(Note: moved from stan-dev/bayes-workflow-book
)
This is the repository for the book Bayesian Workflow Using Stan (working title). The book will have many authors.
The book is in its early stages of development so the content on the master branch will change substantially.
Rules for working on workflow
- Branch (on a well named branch) and then submit a pull request for merging into master.
- At all times the master branch should compile. This is required for merging.
- Keep a list of packages that are needed to compile the book and add to it if you add a package
Directory Structure
*.Rmd
files: book sections to potentially include (not all are currently included)_bookdown.yml
: book includes (only the Rmd files listed here are included in the book)_output.yml
: output configstan/*.stan
: directory of Stan programsdata/{*.R, *.rds}
: directory for data used by programsbibtex/all.bib
: BibTeX file for referencesprograms/{*.R, *.stan}
: legacy programs from old manual (deprecated until they're moved into new style with R inline in .Rmd)
Building the Book from Source
You will need to have RStan installed in the R environment from which you build.
RStudio
In RStudio: to build the project, open index.Rmd
in RStudio and click knit
- change output on first line of index.Rmd
for gitbook
and pdf_book
(not differeing _
)
Outside of RStudio
First, you will need to install pandoc
and pandoc-citeproc
in
addition to the bookdown
package in R. After that, it can be built
from within R in this directory using bookdown::render_book('index.Rmd')
or from the shell using ./build.sh
to build both PDF and HTML
versions.
Style Guide for Authors
-
All lines should be 80 or fewer characters unless absolutely mandated by content
-
y ~ normal(mu, sigma) # Not: N(), not sigma^2, roman font for "normal", LaTeX math for
$y$ ,$\mu$ ,$\sigma$ -
normal(y | mu, sigma) # Vertical bar, not semicolon
-
Poisson, Weibull, LKJ # Use capital letters for distributions that are named after people
-
E(y) # Roman font for E, LaTeX math for
$y$ , parentheses not brackets -
() # Always parentheses, never brackets
-
No special fonts for distributions, just roman and math fonts
-
p(y) # Probability density and probability mass function
-
Pr(A) # probability of an event
-
Follow the Stan style guide for code
- int<lower = 0> N; # Put in the lower bound
- for (n in 1:N); # Not: for (i in 1:n);
- foo_bar # Underscores rather than dots or CamelCase
-
All Stan code should be best practice except when explaining something, in which case we should explicitly show the best-practice alternative
Licensing
The code is licensed under BSD-3 and the text under CC-BY ND 4.0.