This archive provides all code and data necessary to reproduce the analyses in Heard et al. (submitted). 'Synergies between disease and urbanization drive the decline of threatened amphibian populations'. All code is in the form of R scripts, with scripts for the occupancy modelling itself, plus the fitting of the sub-models that contribute covariates to the occupancy model; namely, scripts for fitting the model of seasonal chytrid prevalence, site hydrology and dispersal probability between sites. An R script is also provided to complete the simulations to estimate equilibrium occupancy under the alternate scenarios considered in the paper. Model fitting relies on the MultiBUGS package, called from R. MultiBUGS is a parallel implementation of OpenBUGS (formerly WinBUGS) and allows for parallel computation of MCMC sampling. MultiBUGS can be found here: https://www.multibugs.org/