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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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@ -242,45 +242,45 @@
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<p>Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns <code>se_min</code> and <code>se_max</code>. See <em>Examples</em> for a real live example.</p>
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</div>
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<pre class="usage"><span class='fu'>resistance_predict</span>(
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<span class='kw'>x</span>,
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<span class='kw'>col_ab</span>,
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col_date = <span class='kw'>NULL</span>,
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year_min = <span class='kw'>NULL</span>,
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year_max = <span class='kw'>NULL</span>,
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year_every = <span class='fl'>1</span>,
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minimum = <span class='fl'>30</span>,
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model = <span class='kw'>NULL</span>,
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I_as_S = <span class='fl'>TRUE</span>,
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preserve_measurements = <span class='fl'>TRUE</span>,
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info = <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
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<span class='kw'>...</span>
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)
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<pre class="usage"><span class='fu'>resistance_predict</span><span class='op'>(</span>
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<span class='va'>x</span>,
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<span class='va'>col_ab</span>,
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col_date <span class='op'>=</span> <span class='cn'>NULL</span>,
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year_min <span class='op'>=</span> <span class='cn'>NULL</span>,
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year_max <span class='op'>=</span> <span class='cn'>NULL</span>,
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year_every <span class='op'>=</span> <span class='fl'>1</span>,
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minimum <span class='op'>=</span> <span class='fl'>30</span>,
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model <span class='op'>=</span> <span class='cn'>NULL</span>,
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I_as_S <span class='op'>=</span> <span class='cn'>TRUE</span>,
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preserve_measurements <span class='op'>=</span> <span class='cn'>TRUE</span>,
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info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>,
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<span class='va'>...</span>
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<span class='op'>)</span>
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<span class='fu'>rsi_predict</span>(
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<span class='kw'>x</span>,
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<span class='kw'>col_ab</span>,
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col_date = <span class='kw'>NULL</span>,
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year_min = <span class='kw'>NULL</span>,
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year_max = <span class='kw'>NULL</span>,
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year_every = <span class='fl'>1</span>,
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minimum = <span class='fl'>30</span>,
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model = <span class='kw'>NULL</span>,
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I_as_S = <span class='fl'>TRUE</span>,
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preserve_measurements = <span class='fl'>TRUE</span>,
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info = <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
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<span class='kw'>...</span>
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)
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<span class='fu'>rsi_predict</span><span class='op'>(</span>
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<span class='va'>x</span>,
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<span class='va'>col_ab</span>,
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col_date <span class='op'>=</span> <span class='cn'>NULL</span>,
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year_min <span class='op'>=</span> <span class='cn'>NULL</span>,
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year_max <span class='op'>=</span> <span class='cn'>NULL</span>,
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year_every <span class='op'>=</span> <span class='fl'>1</span>,
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minimum <span class='op'>=</span> <span class='fl'>30</span>,
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model <span class='op'>=</span> <span class='cn'>NULL</span>,
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I_as_S <span class='op'>=</span> <span class='cn'>TRUE</span>,
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preserve_measurements <span class='op'>=</span> <span class='cn'>TRUE</span>,
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info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>,
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<span class='va'>...</span>
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<span class='op'>)</span>
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<span class='co'># S3 method for resistance_predict</span>
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<span class='fu'><a href='plot.html'>plot</a></span>(<span class='kw'>x</span>, main = <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Resistance Prediction of"</span>, <span class='kw'>x_name</span>), <span class='kw'>...</span>)
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<span class='fu'><a href='plot.html'>plot</a></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'>"Resistance Prediction of"</span>, <span class='va'>x_name</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>ggplot_rsi_predict</span>(
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<span class='kw'>x</span>,
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main = <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Resistance Prediction of"</span>, <span class='kw'>x_name</span>),
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ribbon = <span class='fl'>TRUE</span>,
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<span class='kw'>...</span>
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)</pre>
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<span class='fu'>ggplot_rsi_predict</span><span class='op'>(</span>
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<span class='va'>x</span>,
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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 Prediction of"</span>, <span class='va'>x_name</span><span class='op'>)</span>,
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ribbon <span class='op'>=</span> <span class='cn'>TRUE</span>,
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<span class='va'>...</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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@ -395,55 +395,55 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<p>Models: <code><a href='https://rdrr.io/r/stats/lm.html'>lm()</a></code> <code><a href='https://rdrr.io/r/stats/glm.html'>glm()</a></code></p></div>
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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='kw'>x</span> <span class='op'><-</span> <span class='fu'>resistance_predict</span>(<span class='kw'>example_isolates</span>,
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col_ab = <span class='st'>"AMX"</span>,
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year_min = <span class='fl'>2010</span>,
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model = <span class='st'>"binomial"</span>)
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<span class='fu'><a href='plot.html'>plot</a></span>(<span class='kw'>x</span>)
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<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>)) {
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<span class='fu'>ggplot_rsi_predict</span>(<span class='kw'>x</span>)
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}
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<pre class="examples"><span class='va'>x</span> <span class='op'><-</span> <span class='fu'>resistance_predict</span><span class='op'>(</span><span class='va'>example_isolates</span>,
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col_ab <span class='op'>=</span> <span class='st'>"AMX"</span>,
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year_min <span class='op'>=</span> <span class='fl'>2010</span>,
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model <span class='op'>=</span> <span class='st'>"binomial"</span><span class='op'>)</span>
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<span class='fu'><a href='plot.html'>plot</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
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<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>
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<span class='fu'>ggplot_rsi_predict</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
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<span class='op'>}</span>
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<span class='co'># using dplyr:</span>
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<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='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
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<span class='kw'>x</span> <span class='op'><-</span> <span class='kw'>example_isolates</span> <span class='op'>%>%</span>
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<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span>() <span class='op'>%>%</span>
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<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='kw'>mo</span>) <span class='op'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='op'>%>%</span>
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<span class='fu'>resistance_predict</span>(<span class='st'>"PEN"</span>, model = <span class='st'>"binomial"</span>)
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<span class='fu'><a href='plot.html'>plot</a></span>(<span class='kw'>x</span>)
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<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='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='va'>x</span> <span class='op'><-</span> <span class='va'>example_isolates</span> <span class='op'>%>%</span>
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<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='mo_property.html'>mo_genus</a></span><span class='op'>(</span><span class='va'>mo</span><span class='op'>)</span> <span class='op'>==</span> <span class='st'>"Staphylococcus"</span><span class='op'>)</span> <span class='op'>%>%</span>
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<span class='fu'>resistance_predict</span><span class='op'>(</span><span class='st'>"PEN"</span>, model <span class='op'>=</span> <span class='st'>"binomial"</span><span class='op'>)</span>
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<span class='fu'><a href='plot.html'>plot</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
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<span class='co'># get the model from the object</span>
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<span class='kw'>mymodel</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/attributes.html'>attributes</a></span>(<span class='kw'>x</span>)<span class='op'>$</span><span class='kw'>model</span>
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<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='kw'>mymodel</span>)
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}
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<span class='va'>mymodel</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/attributes.html'>attributes</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>$</span><span class='va'>model</span>
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||||
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>mymodel</span><span class='op'>)</span>
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||||
<span class='op'>}</span>
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||||
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<span class='co'># create nice plots with ggplot2 yourself</span>
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||||
<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='https://dplyr.tidyverse.org'>"dplyr"</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='http://ggplot2.tidyverse.org'>"ggplot2"</a></span>)) {
|
||||
<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='https://dplyr.tidyverse.org'>"dplyr"</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='http://ggplot2.tidyverse.org'>"ggplot2"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
|
||||
<span class='kw'>data</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/filter.html'>filter</a></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='fu'>resistance_predict</span>(col_ab = <span class='st'>"AMX"</span>,
|
||||
col_date = <span class='st'>"date"</span>,
|
||||
model = <span class='st'>"binomial"</span>,
|
||||
info = <span class='fl'>FALSE</span>,
|
||||
minimum = <span class='fl'>15</span>)
|
||||
<span class='va'>data</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/filter.html'>filter</a></span><span class='op'>(</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='fu'>resistance_predict</span><span class='op'>(</span>col_ab <span class='op'>=</span> <span class='st'>"AMX"</span>,
|
||||
col_date <span class='op'>=</span> <span class='st'>"date"</span>,
|
||||
model <span class='op'>=</span> <span class='st'>"binomial"</span>,
|
||||
info <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
minimum <span class='op'>=</span> <span class='fl'>15</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='kw'>data</span>,
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span>(x = <span class='kw'>year</span>)) <span class='op'>+</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/geom_bar.html'>geom_col</a></span>(<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span>(y = <span class='kw'>value</span>),
|
||||
fill = <span class='st'>"grey75"</span>) <span class='op'>+</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/geom_linerange.html'>geom_errorbar</a></span>(<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span>(ymin = <span class='kw'>se_min</span>,
|
||||
ymax = <span class='kw'>se_max</span>),
|
||||
colour = <span class='st'>"grey50"</span>) <span class='op'>+</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_continuous.html'>scale_y_continuous</a></span>(limits = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</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>),
|
||||
labels = <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>, <span class='fl'>10</span>), <span class='st'>"%"</span>)) <span class='op'>+</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span>(title = <span class='fu'><a href='https://rdrr.io/r/base/expression.html'>expression</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Forecast of Amoxicillin Resistance in "</span>,
|
||||
<span class='fu'><a href='https://rdrr.io/r/grDevices/plotmath.html'>italic</a></span>(<span class='st'>"E. coli"</span>))),
|
||||
y = <span class='st'>"%R"</span>,
|
||||
x = <span class='st'>"Year"</span>) <span class='op'>+</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggtheme.html'>theme_minimal</a></span>(base_size = <span class='fl'>13</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>,
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span><span class='op'>(</span>x <span class='op'>=</span> <span class='va'>year</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/geom_bar.html'>geom_col</a></span><span class='op'>(</span><span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span><span class='op'>(</span>y <span class='op'>=</span> <span class='va'>value</span><span class='op'>)</span>,
|
||||
fill <span class='op'>=</span> <span class='st'>"grey75"</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/geom_linerange.html'>geom_errorbar</a></span><span class='op'>(</span><span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span><span class='op'>(</span>ymin <span class='op'>=</span> <span class='va'>se_min</span>,
|
||||
ymax <span class='op'>=</span> <span class='va'>se_max</span><span class='op'>)</span>,
|
||||
colour <span class='op'>=</span> <span class='st'>"grey50"</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_continuous.html'>scale_y_continuous</a></span><span class='op'>(</span>limits <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</span>, <span class='fl'>1</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>,
|
||||
labels <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><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'>100</span>, <span class='fl'>10</span><span class='op'>)</span>, <span class='st'>"%"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span><span class='op'>(</span>title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/expression.html'>expression</a></span><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'>"Forecast of Amoxicillin Resistance in "</span>,
|
||||
<span class='fu'><a href='https://rdrr.io/r/grDevices/plotmath.html'>italic</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
|
||||
y <span class='op'>=</span> <span class='st'>"%R"</span>,
|
||||
x <span class='op'>=</span> <span class='st'>"Year"</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggtheme.html'>theme_minimal</a></span><span class='op'>(</span>base_size <span class='op'>=</span> <span class='fl'>13</span><span class='op'>)</span>
|
||||
<span class='op'>}</span>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
@ -460,7 +460,7 @@ 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> 1.5.1.9000.</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