BRugsFit {BRugs} | R Documentation |
BRugs' meta function
Description
This function takes model, data and starting values as input and automatically runs a simulation in BRugs.
Usage
BRugsFit(modelFile, data, inits, numChains = 3, parametersToSave,
nBurnin = 1000, nIter = 1000, nThin = 1, coda = FALSE,
DIC = TRUE, working.directory = NULL, digits = 5, seed=NULL,
BRugsVerbose = getOption("BRugsVerbose"))
Arguments
modelFile |
File containing the model written in OpenBUGS code,
an R function that contains a BUGS model that is written to a temporary model file (see |
data |
Either a named list (names corresponding to variable names in the If a filename of an existing file is given, data are read from that file. |
inits |
A list with If a vector of filenames of existing files is given, inits are read from those files.
Alternatively, if |
numChains |
Number of Markov chains (default: 3). |
parametersToSave |
Character vector of the names of the parameters to save which should be monitored. |
nBurnin |
Length of burn in (before |
nIter |
Number of iterations (without burn in). |
nThin |
Every |
coda |
Determines the output format: if |
DIC |
Logical, whether to calculate and return the DIC. |
working.directory |
Sets working directory during execution of this function;
|
digits |
Number of significant digits used for OpenBUGS input, see |
seed |
Integer value from 1 to 14 defining the state of the random number
generator - default is to not specify the state (see |
BRugsVerbose |
Logical, whether BRugs is supposed to be verbose.
This can be controlled for the whole BRugs package by by the option ‘BRugsVerbose’ (see |
Value
If coda
is set to TRUE, an mcmc.list
object as known from the coda package is returned,
otherwise a list containg components
Stats |
A data frame containing sample statistics. See |
DIC |
The DIC statistics, if |
See Also
BRugs
, help.WinBUGS
.
Andrew Gelman proposes some print
and plot
methods that can be accessed by the
openbugs
(and bugs
) and as.bugs.array
functions in the CRAN package R2WinBUGS.
Examples
## Prepare the example files in a temporary directory
exfiles <- dir(options()$OpenBUGSExamples, pattern="^Rats.*txt$", full.names=TRUE)
ok <- file.copy(exfiles, tempdir())
BRugsFit(data = "Ratsdata.txt", inits = "Ratsinits.txt",
para = c("alpha", "beta"), modelFile = "Ratsmodel.txt",
numChains = 1,
working.directory = tempdir())