reportMC: Reporting MCMC outputs for statistical age models

In numOSL: Numeric Routines for Optically Stimulated Luminescence Dating

Reporting MCMC outputs for statistical age models

Description

Summarizing distributions of parameters simulated from statistical age models using a Markov Chain Monte Carlo method.

Usage

reportMC(obj, burn = 10000, thin = 5, 
         plot = TRUE, outfile = NULL, ...)

Arguments

obj	list(required): an object of S3 class "mcAgeModels", which is produced by function mcFMM or mcMAM
burn	integer(with default): number of iterations (i.e., the initial, non-stationary portion of the chain) to be discarded
thin	integer(with default): take every thin-th iteration
plot	logical(with default): plot the MCMC output or not
outfile	character(optional): if specified, simulated parameters will be written to a CSV file named "outfile" and saved to the current work directory
...	do not use

Details

Function reportMC summarizes the output of a Markov Chain (the mean values, the standard deviations, the mode values, and the 2.5, 25, 50, 75, 97.5 quantiles of the simulated parameters). The initial i (burn=i) samples may have been affected by the inital state and has to be discarded ("burn-in"). Autocorrelation of simulated samples can be reduced by taking every j-th (thin=j) iteration ("thining").

Value

Return a list that contains the following elements:

pars	means, standard deviations, and modes of simulated parameters
quantile	quantiles of simulated parameters
maxlik	maximum logged likelihood values calculated using the means and modes of simulated parameters
bic	Bayesian Information Criterion (BIC) values calculated using the means and modes of simulated parameters

References

Lunn D, Jackson C, Best N, Thomas A, Spiegelhalter D, 2013. The BUGS book: a practical introduction to bayesian analysis. Chapman & Hall/CRC Press.

Gelman A, Carlin JB, Stern HS, Dunson DB, Vehtari A, Rubin DB, 2013. Bayesian data analysis. Chapman & Hall/CRC Press.

Peng J, Dong ZB, Han FQ, 2016. Application of slice sampling method for optimizing OSL age models used for equivalent dose determination. Progress in Geography, 35(1): 78-88. (In Chinese).

See Also

mcFMM; mcMAM

numOSL documentation built on Sept. 18, 2023, 9:07 a.m.