https://github.com/jgabry/bayes-workflow-book

Source files for the book "Bayesian Workflow Using Stan"
https://github.com/jgabry/bayes-workflow-book

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Source files for the book "Bayesian Workflow Using Stan"

• Host: GitHub
• URL: https://github.com/jgabry/bayes-workflow-book
• Owner: jgabry
• Created: 2019-01-03T14:46:39.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2021-10-23T19:32:17.000Z (about 3 years ago)
• Last Synced: 2024-10-31T14:36:45.295Z (2 months ago)
• Language: Jupyter Notebook
• Homepage:
• Size: 5.29 MB
• Stars: 91
• Watchers: 17
• Forks: 14
• Open Issues: 2
• Metadata Files:
  • Readme: README.md

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README

        
(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 config

* `stan/*.stan` : directory of Stan programs

* `data/{*.R, *.rds}` : directory for data used by programs

* `bibtex/all.bib`: BibTeX file for references

* `programs/{*.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 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.