Appendix A. Species- and community-level true positive rate (TPR) and true negative rate (TNR) values for the habitat-only and autologistic models.

Species- and community-level true positive rate (TPR) and true negative rate (TNR) values for the habitat-only and autologistic models

EncHistBuilder_RD

This R script contains functions to subset and format the salamander spreadsheet into a multi-catch SCR encounter history for a robust design analysis

RD JAGS Model

A model file for program JAGS. Contains the actual robust design model whose parameters will be estimated in JAGS. Includes a covariate for sex of the individual

Season3_Closed_Results

The results from the autumn 2014 closed-population analysis

Season2_Closed_Results

The results from the spring 2014 closed-population analysis

ClosedPop JAGS Model

A model file for program JAGS. Contains the actual closed-population model whose parameters will be estimated in JAGS. Includes a covariate for sex of the individual

EncHistBuilder_Closed

This R script contains functions to subset and format the salamander spreadsheet into a multi-catch SCR encounter history for a closed-population analysis

Analysis_RD.R

This R script contains all the steps to load the data, format it, and run the MCMC estimation through program JAGS for the robust design spatial capture-recapture analysis

Analysis_Closed

This R script contains all the steps to load the data, format it, and run the MCMC estimation through program JAGS for the closed-population spatial capture-recapture analysis

Appendix A. Graphs of performance metrics comparing open and closed occupancy models based on expected values data, and a table of model comparisons for three amphibian species.

Graphs of performance metrics comparing open and closed occupancy models based on expected values data, and a table of model comparisons for three amphibian species