mcMAM: Minimum age model optimization (using a Markov chain Monte...

Description Usage Arguments Value References See Also Examples

View source: R/mcMAM.R

Description

Sampling from the joint-likelihood function of the minimum age model using a Markov chain Monte Carlo (MCMC) method .

Usage

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mcMAM(EDdata, ncomp = -1, addsigma = 0, iflog = TRUE, 
      nsim = 50000, inis = list(), control.args = list())

Arguments

EDdata

matrix(required): a two-column matrix (i.e., equivalent dose values and
associated standard errors)

ncomp

integer(with default): number of components, -1=MAM3, -2=MAM4

addsigma

numeric(with default): additional uncertainty

iflog

logical(with default): transform equivalent dose values to log-scale or not

nsim

integer(with default): deseried number of iterations

inis

list(with default): initial state of parameters.
Example: inis=list(p=0.1,gamma=20,sigma=0.5) in MAM3

control.args

list(with default): arguments used by the Slice Sampling algorithm, see function mcFMM for details

Value

Return an invisible list of S3 class object "mcAgeModels". See mcFMM for details.

References

Galbraith RF, Roberts RG, Laslett GM, Yoshida H, Olley JM, 1999. Optical dating of single grains of quartz from Jinmium rock shelter, northern Australia. Part I: experimental design and statistical models. Archaeometry, 41(2): 339-364.

Neal RM, 2003. "Slice sampling" (with discussion). Annals of Statistics, 31(3): 705-767. Software is freely available at http://www.cs.utoronto.ca/~radford/slice.software.html.

See Also

mcFMM; reportSAM; RadialPlotter; EDdata

Examples

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  # Not run.
  # data(EDdata)
  # Construct a MCMC chain for MAM3.
  # obj<-mcMAM(EDdata$al3,ncomp=-1,addsigma=0.1,nsim=5000)
  # reportSAM(obj,burn=1e3,thin=2)
  #
  # The convergence of the simulations may be diagnosed with 
  # the Gelman and Rubin's convergence diagnostic.
  # library(coda)   # Only if package "coda" has been installed.
  # args<-list(nstart=50)
  # inis1<-list(p=0.01,gamma=26,mu=104,sigma=0.01)
  # inis2<-list(p=0.99,gamma=100,mu=104,sigma=4.99)
  # obj1<-mcMAM(EDdata$al3,ncomp=-2,nsim=3000,inis=inis1,control.args=args)
  # obj2<-mcMAM(EDdata$al3,ncomp=-2,nsim=3000,inis=inis2,control.args=args)
  # chain1<-mcmc(obj1$chains)
  # chain2<-mcmc(obj2$chains)
  # chains<-mcmc.list(chain1,chain2)
  # gelman.plot(chains)

numOSL documentation built on July 26, 2018, 9 a.m.