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(v1.1.0.9004) lose dependencies

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dr. M.S. (Matthijs) Berends
2020-05-16 13:05:47 +02:00
parent 9fce546901
commit 7f3da74b17
111 changed files with 3211 additions and 2345 deletions
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34
docs/reference/resistance_predict.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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>
@ -266,7 +266,7 @@
)
<span class='co'># S3 method for resistance_predict</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>main</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Resistance Prediction of"</span>, <span class='no'>x_name</span>), <span class='no'>...</span>)
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>main</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Resistance Prediction of"</span>, <span class='no'>x_name</span>), <span class='no'>...</span>)
<span class='fu'>ggplot_rsi_predict</span>(
<span class='no'>x</span>,
@ -392,25 +392,25 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class='kw'>col_ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
<span class='kw'>year_min</span> <span class='kw'>=</span> <span class='fl'>2010</span>,
<span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"binomial"</span>)
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>x</span>)
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>x</span>)
<span class='fu'>ggplot_rsi_predict</span>(<span class='no'>x</span>)
<span class='co'># use dplyr so you can actually read it:</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span>() <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>) <span class='kw'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>resistance_predict</span>(<span class='st'>"PEN"</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"binomial"</span>)
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>x</span>)
<span class='co'># get the model from the object</span>
<span class='no'>mymodel</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/attributes.html'>attributes</a></span>(<span class='no'>x</span>)$<span class='no'>model</span>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>mymodel</span>)
<span class='co'># using dplyr:</span>
<span class='kw'>if</span> (!<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span>() <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>) <span class='kw'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>resistance_predict</span>(<span class='st'>"PEN"</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"binomial"</span>)
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>x</span>)
<span class='co'># get the model from the object</span>
<span class='no'>mymodel</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/attributes.html'>attributes</a></span>(<span class='no'>x</span>)$<span class='no'>model</span>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>mymodel</span>)
}
<span class='co'># create nice plots with ggplot2 yourself</span>
<span class='kw'>if</span> (!<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>ggplot2</span>)) {
<span class='kw'>if</span> (!<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>ggplot2</span>) <span class='kw'>&amp;</span> !<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
<span class='no'>data</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
@ -451,7 +451,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div>
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