Supplement 1. R code used for conducting the simulations.

File List simulation.r (MD5: 5fc2c0d472f1f3c0971e18872f453b23) Description The file simulation.r is an R script which will replicate the simulations conducted in the study. It (1) produces simulated data sets, (2) fits models to estimate transition probabilities (and, when possible, resampling error rate) using classical likelihood estimator, the method described in Conway-Cranos and Doak (2011) and the multistate dynamic occupancy model, and (3) draws some figures of simulation results.