reportSAM: Report the results of statistical age models
Description
Return a list that summaries the density distributions of the quantities of interest.Usage
reportSAM(obj, burn = 10000, thin = 5,
plot = TRUE, outfile = NULL, ...)Arguments
obj
required: an object of S3 class "mcAgeModels", which is produced by function mcFMM or mcMAM burn
numeric(with default): the number of iterations to be discarded, i.e., the initial, non-stationary portion of the chain thin
numeric(with default): only one sample from each portion that constains every thin values is retained plot
logical(with default): plot the results or not outfile
character(optional): if specified, simulated chain will be written to a file named "outfile" in ".csv" format and saved to the current work directory Value
- Return a list that contains following elements:
- parsparameters and their standard errors
- quantilequantiles of simulated quantities
- maxlikthe logged maximum likelihood value
Details
This function summarizes the output of a Markov chain (the mean values, the standard deviations, and the 95 percent confidence intervals). The numbers of "burn-in" and "thining" are used to refine the simulated chain. The initial portion of the chains may not sufficiently close to stationarity and need to be discarded. The "thining" protocol is used to reduce the posterior correlation of parameters.References
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.Robert CP, Casella G, 2010. Introducing Monte Carlo Methods with R. Springer.