use `select` or `pull` to get your variables</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>()
@ -402,20 +409,20 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># group a variable and analyse another</span>
<span class='no'>septic_patients</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://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>gender</span>)
<span class='co'># get top 10 bugs of hospital A as a vector</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>top_freq</span>(<span class='fl'>10</span>)
<span class='co'># save frequency table to an object</span>
<span class='no'>years</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>year</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>date</span>, <span class='st'>"%Y"</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'>year</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>date</span>, <span class='st'>"%Y"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>year</span>)
@ -466,11 +473,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># only get selected columns</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>item</span>, <span class='no'>percent</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>item</span>, <span class='no'>percent</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(-<span class='no'>count</span>, -<span class='no'>cum_count</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(-<span class='no'>count</span>, -<span class='no'>cum_count</span>)
<span class='co'># check differences between frequency tables</span>