MetaLandSim (version 1.0.4)

ifm.robust.MCMC: Estimate the robust design incidence function model

Description

Estimates the IFM with imperfect detection and missing data.

Usage

ifm.robust.MCMC(niter = 1000, init, det.data, site.distance, site.area, sd.prop.p = 0.1,
sd.prop.mupsi1 = 0.1, sd.prop.e = 0.2, sd.prop.x = 0.2, sd.prop.y = 0.2, sd.prop.b = 0.2,
sd.prop.alpha = 0.2, nthin = 1, nsite.subset = 5, print.by = 100)

Arguments

niter

Number of iterations in the MCMC chain.

init

Named list with values to initialize the chain. E.g.: init1=list(z.data=initocc,z.missing=runif(nmissing),p=runif(nyear, 0.1,1),mupsi1=runif(1),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)). z.data: a matrix with nrows = number of sites and ncol = number of years. Contains NAs for missing values. Contains naive estimates of occupancy elsewhere. z.missing: z.missing: a vector of initial occupancy states for the missing data with length equal to the number of NAs in z.data (i.e., vectorized across years). Can use runif(nmissing). p: vector of length nyears with inital probability of detection in each year mupsi1: probability of initial occupancy in year 1; runif(1) suffices alpha: initial value for alpha in dispersal model; described as 1 / average dispersal distance b: initial value for parameter b in colonization model y: initial value for parameter y in colonization model e: initial value for e in extinction model x: initial value for x in extinction model

det.data

Detection data in an array with dimensions nsites x nyears x nvisits. For removal design, set all values after a detection equal to NA. For missing data in a given year, set all visits to NA.

site.distance

nsite x nsite matrix of distances between sites. The tuning parameters in the example are set for distances less than one, with max distance approximately 0.5. Input data should have a similar scaling.

site.area

Vector of length nsite with areas. The tuning parameters in the example are set for average area approximately equal to 1. Input data should have a similar scaling.

sd.prop.p

Scalar equal to the standard deviation of the proposal distribution for probability of detection, which is a normal distribution centered at current value in the mcmc chain. The same standard deviation is used for all years.

sd.prop.mupsi1

Standard deviation of the proposal distribution for occupancy in year 1.

sd.prop.e

Standard deviation of the proposal distribution for parameter e.

sd.prop.x

Standard deviation of the proposal distribution for parameter x.

sd.prop.y

Standard deviation of the proposal distribution for parameter y.

sd.prop.b

Standard deviation of the proposal distribution for parameter b.

sd.prop.alpha

Standard deviation of the proposal distribution for parameter alpha.

nthin

If specified, keeps only every nthin^th sample from the MCMC chain. Use to save memory or when the chain is moving slowly.

nsite.subset

The number of sites to include in the block sampling, where nsite.subset is equal to the number of sites updated in the same step. Larger values decrease the probability of acceptance.

print.by

Specifies how often to print the number of the current iteration.

Value

z.chain

nsite x nyear x niter array sampled from the posterior distribution of occupancy in each year (if detection occurred at a given year and site, then the value is identically equal to one for all iterations).

muz.chain

nyear x niter matrix posterior sample of the proportion of sites occupied in each year.

muz.missing.chain

nyear x niter matrix posterior sample of the proportion of sites occupied for sites with missing data.

prop.extinct.chain

Extinction rate for all sites.

prop.colon.chain

Colonization rate.

p.chain

nyear x niter sample of detection probabilities.

mupsi1.chain

posterior sample of parameter for occupancy in year 1.

e.chain

posterior sample of e

x.chain

posterior sampmle of x

y.chain

posterior sample of y

b.chain

posterior sample of b

alpha.chain

posterior sample of alpha

latent.deviance.chain

posterior sample of -2*loglik

References

Risk, B. B., De Valpine, P., Beissinger, S. R. (2011). A robust design formulation of the incidence function model of metapopulation dynamics applied to two species of rails. Ecology, 92(2), 462-474.

Examples

# NOT RUN {
# }
# NOT RUN {
data(simulatedifm)
library("coda")

# There are more parameters in this model
# and estimating the posterior requires more iterations:
niter=2000
nsite=nrow(z.sim)
nyear=ncol(z.sim)
nthin=1
nburnin=1000
## NOTE! The notation used here corresponds to MetaLandSim and differs from Risk et al 2011
## Here
## e (in MetaLandSim) = mu (in Risk et al 2011)
## x = chi
## y = gamma
## b = beta
## alpha = alpha
##
# Priors:
#         e: [0,1]
#         x: [0,5]
#         y^2: [0,400]
#         b: [0,5]
#         alpha: [1,30]

# NOTE: If posteriors are truncated at zero, then estimates are biased. Rescale
# distances (e.g., divide by 10,000) and/or areas so that parameters are larger.

# Count number of times a site was never visited in a given year:
nmissing = sum(is.na(z.sim.20))

# Create a dataset with initial guess of true occupancy for sites with visits.
# This dataset should be number of sites by years
# one way of generating these initial values:
initocc <- suppressWarnings(apply(sim.det.20,c(1,2),max,na.rm=TRUE))
# produces warnings but that's okay
initocc[initocc==-Inf]=NA


init1=list(z.data=initocc,z.missing=runif(nmissing),p=runif(nyear,
0.1,1),mupsi1=runif(1),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))

# for diagnosing acceptance rates:
# init1=list(z.data=initocc,z.missing=runif(nmissing),p=runif(nyear,0.1,1),
mupsi1=runif(1),alpha=20, b=0.5,y=7.5,e=0.25,x=0.25)

a = Sys.time()
ir1 <- ifm.robust.MCMC(niter=niter,init=init1, det.data = sim.det.20,
site.distance=sim.distance,site.area=sim.area, sd.prop.p=0.25,sd.prop.mupsi1=0.2, 
sd.prop.alpha=2, sd.prop.b=0.6, sd.prop.y=20, sd.prop.e=0.1, sd.prop.x=0.4, nthin=1)
accept.calculate(ir1,model='robust')
Sys.time() - a

init2=list(z.data=initocc,z.missing=runif(nmissing),p=runif(nyear,
0.1,1),mupsi1=runif(1),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))
ir2 <- ifm.robust.MCMC(niter=niter,init=init2, det.data = sim.det.20,
 site.distance=sim.distance,site.area=sim.area, sd.prop.mupsi1=0.2, sd.prop.alpha=2, sd.prop.b=0.6,
  sd.prop.y=20, sd.prop.e=0.1, sd.prop.x=0.4, sd.prop.p = 0.25, nthin=1)
accept.calculate(ir2,model='robust')

coda.create(ir1,"sim_ir1",par.list=list("mupsi1.chain","e.chain","x.chain",
"alpha.chain","b.chain","y.chain","p.chain"),niter=niter,nthin=nthin)
coda.create(ir2,"sim_ir2",par.list=list("mupsi1.chain","e.chain","x.chain",
"alpha.chain","b.chain","y.chain","p.chain"),niter=niter,nthin=nthin)
coda.sim.ir1=read.coda("sim_ir1.txt","sim_ir1_Index.txt")
coda.sim.ir2=read.coda("sim_ir2.txt","sim_ir2_Index.txt")
coda.sim.ir.list=mcmc.list(coda.sim.ir1,coda.sim.ir2)
sim.ir=combine.chains(ir1,ir2,nburnin=nburnin,nthin=1)
coda.create(sim.ir,"sim_ir",par.list=list("mupsi1.chain","e.chain",
"x.chain","alpha.chain","b.chain","y.chain","p.chain"),niter=(2*niter-2*nburnin),nthin=nthin)
coda.sim.ir.long=read.coda("sim_ir.txt","sim_ir_Index.txt")

summary(coda.sim.ir.list)
summary(coda.sim.ir.long)

gelman.diag(coda.sim.ir.list)

plot(coda.sim.ir.list)
plot(coda.sim.ir.long)
cumuplot(coda.sim.ir.long)

# calculate maximum a posteriori estimates:
m1 <- as.matrix(sim.ir)
e <- calcmode(m1[,1][[1]])
x <- calcmode(m1[,1][[2]])
y <- calcmode(m1[,1][[3]])
b <- calcmode(m1[,1][[4]])
alpha <- calcmode(m1[,1][[5]])
# }