Useful links

Tutorials:

the brms manual
the bayesplot manual
Rewrite of Kruschke’s models using brms (and tidyverse), by A. Solomon Kurz.
Rewrite of Applied longitudinal data analysis using brms (and tidyverse) by A. Solomon Kurz
Stan documentation
- the Reference Manual describes the syntax and workings of a Stan program
- the Functions Reference is where you look up “what’s that function again?”
- the User’s Guide has examples of complex models implemented in Stan, and discusses good programming practice
RStan documentation
Example models in Stan: each contains a Stan program, code for simulating data, real data, and model output and diagnostics
Vignette on stanfit objects
Brief guide to Stan’s warnings

If you are looking for more reference or reading material, these are also good:

Bruce, Bruce, and Gedeck, Practical Statistics for Data Scientists. O’Reilley Publishers. code repository and link to the book
Logan, M. 2010. Biostatistical Design and Analysis Using R. Wiley-Blackwell. A fairly comprehensive book that covers how to use R to do many of the topics in Quinn and Keough.
Wickham, H. & G. Grolemund. 2016. R for Data Science. O’Reilly Publishers. (free web version) How to do many common data analysis tasks in R, specifically in the tidyverse.
Wickham, H. ggplot2: Elegant Graphics for Data Analysis, 2nd edition (free web version of the in-process 3rd edition) A more comprehensive reference to ggplot2 than the chapter of R for data science. Also see the documentation.
Wilke, Claus O. Fundamentals of Data Visualization.. O’Reilly Publishers. (free web version) How to think about visualization (with source code for plots available!).
Haddock, S. and C. Dunn. 2011. Practical Computing for Biologists. Sinauer and Associates.

knitr chunk options for control of Rmarkdown code chunks
Formulae in R and, in more detail, General linear models in R FAQ
How to print the source code for functions that don’t show it to you when you type their names. (tldr; showMethods(fun); getMethod(fun, c(x='class1', y='class2')))