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Built site for AMR: 2.0.0.9030@a4e2e25

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2023-07-10 14:52:49 +00:00
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reference/resistance_predict.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9028</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -299,7 +299,7 @@
<h2 id="interpretation-of-sir">Interpretation of SIR<a class="anchor" aria-label="anchor" href="#interpretation-of-sir"></a></h2>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R as shown below (<a href="https://www.eucast.org/newsiandr/" class="external-link">https://www.eucast.org/newsiandr/</a>):</p><ul><li><p><strong>S - Susceptible, standard dosing regimen</strong><br>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R as shown below (<a href="https://www.eucast.org/newsiandr" class="external-link">https://www.eucast.org/newsiandr</a>):</p><ul><li><p><strong>S - Susceptible, standard dosing regimen</strong><br>
A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
<li><p><strong>I - Susceptible, increased exposure</strong> <em><br>
A microorganism is categorised as "Susceptible, Increased exposure</em>" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.</p></li>
@@ -321,13 +321,14 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span> year_min <span class="op">=</span> <span class="fl">2010</span>,</span></span>
<span class="r-in"><span> model <span class="op">=</span> <span class="st">"binomial"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<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>
<span class="r-plt img"><img src="resistance_predict-1.png" alt="" width="700" height="433"></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'x' not found</span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></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="op">{</span></span></span>
<span class="r-in"><span> <span class="fu">ggplot_sir_predict</span><span class="op">(</span><span class="va">x</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="resistance_predict-2.png" alt="" width="700" height="433"></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error:</span> object 'x' not found</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># using dplyr:</span></span></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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@@ -341,25 +342,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span> <span class="va">mymodel</span> <span class="op">&lt;-</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>
<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>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="resistance_predict-3.png" alt="" width="700" height="433"></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> NULL</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Call:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> glm(formula = df_matrix ~ year, family = binomial)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Coefficients:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Estimate Std. Error z value Pr(&gt;|z|)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> (Intercept) 47.02915 72.98739 0.644 0.519</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> year -0.02280 0.03637 -0.627 0.531</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> (Dispersion parameter for binomial family taken to be 1)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Null deviance: 5.9620 on 11 degrees of freedom</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Residual deviance: 5.5701 on 10 degrees of freedom</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> AIC: 50.533</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Number of Fisher Scoring iterations: 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error:</span> NULL value passed as symbol address</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># create nice plots with ggplot2 yourself</span></span></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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span> <span class="op">&amp;&amp;</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>
@@ -375,7 +358,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<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>
<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>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="resistance_predict-4.png" alt="" width="700" height="433"></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error:</span> In argument: `mo == as.mo("E. coli")`.</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>