BRugs User Manual
( the R interface to BUGS )
Version 1.0, June 2004
Andrew Thomas 1
1 Dept of Mathematics & Statistics,
University of Helsinki
Helsinki
Finland
e-mail: ant@rni.helsinki.fi
This manual describes how to use the BRugs software.
Permission and Disclaimer
please click here to read the legal bit
More informally, potential users are reminded to be extremely careful if using this program for serious statistical analysis. We have tested the program on quite a wide set of examples, but be particularly careful with types of model that are currently not featured. If there is a problem, BRugs might just crash, which is not very good, but it might well carry on and produce answers that are wrong, which is even worse. Please let us know of any successes or failures.
Beware: MCMC sampling can be dangerous!
Contents
Intoduction to BRugs
The Model Functions
General properties
Specification...
Update...
The Inference Functions
General properties
Samples...
Summary...
Rank...
DIC...
Model Specification Language
Graphical models
Graphs as a formal language
The BUGS language: stochastic nodes
Censoring and truncation
Constraints on using certain distributions
Logical nodes
Arrays and indexing
Repeated structures
Data transformations
Nested indexing and mixtures
Formatting of data
Intoduction to BRugs [top]
BRugs is a collection of R functions that allow users to analys graphical models using MCMC techniques. Most of the R functions in BRugs provide a interface to the BRugs dynamic link library (shared object file). The BRugs dynamic link library is able to make use of many of the WinBUGS components, in particular those components concerned with graphical models and MCMC simulation. BRugs lacks the GUI interface of WinBUGS but is able to use R to create graphical displays of the MCMC simulation. BRugs uses the same model specification language as WinBUGS and the same format for data and initial values. However BRugs always uses plain text files for input inplace of WinBUGS compound documents. The BRugs functions can be split into two groups: those associated with setting up and simulating the graphical model and those associated with making statistical inference. In general the R functions in BRugs correspond to the command buttons and and text entry fields in the menus of WinBUGS. Each WinBUGS text entry field splits into two R functions, one to set the quantity and the other to get the value of the quantity.