Code to analyze multi-state, multi-scale dynamic occupancy models for amphibians in Yosemite National Park

The purpose of this study was to evaluate how extreme variation in precipitation in the Sierra Nevada of California, USA, in the early 21st Century affected adult occupancy and the probability of reproduction of amphibians. The study used a 15-year data set to relate site characteristics to initial probability of occurrence of adults, and additional site-specific and dynamic (e.g., weather) variables to evaluate their influence on colonization and extirpation probabilities of adult amphibians and the probability that amphibians would reproduce at each site in each year. The code presented herein reproduces the multi-scale, multi-state occupancy analyses used in the study.