Code to implement analyses for the paper "Simulation-based inference for close-kin mark-recapture: implications for small populations and nonrandom mating" by P. B. Conn
SIMULATION STUDY 1
Examines the performance of different estimators when parents and offspring populations are each sampled once.
The analysis can be conducted using the script /inst/sim_study_one_sample.R
SIMULATION STUDY 2 Examines performance in multi-year CKMR studies where population trend is of interest. This study is run using the script /inst/sim_study_trend.R Note that study also relies on some templated C++ code to conduct pseudo-likelihood inference (via R's TMB package). The pseudo-likelihood code is in the /src directory.
SIMULATION STUDY 3 Examines the performance of different CKMR estimators when applied to a small population with a monogamous mating system. The study is run using the script /inst/sim_monogamous_abc.R
CARIBOU ANALYSIS An example analysis is conducted on the Tonquin caribou herd, using data from 2006-2015. See Mcfarlane et al. (2019, Glabal Ecology and Conservation 16, e00451) and Merriell et al. (2024, Ecology and Evolution 14, e70230) for original description of these data. The analysis is run using inst/caribou_analysis.R, relying on sample sizes and mother-offspring pairs as available in data/caribou.csv