Abundance estimation using capture-recapture models

What it does

This contains R code to estimate abundance using the Cormack-Jolly-Seber (CJS) model. I use RMark because everything can be done in R, and it's cool for reproducible research.

I consider simple CJS models and models with transience. In passing, I also fit models with heterogeneity in the detection process using i) individual random effect and ii) with finite mixtures. The bootstrap is used to obtain confidence intervals. Multi-model inference is also illustrated using bootstrap to perform model selection.

To do

• In the section with heterogeneity, check the calculations for bigU and bigM and make them generic.
• add Jolly-Seber as in Karamanlidis et al. (2015).
• add robust-design as in papers currently in reviews (including model selection with bootstrap).