List of the R-files supplied with the paper: Koshkina et al. "Integrated Species Distribution Models: Combining presence-only data and presence-absence data with imperfect detection"
PBSO-function.r - Fitting PB, SO and Integrated models the data. The data required for the file is stored in the file data.rda and include
- s.occupancy - raster with background covariates that effect occupancy
- s.detection - raster with background covariates that effect detection
- pb.occupancy - matrix with covariates that effect occupancy in the locations of detected presences of the opportunistic survey
- pb.detection - matrix with covariates that effect detection in the locations of detected presences of the opportunistic survey
- y.so - matrix of detection/non detection of the SO surveys
- so.occupancy - matrix with covariates that effect occupancy in the locations of SO survey sites
- so.detection - matrix with covariates that effect detection in the locations of SO survey sites in each survey
sim-data.r - Simulated data generated. Simulates covariates x and w, PB and SO datasets. All the data is saved in a file data.rda
functions.r - Utility and likelihood functions required for PBSO-function.r