Appendix A. Table of model rankings.

Table of model rankings

Appendix B. Large-sample simulation experiments.

Large-sample simulation experiments

Appendix A. Prior specifications, prior sensitivity, and goodness of fit for the harbor seal example.

Prior specifications, prior sensitivity, and goodness of fit for the harbor seal example

Supplement 1. Source code and example data for implementing the Markov chain Monte Carlo algorithm.

<h2>File List</h2><div> <p><a href="MCMCalgorithm.r">MCMCalgorithm.r</a> -- (md5: 66b96318b9d549b5abd7a98178ccc6c8)</p> <p><a href="MCMCalgorithm.c">MCMCalgorithm.c</a> -- (md5: c637bb779c8f04eaf247974a6409ef1b)</p> <p><a href="MCMCalgorithm.dll">MCMCalgorithm.dll</a> -- (md5: 479e438af5b72bb05d8a413b487f8d2e)</p> <p><a href="data.RData">data.RData</a> -- (md5: 25eccac47d5082a651ec6d1040daf939)</p> <p><a href="Initial_values.RData">Initial_values.RData</a> -- (md5: 8da04b2b834f00fe2f7d8669d34e7550)</p> </div><h2>Description</h2><div> <p>MCMCalgorithm.r contains R code for loading the data (data.RData and Initial_values.RData), data pre- and post-processing, loading the dynamic link library file (MCMCalgorithm.dll), and calling the .C function for interfacing the compiled C code (MCMCalgorithm.c) with R (on a machine running Windows). </p> <p>MCMCalgorithm.c contains C code for implementing the MCMC algorithm.</p> <p>MCMCalgorithm.dll is a dynamic link library file containing the compiled C code.</p> <p>data.RData contains the data for 17 harbor seals.</p> <p>Initial_values.RData contains starting values for initialization of the MCMC chain.</p> </div

Appendix C. Posterior summaries for the harbor seal example.

Posterior summaries for the harbor seal example

Appendix B. Markov chain Monte Carlo algorithm.

Markov chain Monte Carlo algorithm

Supplement 1. Example code for constructing A matrix and calculating basis vectors.

<h2>File List</h2><div> <p><a href="integrated_photoID_functions.r">integrated_photoID_functions.r</a> (MD5: 5b24a5e4b384548e2fe751a06e75b8c8)</p> <p><a href="integrated_photoID_example.r">integrated_photoID_example.r</a> (MD5: 49f5760b1a5bc9ffec4193f4fbc7d186)</p> </div><h2>Description</h2><div> <p>integrated_photoID_functions.r contains R code for functions that simulate bilateral encounter data, construct the <b><i>A</i></b> matrix, and calculate the necessary set of basis vectors for the LR, LRB, and LRAB data types.</p> <p>integrated_photoID_example.r demonstrates use of the functions included in integrated_photoID_functions.r.</p> </div

Appendix C. Naïve estimates of occupancy with false positives.

Naïve estimates of occupancy with false positives

Appendix A. Species-specific occupancy analysis results.

Species-specific occupancy analysis results

Appendix A. Details of Bayesian analysis for bilateral photo-identification data.

Details of Bayesian analysis for bilateral photo-identification data