coda.create: Create files for use with R-package coda.

In MetaLandSim: Landscape and Range Expansion Simulation

Create files for use with R-package coda.

Description

Creates two text files, <filename.txt> and filename_Index.txt>, in the format used by OpenBUGS, which can then be read using read.coda() to create an mcmc object for subsequent use of coda diagnostic and plotting functions.

Usage

coda.create(object, file.name, write.index = TRUE, par.list = list("mupsi1.chain", 
"e.chain", "x.chain", "b.chain", "y.chain", "alpha.chain"), niter = 101000, nthin = 10)

Arguments

object	Output from ifm.naive.MCMC, ifm.missing.MCMC, or ifm.robust.MCMC, i.e., a named list with vectors e.chain. x.chain, y.chain, b.chain, alpha.chain, and other parameters depending on the model.
file.name	Name of the text file that will be output in the format used by BUGS and JAGS.
write.index	Logical indicating whether or not to also create file.name_Index.txt. Defaults to TRUE, which allows the subsequent use of read.coda().
par.list	List of parameters to include in the file. Defaults to mupsi1.chain, e.chain, x.chain, b.chain, y.chain, alpha.chain; modify to include additional parameters in ifm.missing.MCMC and ifm.robust.MCMC.
niter	Number of iterations in the original chain (before thinning).
nthin	Thinning used in the original estimation function; this is just bookkeeping, as this function does not perform the thinning.

Details

Writes text files to the current working directory or to the path specified with "file.name".

Author(s)

Benjamin Risk

Examples

## Not run: 

# quick run; actual estimation requires more iterations:

data(simulatedifm)

myniter=100
nsite=nrow(z.sim)
nyear=ncol(z.sim)
nthin=1
nburnin=0
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=myniter,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=1000)

# write files in OpenBUGS format to working directory:
coda.create(inm1,"sim_inm1",par.list=list("e.chain","x.chain","alpha.chain",
"b.chain","y.chain"),niter=myniter,nthin=nthin)

## End(Not run)

MetaLandSim documentation built on Jan. 13, 2023, 1:11 a.m.