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