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.

AuthorPeter Solymos
Date of publication2016-03-12 08:51:14
MaintainerPeter Solymos <solymos@ualberta.ca>
LicenseGPL-2
Version2.1-2
https://groups.google.com/forum/#!forum/dclone-users, http://datacloning.org

View on CRAN

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

update.mcmc.list: Automatic updating of an MCMC object

write.jags.model: Write and remove model file

Functions

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

Files

dclone
dclone/inst
dclone/inst/CITATION
dclone/inst/ChangeLog
dclone/NAMESPACE
dclone/data
dclone/data/ovenbird.rda
dclone/data/regmod.rda
dclone/R
dclone/R/lambdamax.diag.mcmc.list.R dclone/R/dclone.R dclone/R/bugs.fit.R dclone/R/confint.mcmc.list.dc.R dclone/R/quantile.mcmc.list.R dclone/R/clean.jags.model.R dclone/R/extractdcdiag.default.R dclone/R/pairs.mcmc.list.R dclone/R/print.custommodel.R dclone/R/dcFit.R dclone/R/parListModules.R dclone/R/DcloneEnv.R dclone/R/chisq.diag.mcmc.list.R dclone/R/dctable.R dclone/R/dc.fit.R dclone/R/parListFactories.R dclone/R/print.mcmc.list.R dclone/R/dclone.environment.R dclone/R/nclones.list.R dclone/R/parallel.inits.R dclone/R/clusterSplitSB.R dclone/R/update.mcmc.list.R dclone/R/summary.mcmc.list.dc.R dclone/R/dctr.R dclone/R/dcsd.R dclone/R/mclapplySB.R dclone/R/parLapplySB.R dclone/R/extractdctable.default.R dclone/R/parLoadModule.R dclone/R/dclone.default.R dclone/R/parSetFactory.R dclone/R/print.lambdamax.diag.R dclone/R/dcsd.mcmc.list.R dclone/R/dc.parfit.R dclone/R/dclone.dcdim.R dclone/R/plot.dctable.R dclone/R/nclones.default.R dclone/R/dciid.R dclone/R/lambdamax.diag.R dclone/R/codaSamples.R dclone/R/dctable.default.R dclone/R/parUnloadModule.R dclone/R/mcmcapply.R dclone/R/evalParallelArgument.R dclone/R/plot.dcdiag.R dclone/R/parLapplySLB.R dclone/R/plot.chisq.diag.R dclone/R/errlines.default.R dclone/R/parUpdate.R dclone/R/errlines.R dclone/R/quantile.mcmc.R dclone/R/jags.fit.R dclone/R/write.jags.model.R dclone/R/bugs.parfit.R dclone/R/dcdim.R dclone/R/parCodaSamples.R dclone/R/nclones.R dclone/R/stack.mcmc.list.R dclone/R/print.chisq.diag.R dclone/R/custommodel.R dclone/R/extractdcdiag.R dclone/R/dclone.list.R dclone/R/vcov.mcmc.list.dc.R dclone/R/updated.model.mcmc.list.dc.R dclone/R/updated.model.mcmc.list.R dclone/R/coef.mcmc.list.R dclone/R/print.summary.mcmc.list.dc.R dclone/R/Extract.mcmc.list.dc.R dclone/R/dclone.dctr.R dclone/R/dcdiag.R dclone/R/as.mcmc.list.bugs.R dclone/R/jags.parfit.R dclone/R/clusterSize.R dclone/R/plotClusterSize.R dclone/R/coef.mcmc.R dclone/R/vcov.mcmc.R dclone/R/parDosa.R dclone/R/extractdctable.R dclone/R/updated.model.R dclone/R/vcov.mcmc.list.R dclone/R/dcoptions.R dclone/R/dcdiag.default.R dclone/R/zzz.R dclone/R/parJagsModel.R dclone/R/dclone.dciid.R dclone/R/jagsModel.R dclone/R/make.symmetric.R dclone/R/chisq.diag.R
dclone/MD5
dclone/DESCRIPTION
dclone/man
dclone/man/parDosa.Rd dclone/man/parallel.inits.Rd dclone/man/bugs.fit.Rd dclone/man/dctable.Rd dclone/man/dc.fit.Rd dclone/man/parJagsModel.Rd dclone/man/jagsModel.Rd dclone/man/dc.parfit.Rd dclone/man/dclone-package.Rd dclone/man/clusterSize.Rd dclone/man/lambdamax.diag.Rd dclone/man/parLoadModule.Rd dclone/man/write.jags.model.Rd dclone/man/parSetFactory.Rd dclone/man/ovenbird.Rd dclone/man/make.symmetric.Rd dclone/man/parCodaSamples.Rd dclone/man/dcoptions.Rd dclone/man/DcloneEnv.Rd dclone/man/dclone.Rd dclone/man/update.mcmc.list.Rd dclone/man/parUpdate.Rd dclone/man/pairs.mcmc.list.Rd dclone/man/coef.mcmc.list.Rd dclone/man/codaSamples.Rd dclone/man/mclapplySB.Rd dclone/man/errlines.Rd dclone/man/bugs.parfit.Rd dclone/man/jags.fit.Rd dclone/man/dcFit.Rd dclone/man/clusterSplitSB.Rd dclone/man/nclones.Rd dclone/man/regmod.Rd dclone/man/jags.parfit.Rd dclone/man/mcmcapply.Rd dclone/man/evalParallelArgument.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.