setRestartSettings: Set Restart Settings

In AnaCoDa: Analysis of Codon Data under Stationarity using a Bayesian Framework

Description

setRestartSettings sets the needed information (what the file is called, how often the file should be written) to write information to restart the MCMC algorithm from a given point.

Usage

setRestartSettings(mcmc, filename, samples, write.multiple = TRUE)

Arguments

mcmc	MCMC object that will run the model fitting algorithm.
filename	Filename for the restart files to be written.
samples	Number of samples that should occur before a file is written.
write.multiple	Boolean that determines if multiple restart files are written. Default value is TRUE.

Details

setRestartSettings writes a restart file every set amount of samples that occur. Also, if write.multiple is true, instead of overwriting the previous restart file, the sample number is prepended onto the file name and multiple rerstart files are generated for a run.

Value

This function has no return value.

Examples

## set restart settings for checkpointing

samples <- 2500
thinning <- 50
adaptiveWidth <- 25

## estimate all parameter types
mcmc <- initializeMCMCObject(samples = samples, thinning = thinning, 
                             adaptive.width=adaptiveWidth, est.expression=TRUE, 
                             est.csp=TRUE, est.hyper=TRUE, est.mix = TRUE) 
                             
# prompts the mcmc to write a restart file every 100 samples during the run.
setRestartSettings(mcmc = mcmc, filename = "test_restart", samples = 100)

# prompts the mcmc to write a restart file every 100 samples during the run, 
# but will overwrite it each time.
setRestartSettings(mcmc = mcmc, filename = "test_restart", samples = 100, 
                   write.multiple = FALSE)
           

AnaCoDa documentation built on Jan. 8, 2021, 2:37 a.m.