OpenBUGS User Manual
Contents
Introduction
Introduction to WinBUGS
Advice for new users
MCMC methods
Model Specification
Graphical models
Graphs as a formal language
Stochastic nodes
Logical nodes
Arrays and indexing
Repeated structures
Data transformations
Nested indexing and mixtures
Formatting of data
Appendix I Distributions
Appendix II Functions and Functionals
Tutorial
Introduction
Specifying a model in the BUGS language
Running a model in WinBUGS
Monitoring parameter values
Checking convergence
How many iterations after convergence?
Obtaining summaries of the posterior distribution
Advanced use of the BUGS Language
Generic sampling distribution
Specifying a new prior distribution
Using pD and DIC
Mixtures of models of different complexity
Where the size of a set is a random quantity
Assessing sensitivity to prior assumptions
Modelling unknown denominators
Handling unbalanced datasets
Use of the "cut" function
Tips and Troubleshooting
Restrictions when modelling
Some error messages
Some Trap messages
The program hangs
Speeding up sampling
Improving convergence
DoodleBUGS: The Doodle Editor
General properties
Creating a node
Selecting a node
Deleting a node
Moving a node
Creating a plate
Selecting a plate
Deleting a plate
Moving a plate
Resizing a plate
Creating an edge
Deleting an edge
Moving a Doodle
Resizing a Doodle
Scripting and ClassicBUGS
Compound Documents
What is a compound document?
Working with compound documents
Editing compound documents
Compound documents and e-mail
Printing compound documents
Reading in plain text files
The File Menu
General properties
New
Open...
Open Stationary...
Save...
Save As...
Save Copy As...
Close
Page Setup...
Print...
Exit
The Edit Menu
General properties
Undo
Redo
Cut
Copy
Paste
Delete
Copy Properties
Paste Properties
Paste Object
Paste Special...
Paste to Window
Insert Object...
Object Properties...
Object
Select Document
Select All
Select Next Object
Preferences...
The Attributes Menu
General properties
Weight
Fixed Size...
Size...
Fixed Color
Color...
Default Font
Font...
Typeface...
The Tools Menu
General properties
Document Size...
Insert OLE Object...
Insert Header
Create Link
Create Target
Create Fold
Expand All
Collapse All
Fold...
Encode Document
Encode Selection
Encode File...
Encode File List
Decode
About Encoded Material
The Text Menu
General properties
Find/Replace...
Find Again
Find Previous
Find First
Find Last
Shift Left
Shift Right
Insert Paragraph
Insert Ruler
Insert-Soft-Hyphen
Insert Non-Brk-Hyphen
Insert Non-Brk-Space
Insert Digit Space
Show/Hide Marks
Make Default Attributes
Make Default Ruler
The Info Menu
General properties
Open Log
Clear Log
Node info...
Uninitialized nodes
Updaters by name
Updaters by depth
Modules
The Model Menu
General properties
Specification...
Update...
Save State
Random number generator...
Script
Pretty printing
Latex
Input / Output options...
Compile options...
Updater options...
Externalize
Internalize
The Inference Menu
General properties
Samples...
Compare...
Correlations...
Summary...
Rank...
DIC...
The Examples Menu
The Manuals Menu
The Help Menu
WinBUGS Graphics
General properties
Margins
Axis Bounds
Titles
All Plots
Fonts
Specific properties (via Special)
Density plot
Box plot
Caterpillar plot
Model fit plot
Scatterplot
References