R and TMB codes for fitting multievent SIR models to capture-recapture data

We provide here the R and TMB codes associated with the paper Eco-epidemiological capture-recapture parameter estimates are robust to variation in infection state uncertainty by Sarah Benhaiem, Lucile Marescot, Heribert Hofer, Marion L. East, J-D Lebreton, Stephanie Kramer-Schadt, Olivier Gimenez.

First, we present a benchmark analysis to compare a native R vs. TMB (Kristensen et al. 2016) implementation of the optimization procedure.

Second, we provide the R and TMB codes to run a Monte Carlo simulation study to assess the bias and mean square error of the multievent SIR capture-recapture model parameters estimators.