Data Cloning and MCMC Tools for Maximum Likelihood Methods
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Documentation for package ‘dclone’ version 2.3-3
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 |