dclone: Data Cloning and MCMC Tools for Maximum Likelihood Methods

Low level functions for implementing maximum likelihood estimating procedures for complex models using data cloning and Bayesian Markov chain Monte Carlo methods. Sequential and parallel MCMC support for JAGS, WinBUGS and OpenBUGS.

Author
Peter Solymos
Date of publication
2013-10-01 19:05:32
Maintainer
Peter Solymos <solymos@ualberta.ca>
License
GPL-2
Version
2.0-0
URLs

View on R-Forge

Man pages

bugs.fit
Fit BUGS models with cloned data
bugs.parfit
Parallel computing with WinBUGS/OpenBUGS
clusterSize
Optimizing the number of workers
clusterSplitSB
Size balancing
codaSamples
Generate posterior samples in mcmc.list format
coef.mcmc.list
Methods for the 'mcmc.list' class
dc.fit
Iterative model fitting with data cloning
dcFit
Internal function for iterative model fitting with data...
dclone
Cloning R objects
DcloneEnv
Manipulating dclone environments
dclone-package
Data Cloning
dcoptions
Setting Options
dc.parfit
Parallel model fitting with data cloning
dctable
Retrieve descriptive statistics from fitted objects to...
errlines
Plot error bars
evalParallelArgument
Evaluates parallel argument
jags.fit
Fit JAGS models with cloned data
jagsModel
Create a JAGS model object
jags.parfit
Parallel computing with JAGS
lambdamax.diag
Data Cloning Diagnostics
make.symmetric
Make a square matrix symmetric by averaging.
mclapplySB
Size balancing version of mclapply
mcmcapply
Calculations on 'mcmc.list' objects
nclones
Number of Clones
ovenbird
Abundances of ovenbird in Alberta
pairs.mcmc.list
Scatterplot Matrices for 'mcmc.list' Objects
parallel.inits
Parallel RNGs for initial values
parCodaSamples
Generate posterior samples in 'mcmc.list' format on parallel...
parDosa
Parallel wrapper function to call from within a function
parJagsModel
Create a JAGS model object on parallel workers
parLoadModule
Dynamically load JAGS modules on parallel workers
parSetFactory
Advanced control over JAGS on parallel workers
parUpdate
Update jags models on parallel workers
regmod
Exemplary MCMC list object
snowWrapper
Parallel wrapper function to call from within a function
update.mcmc.list
Automatic updating of an MCMC object
write.jags.model
Write and remove model file

Files in this package

dclone/DESCRIPTION
dclone/NAMESPACE
dclone/R
dclone/R/DcloneEnv.R
dclone/R/Extract.mcmc.list.dc.R
dclone/R/as.mcmc.list.bugs.R
dclone/R/bugs.fit.R
dclone/R/bugs.parfit.R
dclone/R/chisq.diag.R
dclone/R/chisq.diag.mcmc.list.R
dclone/R/clean.jags.model.R
dclone/R/clusterSize.R
dclone/R/clusterSplitSB.R
dclone/R/codaSamples.R
dclone/R/coef.mcmc.R
dclone/R/coef.mcmc.list.R
dclone/R/confint.mcmc.list.dc.R
dclone/R/custommodel.R
dclone/R/dc.fit.R
dclone/R/dc.parfit.R
dclone/R/dcFit.R
dclone/R/dcdiag.R
dclone/R/dcdiag.default.R
dclone/R/dcdim.R
dclone/R/dciid.R
dclone/R/dclone.R
dclone/R/dclone.dcdim.R
dclone/R/dclone.dciid.R
dclone/R/dclone.dctr.R
dclone/R/dclone.default.R
dclone/R/dclone.environment.R
dclone/R/dclone.list.R
dclone/R/dcoptions.R
dclone/R/dcsd.R
dclone/R/dcsd.mcmc.list.R
dclone/R/dctable.R
dclone/R/dctable.default.R
dclone/R/dctr.R
dclone/R/errlines.R
dclone/R/errlines.default.R
dclone/R/evalParallelArgument.R
dclone/R/extractdcdiag.R
dclone/R/extractdcdiag.default.R
dclone/R/extractdctable.R
dclone/R/extractdctable.default.R
dclone/R/jags.fit.R
dclone/R/jags.parfit.R
dclone/R/jagsModel.R
dclone/R/lambdamax.diag.R
dclone/R/lambdamax.diag.mcmc.list.R
dclone/R/make.symmetric.R
dclone/R/mclapplySB.R
dclone/R/mcmcapply.R
dclone/R/nclones.R
dclone/R/nclones.default.R
dclone/R/nclones.list.R
dclone/R/pairs.mcmc.list.R
dclone/R/parCodaSamples.R
dclone/R/parDosa.R
dclone/R/parJagsModel.R
dclone/R/parLapplySB.R
dclone/R/parLapplySLB.R
dclone/R/parListFactories.R
dclone/R/parListModules.R
dclone/R/parLoadModule.R
dclone/R/parSetFactory.R
dclone/R/parUnloadModule.R
dclone/R/parUpdate.R
dclone/R/parallel.inits.R
dclone/R/plot.chisq.diag.R
dclone/R/plot.dcdiag.R
dclone/R/plot.dctable.R
dclone/R/plotClusterSize.R
dclone/R/print.chisq.diag.R
dclone/R/print.custommodel.R
dclone/R/print.lambdamax.diag.R
dclone/R/print.mcmc.list.R
dclone/R/print.summary.mcmc.list.dc.R
dclone/R/quantile.mcmc.R
dclone/R/quantile.mcmc.list.R
dclone/R/snowWrapper.R
dclone/R/stack.mcmc.list.R
dclone/R/summary.mcmc.list.dc.R
dclone/R/update.mcmc.list.R
dclone/R/updated.model.R
dclone/R/updated.model.mcmc.list.R
dclone/R/updated.model.mcmc.list.dc.R
dclone/R/vcov.mcmc.R
dclone/R/vcov.mcmc.list.R
dclone/R/vcov.mcmc.list.dc.R
dclone/R/write.jags.model.R
dclone/R/zzz.R
dclone/data
dclone/data/ovenbird.rda
dclone/data/regmod.rda
dclone/inst
dclone/inst/CITATION
dclone/inst/ChangeLog
dclone/man
dclone/man/DcloneEnv.Rd
dclone/man/bugs.fit.Rd
dclone/man/bugs.parfit.Rd
dclone/man/clusterSize.Rd
dclone/man/clusterSplitSB.Rd
dclone/man/codaSamples.Rd
dclone/man/coef.mcmc.list.Rd
dclone/man/dc.fit.Rd
dclone/man/dc.parfit.Rd
dclone/man/dcFit.Rd
dclone/man/dclone-package.Rd
dclone/man/dclone.Rd
dclone/man/dcoptions.Rd
dclone/man/dctable.Rd
dclone/man/errlines.Rd
dclone/man/evalParallelArgument.Rd
dclone/man/jags.fit.Rd
dclone/man/jags.parfit.Rd
dclone/man/jagsModel.Rd
dclone/man/lambdamax.diag.Rd
dclone/man/make.symmetric.Rd
dclone/man/mclapplySB.Rd
dclone/man/mcmcapply.Rd
dclone/man/nclones.Rd
dclone/man/ovenbird.Rd
dclone/man/pairs.mcmc.list.Rd
dclone/man/parCodaSamples.Rd
dclone/man/parDosa.Rd
dclone/man/parJagsModel.Rd
dclone/man/parLoadModule.Rd
dclone/man/parSetFactory.Rd
dclone/man/parUpdate.Rd
dclone/man/parallel.inits.Rd
dclone/man/regmod.Rd
dclone/man/snowWrapper.Rd
dclone/man/update.mcmc.list.Rd
dclone/man/write.jags.model.Rd