reportSAM: Report the results of statistical age models

Description

Return a plot and a list that summaries the posterior density distributions of the quantities of interest in a specified age model, the history of simulations and the auto-correlations of these parameters.

Usage

reportSAM(obj, burn = NULL, thin = NULL, plot = TRUE, outfile = NULL, ...)

Arguments

obj

required: an object of class "mcAgeModels", which is produced by function mcFMM or mcMAM

burn

numeric(with default): the number of simulations to be discarded, i.e. the initial, non-stationary portion of the chains, default burn=floor(nsim/5L)

thin

numeric(with default): only one value from each portion that constains every thin values is retained, default thin=5

plot

logical(with default): plot the results or not

outfile

character(optional): if specified, simulated chains will be written to a file named "outfile" in ".csv" format and will be saved to the current work directory

...

do not use

Value

Return list that contains following elements:
parsestimates and their standard errors
quantilequantiles of simulated variables
maxlikthe estimated logged maximum likelihood value

Details

The numbers of "burn-in" and "thining" are used to refine the simulated chains in order to obtain more reliable inference. The initial portion of the chains may not sufficiently close to stationarity and need to be discarded. Where the "thining" protocol is used to reduce the posterior correlation between parameters.

References

Robert, C.P., Casella, G., 2010. Introducing Monte Carlo Methods with R. New York: Springer.

Lunn, D., Jackson, C., Best, N., Thomas, A., Spiegelhalter, D., 2013. The BUGS Book: A Practical Introduction to Bayesian Analysis. Boca Raton, Florida: CRC Press.