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<title>Weighted two-stage analyses</title>
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<h1 class="title toc-ignore">Weighted two-stage analyses</h1>
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<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="co"># packages</span></a>
<a class="sourceLine" id="cb1-2" title="2">pacman<span class="op">::</span><span class="kw">p_load</span>(dplyr, purrr, tibble, tidyr, stringr, <span class="co"># data handling</span></a>
<a class="sourceLine" id="cb1-3" title="3"> nlme, lme4, glmmTMB, sommer, <span class="co"># mixed modelling</span></a>
<a class="sourceLine" id="cb1-4" title="4"> AICcmodavg, mixedup) <span class="co"># mixed model extractions</span></a>
<a class="sourceLine" id="cb1-5" title="5"></a>
<a class="sourceLine" id="cb1-6" title="6"><span class="co"># data</span></a>
<a class="sourceLine" id="cb1-7" title="7">dat <-<span class="st"> </span>readr<span class="op">::</span><span class="kw">read_csv</span>(<span class="st">"data/Winter Wheat 2016.csv"</span>) <span class="op">%>%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb1-8" title="8"><span class="st"> </span>dplyr<span class="op">::</span><span class="kw">select</span>(Year, <span class="kw">everything</span>()) <span class="op">%>%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb1-9" title="9"><span class="st"> </span><span class="kw">mutate_at</span>(<span class="kw">vars</span>(Year<span class="op">:</span>Cultivar), as.factor)</a></code></pre></div>
<div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:200px; ">
<table class="table table-bordered table-hover table-condensed table-responsive" style="width: auto !important; margin-left: auto; margin-right: auto;">
<thead>
<tr>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;">
Year
</th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;">
Zone
</th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;">
Location
</th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;">
Rep
</th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;">
Alpha
</th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;">
Cultivar
</th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;">
Yield
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
2016
</td>
<td style="text-align:left;">
South
</td>
<td style="text-align:left;">
07BM20
</td>
<td style="text-align:left;">
1
</td>
<td style="text-align:left;">
2
</td>
<td style="text-align:left;">
22455
</td>
<td style="text-align:right;">
727.3249
</td>
</tr>
<tr>
<td style="text-align:left;">
2016
</td>
<td style="text-align:left;">
South
</td>
<td style="text-align:left;">
07BM20
</td>
<td style="text-align:left;">
2
</td>
<td style="text-align:left;">
3
</td>
<td style="text-align:left;">
22455
</td>
<td style="text-align:right;">
721.4117
</td>
</tr>
<tr>
<td style="text-align:left;">
2016
</td>
<td style="text-align:left;">
South
</td>
<td style="text-align:left;">
07BM20
</td>
<td style="text-align:left;">
1
</td>
<td style="text-align:left;">
7
</td>
<td style="text-align:left;">
23286
</td>
<td style="text-align:right;">
830.3894
</td>
</tr>
<tr>
<td style="text-align:left;">
2016
</td>
<td style="text-align:left;">
South
</td>
<td style="text-align:left;">
07BM20
</td>
<td style="text-align:left;">
2
</td>
<td style="text-align:left;">
4
</td>
<td style="text-align:left;">
23286
</td>
<td style="text-align:right;">
806.8322
</td>
</tr>
<tr>
<td style="text-align:left;">
2016
</td>
<td style="text-align:left;">
South
</td>
<td style="text-align:left;">
07BM20
</td>
<td style="text-align:left;">
1
</td>
<td style="text-align:left;">
7
</td>
<td style="text-align:left;">
23524
</td>
<td style="text-align:right;">
810.4373
</td>
</tr>
<tr>
<td style="text-align:left;">
2016
</td>
<td style="text-align:left;">
South
</td>
<td style="text-align:left;">
07BM20
</td>
<td style="text-align:left;">
2
</td>
<td style="text-align:left;">
8
</td>
<td style="text-align:left;">
23524
</td>
<td style="text-align:right;">
833.9282
</td>
</tr>
<tr>
<td style="text-align:left;">
2016
</td>
<td style="text-align:left;">
South
</td>
<td style="text-align:left;">
07BM20
</td>
<td style="text-align:left;">
1
</td>
<td style="text-align:left;">
4
</td>
<td style="text-align:left;">
24054
</td>
<td style="text-align:right;">
898.0152
</td>
</tr>
<tr>
<td style="text-align:left;">
2016
</td>
<td style="text-align:left;">
South
</td>
<td style="text-align:left;">
07BM20
</td>
<td style="text-align:left;">
2
</td>
<td style="text-align:left;">
1
</td>
<td style="text-align:left;">
24054
</td>
<td style="text-align:right;">
874.5377
</td>
</tr>
<tr>
<td style="text-align:left;">
2016
</td>
<td style="text-align:left;">
South
</td>
<td style="text-align:left;">
07BM20
</td>
<td style="text-align:left;">
1
</td>
<td style="text-align:left;">
1
</td>
<td style="text-align:left;">
24521
</td>
<td style="text-align:right;">
852.6834
</td>
</tr>
<tr>
<td style="text-align:left;">
2016
</td>
<td style="text-align:left;">
South
</td>
<td style="text-align:left;">
07BM20
</td>
<td style="text-align:left;">
2
</td>
<td style="text-align:left;">
2
</td>
<td style="text-align:left;">
24521
</td>
<td style="text-align:right;">
846.8028
</td>
</tr>
<tr>
<td style="text-align:left;">
2016
</td>
<td style="text-align:left;">
South
</td>
<td style="text-align:left;">
07BM20
</td>
<td style="text-align:left;">
1
</td>
<td style="text-align:left;">
3
</td>
<td style="text-align:left;">
24984
</td>
<td style="text-align:right;">
768.3876
</td>
</tr>
<tr>
<td style="text-align:left;">
2016
</td>
<td style="text-align:left;">
South
</td>
<td style="text-align:left;">
07BM20
</td>
<td style="text-align:left;">
2
</td>
<td style="text-align:left;">
3
</td>
<td style="text-align:left;">
24984
</td>
<td style="text-align:right;">
837.1984
</td>
</tr>
<tr>
<td style="text-align:left;">
2016
</td>
<td style="text-align:left;">
South
</td>
<td style="text-align:left;">
07BM20
</td>
<td style="text-align:left;">
1
</td>
<td style="text-align:left;">
1
</td>
<td style="text-align:left;">
25512
</td>
<td style="text-align:right;">
829.0663
</td>
</tr>
<tr>
<td style="text-align:left;">
2016
</td>
<td style="text-align:left;">
South
</td>
<td style="text-align:left;">
07BM20
</td>
<td style="text-align:left;">
2
</td>
<td style="text-align:left;">
1
</td>
<td style="text-align:left;">
25512
</td>
<td style="text-align:right;">
811.6733
</td>
</tr>
<tr>
<td style="text-align:left;">
2016
</td>
<td style="text-align:left;">
South
</td>
<td style="text-align:left;">
07BM20
</td>
<td style="text-align:left;">
1
</td>
<td style="text-align:left;">
6
</td>
<td style="text-align:left;">
25965
</td>
<td style="text-align:right;">
872.8433
</td>
</tr>
<tr>
<td style="text-align:left;">
2016
</td>
<td style="text-align:left;">
South
</td>
<td style="text-align:left;">
07BM20
</td>
<td style="text-align:left;">
2
</td>
<td style="text-align:left;">
8
</td>
<td style="text-align:left;">
25965
</td>
<td style="text-align:right;">
849.0925
</td>
</tr>
<tr>
<td style="text-align:left;">
2016
</td>
<td style="text-align:left;">
South
</td>
<td style="text-align:left;">
07BM20
</td>
<td style="text-align:left;">
1
</td>
<td style="text-align:left;">
1
</td>
<td style="text-align:left;">
26362
</td>
<td style="text-align:right;">
877.3207
</td>
</tr>
<tr>
<td style="text-align:left;">
2016
</td>
<td style="text-align:left;">
South
</td>
<td style="text-align:left;">
07BM20
</td>
<td style="text-align:left;">
2
</td>
<td style="text-align:left;">
7
</td>
<td style="text-align:left;">
26362
</td>
<td style="text-align:right;">
929.6114
</td>
</tr>
<tr>
<td style="text-align:left;">
2016
</td>
<td style="text-align:left;">