P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 20:21:55 +02:00
Code Releases Activity

(v1.5.0.9027) website update

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-02-26 12:11:29 +01:00
parent 1737d56ae4
commit 41f94cde97
45 changed files with 491 additions and 425 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
docs/reference/as.mic.html
View File

@ -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">1.5.0.9025</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9027</span>
</span>
</div>

16
docs/reference/ggplot_rsi.html
View File

@ -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">1.5.0.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9027</span>
</span>
</div>
@ -285,11 +285,7 @@
<span class='fu'>scale_y_percent</span><span class='op'>(</span>breaks <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span><span class='op'>)</span>, limits <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>scale_rsi_colours</span><span class='op'>(</span>
colours <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>S <span class='op'>=</span> <span class='st'>"#3CAEA3"</span>, SI <span class='op'>=</span> <span class='st'>"#3CAEA3"</span>, I <span class='op'>=</span> <span class='st'>"#F6D55C"</span>, IR <span class='op'>=</span> <span class='st'>"#ED553B"</span>, R <span class='op'>=</span>
<span class='st'>"#ED553B"</span><span class='op'>)</span>,
aesthetics <span class='op'>=</span> <span class='st'>"fill"</span>
<span class='op'>)</span>
<span class='fu'>scale_rsi_colours</span><span class='op'>(</span><span class='va'>...</span>, aesthetics <span class='op'>=</span> <span class='st'>"fill"</span><span class='op'>)</span>
<span class='fu'>theme_rsi</span><span class='op'>(</span><span class='op'>)</span>
@ -362,7 +358,7 @@
</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> for standard <a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot2</a> colours. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red.</p></td>
<td><p>a named vactor with colour to be used for filling. The default colours are colour-blind friendly.</p></td>
</tr>
<tr>
<th>datalabels</th>
@ -398,11 +394,11 @@
</tr>
<tr>
<th>...</th>
<td><p>other arguments passed on to <code>geom_rsi()</code></p></td>
<td><p>other arguments passed on to <code>geom_rsi()</code> or, in case of <code>scale_rsi_colours()</code>, named values to set colours. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red. See <em>Examples</em>.</p></td>
</tr>
<tr>
<th>aesthetics</th>
<td><p>aesthetics to apply the colours to, defaults to "fill" but can also be "colour" or "both"</p></td>
<td><p>aesthetics to apply the colours to, defaults to "fill" but can also be (a combination of) "alpha", "colour", "fill", "linetype", "shape" or "size"</p></td>
</tr>
</table>
@ -414,7 +410,7 @@
<p><code>geom_rsi()</code> will take any variable from the data that has an <code><a href='as.rsi.html'>rsi</a></code> class (created with <code><a href='as.rsi.html'>as.rsi()</a></code>) using <code><a href='proportion.html'>rsi_df()</a></code> and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.</p>
<p><code>facet_rsi()</code> creates 2d plots (at default based on S/I/R) using <code><a href='https://ggplot2.tidyverse.org/reference/facet_wrap.html'>ggplot2::facet_wrap()</a></code>.</p>
<p><code>scale_y_percent()</code> transforms the y axis to a 0 to 100% range using <code><a href='https://ggplot2.tidyverse.org/reference/scale_continuous.html'>ggplot2::scale_y_continuous()</a></code>.</p>
<p><code>scale_rsi_colours()</code> sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using <code><a href='https://ggplot2.tidyverse.org/reference/scale_manual.html'>ggplot2::scale_fill_manual()</a></code>.</p>
<p><code>scale_rsi_colours()</code> sets colours to the bars (green for S, yellow for I, and red for R). with multilingual support. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red.</p>
<p><code>theme_rsi()</code> is a [ggplot2 theme][<code><a href='https://ggplot2.tidyverse.org/reference/theme.html'>ggplot2::theme()</a></code> with minimal distraction.</p>
<p><code>labels_rsi_count()</code> print datalabels on the bars with percentage and amount of isolates using <code><a href='https://ggplot2.tidyverse.org/reference/geom_text.html'>ggplot2::geom_text()</a></code>.</p>
<p><code>ggplot_rsi()</code> is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (<code>%&gt;%</code>). See <em>Examples</em>.</p>

4
docs/reference/index.html
View File

@ -81,7 +81,7 @@
</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">1.5.0.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9027</span>
</span>
</div>
@ -453,7 +453,7 @@
</tr><tr>
<td>
<p><code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;rsi&gt;</i>)</a></code> </p>
<p><code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;rsi&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;rsi&gt;</i>)</a></code> </p>
</td>
<td><p>Plotting for Classes <code>rsi</code>, <code>mic</code> and <code>disk</code></p></td>
</tr><tr>

2
docs/reference/like.html
View File

@ -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">1.5.0.9025</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9027</span>
</span>
</div>

20
docs/reference/plot.html
View File

@ -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">1.5.0.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9027</span>
</span>
</div>
@ -274,7 +274,7 @@
<span class='co'># S3 method for disk</span>
<span class='fu'>plot</span><span class='op'>(</span>
<span class='va'>x</span>,
main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Disk zones values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Disk zones of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
xlab <span class='op'>=</span> <span class='st'>"Disk diffusion diameter (mm)"</span>,
mo <span class='op'>=</span> <span class='cn'>NULL</span>,
@ -289,7 +289,7 @@
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Disk zones values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Disk zones of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
xlab <span class='op'>=</span> <span class='st'>"Disk diffusion diameter (mm)"</span>,
mo <span class='op'>=</span> <span class='cn'>NULL</span>,
@ -307,6 +307,17 @@
xlab <span class='op'>=</span> <span class='st'>"Antimicrobial Interpretation"</span>,
main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='co'># S3 method for rsi</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
xlab <span class='op'>=</span> <span class='st'>"Antimicrobial Interpretation"</span>,
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
colours_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"#ED553B"</span>, <span class='st'>"#3CAEA3"</span>, <span class='st'>"#F6D55C"</span><span class='op'>)</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@ -378,9 +389,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='va'>some_mic_values</span> <span class='op'>&lt;-</span> <span class='fu'><a href='random.html'>random_mic</a></span><span class='op'>(</span>size <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>
<span class='va'>some_disk_values</span> <span class='op'>&lt;-</span> <span class='fu'><a href='random.html'>random_disk</a></span><span class='op'>(</span>size <span class='op'>=</span> <span class='fl'>100</span>, mo <span class='op'>=</span> <span class='st'>"Escherichia coli"</span>, ab <span class='op'>=</span> <span class='st'>"cipro"</span><span class='op'>)</span>
<span class='va'>some_rsi_values</span> <span class='op'>&lt;-</span> <span class='fu'><a href='random.html'>random_rsi</a></span><span class='op'>(</span><span class='fl'>50</span>, prob_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.30</span>, <span class='fl'>0.55</span>, <span class='fl'>0.05</span><span class='op'>)</span><span class='op'>)</span>
<span class='fu'>plot</span><span class='op'>(</span><span class='va'>some_mic_values</span><span class='op'>)</span>
<span class='fu'>plot</span><span class='op'>(</span><span class='va'>some_disk_values</span><span class='op'>)</span>
<span class='fu'>plot</span><span class='op'>(</span><span class='va'>some_rsi_values</span><span class='op'>)</span>
<span class='co'># when providing the microorganism and antibiotic, colours will show interpretations:</span>
<span class='fu'>plot</span><span class='op'>(</span><span class='va'>some_mic_values</span>, mo <span class='op'>=</span> <span class='st'>"S. aureus"</span>, ab <span class='op'>=</span> <span class='st'>"ampicillin"</span><span class='op'>)</span>
@ -389,6 +402,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='http://ggplot2.tidyverse.org'>"ggplot2"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>some_mic_values</span><span class='op'>)</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>some_disk_values</span>, mo <span class='op'>=</span> <span class='st'>"Escherichia coli"</span>, ab <span class='op'>=</span> <span class='st'>"cipro"</span><span class='op'>)</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>some_rsi_values</span><span class='op'>)</span>
<span class='op'>}</span>
</pre>
</div>

2
docs/reference/random.html
View File

@ -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">1.5.0.9025</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9027</span>
</span>
</div>