bad enough to turn into something good

First draft done
adknudson · Nov 10, 2020 · b457d9a · b457d9a
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diff --git a/050-predictive-inference.Rmd b/050-predictive-inference.Rmd
diff --git a/docs/050-predictive-inference.md b/docs/050-predictive-inference.md
diff --git a/docs/050-predictive-inference_files/figure-html/ch050-Cold-Fish-1.png b/docs/050-predictive-inference_files/figure-html/ch050-Cold-Fish-1.png
diff --git a/docs/050-predictive-inference_files/figure-html/ch050-Moving-Moose-1.png b/docs/050-predictive-inference_files/figure-html/ch050-Moving-Moose-1.png
diff --git a/docs/050-predictive-inference_files/figure-html/ch050-Olive-Screwdriver-1.png b/docs/050-predictive-inference_files/figure-html/ch050-Olive-Screwdriver-1.png
diff --git a/docs/050-predictive-inference_files/figure-html/ch050-Strawberry-Swallow-1.png b/docs/050-predictive-inference_files/figure-html/ch050-Strawberry-Swallow-1.png
diff --git a/docs/conclusion.html b/docs/conclusion.html
@@ -156,7 +156,11 @@
 </ul></li>
 <li class="chapter" data-level="4.2" data-path="model-checking.html"><a href="model-checking.html#prior-predictive-checks"><i class="fa fa-check"></i><b>4.2</b> Prior Predictive Checks</a></li>
 </ul></li>
-<li class="chapter" data-level="5" data-path="predictive-inferences.html"><a href="predictive-inferences.html"><i class="fa fa-check"></i><b>5</b> Predictive Inference</a></li>
+<li class="chapter" data-level="5" data-path="predictive-inferences.html"><a href="predictive-inferences.html"><i class="fa fa-check"></i><b>5</b> Predictive Inference</a><ul>
+<li class="chapter" data-level="5.1" data-path="predictive-inferences.html"><a href="predictive-inferences.html#model-comparison-via-predictive-performance"><i class="fa fa-check"></i><b>5.1</b> Model Comparison via Predictive Performance</a><ul>
+<li class="chapter" data-level="5.1.1" data-path="predictive-inferences.html"><a href="predictive-inferences.html#loocv-and-importance-sampling"><i class="fa fa-check"></i><b>5.1.1</b> LOOCV and Importance Sampling</a></li>
+</ul></li>
+</ul></li>
 <li class="chapter" data-level="6" data-path="results.html"><a href="results.html"><i class="fa fa-check"></i><b>6</b> Psychometric Results</a><ul>
 <li class="chapter" data-level="6.1" data-path="results.html"><a href="results.html#affect-of-adaptation-across-age-groups"><i class="fa fa-check"></i><b>6.1</b> Affect of Adaptation across Age Groups</a><ul>
 <li class="chapter" data-level="6.1.1" data-path="results.html"><a href="results.html#on-perceptual-synchrony"><i class="fa fa-check"></i><b>6.1.1</b> On Perceptual Synchrony</a></li>

diff --git a/docs/discussion.html b/docs/discussion.html
diff --git a/docs/index.html b/docs/index.html
@@ -156,7 +156,11 @@
 </ul></li>
 <li class="chapter" data-level="4.2" data-path="model-checking.html"><a href="model-checking.html#prior-predictive-checks"><i class="fa fa-check"></i><b>4.2</b> Prior Predictive Checks</a></li>
 </ul></li>
-<li class="chapter" data-level="5" data-path="predictive-inferences.html"><a href="predictive-inferences.html"><i class="fa fa-check"></i><b>5</b> Predictive Inference</a></li>
+<li class="chapter" data-level="5" data-path="predictive-inferences.html"><a href="predictive-inferences.html"><i class="fa fa-check"></i><b>5</b> Predictive Inference</a><ul>
+<li class="chapter" data-level="5.1" data-path="predictive-inferences.html"><a href="predictive-inferences.html#model-comparison-via-predictive-performance"><i class="fa fa-check"></i><b>5.1</b> Model Comparison via Predictive Performance</a><ul>
+<li class="chapter" data-level="5.1.1" data-path="predictive-inferences.html"><a href="predictive-inferences.html#loocv-and-importance-sampling"><i class="fa fa-check"></i><b>5.1.1</b> LOOCV and Importance Sampling</a></li>
+</ul></li>
+</ul></li>
 <li class="chapter" data-level="6" data-path="results.html"><a href="results.html"><i class="fa fa-check"></i><b>6</b> Psychometric Results</a><ul>
 <li class="chapter" data-level="6.1" data-path="results.html"><a href="results.html#affect-of-adaptation-across-age-groups"><i class="fa fa-check"></i><b>6.1</b> Affect of Adaptation across Age Groups</a><ul>
 <li class="chapter" data-level="6.1.1" data-path="results.html"><a href="results.html#on-perceptual-synchrony"><i class="fa fa-check"></i><b>6.1.1</b> On Perceptual Synchrony</a></li>

diff --git a/docs/model-checking.html b/docs/model-checking.html
@@ -156,7 +156,11 @@
 </ul></li>
 <li class="chapter" data-level="4.2" data-path="model-checking.html"><a href="model-checking.html#prior-predictive-checks"><i class="fa fa-check"></i><b>4.2</b> Prior Predictive Checks</a></li>
 </ul></li>
-<li class="chapter" data-level="5" data-path="predictive-inferences.html"><a href="predictive-inferences.html"><i class="fa fa-check"></i><b>5</b> Predictive Inference</a></li>
+<li class="chapter" data-level="5" data-path="predictive-inferences.html"><a href="predictive-inferences.html"><i class="fa fa-check"></i><b>5</b> Predictive Inference</a><ul>
+<li class="chapter" data-level="5.1" data-path="predictive-inferences.html"><a href="predictive-inferences.html#model-comparison-via-predictive-performance"><i class="fa fa-check"></i><b>5.1</b> Model Comparison via Predictive Performance</a><ul>
+<li class="chapter" data-level="5.1.1" data-path="predictive-inferences.html"><a href="predictive-inferences.html#loocv-and-importance-sampling"><i class="fa fa-check"></i><b>5.1.1</b> LOOCV and Importance Sampling</a></li>
+</ul></li>
+</ul></li>
 <li class="chapter" data-level="6" data-path="results.html"><a href="results.html"><i class="fa fa-check"></i><b>6</b> Psychometric Results</a><ul>
 <li class="chapter" data-level="6.1" data-path="results.html"><a href="results.html#affect-of-adaptation-across-age-groups"><i class="fa fa-check"></i><b>6.1</b> Affect of Adaptation across Age Groups</a><ul>
 <li class="chapter" data-level="6.1.1" data-path="results.html"><a href="results.html#on-perceptual-synchrony"><i class="fa fa-check"></i><b>6.1.1</b> On Perceptual Synchrony</a></li>
@@ -228,7 +232,7 @@ <h4><span class="header-section-number">4.1.1.1</span> Trace Plots</h4>
 Figure 4.2: An example of healthy chains.
 </p>
 </div>
-<p>There is a similar diagnostic plot called the rank histogram plot (or <em>trank</em> plot for trace rank plot). <span class="citation">Vehtari et al. (<a href="#ref-vehtari2020rank" role="doc-biblioref">2020</a>)</span> details the motivation for trank plots, but in short if the chains are all exploring the posterior efficiently, then the histograms will be similar and uniform. Figure <a href="model-checking.html#fig:ch040-Dog-Reborn">4.3</a> is from the same model as above but for the rank histogram.</p>
+<p>There is a similar diagnostic plot called the rank histogram plot (or <em>trank</em> plot for trace rank plot). <span class="citation">Vehtari, Gelman, et al. (<a href="#ref-vehtari2020rank" role="doc-biblioref">2020</a>)</span> details the motivation for trank plots, but in short if the chains are all exploring the posterior efficiently, then the histograms will be similar and uniform. Figure <a href="model-checking.html#fig:ch040-Dog-Reborn">4.3</a> is from the same model as above but for the rank histogram.</p>
 <div class="figure" style="text-align: center"><span id="fig:ch040-Dog-Reborn"></span>
 <img src="040-model-checking_files/figure-html/ch040-Dog-Reborn-1.png" alt="A trank plot of healthy chains." width="85%" />
 <p class="caption">

diff --git a/docs/motivating-data.html b/docs/motivating-data.html
@@ -156,7 +156,11 @@
 </ul></li>
 <li class="chapter" data-level="4.2" data-path="model-checking.html"><a href="model-checking.html#prior-predictive-checks"><i class="fa fa-check"></i><b>4.2</b> Prior Predictive Checks</a></li>
 </ul></li>
-<li class="chapter" data-level="5" data-path="predictive-inferences.html"><a href="predictive-inferences.html"><i class="fa fa-check"></i><b>5</b> Predictive Inference</a></li>
+<li class="chapter" data-level="5" data-path="predictive-inferences.html"><a href="predictive-inferences.html"><i class="fa fa-check"></i><b>5</b> Predictive Inference</a><ul>
+<li class="chapter" data-level="5.1" data-path="predictive-inferences.html"><a href="predictive-inferences.html#model-comparison-via-predictive-performance"><i class="fa fa-check"></i><b>5.1</b> Model Comparison via Predictive Performance</a><ul>
+<li class="chapter" data-level="5.1.1" data-path="predictive-inferences.html"><a href="predictive-inferences.html#loocv-and-importance-sampling"><i class="fa fa-check"></i><b>5.1.1</b> LOOCV and Importance Sampling</a></li>
+</ul></li>
+</ul></li>
 <li class="chapter" data-level="6" data-path="results.html"><a href="results.html"><i class="fa fa-check"></i><b>6</b> Psychometric Results</a><ul>
 <li class="chapter" data-level="6.1" data-path="results.html"><a href="results.html#affect-of-adaptation-across-age-groups"><i class="fa fa-check"></i><b>6.1</b> Affect of Adaptation across Age Groups</a><ul>
 <li class="chapter" data-level="6.1.1" data-path="results.html"><a href="results.html#on-perceptual-synchrony"><i class="fa fa-check"></i><b>6.1.1</b> On Perceptual Synchrony</a></li>