getACinCore: Extract an MCMC chain for number of Activity Centres in the...

In mikemeredith/makeJAGSmask: Construct a Habitat Matrix for Use with SECR Analysis in JAGS or BUGS

Description

Often we are interested in the number of activity centres in a core area which is smaller than the full extent of the available habitat. This function produces an MCMC chain for the posterior distribution of the number of activity centres in the core.

Usage

getACinCore(S, w, JAGSmask)

Arguments

S	A 3D array of MCMC output, iterations x animals x 2, with the x and y coordinates of the activity centres on the pixels scale. Typically this would be output from JAGS.
w	A 1/0 matrix of MCMC output, iterations x animals, with 1 if the animal is in the study area and available for capture, 0 otherwise. Typically this would be output from JAGS. May be missing if (1) data augmentation was not used or (2) if relevant entries in S have been replaced with NA.
JAGSmask	An object of class JAGSmask which includes information on the core, see addCore.

Value

Returns an MCMC chain with the posterior distribution for the number of activity centres located inside the core area.

Author(s)

Mike Meredith

Examples

## See the examples for addCore.

mikemeredith/makeJAGSmask documentation built on May 19, 2021, 1:10 a.m.