major revision

.gitignore

@@ -1,3 +1,8 @@
 .httr-oauth
 .Rproj.user
 *_cache
+*.md
+*_files/
+*.acorn
+*.mov
+myplot.pdf

_bookdown.yml

@@ -3,6 +3,7 @@ new_session: yes
 output_dir: "docs"
 
 rmd_files:
+
   [ "index.Rmd",
     "start_here.Rmd",
 
@@ -22,34 +23,39 @@ rmd_files:
 
     "linear-models.Rmd",
     "anova.Rmd",
-    "anova-cookbook.Rmd",
 
     "understanding-interactions.Rmd",
     "predictions-and-margins.Rmd",
 
     "general-linear-models.Rmd",
     "mediation.Rmd",
     "multilevel-models.Rmd",
-    "cfa.Rmd",
-    "sem.Rmd",
+    "cfa-sem.Rmd",
     "power-analysis.Rmd",
-    "meta-analysis.Rmd",
-    "bayes-factors.Rmd",
-    "bayes-mcmc.Rmd",
+
 
+    "additional-stubs.Rmd",
+    "bayes-mcmc.Rmd",
 
+
     "statistical-explanations.Rmd",
     "confidence-vs-prediction-intervals.Rmd",
     "multiple-comparisons.Rmd",
+    "link-functions.Rmd",
+    "over-fitting.Rmd",
+    "gof.Rmd",
 
 
     "loose-ends.Rmd",
     "installation.Rmd",
     "packages.Rmd",
+    "colours.Rmd",
     "help.Rmd",
-    "rmarkdown-tricks.Rmd",
-    "sharing-and-publishing.Rmd",
+    "functions.Rmd",
 
+
+    "sharing-and-publishing.Rmd",
+
     "references.Rmd"
   ]
 

additional-stubs.Rmd

@@ -0,0 +1,52 @@
+---
+title: 'Bayes factors'
+output: bookdown::tufte_html2
+---
+
+
+```{r, include=FALSE}
+# ignore all this for the moment
+knitr::opts_chunk$set(echo = TRUE, collapse=TRUE, cache=TRUE)
+library(tidyverse)
+library(pander)
+library(lmerTest)
+
+```
+
+
+
+# Additional stub articles
+
+These hopefully to be fleshed out soon. Contributions welcome!
+
+
+
+## Meta analysis {- #meta-analysis}
+
+
+For the moment, [see this introduction to meta analysis in R](https://www.r-bloggers.com/r-and-meta-analysis/)
+
+
+## Bayes factors {- #bayes-factors}
+
+
+TODO
+
+Tongue in cheek Chapter that Andy proposed as a Stage 4 option: "doing BF for rubbish data..."
+
+Cover:
+
+- What is a BF: http://bayesfactor.blogspot.co.uk/2014/02/the-bayesfactor-package-this-blog-is.html
+https://en.wikipedia.org/wiki/Bayes_factor#Interpretation
+
+- BF package manual http://bayesfactorpcl.r-forge.r-project.org/#twosample
+
+- BayesFactors not (too) sensitive to choice of priors:  http://www.nicebread.de/interactive-exploration-of-a-priors-impact/
+
+
+
+Also explore parameter estimation and inference from posterior of parameters as an alternative approach (see Krusche chapter, and Gelman papers).
+
+
+
+