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@ -255,7 +255,7 @@
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
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<span class='no'>genus</span> <span class='kw'>==</span> <span class='st'>"Haemophilus"</span>) <span class='kw'>%>%</span>
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<span class='fu'>resistance_predict</span>(<span class='no'>amcl</span>, <span class='no'>date</span>)
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<span class='co'># }</span><span class='co'># NOT RUN {</span>
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<span class='co'># }</span><div class='input'>
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<span class='co'># real live example:</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
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@ -273,8 +273,56 @@
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<span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
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<span class='kw'>year_max</span> <span class='kw'>=</span> <span class='fl'>2025</span>,
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<span class='kw'>preserve_measurements</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
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<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>0</span>)
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<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>0</span>)</div><div class='output co'>#> <span class='message'><span style='color: #0000BB;'>NOTE: Using column `</span><span style='color: #0000BB;font-weight: bold;'>mo</span><span style='color: #0000BB;'>` as input for `col_mo`.</span><span></span></div><div class='output co'>#> <span class='message'></span><span style='color: #0000BB;'>NOTE: Using column `</span><span style='color: #0000BB;font-weight: bold;'>date</span><span style='color: #0000BB;'>` as input for `col_date`.</span><span></span></div><div class='output co'>#> <span class='message'></span><span style='color: #0000BB;'>NOTE: Using column `</span><span style='color: #0000BB;font-weight: bold;'>patient_id</span><span style='color: #0000BB;'>` as input for `col_patient_id`.</span><span></span></div><div class='output co'>#> <span class='message'>=> Found </span><span style='font-weight: bold;'>1,317 first isolates</span><span> (65.9% of total)</span></div><div class='output co'>#>
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#> Logistic regression model (logit) with binomial distribution
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#> ------------------------------------------------------------
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#>
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#> Call:
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#> glm(formula = cbind(R, S) ~ year, family = binomial)
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#>
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#> Deviance Residuals:
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#> Min 1Q Median 3Q Max
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#> -1.0751 -0.4675 -0.2840 -0.1530 1.5028
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#>
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#> Coefficients:
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#> Estimate Std. Error z value Pr(>|z|)
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#> (Intercept) -686.7518 342.1219 -2.007 0.0447 *
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#> year 0.3393 0.1698 1.998 0.0457 *
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#> ---
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#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
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#>
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#> (Dispersion parameter for binomial family taken to be 1)
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#>
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#> Null deviance: 13.5547 on 15 degrees of freedom
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#> Residual deviance: 6.8145 on 14 degrees of freedom
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#> AIC: 19.128
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#>
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#> Number of Fisher Scoring iterations: 6
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#> </div><div class='output co'>#> year value se_min se_max observations observed estimated
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#> 1 2002 0.00000000 NA NA 12 0.00000000 0.0005265096
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#> 2 2003 0.00000000 NA NA 13 0.00000000 0.0007390158
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#> 3 2004 0.00000000 NA NA 12 0.00000000 0.0010372031
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#> 4 2005 0.00000000 NA NA 15 0.00000000 0.0014555316
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#> 5 2006 0.00000000 NA NA 16 0.00000000 0.0020422369
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#> 6 2007 0.00000000 NA NA 17 0.00000000 0.0028647568
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#> 7 2008 0.00000000 NA NA 17 0.00000000 0.0040172166
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#> 8 2009 0.00000000 NA NA 18 0.00000000 0.0056306802
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#> 9 2010 0.00000000 NA NA 13 0.00000000 0.0078870391
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#> 10 2011 0.04761905 NA NA 21 0.04761905 0.0110375429
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#> 11 2012 0.00000000 NA NA 10 0.00000000 0.0154269569
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#> 12 2013 0.00000000 NA NA 13 0.00000000 0.0215239636
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#> 13 2014 0.00000000 NA NA 19 0.00000000 0.0299572977
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#> 14 2015 0.14285714 NA NA 14 0.14285714 0.0415545799
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#> 15 2016 0.04761905 NA NA 21 0.04761905 0.0573759332
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#> 16 2017 0.05000000 NA NA 20 0.05000000 0.0787262663
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#> 17 2018 0.10711851 0.03829468 0.1759423 NA NA 0.1071185079
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#> 18 2019 0.14414813 0.03838570 0.2499106 NA NA 0.1441481336
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#> 19 2020 0.19123682 0.03582031 0.3466533 NA NA 0.1912368226
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#> 20 2021 0.24922848 0.03244999 0.4660070 NA NA 0.2492284792
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#> 21 2022 0.31789357 0.03249431 0.6032928 NA NA 0.3178935725
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#> 22 2023 0.39551054 0.04249603 0.7485251 NA NA 0.3955105423
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#> 23 2024 0.47877663 0.06981495 0.8877383 NA NA 0.4787766284
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#> 24 2025 0.56323896 0.11983506 1.0000000 NA NA 0.5632389556</div><div class='input'>
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<span class='co'># create nice plots with ggplot</span>
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<span class='kw'>if</span> (!<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>require</a></span>(<span class='no'>ggplot2</span>)) {
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@ -300,8 +348,7 @@
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<span class='kw'>y</span> <span class='kw'>=</span> <span class='st'>"%IR"</span>,
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<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Year"</span>) +
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<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggtheme.html'>theme_minimal</a></span>(<span class='kw'>base_size</span> <span class='kw'>=</span> <span class='fl'>13</span>)
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}
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<span class='co'># }</span></pre>
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}</div></span></pre>
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</div>
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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<h2>Contents</h2>
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