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(v1.3.0.9035) mdro() for EUCAST 3.2, examples cleanup

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dr. M.S. (Matthijs) Berends
2020-09-29 23:35:46 +02:00
parent 68e6e1e329
commit 4e0374af29
94 changed files with 1143 additions and 1165 deletions
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11
docs/reference/ggplot_rsi.html
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@ -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">1.3.0.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9035</span>
</span>
</div>
@ -467,14 +467,14 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
}
<span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># \donttest{</span>
<span class='co'># resistance of ciprofloxacine per age group</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(first_isolate = <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='kw'>.</span>)) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='kw'>first_isolate</span> <span class='op'>==</span> <span class='fl'>TRUE</span>,
<span class='kw'>mo</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='op'>%&gt;%</span>
<span class='co'># `age_group` is also a function of this package:</span>
<span class='co'># `age_groups` is also a function of this AMR package:</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(age_group = <span class='fu'><a href='age_groups.html'>age_groups</a></span>(<span class='kw'>age</span>)) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>age_group</span>,
<span class='kw'>CIP</span>) <span class='op'>%&gt;%</span>
@ -483,7 +483,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='co'># for colourblind mode, use divergent colours from the viridis package:</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>NIT</span>, <span class='kw'>FOS</span>, <span class='kw'>TMP</span>, <span class='kw'>CIP</span>) <span class='op'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>() <span class='op'>+</span> <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_fill_viridis_d</a></span>()
<span class='fu'>ggplot_rsi</span>() <span class='op'>+</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_fill_viridis_d</a></span>()
<span class='co'># a shorter version which also adjusts data label colours:</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>NIT</span>, <span class='kw'>FOS</span>, <span class='kw'>TMP</span>, <span class='kw'>CIP</span>) <span class='op'>%&gt;%</span>
@ -500,7 +501,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
title = <span class='st'>"AMR of Anti-UTI Drugs Per Hospital"</span>,
x.title = <span class='st'>"Hospital"</span>,
datalabels = <span class='fl'>FALSE</span>)
}
<span class='co'># }</span>
</pre>
</div>
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