some minor updates

psych252 · Jan 7, 2024 · 7bf0528 · 7bf0528
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diff --git a/01-introduction.Rmd b/01-introduction.Rmd
@@ -44,6 +44,7 @@ Special thanks go to my teaching teams:
   - Satchel Grant 
   - Shawn Schwartz
 - 2023: 
+  - Nilam Ram (instructor)
   - Ari Beller
   - Yoonji Lee
   - Satchel Grant 

diff --git a/02-visualization1.Rmd b/02-visualization1.Rmd
@@ -28,6 +28,10 @@ The `tidyverse` is a collection of packages that includes `ggplot2`.
 
 ## Why visualize data?
 
+```{r hiding, echo=FALSE, fig.cap="Are you hiding anything?", out.width="95%"}
+include_graphics("figures/hiding_data.png")
+```
+
 > The greatest value of a picture is when it forces us to notice what we never expected to see. — John Tukey
 
 > There is no single statistical tool that is as powerful as a well‐chosen graph. [@chambers1983graphical]

diff --git a/08-simulation2.Rmd b/08-simulation2.Rmd
@@ -652,6 +652,10 @@ ggplot(data = as_tibble(bootstraps),
 
 ## Additional resources
 
+### Misc 
+
+- [Nice illustration of the permutation test](https://www.jwilber.me/permutationtest/?s=09)
+
 ### Datacamp
 
 - [Foundations of Inference](https://www.datacamp.com/courses/foundations-of-inference)

diff --git a/14-power_analysis.Rmd b/14-power_analysis.Rmd
@@ -874,6 +874,8 @@ set.seed(1)
 
 ### Misc
 
+- [Sample size justification](https://lakens.github.io/statistical_inferences/08-samplesizejustification.html)
+- [Guide to reporting effect sizes and confidence intervals](https://matthewbjane.quarto.pub/)
 - [Getting started with `pwr`](https://cran.r-project.org/web/packages/pwr/vignettes/pwr-vignette.html)
 - [Visualize power](https://rpsychologist.com/d3/NHST/)
 - [Calculating and reporting effect sizes to facilitate cumulative science: a practical primer for t-tests and ANOVAs](https://www.frontiersin.org/articles/10.3389/fpsyg.2013.00863/full)

diff --git a/24-bayesian_data_analysis3.Rmd b/24-bayesian_data_analysis3.Rmd
@@ -622,6 +622,7 @@ loo_compare(fit.brm_ordinal, fit.brm_ordinal_variance)
 - [Hypothetical outcome plots](https://mucollective.northwestern.edu/files/2018-HOPsTrends-InfoVis.pdf)
 - [Visual MCMC diagnostics](https://cran.r-project.org/web/packages/bayesplot/vignettes/visual-mcmc-diagnostics.html#general-mcmc-diagnostics)
 - [Visualiztion of different MCMC algorithms](https://chi-feng.github.io/mcmc-demo/)
+- [Frequentist equivalence test](https://www.carlislerainey.com/blog/2023-08-18-equivalence-tests/?s=09)
 
 
 For additional resources, I highly recommend the brms and tidyverse implementations of the Statistical rethinking book [@mcelreath2020statistical], as well as of the Doing Bayesian Data analysis book [@kruschke2014doing], by Solomon Kurz [@kurz2020statistical; @kurz2022doingbayesian]. 

diff --git a/26-reporting.Rmd b/26-reporting.Rmd
@@ -112,8 +112,11 @@ apa_table(results_regression$table,
           escape = FALSE)
 ```
 
+## Additional resources
 
-<!-- ### Bayesian statistics -->
+### Misc
+
+- [Guide to reporting effect sizes and confidence intervals](https://matthewbjane.quarto.pub/)
 
 ## Session info
 

diff --git a/docs/404.html b/docs/404.html
@@ -23,7 +23,7 @@
 <meta name="author" content="Tobias Gerstenberg" />
 
 
-<meta name="date" content="2024-01-06" />
+<meta name="date" content="2024-01-07" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -51,8 +51,6 @@
 <link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
 <link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
 <script src="libs/anchor-sections-1.1.0/anchor-sections.js"></script>
-<script src="libs/kePrint-0.0.1/kePrint.js"></script>
-<link href="libs/lightable-0.0.1/lightable.css" rel="stylesheet" />
 
 
 <style type="text/css">
@@ -124,6 +122,28 @@
 
   div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
 </style>
+<style type="text/css">
+/* Used with Pandoc 2.11+ new --citeproc when CSL is used */
+div.csl-bib-body { }
+div.csl-entry {
+  clear: both;
+}
+.hanging div.csl-entry {
+  margin-left:2em;
+  text-indent:-2em;
+}
+div.csl-left-margin {
+  min-width:2em;
+  float:left;
+}
+div.csl-right-inline {
+  margin-left:2em;
+  padding-left:1em;
+}
+div.csl-indent {
+  margin-left: 2em;
+}
+</style>
 
 <link rel="stylesheet" href="style.css" type="text/css" />
 </head>
@@ -379,7 +399,8 @@
 </ul></li>
 <li class="chapter" data-level="8.5" data-path="simulation-2.html"><a href="simulation-2.html#additional-resources-6"><i class="fa fa-check"></i><b>8.5</b> Additional resources</a>
 <ul>
-<li class="chapter" data-level="8.5.1" data-path="simulation-2.html"><a href="simulation-2.html#datacamp-1"><i class="fa fa-check"></i><b>8.5.1</b> Datacamp</a></li>
+<li class="chapter" data-level="8.5.1" data-path="simulation-2.html"><a href="simulation-2.html#misc-3"><i class="fa fa-check"></i><b>8.5.1</b> Misc</a></li>
+<li class="chapter" data-level="8.5.2" data-path="simulation-2.html"><a href="simulation-2.html#datacamp-1"><i class="fa fa-check"></i><b>8.5.2</b> Datacamp</a></li>
 </ul></li>
 <li class="chapter" data-level="8.6" data-path="simulation-2.html"><a href="simulation-2.html#session-info-7"><i class="fa fa-check"></i><b>8.6</b> Session info</a></li>
 </ul></li>
@@ -394,7 +415,7 @@
 </ul></li>
 <li class="chapter" data-level="9.3" data-path="modeling-data.html"><a href="modeling-data.html#hypothesis-testing-one-sample-t-test"><i class="fa fa-check"></i><b>9.3</b> Hypothesis testing: “One-sample t-test”</a></li>
 <li class="chapter" data-level="9.4" data-path="modeling-data.html"><a href="modeling-data.html#building-a-sampling-distribution-of-pre"><i class="fa fa-check"></i><b>9.4</b> Building a sampling distribution of PRE</a></li>
-<li class="chapter" data-level="9.5" data-path="modeling-data.html"><a href="modeling-data.html#misc-3"><i class="fa fa-check"></i><b>9.5</b> Misc</a></li>
+<li class="chapter" data-level="9.5" data-path="modeling-data.html"><a href="modeling-data.html#misc-4"><i class="fa fa-check"></i><b>9.5</b> Misc</a></li>
 <li class="chapter" data-level="9.6" data-path="modeling-data.html"><a href="modeling-data.html#additional-resources-7"><i class="fa fa-check"></i><b>9.6</b> Additional resources</a>
 <ul>
 <li class="chapter" data-level="9.6.1" data-path="modeling-data.html"><a href="modeling-data.html#reading"><i class="fa fa-check"></i><b>9.6.1</b> Reading</a></li>
@@ -415,7 +436,7 @@
 <li class="chapter" data-level="10.5" data-path="linear-model-1.html"><a href="linear-model-1.html#additional-resources-8"><i class="fa fa-check"></i><b>10.5</b> Additional resources</a>
 <ul>
 <li class="chapter" data-level="10.5.1" data-path="linear-model-1.html"><a href="linear-model-1.html#datacamp-3"><i class="fa fa-check"></i><b>10.5.1</b> Datacamp</a></li>
-<li class="chapter" data-level="10.5.2" data-path="linear-model-1.html"><a href="linear-model-1.html#misc-4"><i class="fa fa-check"></i><b>10.5.2</b> Misc</a></li>
+<li class="chapter" data-level="10.5.2" data-path="linear-model-1.html"><a href="linear-model-1.html#misc-5"><i class="fa fa-check"></i><b>10.5.2</b> Misc</a></li>
 </ul></li>
 <li class="chapter" data-level="10.6" data-path="linear-model-1.html"><a href="linear-model-1.html#session-info-9"><i class="fa fa-check"></i><b>10.6</b> Session info</a></li>
 </ul></li>
@@ -447,7 +468,7 @@
 <li class="chapter" data-level="11.8" data-path="linear-model-2.html"><a href="linear-model-2.html#additional-resources-9"><i class="fa fa-check"></i><b>11.8</b> Additional resources</a>
 <ul>
 <li class="chapter" data-level="11.8.1" data-path="linear-model-2.html"><a href="linear-model-2.html#datacamp-4"><i class="fa fa-check"></i><b>11.8.1</b> Datacamp</a></li>
-<li class="chapter" data-level="11.8.2" data-path="linear-model-2.html"><a href="linear-model-2.html#misc-5"><i class="fa fa-check"></i><b>11.8.2</b> Misc</a></li>
+<li class="chapter" data-level="11.8.2" data-path="linear-model-2.html"><a href="linear-model-2.html#misc-6"><i class="fa fa-check"></i><b>11.8.2</b> Misc</a></li>
 </ul></li>
 <li class="chapter" data-level="11.9" data-path="linear-model-2.html"><a href="linear-model-2.html#session-info-10"><i class="fa fa-check"></i><b>11.9</b> Session info</a></li>
 <li class="chapter" data-level="11.10" data-path="linear-model-2.html"><a href="linear-model-2.html#references"><i class="fa fa-check"></i><b>11.10</b> References</a></li>
@@ -478,7 +499,7 @@
 <li class="chapter" data-level="12.7" data-path="linear-model-3.html"><a href="linear-model-3.html#additional-resources-10"><i class="fa fa-check"></i><b>12.7</b> Additional resources</a>
 <ul>
 <li class="chapter" data-level="12.7.1" data-path="linear-model-3.html"><a href="linear-model-3.html#datacamp-5"><i class="fa fa-check"></i><b>12.7.1</b> Datacamp</a></li>
-<li class="chapter" data-level="12.7.2" data-path="linear-model-3.html"><a href="linear-model-3.html#misc-6"><i class="fa fa-check"></i><b>12.7.2</b> Misc</a></li>
+<li class="chapter" data-level="12.7.2" data-path="linear-model-3.html"><a href="linear-model-3.html#misc-7"><i class="fa fa-check"></i><b>12.7.2</b> Misc</a></li>
 </ul></li>
 <li class="chapter" data-level="12.8" data-path="linear-model-3.html"><a href="linear-model-3.html#session-info-11"><i class="fa fa-check"></i><b>12.8</b> Session info</a></li>
 </ul></li>
@@ -498,7 +519,7 @@
 </ul></li>
 <li class="chapter" data-level="13.6" data-path="linear-model-4.html"><a href="linear-model-4.html#additional-resources-11"><i class="fa fa-check"></i><b>13.6</b> Additional resources</a>
 <ul>
-<li class="chapter" data-level="13.6.1" data-path="linear-model-4.html"><a href="linear-model-4.html#misc-7"><i class="fa fa-check"></i><b>13.6.1</b> Misc</a></li>
+<li class="chapter" data-level="13.6.1" data-path="linear-model-4.html"><a href="linear-model-4.html#misc-8"><i class="fa fa-check"></i><b>13.6.1</b> Misc</a></li>
 </ul></li>
 <li class="chapter" data-level="13.7" data-path="linear-model-4.html"><a href="linear-model-4.html#session-info-12"><i class="fa fa-check"></i><b>13.7</b> Session info</a></li>
 </ul></li>
@@ -521,7 +542,7 @@
 <ul>
 <li class="chapter" data-level="14.7.1" data-path="power-analysis.html"><a href="power-analysis.html#datacamp-6"><i class="fa fa-check"></i><b>14.7.1</b> Datacamp</a></li>
 <li class="chapter" data-level="14.7.2" data-path="power-analysis.html"><a href="power-analysis.html#cheatsheets-5"><i class="fa fa-check"></i><b>14.7.2</b> Cheatsheets</a></li>
-<li class="chapter" data-level="14.7.3" data-path="power-analysis.html"><a href="power-analysis.html#misc-8"><i class="fa fa-check"></i><b>14.7.3</b> Misc</a></li>
+<li class="chapter" data-level="14.7.3" data-path="power-analysis.html"><a href="power-analysis.html#misc-9"><i class="fa fa-check"></i><b>14.7.3</b> Misc</a></li>
 </ul></li>
 <li class="chapter" data-level="14.8" data-path="power-analysis.html"><a href="power-analysis.html#session-info-13"><i class="fa fa-check"></i><b>14.8</b> Session info</a></li>
 </ul></li>
@@ -576,7 +597,7 @@
 <ul>
 <li class="chapter" data-level="16.8.1" data-path="causation.html"><a href="causation.html#books"><i class="fa fa-check"></i><b>16.8.1</b> Books</a></li>
 <li class="chapter" data-level="16.8.2" data-path="causation.html"><a href="causation.html#tutorials-1"><i class="fa fa-check"></i><b>16.8.2</b> Tutorials</a></li>
-<li class="chapter" data-level="16.8.3" data-path="causation.html"><a href="causation.html#misc-9"><i class="fa fa-check"></i><b>16.8.3</b> Misc</a></li>
+<li class="chapter" data-level="16.8.3" data-path="causation.html"><a href="causation.html#misc-10"><i class="fa fa-check"></i><b>16.8.3</b> Misc</a></li>
 </ul></li>
 <li class="chapter" data-level="16.9" data-path="causation.html"><a href="causation.html#session-info-15"><i class="fa fa-check"></i><b>16.9</b> Session info</a></li>
 </ul></li>
@@ -681,7 +702,7 @@
 <li class="chapter" data-level="21.7" data-path="generalized-linear-model.html"><a href="generalized-linear-model.html#logistic-mixed-effects-model"><i class="fa fa-check"></i><b>21.7</b> Logistic mixed effects model</a></li>
 <li class="chapter" data-level="21.8" data-path="generalized-linear-model.html"><a href="generalized-linear-model.html#additional-information"><i class="fa fa-check"></i><b>21.8</b> Additional information</a>
 <ul>
-<li class="chapter" data-level="21.8.1" data-path="generalized-linear-model.html"><a href="generalized-linear-model.html#misc-10"><i class="fa fa-check"></i><b>21.8.1</b> Misc</a></li>
+<li class="chapter" data-level="21.8.1" data-path="generalized-linear-model.html"><a href="generalized-linear-model.html#misc-11"><i class="fa fa-check"></i><b>21.8.1</b> Misc</a></li>
 <li class="chapter" data-level="21.8.2" data-path="generalized-linear-model.html"><a href="generalized-linear-model.html#datacamp-7"><i class="fa fa-check"></i><b>21.8.2</b> Datacamp</a></li>
 </ul></li>
 <li class="chapter" data-level="21.9" data-path="generalized-linear-model.html"><a href="generalized-linear-model.html#session-info-20"><i class="fa fa-check"></i><b>21.9</b> Session info</a></li>
@@ -804,7 +825,11 @@
 <ul>
 <li class="chapter" data-level="26.2.1" data-path="reporting-statistics.html"><a href="reporting-statistics.html#frequentist-statistics"><i class="fa fa-check"></i><b>26.2.1</b> Frequentist statistics</a></li>
 </ul></li>
-<li class="chapter" data-level="26.3" data-path="reporting-statistics.html"><a href="reporting-statistics.html#session-info-25"><i class="fa fa-check"></i><b>26.3</b> Session info</a></li>
+<li class="chapter" data-level="26.3" data-path="reporting-statistics.html"><a href="reporting-statistics.html#additional-resources-21"><i class="fa fa-check"></i><b>26.3</b> Additional resources</a>
+<ul>
+<li class="chapter" data-level="26.3.1" data-path="reporting-statistics.html"><a href="reporting-statistics.html#misc-12"><i class="fa fa-check"></i><b>26.3.1</b> Misc</a></li>
+</ul></li>
+<li class="chapter" data-level="26.4" data-path="reporting-statistics.html"><a href="reporting-statistics.html#session-info-25"><i class="fa fa-check"></i><b>26.4</b> Session info</a></li>
 </ul></li>
 <li class="chapter" data-level="27" data-path="cheatsheets-6.html"><a href="cheatsheets-6.html"><i class="fa fa-check"></i><b>27</b> Cheatsheets</a>
 <ul>

diff --git a/docs/figures/hiding_data.png b/docs/figures/hiding_data.png