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dclone (version 2.3-0)

Data Cloning and MCMC Tools for Maximum Likelihood Methods

Description

Low level functions for implementing maximum likelihood estimating procedures for complex models using data cloning and Bayesian Markov chain Monte Carlo methods as described in Solymos 2010 (R Journal 2(2):29--37). Sequential and parallel MCMC support for 'JAGS', 'WinBUGS', 'OpenBUGS', and 'Stan'.

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Version

Install

install.packages('dclone')

Monthly Downloads

470

Version

2.3-0

License

GPL-2

Maintainer

Peter Solymos

Last Published

March 22nd, 2019

Functions in dclone (2.3-0)

clusterSplitSB

Size balancing
mclapplySB

Size balancing version of mclapply
DcloneEnv

Manipulating dclone environments
bugs.fit

Fit BUGS models with cloned data
write.jags.model

Write and remove model file
errlines

Plot error bars
mcmc.list-methods

Methods for the 'mcmc.list' class
evalParallelArgument

Evaluates parallel argument
mcmcapply

Calculations on 'mcmc.list' objects
dc.fit

Iterative model fitting with data cloning
dc.parfit

Parallel model fitting with data cloning
bugs.parfit

Parallel computing with WinBUGS/OpenBUGS
.dcFit

Internal function for iterative model fitting with data cloning
jags.fit

Fit JAGS models with cloned data
jags.parfit

Parallel computing with JAGS
dcoptions

Setting Options
nclones

Number of Clones
clusterSize

Optimizing the number of workers
stan.fit

Fit Stan models with cloned data
update.mcmc.list

Automatic updating of an MCMC object from JAGS
dclone-package

Data Cloning
dctable

Retrieve descriptive statistics from fitted objects to evaluate convergence
parJagsModel

Create a JAGS model object on parallel workers
parLoadModule

Dynamically load JAGS modules on parallel workers
parallel.inits

Parallel RNGs for initial values
dclone

Cloning R objects
regmod

Exemplary MCMC list object
ovenbird

Abundances of ovenbird in Alberta
pairs.mcmc.list

Scatterplot Matrices for 'mcmc.list' Objects
jagsModel

Create a JAGS model object
lambdamax.diag

Data Cloning Diagnostics
parDosa

Parallel wrapper function to call from within a function
parCodaSamples

Generate posterior samples in 'mcmc.list' format on parallel workers
parSetFactory

Advanced control over JAGS on parallel workers
parUpdate

Update jags models on parallel workers
codaSamples

Generate posterior samples in mcmc.list format
make.symmetric

Make a square matrix symmetric by averaging.