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

Details of Bayesian analysis for bilateral photo-identification data

Appendix B. Simulation methods and results.

Simulation methods and results

Appendix C. Description of the bobcat data and integrated analysis.

Description of the bobcat data and integrated analysis

Mark-Recapture and Mark-Resight Methods for Estimating Abundance with Remote Cameras: A Carnivore Case Study

<div><p>Abundance estimation of carnivore populations is difficult and has prompted the use of non-invasive detection methods, such as remotely-triggered cameras, to collect data. To analyze photo data, studies focusing on carnivores with unique pelage patterns have utilized a mark-recapture framework and studies of carnivores without unique pelage patterns have used a mark-resight framework. We compared mark-resight and mark-recapture estimation methods to estimate bobcat (<i>Lynx rufus</i>) population sizes, which motivated the development of a new "hybrid" mark-resight model as an alternative to traditional methods. We deployed a sampling grid of 30 cameras throughout the urban southern California study area. Additionally, we physically captured and marked a subset of the bobcat population with GPS telemetry collars. Since we could identify individual bobcats with photos of unique pelage patterns and a subset of the population was physically marked, we were able to use traditional mark-recapture and mark-resight methods, as well as the new “hybrid” mark-resight model we developed to estimate bobcat abundance. We recorded 109 bobcat photos during 4,669 camera nights and physically marked 27 bobcats with GPS telemetry collars. Abundance estimates produced by the traditional mark-recapture, traditional mark-resight, and “hybrid” mark-resight methods were similar, however precision differed depending on the models used. Traditional mark-recapture and mark-resight estimates were relatively imprecise with percent confidence interval lengths exceeding 100% of point estimates. Hybrid mark-resight models produced better precision with percent confidence intervals not exceeding 57%. The increased precision of the hybrid mark-resight method stems from utilizing the complete encounter histories of physically marked individuals (including those never detected by a camera trap) and the encounter histories of naturally marked individuals detected at camera traps. This new estimator may be particularly useful for estimating abundance of uniquely identifiable species that are difficult to sample using camera traps alone.</p></div

Camera survey model-averaged mark-recapture and mark-resight bobcat <i>Lynx rufus</i> abundance (N^) and density/km² (D^) estimates in the San Joaquin Hills study area, Orange County, California.

<p>Right-side (RS) and left-side (LS) analyses were conducted for the mark-recapture and hybrid mark-resight estimators. Separate density estimates were derived from the estimated radius (</p><p></p><p></p><p></p><p></p><p><mi>D</mi><mo>^</mo></p><mi>r</mi><p></p><p></p><p></p><p></p>) and diameter (<p></p><p></p><p></p><p></p><p><mi>D</mi><mo>^</mo></p><mi>d</mi><p></p><p></p><p></p><p></p>) of average home range size. % CIL denotes the 95% confidence (or highest posterior density) interval length relative to <p></p><p></p><p><mi>N</mi><mo>^</mo></p><p></p><p></p> and <p></p><p></p><p><mi>D</mi><mo>^</mo></p><p></p><p></p>.<p></p><p>Camera survey model-averaged mark-recapture and mark-resight bobcat <i>Lynx rufus</i> abundance (</p><p></p><p></p><p><mi>N</mi><mo>^</mo></p><p></p><p></p>) and density/km² (<p></p><p></p><p><mi>D</mi><mo>^</mo></p><p></p><p></p>) estimates in the San Joaquin Hills study area, Orange County, California.<p></p

The San Joaquin Hills study area, Orange County, California.

<p>The sampling unit grid (dashed lines) was used to determine the locations of remote camera stations. Map figure base layers from SCAG [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123032#pone.0123032.ref035" target="_blank">35</a>] and StreetMap USA for ESRI ArcGIS 9.3, for representational purposes only.</p