dclone: Data Cloning and MCMC Tools for Maximum Likelihood Methods
Version 2.0-0

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.

Browse man pages Browse package API and functions Browse package files

AuthorPeter Solymos
Date of publication2013-10-01 19:05:32
MaintainerPeter Solymos <solymos@ualberta.ca>
LicenseGPL-2
Version2.0-0
URL http://cran.r-project.org/package=dclone http://dcr.r-forge.r-project.org/
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("dclone", repos="http://R-Forge.R-project.org")

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

Functions

.DcloneEnvModel Man page
.DcloneEnvResults Man page
.dcFit Man page
DcloneEnv Man page
as.mcmc.list.bugs Man page Source code
bugs.fit Man page Source code
bugs.parfit Man page Source code
chisq.diag Man page Source code
chisq.diag.mcmc.list Man page Source code
clean.jags.model Man page Source code
clearDcloneEnv Man page Source code
clusterSize Man page Source code
clusterSplitSB Man page Source code
codaSamples Man page Source code
coef.mcmc Source code
coef.mcmc.list Man page Source code
confint.mcmc.list.dc Man page Source code
custommodel Man page Source code
dc.fit Man page Source code
dc.parfit Man page Source code
dcFit Source code
dcdiag Man page Source code
dcdiag.default Man page Source code
dcdim Man page Source code
dciid Man page Source code
dclone Man page Source code
dclone-package Man page
dclone.dcdim Man page Source code
dclone.dciid Man page Source code
dclone.dctr Man page Source code
dclone.default Man page Source code
dclone.environment Man page Source code
dclone.list Man page Source code
dcoptions Man page Source code
dcsd Man page Source code
dcsd.mcmc.list Man page Source code
dctable Man page Source code
dctable.default Man page Source code
dctr Man page Source code
errlines Man page Source code
errlines.default Man page Source code
evalParallelArgument Man page Source code
existsDcloneEnv Man page Source code
extractdcdiag Man page Source code
extractdcdiag.default Man page Source code
extractdctable Man page Source code
extractdctable.default Man page Source code
jags.fit Man page Source code
jags.parfit Man page Source code
jagsModel Man page Source code
lambdamax.diag Man page Source code
lambdamax.diag.mcmc.list Man page Source code
listDcloneEnv Man page Source code
make.symmetric Man page Source code
mclapplySB Man page Source code
mcmcapply Man page Source code
nclones Man page Source code
nclones.default Man page Source code
nclones.list Man page Source code
onAttach Source code
onLoad Source code
onUnload Source code
ovenbird Man page
pairs.mcmc.list Man page Source code
parCodaSamples Man page Source code
parDosa Man page Source code
parJagsModel Man page Source code
parLapplySB Man page Source code
parLapplySLB Man page Source code
parListFactories Man page Source code
parListModules Man page Source code
parLoadModule Man page Source code
parSetFactory Man page Source code
parUnloadModule Man page Source code
parUpdate Man page Source code
parallel.inits Man page Source code
plot.chisq.diag Source code
plot.dcdiag Man page Source code
plot.dctable Man page Source code
plotClusterSize Man page Source code
print.chisq.diag Source code
print.custommodel Source code
print.lambdamax.diag Source code
print.mcmc.list Source code
print.summary.mcmc.dc Source code
pullDcloneEnv Man page Source code
pushDcloneEnv Man page Source code
quantile.mcmc Source code
quantile.mcmc.list Man page Source code
regmod Man page
snowWrapper Man page Source code
stack.mcmc.list Man page Source code
summary.mcmc.list.dc Source code
update.mcmc.list Man page Source code
updated.model Man page Source code
updated.model.mcmc.list Source code
updated.model.mcmc.list.dc Source code
vcov.mcmc Source code
vcov.mcmc.list Man page Source code
vcov.mcmc.list.dc Man page Source code
write.jags.model Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/DcloneEnv.R
R/Extract.mcmc.list.dc.R
R/as.mcmc.list.bugs.R
R/bugs.fit.R
R/bugs.parfit.R
R/chisq.diag.R
R/chisq.diag.mcmc.list.R
R/clean.jags.model.R
R/clusterSize.R
R/clusterSplitSB.R
R/codaSamples.R
R/coef.mcmc.R
R/coef.mcmc.list.R
R/confint.mcmc.list.dc.R
R/custommodel.R
R/dc.fit.R
R/dc.parfit.R
R/dcFit.R
R/dcdiag.R
R/dcdiag.default.R
R/dcdim.R
R/dciid.R
R/dclone.R
R/dclone.dcdim.R
R/dclone.dciid.R
R/dclone.dctr.R
R/dclone.default.R
R/dclone.environment.R
R/dclone.list.R
R/dcoptions.R
R/dcsd.R
R/dcsd.mcmc.list.R
R/dctable.R
R/dctable.default.R
R/dctr.R
R/errlines.R
R/errlines.default.R
R/evalParallelArgument.R
R/extractdcdiag.R
R/extractdcdiag.default.R
R/extractdctable.R
R/extractdctable.default.R
R/jags.fit.R
R/jags.parfit.R
R/jagsModel.R
R/lambdamax.diag.R
R/lambdamax.diag.mcmc.list.R
R/make.symmetric.R
R/mclapplySB.R
R/mcmcapply.R
R/nclones.R
R/nclones.default.R
R/nclones.list.R
R/pairs.mcmc.list.R
R/parCodaSamples.R
R/parDosa.R
R/parJagsModel.R
R/parLapplySB.R
R/parLapplySLB.R
R/parListFactories.R
R/parListModules.R
R/parLoadModule.R
R/parSetFactory.R
R/parUnloadModule.R
R/parUpdate.R
R/parallel.inits.R
R/plot.chisq.diag.R
R/plot.dcdiag.R
R/plot.dctable.R
R/plotClusterSize.R
R/print.chisq.diag.R
R/print.custommodel.R
R/print.lambdamax.diag.R
R/print.mcmc.list.R
R/print.summary.mcmc.list.dc.R
R/quantile.mcmc.R
R/quantile.mcmc.list.R
R/snowWrapper.R
R/stack.mcmc.list.R
R/summary.mcmc.list.dc.R
R/update.mcmc.list.R
R/updated.model.R
R/updated.model.mcmc.list.R
R/updated.model.mcmc.list.dc.R
R/vcov.mcmc.R
R/vcov.mcmc.list.R
R/vcov.mcmc.list.dc.R
R/write.jags.model.R
R/zzz.R
data
data/ovenbird.rda
data/regmod.rda
inst
inst/CITATION
inst/ChangeLog
man
man/DcloneEnv.Rd
man/bugs.fit.Rd
man/bugs.parfit.Rd
man/clusterSize.Rd
man/clusterSplitSB.Rd
man/codaSamples.Rd
man/coef.mcmc.list.Rd
man/dc.fit.Rd
man/dc.parfit.Rd
man/dcFit.Rd
man/dclone-package.Rd
man/dclone.Rd
man/dcoptions.Rd
man/dctable.Rd
man/errlines.Rd
man/evalParallelArgument.Rd
man/jags.fit.Rd
man/jags.parfit.Rd
man/jagsModel.Rd
man/lambdamax.diag.Rd
man/make.symmetric.Rd
man/mclapplySB.Rd
man/mcmcapply.Rd
man/nclones.Rd
man/ovenbird.Rd
man/pairs.mcmc.list.Rd
man/parCodaSamples.Rd
man/parDosa.Rd
man/parJagsModel.Rd
man/parLoadModule.Rd
man/parSetFactory.Rd
man/parUpdate.Rd
man/parallel.inits.Rd
man/regmod.Rd
man/snowWrapper.Rd
man/update.mcmc.list.Rd
man/write.jags.model.Rd
dclone documentation built on May 21, 2017, 3:37 a.m.