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Built site for AMR: 1.8.1.9045@e7af5fc
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@ -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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@ -283,10 +283,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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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="va">x</span> <span class="op"><-</span> <span class="fu">resistance_predict</span><span class="op">(</span><span class="va">example_isolates</span>, </span></span>
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<span class="r-in"><span> col_ab <span class="op">=</span> <span class="st">"AMX"</span>,</span></span>
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<span class="r-in"><span> year_min <span class="op">=</span> <span class="fl">2010</span>,</span></span>
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<span class="r-in"><span> model <span class="op">=</span> <span class="st">"binomial"</span><span class="op">)</span></span></span>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><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>,</span></span>
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<span class="r-in"><span> col_ab <span class="op">=</span> <span class="st">"AMX"</span>,</span></span>
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<span class="r-in"><span> year_min <span class="op">=</span> <span class="fl">2010</span>,</span></span>
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<span class="r-in"><span> model <span class="op">=</span> <span class="st">"binomial"</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-msg co"><span class="r-pr">#></span> ℹ Using column 'date' as input for `col_date`.</span>
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<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
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<span class="r-plt img"><img src="resistance_predict-1.png" alt="" width="700" height="433"></span>
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@ -302,14 +303,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<span class="r-in"><span> <span class="fu"><a href="first_isolate.html">filter_first_isolate</a></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>
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<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_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"><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">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></span></span>
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<span class="r-in"><span> <span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">x</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 the model from the object</span></span></span>
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<span class="r-in"><span> <span class="va">mymodel</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/attributes.html" class="external-link">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></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mymodel</span><span class="op">)</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-msg co"><span class="r-pr">#></span> Including isolates from ICU.</span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'date' as input for `col_date`.</span>
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<span class="r-plt img"><img src="resistance_predict-3.png" alt="" width="700" height="433"></span>
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<span class="r-out co"><span class="r-pr">#></span> NULL</span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> Call:</span>
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<span class="r-out co"><span class="r-pr">#></span> glm(formula = df_matrix ~ year, family = binomial)</span>
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@ -333,15 +336,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<span class="r-out co"><span class="r-pr">#></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"># create nice plots with ggplot2 yourself</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://dplyr.tidyverse.org" class="external-link">"dplyr"</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://ggplot2.tidyverse.org" class="external-link">"ggplot2"</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://dplyr.tidyverse.org" class="external-link">"dplyr"</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://ggplot2.tidyverse.org" class="external-link">"ggplot2"</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 class="va">data</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></span>
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<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">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>
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<span class="r-in"><span> <span class="fu">resistance_predict</span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"AMX"</span>,</span></span>
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<span class="r-in"><span> col_date <span class="op">=</span> <span class="st">"date"</span>,</span></span>
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<span class="r-in"><span> model <span class="op">=</span> <span class="st">"binomial"</span>,</span></span>
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<span class="r-in"><span> info <span class="op">=</span> <span class="cn">FALSE</span>,</span></span>
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<span class="r-in"><span> minimum <span class="op">=</span> <span class="fl">15</span><span class="op">)</span></span></span>
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<span class="r-in"><span> <span class="fu">resistance_predict</span><span class="op">(</span></span></span>
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<span class="r-in"><span> col_ab <span class="op">=</span> <span class="st">"AMX"</span>,</span></span>
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<span class="r-in"><span> col_date <span class="op">=</span> <span class="st">"date"</span>,</span></span>
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<span class="r-in"><span> model <span class="op">=</span> <span class="st">"binomial"</span>,</span></span>
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<span class="r-in"><span> info <span class="op">=</span> <span class="cn">FALSE</span>,</span></span>
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<span class="r-in"><span> minimum <span class="op">=</span> <span class="fl">15</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-in"><span> <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data</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/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">data</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="op">}</span></span></span>
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