writeMCMCObject: Write MCMC Object

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

Description

writeMCMCObject stores the MCMC information from the model fitting run in a file.

Usage

writeMCMCObject(mcmc, file)

Arguments

mcmc	MCMC object that has run the model fitting algorithm.
file	A filename where the data will be stored.

Value

This function has no return value.

Examples

## saving the MCMC object after model fitting
genome_file <- system.file("extdata", "genome.fasta", package = "AnaCoDa")

genome <- initializeGenomeObject(file = genome_file)
sphi_init <- c(1,1)
numMixtures <- 2
geneAssignment <- c(rep(1,floor(length(genome)/2)),rep(2,ceiling(length(genome)/2)))
parameter <- initializeParameterObject(genome = genome, sphi = sphi_init, 
                                       num.mixtures = numMixtures, 
                                       gene.assignment = geneAssignment, 
                                       mixture.definition = "allUnique")
samples <- 2500
thinning <- 50
adaptiveWidth <- 25
mcmc <- initializeMCMCObject(samples = samples, thinning = thinning, 
                             adaptive.width=adaptiveWidth, est.expression=TRUE, 
                             est.csp=TRUE, est.hyper=TRUE, est.mix = TRUE) 
divergence.iteration <- 10
## Not run: 
runMCMC(mcmc = mcmc, genome = genome, model = model, 
        ncores = 4, divergence.iteration = divergence.iteration)
writeMCMCObject(mcmc = mcmc, file = file.path(tempdir(), "file.Rda"))


## End(Not run)

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