mcmcListExample {mcmcOutput}

An object of class mcmc.list produced by rjags::coda.samples

Description

This is the output of a basic occupancy model applied to detection/non-detection data for blue ridge salamanders (Eurycea wilderae) in Great Smoky Mountains National Park (MacKenzie et al, 2006 p99). Detections were recorded for 5 visits to each of 39 sites, and the data are the number of visits where the species was detected.

The model has five parameters:

psi

scalar, the probability of occupancy.

p

p[1,1] is the probability of detection given presence; p[2,2] is a dummy variable with values drawn from a Beta(0.5,0.5) distribution; p[1,2] and p[2,1] are not defined, so p is a "ragged array".

z

a vector of length 39, one value for each site.

Tobs

scalar, the Freeman-Tukey discrepancy for the observed data.

Tsim

scalar, the Freeman-Tukey discrepancy for the simulated data.

The number of nodes monitored is 44 (p[1,2] and p[2,1] are not monitored).

Three MCMC chains were run, with 1000 adaptation iterations, 1000 burn-in, and 1000 iterations saved per chain after thinning by 10.

Usage

data("mcmcListExample")

Format

mcmcListExample is mcmc.list object as defined in package coda.

References

MacKenzie, D I; J D Nichols; A J Royle; K H Pollock; L L Bailey; J E Hines 2006. Occupancy estimation and modeling : inferring patterns and dynamics of species occurrence. Elsevier Publishing.

Examples

data(mcmcListExample)
str(mcmcListExample)

# convert to class mcmcOutput
( mco <- mcmcOutput(mcmcListExample) )
summary(mco)

# Extract with "$"
p <- mco$p
str(p)
p[1:5,,]  # Elements of p not defined in the model are filled with NAs

# "[" with one index, produces new mcmcOutput object
head(mco[4:5])
print(mco[c("z[35]", "z[39]")])

# "[" with two indices
mco[1:5, "psi"]  # First 5 values for psi (chain #1)

# "[" with three indices
mco[1:5, 2, "psi"] # First 5 values for psi in chain #2