Welcome to the 'Occupancy in E-SURGE' project. This is the Wiki page associated to the our paper Fitting occupancy models with E-SURGE: hidden Markov modelling of presence-absence data published in 2014 in Methods in Ecology and Evolution.
You will find here the ingredients to implement various occupancy models in program E-SURGE. We recommend you check Choquet (2008), Choquet et al. (2009) and the user's manual if you have any questions. Also, there's a FAQ site here. Otherwise, just email us.
To install E-SURGE 1.9.1, go here and follow the instructions.
- single-season (static) models
- multiple-season (dynamic) models
- occupancy models with species misidentification (aka false positive errors)
- single- and multiple-season models, with random effects here
- published examples of occupancy models fitted in E-SURGE (check out the appendices for E-SURGE details)
- Cayuela, H., Besnard, A. & Joly, P. (2013) Multi-event models reveal the absence of interaction between an invasive frog and a native endangered amphibian. Biological Invasions, 15: 2001–2012.
- Fréville, H., Choquet, R., Pradel, R. & Cheptou, P.-O. (2013) Inferring Seed Bank From Hidden Markov Models: New Insights Into Metapopulation Dynamics In Plants. Journal of Ecology, 101: 1572–1580
- Lorentzen, E., R. Choquet, H. Steen. (2012) Modelling state uncertainty with photo series data for the estimation of breeding success in a cliff-nesting seabird. Journal of Ornithology, 152 (suppl 2): 477-483.
- Véran, S., Kleiner, D., Choquet, R., Collazo, J. & Nichols, J.D. (2012) Modeling habitat dynamics accounting for possible misclassification. Landscape Ecology, 27: 943–956.