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(v1.4.0.9026) docu update

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dr. M.S. (Matthijs) Berends
2020-11-24 11:47:54 +01:00
parent b045b571a6
commit 7b42b15c90
21 changed files with 47 additions and 50 deletions
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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">1.4.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9026</span>
</span>
</div>
@ -361,7 +361,7 @@
</tr>
<tr>
<th>colours</th>
<td><p>a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be <code>FALSE</code> to use default [ggplot2][<code><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot2::ggplot()</a></code> colours.</p></td>
<td><p>a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be <code>FALSE</code> to use default <a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot2</a> colours.</p></td>
</tr>
<tr>
<th>datalabels</th>
@ -468,13 +468,12 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='op'>}</span>
<span class='co'># \donttest{</span>
<span class='co'># resistance of ciprofloxacine per age group</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>first_isolate <span class='op'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span><span class='op'>(</span><span class='va'>.</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>first_isolate</span> <span class='op'>==</span> <span class='cn'>TRUE</span>,
<span class='va'>mo</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='co'># `age_groups` is also a function of this AMR package:</span>
<span class='co'># age_groups() is also a function in this AMR package:</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span>age_group <span class='op'>=</span> <span class='fu'><a href='age_groups.html'>age_groups</a></span><span class='op'>(</span><span class='va'>age</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>age_group</span>,
<span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span>