The files in this folder demonstrate how spatial capture–recapture (SCR) methods can be adapted to model movement and space use in aquatic systems. Appenidx_1A_MvmtAssistedLocalization.R simulates and analyzes acoustic telemetry data in an SCR framework. sim_SCR_mvmt.R simulates and models an integrated SCR–movement model that jointly quantifies abundance, distribution, and movement of individuals using capture-recapture and telemetry data motivated by polar bear studies in the eastern Chukchi Sea. Finally, three files are used to simulate and model an age-structured capture-recapture model that incorporates age and capture-recapture data to provide comprehensive information on population dynamics including abundance, age-dependent survival, recruitment, age structure, and population growth rates. The motivating polar bear data from the western Hudson Bay are included in SupplementS3_CaseStudyData.txt.

Seals, polar bears, and polar bear track counts were summarized from U.S. and Russian survey flights over the Chukchi Sea during aerial surveys in April and May of 2016. Seal detections were made using using infrared imagery, with corresponding digital photographs providing information on species identification, where possible. Polar bear detections were made using a variety of methods, including infrared (thermal) detections, in situ observations by human observers, and through post hoc searching of photographs. These observations are summarized within a discretized study area, where grid cells are approximately 625 km^2, with the intention of estimating the distribution and abundance of all three species (bearded seals, Erignathus barbatus; ringed seals, Pusa hispida; and polar bears, Ursus maritimus). Data are provided in 5 .csv (comma delimited text) files, summarizing (1) the location of grid cells, and some associated environmental and physiographic covariates (CHESS_grid_axiom.csv), (2) survey effort per grid cell in U.S. airspace, including counts of seals and information on polar bear tracks (effort_us.csv), (3) survey effort per grid cell in Russian airspace, including counts of seals and polar bear tracks (effort_russia.csv), (4) locations, group sizes, and detection types for polar bear groups encountered in surveys within U.S. airspace (pb_encounters_us.csv), and (5) locations, group sizes, and horizontal distances for polar bear groups detected in surveys over Russian airspace. Owing to differences in detection methods for polar bears, we advocate using a distance sampling approach for analyzing Russian polar bear detections, and a strip transect approach to analyzing seal and U.S. polar bear detections.