BRugsFit {BRugs} | R Documentation |
This function takes model, data and starting values as input and automatically runs a simulation in BRugs.
BRugsFit(modelFile, data, inits, numChains = 3, parametersToSave, nBurnin = 1000, nIter = 1000, nThin = 1, DIC = TRUE, working.directory = NULL, digits = 5, BRugsVerbose = getOption("BRugsVerbose"))
modelFile |
File containing the model written in OpenBUGS code. |
data |
Either a named list (names corresponding to variable names in the modelFile )
of the data for the OpenBUGS model, or
a vector or list of the names of the data objects used by the model.
In these cases data are written into a file ‘data.txt’ into the working directory.
If a filename of an existing file is given, data are read from that file. |
inits |
A list with numChains elements; each element of the list is
itself a list of starting values for the OpenBUGS model, or
a function creating (possibly random) initial values.
In these cases inits are written into files ‘inits1.txt’, ..., ‘initsN.txt’ into the working directory.
If a vector of filenames of existing files is given, inits are read from those files. Alternatively, if inits is not specified, initial values are generated by OpenBUGS. |
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 iterations start). |
nIter |
Number of iterations (without burn in). |
nThin |
Every nThin -th iteration of each chain is stored. |
DIC |
Logical, whether to calculate and return the DIC. |
working.directory |
Sets working directory during execution of this function;
data , inits and other files are written to / read from this directory if no other directory
is explicitly given in those arguments.
If NULL , the current working directory is chosen. |
digits |
Number of significant digits used for OpenBUGS input, see formatC . |
BRugsVerbose |
Logical, whether BRugs is supposed to be verbose.
This can be controlled for the whole BRugs package by by the option ‘BRugsVerbose’ (see options )
which is set to TRUE by default. |
A list containg components
Stats |
A data frame containing sample statistics. See samplesStats . |
DIC |
The DIC statistics, if DIC=TRUE , else NULL . See dicStats . |
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.
BRugsFit(data = "ratsdata.txt", inits = "ratsinits.txt", para = c("alpha", "beta"), modelFile = "ratsmodel.txt", numChains = 1, working.directory = system.file("OpenBUGS", "Examples", package = "BRugs"))