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Built site for AMR: 1.8.1.9045@e7af5fc
This commit is contained in:
github-actions
@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -311,12 +311,15 @@
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \donttest{</span></span></span>
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<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
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<span class="r-in"><span> </span></span>
|
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<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span> <span class="co"># get antimicrobial results for drugs against a UTI:</span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">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></span>
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||||
<span class="r-in"><span> <span class="fu">geom_rsi</span><span class="op">(</span><span class="op">)</span></span></span>
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||||
<span class="r-in"><span> </span></span>
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-plt img"><img src="ggplot_rsi-1.png" alt="" width="700" height="433"></span>
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<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span> <span class="co"># prettify the plot using some additional functions:</span></span></span>
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<span class="r-in"><span> <span class="va">df</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">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></span>
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||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">df</span><span class="op">)</span> <span class="op">+</span></span></span>
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@ -325,74 +328,105 @@
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<span class="r-in"><span> <span class="fu">scale_rsi_colours</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
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<span class="r-in"><span> <span class="fu">labels_rsi_count</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
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||||
<span class="r-in"><span> <span class="fu">theme_rsi</span><span class="op">(</span><span class="op">)</span></span></span>
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<span class="r-in"><span> </span></span>
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||||
<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-plt img"><img src="ggplot_rsi-2.png" alt="" width="700" height="433"></span>
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||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span> <span class="co"># or better yet, simplify this using the wrapper function - a single command:</span></span></span>
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<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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||||
<span class="r-in"><span> <span class="fu">ggplot_rsi</span><span class="op">(</span><span class="op">)</span></span></span>
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||||
<span class="r-in"><span> </span></span>
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||||
<span class="r-in"><span><span class="op">}</span></span></span>
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||||
<span class="r-plt img"><img src="ggplot_rsi-3.png" alt="" width="700" height="433"></span>
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||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
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||||
<span class="r-in"><span></span></span>
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||||
<span class="r-in"><span> <span class="co"># get only proportions and no counts:</span></span></span>
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||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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||||
<span class="r-in"><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></span>
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||||
<span class="r-in"><span> </span></span>
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||||
<span class="r-in"><span><span class="op">}</span></span></span>
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||||
<span class="r-plt img"><img src="ggplot_rsi-4.png" alt="" width="700" height="433"></span>
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||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
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||||
<span class="r-in"><span></span></span>
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||||
<span class="r-in"><span> <span class="co"># add other ggplot2 arguments as you like:</span></span></span>
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||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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||||
<span class="r-in"><span> <span class="fu">ggplot_rsi</span><span class="op">(</span>width <span class="op">=</span> <span class="fl">0.5</span>,</span></span>
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||||
<span class="r-in"><span> colour <span class="op">=</span> <span class="st">"black"</span>,</span></span>
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||||
<span class="r-in"><span> size <span class="op">=</span> <span class="fl">1</span>,</span></span>
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||||
<span class="r-in"><span> linetype <span class="op">=</span> <span class="fl">2</span>,</span></span>
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||||
<span class="r-in"><span> alpha <span class="op">=</span> <span class="fl">0.25</span><span class="op">)</span></span></span>
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||||
<span class="r-in"><span> <span class="fu">ggplot_rsi</span><span class="op">(</span></span></span>
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||||
<span class="r-in"><span> width <span class="op">=</span> <span class="fl">0.5</span>,</span></span>
|
||||
<span class="r-in"><span> colour <span class="op">=</span> <span class="st">"black"</span>,</span></span>
|
||||
<span class="r-in"><span> size <span class="op">=</span> <span class="fl">1</span>,</span></span>
|
||||
<span class="r-in"><span> linetype <span class="op">=</span> <span class="fl">2</span>,</span></span>
|
||||
<span class="r-in"><span> alpha <span class="op">=</span> <span class="fl">0.25</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="ggplot_rsi-5.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># you can alter the colours with colour names:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><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" class="external-link">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></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="ggplot_rsi-6.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># but you can also use the built-in colour-blind friendly colours for</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># your plots, where "S" is green, "I" is yellow and "R" is red:</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Value1"</span>, <span class="st">"Value2"</span>, <span class="st">"Value3"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> y <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> z <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Value4"</span>, <span class="st">"Value5"</span>, <span class="st">"Value6"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Value1"</span>, <span class="st">"Value2"</span>, <span class="st">"Value3"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> y <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> z <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Value4"</span>, <span class="st">"Value5"</span>, <span class="st">"Value6"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html" class="external-link">geom_col</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">x</span>, y <span class="op">=</span> <span class="va">y</span>, fill <span class="op">=</span> <span class="va">z</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">scale_rsi_colours</span><span class="op">(</span>Value4 <span class="op">=</span> <span class="st">"S"</span>, Value5 <span class="op">=</span> <span class="st">"I"</span>, Value6 <span class="op">=</span> <span class="st">"R"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="ggplot_rsi-7.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># resistance of ciprofloxacine per age group</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">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="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first_isolate</span> <span class="op">==</span> <span class="cn">TRUE</span>,</span></span>
|
||||
<span class="r-in"><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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">first_isolate</span> <span class="op">==</span> <span class="cn">TRUE</span>,</span></span>
|
||||
<span class="r-in"><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">"Escherichia coli"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># age_groups() is also a function in this AMR package:</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><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></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Including isolates from ICU.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Removed 6 rows containing missing values (position_stack).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Removed 6 rows containing missing values (position_stack).</span>
|
||||
<span class="r-plt img"><img src="ggplot_rsi-8.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># a shorter version which also adjusts data label colours:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><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></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="ggplot_rsi-9.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># it also supports groups (don't forget to use the group var on `x` or `facet`):</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">ward</span> <span class="op">!=</span> <span class="st">"Outpatient"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># select only UTI-specific drugs</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">ggplot_rsi</span><span class="op">(</span>x <span class="op">=</span> <span class="st">"hospital_id"</span>,</span></span>
|
||||
<span class="r-in"><span> facet <span class="op">=</span> <span class="st">"antibiotic"</span>,</span></span>
|
||||
<span class="r-in"><span> nrow <span class="op">=</span> <span class="fl">1</span>,</span></span>
|
||||
<span class="r-in"><span> title <span class="op">=</span> <span class="st">"AMR of Anti-UTI Drugs Per Hospital"</span>,</span></span>
|
||||
<span class="r-in"><span> x.title <span class="op">=</span> <span class="st">"Hospital"</span>,</span></span>
|
||||
<span class="r-in"><span> datalabels <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">ward</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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">ggplot_rsi</span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> x <span class="op">=</span> <span class="st">"ward"</span>,</span></span>
|
||||
<span class="r-in"><span> facet <span class="op">=</span> <span class="st">"antibiotic"</span>,</span></span>
|
||||
<span class="r-in"><span> nrow <span class="op">=</span> <span class="fl">1</span>,</span></span>
|
||||
<span class="r-in"><span> title <span class="op">=</span> <span class="st">"AMR of Anti-UTI Drugs Per Ward"</span>,</span></span>
|
||||
<span class="r-in"><span> x.title <span class="op">=</span> <span class="st">"Ward"</span>,</span></span>
|
||||
<span class="r-in"><span> datalabels <span class="op">=</span> <span class="cn">FALSE</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `mo_is_gram_negative()`</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Removed 6 rows containing missing values (position_stack).</span>
|
||||
<span class="r-plt img"><img src="ggplot_rsi-1.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-plt img"><img src="ggplot_rsi-10.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
Reference in New Issue
Block a user