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Built site for AMR: 1.8.2.9111@aa48c6b

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2023-02-08 16:01:47 +00:00
parent c43e91eaee
commit 769ace0b66
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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="">1.8.2.9103</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</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">
@ -42,6 +42,11 @@
Conduct AMR Analysis
</a>
<a class="dropdown-item" href="../reference/antibiogram.html">
<span class="fa fa-file-prescription"></span>
Generate Antibiogram (Trad./Syndromic/WISCA)
</a>
<a class="dropdown-item" href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
@ -299,7 +304,6 @@ 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-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'date' as input for col_date.</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-in"><span><span class="co"># \donttest{</span></span></span>
@ -320,7 +324,6 @@ 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-msg co"><span class="r-pr">#&gt;</span> Including isolates from ICU.</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>
@ -329,18 +332,18 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Deviance Residuals: </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Min 1Q Median 3Q Max </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> -1.4150 -0.1855 0.0000 0.4096 0.9277 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> -1.3342 -0.1917 0.0000 0.5364 1.2073 </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> (Intercept) 72.77752 65.66452 1.108 0.268</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> year -0.03557 0.03272 -1.087 0.277</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> Null deviance: 7.6911 on 11 degrees of freedom</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Residual deviance: 6.5141 on 10 degrees of freedom</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> AIC: 53.694</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>