Supplement 1. Program R code to fit a movement model to simulated data.

File List Run_Geremia_et_al_2013.R (MD5: 6473a85544c5ad4c1364156d539084fc) Simdata_Geremia_et_al_2013.R (MD5: 39d43c44eba8cbabcfc1901143a7289b) Markov_movementmodel_mcmc.R (MD5: ce270c6e117c0fa67c133744fb96ff66) Description This supplement provides code for simulating data and fitting those data to a hierarchical Bayesian state-space movement model. All files are provided as R code (R Code Development Team. 2013. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. Retrieved from http://www.R-project.org). The model coded within this supplement is a simplification of the model described in Appendix A. We assume that there are five wintering areas that are sequential and connected by one migration route each. The transition matrix A describes movements between these areas, where -- IMAGE: Please see in attached file. -- All animals are assumed to survive and we do not estimate a survival parameter in this example. The user can manipulate the number of movement covariates, parameter values, number of model updates within and between years, number of animals in the population, and number of GPS collared animals to explore the model. Users should begin by opening the file Run_Geremia_et_al_2013.R in Program R. Run_Geremia_et_al_2013.R internally sources the other files Simdata_Geremia_et_al_2013.R and Markov_movementmodel_mcmc.R. Within Run_Geremia_et_al_2013.R, users can manipulate variables and parameters. Users then run commands to simulate data given the specified variables and parameter values and recover those values using the model. Advanced users can adjust the files Simdata_Geremia_et_al_2013.R and Markov_movementmodel_mcmc.R for alternative spatial graphs that are appropriate for their data.