Summarizing distributions of parameters simulated from statistical age models.
reportSAM(obj, burn = 10000, thin = 5,
plot = TRUE, outfile = NULL, ...)integer(with default): number of iterations (i.e., the initial, non-stationary portion of the chain) to be discarded
integer(with default): take every thin-th iteration
logical(with default): plot the MCMC output or not
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
Return a list that contains the following elements:
parameters and relevant statistics
quantiles of simulated parameters
calculated maximum logged likelihood value
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").
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.