mirror of
https://github.com/msberends/AMR.git
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(v1.4.0.9000) more extensive unit tests
This commit is contained in:
@ -82,7 +82,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
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</span>
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</div>
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@ -242,67 +242,67 @@
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<p>Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on <a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot2</a> functions.</p>
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</div>
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<pre class="usage"><span class='fu'>ggplot_rsi</span>(
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<span class='kw'>data</span>,
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position = <span class='kw'>NULL</span>,
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x = <span class='st'>"antibiotic"</span>,
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fill = <span class='st'>"interpretation"</span>,
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facet = <span class='kw'>NULL</span>,
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breaks = <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>),
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limits = <span class='kw'>NULL</span>,
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translate_ab = <span class='st'>"name"</span>,
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combine_SI = <span class='fl'>TRUE</span>,
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combine_IR = <span class='fl'>FALSE</span>,
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minimum = <span class='fl'>30</span>,
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language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
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nrow = <span class='kw'>NULL</span>,
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colours = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(S = <span class='st'>"#61a8ff"</span>, SI = <span class='st'>"#61a8ff"</span>, I = <span class='st'>"#61f7ff"</span>, IR = <span class='st'>"#ff6961"</span>, R =
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<span class='st'>"#ff6961"</span>),
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datalabels = <span class='fl'>TRUE</span>,
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datalabels.size = <span class='fl'>2.5</span>,
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datalabels.colour = <span class='st'>"gray15"</span>,
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title = <span class='kw'>NULL</span>,
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subtitle = <span class='kw'>NULL</span>,
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caption = <span class='kw'>NULL</span>,
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x.title = <span class='st'>"Antimicrobial"</span>,
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y.title = <span class='st'>"Proportion"</span>,
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<span class='kw'>...</span>
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)
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<pre class="usage"><span class='fu'>ggplot_rsi</span><span class='op'>(</span>
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<span class='va'>data</span>,
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position <span class='op'>=</span> <span class='cn'>NULL</span>,
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x <span class='op'>=</span> <span class='st'>"antibiotic"</span>,
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fill <span class='op'>=</span> <span class='st'>"interpretation"</span>,
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facet <span class='op'>=</span> <span class='cn'>NULL</span>,
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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>,
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limits <span class='op'>=</span> <span class='cn'>NULL</span>,
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translate_ab <span class='op'>=</span> <span class='st'>"name"</span>,
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combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
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combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>,
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minimum <span class='op'>=</span> <span class='fl'>30</span>,
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language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
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nrow <span class='op'>=</span> <span class='cn'>NULL</span>,
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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'>"#61a8ff"</span>, SI <span class='op'>=</span> <span class='st'>"#61a8ff"</span>, I <span class='op'>=</span> <span class='st'>"#61f7ff"</span>, IR <span class='op'>=</span> <span class='st'>"#ff6961"</span>, R <span class='op'>=</span>
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<span class='st'>"#ff6961"</span><span class='op'>)</span>,
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datalabels <span class='op'>=</span> <span class='cn'>TRUE</span>,
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datalabels.size <span class='op'>=</span> <span class='fl'>2.5</span>,
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datalabels.colour <span class='op'>=</span> <span class='st'>"gray15"</span>,
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title <span class='op'>=</span> <span class='cn'>NULL</span>,
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subtitle <span class='op'>=</span> <span class='cn'>NULL</span>,
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caption <span class='op'>=</span> <span class='cn'>NULL</span>,
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x.title <span class='op'>=</span> <span class='st'>"Antimicrobial"</span>,
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y.title <span class='op'>=</span> <span class='st'>"Proportion"</span>,
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<span class='va'>...</span>
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<span class='op'>)</span>
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<span class='fu'>geom_rsi</span>(
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position = <span class='kw'>NULL</span>,
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x = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"antibiotic"</span>, <span class='st'>"interpretation"</span>),
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fill = <span class='st'>"interpretation"</span>,
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translate_ab = <span class='st'>"name"</span>,
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minimum = <span class='fl'>30</span>,
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language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
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combine_SI = <span class='fl'>TRUE</span>,
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combine_IR = <span class='fl'>FALSE</span>,
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<span class='kw'>...</span>
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)
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<span class='fu'>geom_rsi</span><span class='op'>(</span>
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position <span class='op'>=</span> <span class='cn'>NULL</span>,
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x <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'>"antibiotic"</span>, <span class='st'>"interpretation"</span><span class='op'>)</span>,
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fill <span class='op'>=</span> <span class='st'>"interpretation"</span>,
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translate_ab <span class='op'>=</span> <span class='st'>"name"</span>,
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minimum <span class='op'>=</span> <span class='fl'>30</span>,
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language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
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combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
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combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>,
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<span class='va'>...</span>
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<span class='op'>)</span>
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<span class='fu'>facet_rsi</span>(facet = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"interpretation"</span>, <span class='st'>"antibiotic"</span>), nrow = <span class='kw'>NULL</span>)
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<span class='fu'>facet_rsi</span><span class='op'>(</span>facet <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'>"interpretation"</span>, <span class='st'>"antibiotic"</span><span class='op'>)</span>, nrow <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
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<span class='fu'>scale_y_percent</span>(breaks = <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>), limits = <span class='kw'>NULL</span>)
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<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>
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<span class='fu'>scale_rsi_colours</span>(
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colours = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(S = <span class='st'>"#61a8ff"</span>, SI = <span class='st'>"#61a8ff"</span>, I = <span class='st'>"#61f7ff"</span>, IR = <span class='st'>"#ff6961"</span>, R =
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<span class='st'>"#ff6961"</span>)
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)
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<span class='fu'>scale_rsi_colours</span><span class='op'>(</span>
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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'>"#61a8ff"</span>, SI <span class='op'>=</span> <span class='st'>"#61a8ff"</span>, I <span class='op'>=</span> <span class='st'>"#61f7ff"</span>, IR <span class='op'>=</span> <span class='st'>"#ff6961"</span>, R <span class='op'>=</span>
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<span class='st'>"#ff6961"</span><span class='op'>)</span>
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<span class='op'>)</span>
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<span class='fu'>theme_rsi</span>()
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<span class='fu'>theme_rsi</span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'>labels_rsi_count</span>(
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position = <span class='kw'>NULL</span>,
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x = <span class='st'>"antibiotic"</span>,
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translate_ab = <span class='st'>"name"</span>,
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minimum = <span class='fl'>30</span>,
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language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
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combine_SI = <span class='fl'>TRUE</span>,
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combine_IR = <span class='fl'>FALSE</span>,
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datalabels.size = <span class='fl'>3</span>,
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datalabels.colour = <span class='st'>"gray15"</span>
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)</pre>
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<span class='fu'>labels_rsi_count</span><span class='op'>(</span>
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position <span class='op'>=</span> <span class='cn'>NULL</span>,
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x <span class='op'>=</span> <span class='st'>"antibiotic"</span>,
|
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translate_ab <span class='op'>=</span> <span class='st'>"name"</span>,
|
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minimum <span class='op'>=</span> <span class='fl'>30</span>,
|
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language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
|
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combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
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combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
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datalabels.size <span class='op'>=</span> <span class='fl'>3</span>,
|
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datalabels.colour <span class='op'>=</span> <span class='st'>"gray15"</span>
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<span class='op'>)</span></pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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@ -403,7 +403,7 @@
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p>At default, the names of antibiotics will be shown on the plots using <code><a href='ab_property.html'>ab_name()</a></code>. This can be set with the <code>translate_ab</code> parameter. See <code><a href='count.html'>count_df()</a></code>.</p><h3>The functions</h3>
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<p>At default, the names of antibiotics will be shown on the plots using <code><a href='ab_property.html'>ab_name()</a></code>. This can be set with the <code>translate_ab</code> parameter. See <code><a href='count.html'>count_df()</a></code>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>The functions</h3>
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<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>
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@ -427,80 +427,80 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
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<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
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<pre class="examples"><span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='http://ggplot2.tidyverse.org'>"ggplot2"</a></span>) <span class='op'>&</span> <span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
|
||||
<pre class="examples"><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='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
|
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<span class='co'># get antimicrobial results for drugs against a UTI:</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='kw'>example_isolates</span> <span class='op'>%>%</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'>+</span>
|
||||
<span class='fu'>geom_rsi</span>()
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'>geom_rsi</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># prettify the plot using some additional functions:</span>
|
||||
<span class='kw'>df</span> <span class='op'><-</span> <span class='kw'>example_isolates</span> <span class='op'>%>%</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='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='kw'>df</span>) <span class='op'>+</span>
|
||||
<span class='fu'>geom_rsi</span>() <span class='op'>+</span>
|
||||
<span class='fu'>scale_y_percent</span>() <span class='op'>+</span>
|
||||
<span class='fu'>scale_rsi_colours</span>() <span class='op'>+</span>
|
||||
<span class='fu'>labels_rsi_count</span>() <span class='op'>+</span>
|
||||
<span class='fu'>theme_rsi</span>()
|
||||
<span class='va'>df</span> <span class='op'><-</span> <span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</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'>df</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'>geom_rsi</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'>scale_y_percent</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'>scale_rsi_colours</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'>labels_rsi_count</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'>theme_rsi</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># or better yet, simplify this using the wrapper function - a single command:</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</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'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>()
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># get only proportions and no counts:</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</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'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>(datalabels = <span class='fl'>FALSE</span>)
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span><span class='op'>(</span>datalabels <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># add other ggplot2 parameters as you like:</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</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'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>(width = <span class='fl'>0.5</span>,
|
||||
colour = <span class='st'>"black"</span>,
|
||||
size = <span class='fl'>1</span>,
|
||||
linetype = <span class='fl'>2</span>,
|
||||
alpha = <span class='fl'>0.25</span>)
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span><span class='op'>(</span>width <span class='op'>=</span> <span class='fl'>0.5</span>,
|
||||
colour <span class='op'>=</span> <span class='st'>"black"</span>,
|
||||
size <span class='op'>=</span> <span class='fl'>1</span>,
|
||||
linetype <span class='op'>=</span> <span class='fl'>2</span>,
|
||||
alpha <span class='op'>=</span> <span class='fl'>0.25</span><span class='op'>)</span>
|
||||
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>(colours = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(SI = <span class='st'>"yellow"</span>))
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</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>SI <span class='op'>=</span> <span class='st'>"yellow"</span><span class='op'>)</span><span class='op'>)</span>
|
||||
|
||||
}
|
||||
<span class='op'>}</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'>%>%</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'>%>%</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'>%>%</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</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'>%>%</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'>%>%</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'>%>%</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'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>(x = <span class='st'>"age_group"</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'>%>%</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'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span><span class='op'>(</span>x <span class='op'>=</span> <span class='st'>"age_group"</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># for colourblind mode, use divergent colours from the viridis package:</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</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'>%>%</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='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span><span class='op'>(</span><span class='op'>)</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='op'>(</span><span class='op'>)</span>
|
||||
<span class='co'># a shorter version which also adjusts data label colours:</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</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'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>(colours = <span class='fl'>FALSE</span>)
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span><span class='op'>(</span>colours <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
|
||||
<span class='co'># it also supports groups (don't forget to use the group var on `x` or `facet`):</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>hospital_id</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'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>(x = <span class='st'>"hospital_id"</span>,
|
||||
facet = <span class='st'>"antibiotic"</span>,
|
||||
nrow = <span class='fl'>1</span>,
|
||||
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='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>hospital_id</span>, <span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span><span class='op'>(</span>x <span class='op'>=</span> <span class='st'>"hospital_id"</span>,
|
||||
facet <span class='op'>=</span> <span class='st'>"antibiotic"</span>,
|
||||
nrow <span class='op'>=</span> <span class='fl'>1</span>,
|
||||
title <span class='op'>=</span> <span class='st'>"AMR of Anti-UTI Drugs Per Hospital"</span>,
|
||||
x.title <span class='op'>=</span> <span class='st'>"Hospital"</span>,
|
||||
datalabels <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
<span class='co'># }</span>
|
||||
</pre>
|
||||
</div>
|
||||
@ -518,7 +518,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
Reference in New Issue
Block a user