as.mcmc.mcmcComposite: Extract mcmc object from a mcmcComposite object

In HelpersMG: Tools for Environmental Analyses, Ecotoxicology and Various R Functions

Extract mcmc object from a mcmcComposite object

Description

Take a mcmcComposite object and create a mcmc.list object to be used with coda package.

Usage

## S3 method for class 'mcmcComposite'
as.mcmc(x, ...)

Arguments

x	A mcmcComposite obtained as a result of MHalgoGen() function
...	Not used

Details

as.mcmc Extract mcmc object from the result of phenology_MHmcmc to be used with coda package

Value

A mcmc.list object

Author(s)

Marc Girondot [e-mail]

See Also

Other mcmcComposite functions: MHalgoGen(), as.parameters(), as.quantiles(), merge.mcmcComposite(), plot.PriorsmcmcComposite(), plot.mcmcComposite(), setPriors(), summary.mcmcComposite()

Examples

## Not run: 
library(HelpersMG)
require(coda)
x <- rnorm(30, 10, 2)
dnormx <- function(data, x) {
 data <- unlist(data)
 return(-sum(dnorm(data, mean=x['mean'], sd=x['sd'], log=TRUE)))
}
parameters_mcmc <- data.frame(Density=c('dnorm', 'dlnorm'), 
Prior1=c(10, 0.5), Prior2=c(2, 0.5), SDProp=c(1, 1), 
Min=c(-3, 0), Max=c(100, 10), Init=c(10, 2), stringsAsFactors = FALSE, 
row.names=c('mean', 'sd'))
mcmc_run <- MHalgoGen(n.iter=1000, parameters=parameters_mcmc, data=x, 
likelihood=dnormx, n.chains=1, n.adapt=100, thin=1, trace=1)
plot(mcmc_run, xlim=c(0, 20))
plot(mcmc_run, xlim=c(0, 10), parameters="sd")
mcmcforcoda <- as.mcmc(mcmc_run)
#' heidel.diag(mcmcforcoda)
raftery.diag(mcmcforcoda)
autocorr.diag(mcmcforcoda)
acf(mcmcforcoda[[1]][,"mean"], lag.max=20, bty="n", las=1)
acf(mcmcforcoda[[1]][,"sd"], lag.max=20, bty="n", las=1)
batchSE(mcmcforcoda, batchSize=100)
# The batch standard error procedure is usually thought to 
# be not as accurate as the time series methods used in summary
summary(mcmcforcoda)$statistics[,"Time-series SE"]
summary(mcmc_run)
as.parameters(mcmc_run)
lastp <- as.parameters(mcmc_run, index="last")
parameters_mcmc[,"Init"] <- lastp
# The n.adapt set to 1 is used to not record the first set of parameters
# then it is not duplicated (as it is also the last one for 
# the object mcmc_run)
mcmc_run2 <- MHalgoGen(n.iter=1000, parameters=parameters_mcmc, data=x, 
likelihood=dnormx, n.chains=1, n.adapt=1, thin=1, trace=1)
mcmc_run3 <- merge(mcmc_run, mcmc_run2)
####### no adaptation, n.adapt must be 0
parameters_mcmc[,"Init"] <- c(mean(x), sd(x))
mcmc_run3 <- MHalgoGen(n.iter=1000, parameters=parameters_mcmc, data=x, 
likelihood=dnormx, n.chains=1, n.adapt=0, thin=1, trace=1)

## End(Not run)

HelpersMG documentation built on Sept. 12, 2024, 9:35 a.m.