Books

Stan translation by Hiroki Itô of Bayesian Population Analysis using WinBUGS

Bayesian Data Analysis in Ecology Using Linear Models with R, BUGS, and Stan

Online Resources + Case Studies

Introduction to Stan

• Fitting Bayesian models using Stan and R: An introduction to fitting Bayesian models using Stan and R
• A practical introduction to Stan

Other

• Exact sparse Conditionally Autoregressive models in Stan
• Applied time series analysis in R with Stan. Allows fast Bayesian fitting of multivariate time-series models.
• Bayesian spatial filtering
• Case study: hierarchical model for cherry flowering (In French)
• A step-by-step guide to marginalizing over discrete parameters for ecologists using Stan
• hidden Markov models for animal movement: Discussion and code comparing moveHMM and Stan and another here
• hidden Markov model R package BayesHMM
• Predator-Prey Population Dynamics: the Lotka-Volterra model in Stan
• Multiple Species-Site Occupancy Model
• Fitting the Cormack-Jolly-Seber (CJS) model
• Fitting a Generalized Bayesian Factor Model with Stan
• Dirichlet regression and the 2018 Quebec Elections (with brms)
• Series of blog posts on: Selecting covariates in multiple regression
• Spatial capture-recapture models in Stan