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| ################################################# | |
| ## Run OpenBUGS through R2OpenBUGS on Mac OS X ## | |
| ################################################# | |
| # Johannes Karreth | |
| # jkarreth@albany.edu | |
| # The code below uses the help file for bugs() | |
| # Adjust file paths to your system | |
| library(R2OpenBUGS) | |
| model.file <- system.file(package="R2WinBUGS", "model", "schools.txt") | |
| # Some example data (see ?schools for details): | |
| data(schools) | |
| J <- nrow(schools) | |
| y <- schools$estimate | |
| sigma.y <- schools$sd | |
| data <- list(J=J, y=y, sigma.y=sigma.y) | |
| inits <- function(){ | |
| list(theta=rnorm(J, 0, 100), mu.theta=rnorm(1, 0, 100), | |
| sigma.theta=runif(1, 0, 100)) | |
| } | |
| ## or alternatively something like: | |
| # inits <- list( | |
| # list(theta=rnorm(J, 0, 90), mu.theta=rnorm(1, 0, 90), | |
| # sigma.theta=runif(1, 0, 90)), | |
| # list(theta=rnorm(J, 0, 100), mu.theta=rnorm(1, 0, 100), | |
| # sigma.theta=runif(1, 0, 100)) | |
| # list(theta=rnorm(J, 0, 110), mu.theta=rnorm(1, 0, 110), | |
| # sigma.theta=runif(1, 0, 110))) | |
| parameters <- c("theta", "mu.theta", "sigma.theta") | |
| schools.sim <- bugs(data = data, | |
| inits = inits, | |
| parameters = parameters, | |
| model.file = model.file, | |
| n.chains=3, | |
| n.burnin = 2500, | |
| n.iter=5000, | |
| debug = FALSE, | |
| OpenBUGS.pgm = "/Applications/Wineskin/OpenBUGS.app/Contents/Resources/drive_c/Program Files/OpenBUGS/OpenBUGS323/OpenBUGS.exe", | |
| working.directory = "/Users/johanneskarreth/R/Bayes/R2OpenBUGS", # Note: spaces in this path will create errors! | |
| useWINE = TRUE, | |
| bugs.seed = 12) | |
| print(schools.sim) | |
| plot(schools.sim) | |
| # For a function to create a barebones summary table, use | |
| # https://github.com/jkarreth/JKmisc/blob/master/mcmctab.R | |
| # install.packages("devtools") | |
| devtools::source_url("https://raw.githubusercontent.com/jkarreth/JKmisc/master/mcmctab.R") | |
| mcmctab(schools.sim) | |
| # Access posterior draws for postestimation | |
| # Rows are draws, columns are parameters | |
| schools.out <- schools.sim$sims.matrix |