bmksensitive: Hellinger distance between two MCMC chains for sensitivity...

In bmk: MCMC diagnostics package

Description

Determine if two identically dimensioned sets of chains match. This is good for conducting sensitivity studies.

Usage

  bmksensitive(inputlist1, inputlist2)

Arguments

inputlist1	A list of the combined MCMC chains for all samples from one scenario.
inputlist2	A list of the combined MCMC chains for all samples from another scenario.

References

Boone EL, Merrick JR and Krachey MJ. A Hellinger distance approach to MCMC diagnostics. Journal of Statistical Computation and Simulation, DOI:10.1080/00949655.2012.729588.

Examples

data(MCMCsamples)
 bmksensitive(MCMC.one.mean0, MCMC.one.mean1)
 ## Not run: 
 library(dismo); library(MCMCpack)
 data(Anguilla_train)
 b0mean0 <- 0
 b0mean1 <- 1
 b0precision <- (1/5)^2
 mcmclen = 1000
 burn=10000
 MCMC.one.mean0 <- MCMClogit(Angaus ~ SegSumT+DSDist+USNative+as.factor(Method)+DSMaxSlope+USSlope,
                  data=Anguilla_train,burnin=burn, mcmc=mcmclen, beta.start=-1,
                  b0=b0mean0, B0=b0precision)
 MCMC.one.mean1 <- MCMClogit(Angaus ~ SegSumT+DSDist+USNative+as.factor(Method)+DSMaxSlope+USSlope,
                  data=Anguilla_train,burnin=burn, mcmc=mcmclen, beta.start=-.5,
                  b0=b0mean1, B0=b0precision)
 bmksensitive(one, two)
 
## End(Not run)

bmk documentation built on May 1, 2019, 8:21 p.m.