accept.calculate: Calculate acceptance rates in MCMC chains

In MetaLandSim: Landscape and Range Expansion Simulation

Calculate acceptance rates in MCMC chains

Description

Calculate acceptance rates of parameters in the IFM.

Usage

accept.calculate(x, model = c("naive", "missing", "robust"))

Arguments

x	A named list with the MCMC chains estimated by ifm.naive.MCMC, ifm.missing.MCMC, or ifm.robust.MCMC.
model	Either "naive", "missing", or "robust"

Value

Named list containing MCMC chain acceptance rates. Names are built from the input list, e.g., for model=“naive":

acc.b.chain	Acceptance rates of parameter b
acc.e.chain	Acceptance rates of parameter e
acc.y.chain	Acceptance rates of parameter y
acc.alpha.chain	Acceptance rates of parameter alpha
acc.x.chain	Acceptance rates of parameter x

Author(s)

Benjamin Risk

Examples

data(simulatedifm)

# Here, we run a chain with random initial values:
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=1000,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)
accept.calculate(inm1,model='naive')

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