Summary statistics for spatial capture-recapture parameters across 100 simulations for four simulation scenarios.

<p>Mean, relative root mean squared error (rrmse) of the mean, mode, 2.5% and 97.5% quantiles, relative bias of mean (RB) and 95BCI coverage (BCI) for spatial capture-recapture parameters across 100 simulations for four simulation scenarios, define by the input value of movement parameter <i>σ</i>. <i>N</i> = number of individuals in the state space; <i>λ₀</i> = baseline trap encounter rate.</p

Estimates of baseline trap encounter rates <i>λ_k</i> (SE) for black bears sampled with hair snares.

<p>Estimates of baseline trap encounter rates <i>λ_k</i> (SE) for black bears sampled with hair snares over four 14-day occasions in Pictured Rocks National Lakeshore, Michigan, estimated with spatial capture-recapture models for the full data set and three reduced data sets. Values correspond to female <i>λ_k</i>, <i>β</i>(male) is the effect of being a male on <i>λ_k</i> on the log-scale.</p>*<p>Reduced trap array area – 50% innermost traps used.</p>**<p>Reduced trap array area – 20% southernmost traps used.</p>***<p>Increased trap spacing by random removal of 50% of the traps.</p

Location of the study area.

<p>Location of the study area in Pictured Rocks National Lakeshore, Michigan (rectangle in inset map), and state-space with trap array layouts for the full (A) and three reduced sets of black bear hair snare data; B) 50% of all traps chosen at random; C) 50% of traps in the centre of the grid; and D) 20% of traps in the South of the grid.</p

Posterior summaries of SCR model parameters for black bears.

<p>Posterior summaries of SCR model parameters for black bears sampled with hair snares over four 14-day occasions in Pictured Rocks National Lakeshore, Michigan, for the full data set and three reduced data sets. <i>D</i> = density, <i>σ</i> = movement parameter.</p>*<p>Reduced trap array area – 50% innermost traps used.</p>**<p>Reduced trap array area – 20% southernmost traps used.</p>***<p>Increased trap spacing by random removal of 50% of the traps.</p

Supplement 1. The R code with embedded WinBUGS specification to run the simulation study and a separate WinBUGS file with specification for the spatially explicit open population model used in the Pampas cat study.

<h2>File List</h2><blockquote> <p><a href="RCODE.txt">RCODE.txt</a></p><br> <p><a href="WINBUGS.txt">WINBUGS.txt</a></p> </blockquote><h2>Description</h2><blockquote> <p>"RCODE.txt" : This file contains the R code with the WinBUGS specification to run the simulation study with <i>T</i> = 3 for the spatially explicit open population model. N, φ, σ, M, and other parameters can be adjusted to simulate various size data sets. In the specification, we create some data such as “grid”, a J × 2 matrix of the (x,y) locations of the traps and we estimate other parameters such as the SX and SY, the estimated (x,y) locations of the activity centers. This code calls WinBUGS from within R using the R2WinBUGS package.</p> <p>"WINBUGS.txt" : WinBugs specification for the spatially explicit open population model used in the Pampas cat study. There are only <i>T</i> = 2 time periods in this specification. Here, “trapmat” is a J × 2 matrix of the (x,y) locations of the traps and SX and SY are the estimated (x,y) locations of the activity centers. “year” is an indicator variable that tells if a trap <i>j</i> was operational during year <i>t</i> of the survey.</p> </blockquote

Appendix C. Details of the simulation study of the Jolly-Seber extension to our spatially explicit capture–recapture model.

Details of the simulation study of the Jolly-Seber extension to our spatially explicit capture–recapture model

Appendix A. Details about Pampas cats and the Pampas cat study.

Details about Pampas cats and the Pampas cat study

Appendix B. Survival and recruitment for T > 2.

Survival and recruitment for T > 2

Supplement 1. Model implementation detail, R ,and WinBUGS code, and data for the Wood Thrush example presented in the paper.

<h2>File List</h2><blockquote> <a href="carCJS.r">carCJS.r</a> - R script used to read in wood thrush data, create data objects for the spatial CJS model, specify the model in WinBUGS, call WinBUGS to run model and save output, and create ASCII grids for mapping ouput<br> <a href="woth.txt">woth.txt</a> - Capture history file for wood thrush example</blockquote><h2>Description</h2><blockquote> <p>The 'carCJS.r' script requires the following R packages: boot, coda, deldir, gpclib, maptools, Matrix, R2WinBUGS, spam, spatstat, spdep, and tripack. The script reads in data; and creates a base 1-degree ASCII grid ('MAPSgrid.txt'), a model file for WinBUGS ('spatialcjs.txt'), and objects needed to run the model in WinBUGS. The script calls WinBUGS and stores output in an R list called 'out'. The script also creates objects for creating spatial maps of survival and residency (as in Fig. 3) within R and writes ASCII grids for making maps with GIS software outside of R. </p> <p>The data in 'woth.txt' are capture histories derived from the Monitoring Avian Productivity and Survivorship (MAPS) program. Included are all records of adult birds (i.e., ‘after-hatch-year’) of both sexes at stations where the species is known to breed. Fields in ‘woth.txt’ include:</p> <ol> <li>SPEC – Species 4-letter code. WOTH = wood thrush (<i>Hylocichla mustelina</i>)</li> <li>STA2 – MAPS station 4-character code. Stations consist of about 10 mist nets that sample an area of approximately 20 ha. Multiple stations < 1 km apart were considered a single station</li> <li>BAND – USGS Bird Banding Laboratory band number</li> <li>R – Indicates whether predetermined resident (M) or not (U)</li> <li>Y1 – Indicator variable denoting whether captured (1) or not captured (0) in year 1. Y1 corresponds to 1992, the first year of the study (first year of standardized MAPS protocol)</li> <li>Y2 – Indicator variable denoting whether captured (1) or not captured (0) in year 2 (1993)</li> <li>Y3 – Indicator variable denoting whether captured (1) or not captured (0) in year 3 (1994)</li> <li>Y4 – Indicator variable denoting whether captured (1) or not captured (0) in year 4 (1995)</li> <li>Y5 – Indicator variable denoting whether captured (1) or not captured (0) in year 5 (1996)</li> <li>Y6 – Indicator variable denoting whether captured (1) or not captured (0) in year 6 (1997)</li> <li>Y7 – Indicator variable denoting whether captured (1) or not captured (0) in year 7 (1998)</li> <li>Y8 – Indicator variable denoting whether captured (1) or not captured (0) in year 8 (1999)</li> <li>Y9 – Indicator variable denoting whether captured (1) or not captured (0) in year 9 (2000)</li> <li>Y10 – Indicator variable denoting whether captured (1) or not captured (0) in year 10 (2001)</li> <li>Y11 – Indicator variable denoting whether captured (1) or not captured (0) in year 11 (2002)</li> <li>Y12 – Indicator variable denoting whether captured (1) or not captured (0) in year 12 (2003)</li> <li>LAT – Latitude of the MAPS station in decimal degrees</li> <li>LONG – Longitude of the MAPS station in decimal degrees</li> <li>CAP – Mean no. of within-year captures per individual at the station</li> </ol> <p>Note that although 6,645 birds are included in the woth.txt, only 6,241 of these birds that were captured for the first time prior to the last year of the study are read into the data object used in the model.</p> </blockquote

Estimating Population Size for Capercaillie (<i>Tetrao urogallus - Fig 3 </i> L.) with Spatial Capture-Recapture Models Based on Genotypes from One Field Sample

<p>(a) Posterior distribution of the total Capercaillie population size in the study area based on the SCR model. (b) Posterior distribution of the number of males. (c) Posterior distribution of the number of females. (d) Posterior distribution of the sex ratio (proportion males). Grey line with x: observed numbers of individuals, grey arrow: posterior means. The y axis shows the density.</p