This contains R code to build a map of occupancy probability estimates, using a case study on lynx in the French Alps. A single-season occupancy model was fitted to detection/non-detection data. Initial occupancy was a function of forest cover while species detection had a site-random effect on it.
More details on the data and the estimation step in Gimenez, O., L. Blanc, A. Besnard, R. Pradel, P. F. Doherty Jr, E. Marboutin and R. Choquet (2014). Fitting occupancy models with E-SURGE: hidden-Markov modelling of presence-absence data. Methods in Ecology and Evolution. 5: 592–597.