R: Data Cloning and MCMC Tools for Maximum Likelihood Methods

# Data Cloning and MCMC Tools for Maximum Likelihood Methods

## Documentation for package ‘dclone’ version 2.3-3

- DESCRIPTION file.
- Package NEWS.

## Help Pages

dclone-package | Data Cloning
.dcFit | Internal function for iterative model fitting with data cloning
.DcloneEnvModel | Manipulating dclone environments
.DcloneEnvResults | Manipulating dclone environments
as.mcmc.list.bugs | Fit BUGS models with cloned data
bugs.fit | Fit BUGS models with cloned data
bugs.parfit | Parallel computing with WinBUGS/OpenBUGS
chisq.diag | Data Cloning Diagnostics
chisq.diag.mcmc.list | Data Cloning Diagnostics
clean.jags.model | Write and remove model file
clearDcloneEnv | Manipulating dclone environments
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
confint.mcmc.list.dc | Methods for the 'mcmc.list' class
custommodel | Write and remove model file
dc.fit | Iterative model fitting with data cloning
dc.parfit | Parallel model fitting with data cloning
dcdiag | Retrieve descriptive statistics from fitted objects to evaluate convergence
dcdiag.default | Retrieve descriptive statistics from fitted objects to evaluate convergence
dcdim | Cloning R objects
dciid | Cloning R objects
dclone | Cloning R objects
dclone.dcdim | Cloning R objects
dclone.dciid | Cloning R objects
dclone.dctr | Cloning R objects
dclone.default | Cloning R objects
dclone.environment | Cloning R objects
dclone.list | Cloning R objects
DcloneEnv | Manipulating dclone environments
dcoptions | Setting Options
dcsd | Methods for the 'mcmc.list' class
dcsd.mcmc.list | Methods for the 'mcmc.list' class
dctable | Retrieve descriptive statistics from fitted objects to evaluate convergence
dctable.default | Retrieve descriptive statistics from fitted objects to evaluate convergence
dctr | Cloning R objects
errlines | Plot error bars
errlines.default | Plot error bars
evalParallelArgument | Evaluates parallel argument
existsDcloneEnv | Manipulating dclone environments
extractdcdiag | Retrieve descriptive statistics from fitted objects to evaluate convergence
extractdcdiag.default | Retrieve descriptive statistics from fitted objects to evaluate convergence
extractdctable | Retrieve descriptive statistics from fitted objects to evaluate convergence
extractdctable.default | Retrieve descriptive statistics from fitted objects to evaluate convergence
jags.fit | Fit JAGS models with cloned data
jags.parfit | Parallel computing with JAGS
jagsModel | Create a JAGS model object
lambdamax.diag | Data Cloning Diagnostics
lambdamax.diag.mcmc.list | Data Cloning Diagnostics
listDcloneEnv | Manipulating dclone environments
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
nclones.default | Number of Clones
nclones.list | 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 workers
parDosa | Parallel wrapper function to call from within a function
parJagsModel | Create a JAGS model object on parallel workers
parLapplySB | Size balancing
parLapplySLB | Size balancing
parListFactories | Advanced control over JAGS on parallel workers
parListModules | Dynamically load JAGS modules on parallel workers
parLoadModule | Dynamically load JAGS modules on parallel workers
parSetFactory | Advanced control over JAGS on parallel workers
parUnloadModule | Dynamically load JAGS modules on parallel workers
parUpdate | Update jags models on parallel workers
plot.dcdiag | Retrieve descriptive statistics from fitted objects to evaluate convergence
plot.dctable | Retrieve descriptive statistics from fitted objects to evaluate convergence
plotClusterSize | Optimizing the number of workers
pullDcloneEnv | Manipulating dclone environments
pushDcloneEnv | Manipulating dclone environments
quantile.mcmc.list | Methods for the 'mcmc.list' class
regmod | Exemplary MCMC list object
stack.mcmc.list | Calculations on 'mcmc.list' objects
stan.fit | Fit Stan models with cloned data
stan.model | Fit Stan models with cloned data
stan.parfit | Fit Stan models with cloned data
update.mcmc.list | Automatic updating of an MCMC object from JAGS
updated.model | Automatic updating of an MCMC object from JAGS
vcov.mcmc.list | Methods for the 'mcmc.list' class
vcov.mcmc.list.dc | Methods for the 'mcmc.list' class
write.jags.model | Write and remove model file