pbugs
is an R
package devised to run WinBUGS
or OpenBUGS
models
in parallel. Each chain is run in a different BUGS
instance so it is
computed in a different core of your machine. Ideally, if n.chains
are
simulated (and your simulation is long enough) this should yield
computing time improvements close to 1 / n.chains
.
The pbugs
package heavily depends on the
R2WinBUGS
and
R2OpenBUGS
libraries. Indeed, any R
syntax calling to any R2WinBUGS
or
R2OpenBUGS
should work equally when using the pbugs
package by
simply replacing any bugs(...)
sentence by the corresponding
pbugs(...)
sentence. We have tried to preserve the original syntax so
that your old code using this package works also when the pbugs
package is used instead, by simply changing bugs
by pbugs
. Anyway,
when pbugs
is used that same code should run substantially faster.
Aditionally, the pbugs
package contains also some improvements over
R2WinBUGS
and R2OpenBUGS
that we have thought interesting to
implement as former R2WinBUGS
users. These main improvements could be
summarized as:
pbugs
objects keep the structure and functionality of bugs
objects with some enhancements, so anything that you did with your
bugs
will be also possible to do with your pbugs
object.pbugs
automatically saves the computing time taken to run the
sentence generating that object. This is saved at the exec.time
component of any pbugs
object.pbugs
makes it possible to change and control the default sampling
methods when using WinBUGS
(as described at the ‘Changing MCMC
defaults’ section of the WinBUGS
help) automatically.WinBUGS
chains crashes during the MCMC simulation
process for some reason, pbugs
will retrieve the results of the
rest of chains and will build the corresponding pbugs
object. In
this manner you will not lose the results for the rest of chains.print
and summary
methods for pbugs
objects, allowing for example ordering variables in summaries by
their values of their convergence statistics.pbugs
objects (traceplot
)
has been included into the package. This function automatically
plots those parameters with deficient convergence criteria.pbugs
has been substantially tested on Linux workstations, we have
also substantially tested the package on Windows machines, but although
tested, our experience on ‘Mac’ systems is much lower. Thus, if you
found some issue on the running of this package on some of these
different environments please do not doubt to let us
know*.
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