Reporting MCMC outputs for statistical age models

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Description

Summarizing distributions of parameters simulated from statistical age models.

Usage

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reportSAM(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 reportSAM summarizes the output of a Markov chain (the mean values, the standard deviations, and the 95 percent confidence intervals). 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

parameters and relevant statistics

quantile

quantiles of simulated parameters

maxlik

calculated maximum logged likelihood value

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.

See Also

mcFMM; mcMAM