Supplement 1. R and JAGS code needed for model.

File List /Model Code/ A_WORKFLOW.R (MD5: ) Generate initial state matrix.R (MD5: ) /Model Code/Analyses/ Final Analysis of R0 for submission.R (MD5: ) Final Analysis of lambda for submission.R (MD5: ) /Model Code/Density Dependent/ Call_one_beta_model_final.R (MD5: ) One_beta_model_finalJAGS.R (MD5: ) /Model Code/Figures and tables/ Calls for effect of management plots.R (MD5: ) Table and plotting code final IV.R (MD5: ) Effect of management plotsII.R (MD5: ) data_plot.R (MD5: ) /Model Code/Forecasts/With management uncertainty/ Call_one_beta_model_final_mgmt_unc_IV.R (MD5: ) One_beta_model_finalJAGS.R (MD5: ) /Model Code/Forecasts/Without management uncertainty/ Call_one_beta_model_final_VII_revised.R (MD5: ) One_beta_model_finalJAGS_VII_revised.R (MD5: ) /Model Code/Freq and Dens Dependent/ Call_one_beta_model_final.R (MD5: ) One_beta_model_finalJAGS.R (MD5: ) /Model Code/Frequency Dependent/ Call_one_beta_model_final.R (MD5: ) One_beta_model_finalJAGS.R (MD5: ) Description /Model Code/ A_WORKFLOW.R -- R script for linking all scripts below to recreate the entire analysis reported in the manuscript Generate initial state matrix.R -- R script for generating initial values for population states /Model Code/Analyses/ Final Analysis of R0 for submission.R -- R script for computing posterior distribution of the basic reproductive ratio Final Analysis of lambda for submission.R -- R script for computing posterior distribution of population growth rates /Model Code/Density Dependent/ Call_one_beta_model_final.R -- R script for implementing JAGS model of density dependent model of transmission One_beta_model_finalJAGS.R -- JAGS code for density dependent model of transmission /Model Code/Figures and tables/ Calls for effect of management plots.R -- R script for producing Figure 14 Table and plotting code final IV.R -- R script for creating manuscript tables and figures Effect of management plotsII.R -- R script for function needed by Calls for effect of management plots.R data_plot.R -- R script for producing Figure 1 of manuscript /Model Code/Forecasts/With management uncertainty/ Call_one_beta_model_final_mgmt_unc_IV.R -- R script for implementing analysis of alternatives for management including uncertainty in ability to implement alternatives One_beta_model_finalJAGS.R -- JAGS code for analysis of alternatives for management including uncertainty in ability to implement alternatives /Model Code/Forecasts/Without management uncertainty/ Call_one_beta_model_final_VII_revised.R -- R script for implementing analysis of alternatives for management without uncertainty in ability to implement alternatives One_beta_model_finalJAGS_VII_revised.R JAGS code for analysis of alternatives for management without uncertainty in ability to implement alternatives /Model Code/Freq and Dens Dependent/ Call_one_beta_model_final.R -- R script for implementing JAGS model of combined transmission One_beta_model_finalJAGS.R JAGS code for the combined model of transmission /Model Code/Frequency Dependent/ Call_one_beta_model_final.R -- R script for implementing JAGS model of combined transmission One_beta_model_finalJAGS.R -- JAGS code for frequency dependent model of transmission