calc.GR {mixstock} | R Documentation

## Run chains and calculate Gelman and Rubin diagnostics for mixed stock analyses

### Description

For a mixed stock analysis data set with `R` sources, runs `R` Gibbs-sampler chains (one starting from a majority of the contribution from each source) and calculates Gelman and Rubin diagnostics on the combined set of chains.

### Usage

    calc.GR(data, tot=20000, burn=1, verbose=FALSE, rseed=1001,
               chainfrac=NULL)

### Arguments

`data` | A mixed stock analysis data set (either an object of type `mixstock.data`, or any list containing appropriate `sourcesamp` and `mixsamp` objects)
`tot` | Total length of each MCMC chain
`burn` | Burn-in time for MCMC chains
`verbose` | Produce verbose output?
`chainfrac` | Fraction of each chain to discard. By default, chainfrac is set to (1-1/R), so that the total length of the combined chain is equal to (R*tot/R=tot).
`rseed` | Seed for random-number generator

### Details

calls CODA function `gelman.diag`

### Value

Returns the diagnostic from the CODA function

### Author(s)

Ben Bolker

[Package mixstock version 0.9.2 Index]