Supplement 1. BUGS-language model specification of hierarchical community occupancy model.

BUGS_code.txt (MD5: 5101dc4c7becb6442fbaed48ca40bc88)

BUGS_code.text: Provided in this file is the BUGS-language code for specification of the hierarchical community occupancy model presented in the associated publication. The code expects several data variables to be available and these are specified as follows: n the number of species; nzeroes the number of “zero species” added during data augmentation; era the time period during which a site is surveyed (0 = historical; 1 = modern); elev the standardized elevation; elev2 the squared elevation; R1 a dummy variable representing one of the three regions; R2 a dummy variable representing one of the three regions; jday the standardized day of year; jday2 the squared day of year; X the multi-dimensional occurrence history array; J the number of sites; K a vector of the number of surveys per site (per era); zone_LS, zone_US, zone_TR, zone_CA, zone_HU, zone_XX dummy variables indicating whether a species belongs in a certain life zone grouping; H a vector indicating which paired sites belong in the historic time period; M a vector indicating which paired sites belong in the modern time period; L the number of paired sites per era.