Combining individual and close-kin mark-recapture to design an effective wildlife population survey (dataset)

This repository contains code to reproduce the analyses presented in: Jacobson, E. K., M. V. Bravington, D. L. Miller, I. S. Trukhanova, R. L. Taylor, and W. S. Beatty. Combining close-kin and self-mark-recapture to design an effective wildlife population survey.

The folder Simulation contains scripts to run the simulation.
The package fishSim must be installed from https://github.com/SMBaylis/fishSim

runSimScenarios.R runs the walrus simulation given demographic parameters of interest.

The folder CKMRModels contains the ICKMR model code.
The following packages must be installed from Mark's repo at https://markbravington.r-universe.dev/builds

mvbutils
offarray
despack
TMBO
debug
kinsimmer
atease

Additional packages required from CRAN:

doParallel
fastmatch

Order of Operations:

fit_walrus_ckmR.R runs the CKMR code on a file of simulated data.

from here, you can either

compare2sims.R compares model expected values to simulated values
design_eg.R generates expected precision associated with designs