MetaLandSim (version 2.0.0)

combine.chains: Combines two chains into a single chain.

Description

Combines two lists of chains from ifm.naive.MCMC, ifm.missing.MCMC, or ifm.robust.MCMC into one list where each element is the concatenated chains.

Usage

combine.chains(x1, x2, nburnin, nthin = 1, z.thin = TRUE)

Value

Named list with the same names as the inputs x1 and x2

Arguments

x1

First list of chains.

x2

Second list of chains.

nburnin

Number of initial iterations to discard.

nthin

If nthin>1, subsets to every nthin^th sample

z.thin

logical; defaults to TRUE. Thinning for the posterior sample of the occupancy states. If true, uses thinning equal to 5. The posterior sample of occupancy states is a large nsite x nyear x niter array, and this option reduces memory usage. Ignored if the chain is from the ifm.naive.MCMC (where occupancy states are fixed).

Author

Benjamin Risk

Examples

data(simulatedifm)

init1=list(alpha=runif(1,1,30), b=runif(1,0,5),y=runif(1,0,20),e=runif(1,0,1),x=runif(1,0,5))

inm1 <- ifm.naive.MCMC(niter=500,init=init1,z.data =
 z.sim,site.distance=sim.distance,site.area=sim.area,
  sd.prop.alpha=4,sd.prop.b=0.6,sd.prop.y=40,sd.prop.e=0.05,sd.prop.x=0.4,nthin=1,print.by=100)
  
init1=list(alpha=runif(1,1,30), b=runif(1,0,5),y=runif(1,0,20),e=runif(1,0,1),x=runif(1,0,5))

inm2 <- ifm.naive.MCMC(niter=500,init=init1,z.data =
 z.sim,site.distance=sim.distance,site.area=sim.area,
  sd.prop.alpha=4,sd.prop.b=0.6,sd.prop.y=40,sd.prop.e=0.05,sd.prop.x=0.4,nthin=1,print.by=100)

sim.inm=combine.chains(inm1,inm2,nburnin=0,nthin=1)