Functions to fit point process models using the Palm likelihood. First proposed by Tanaka, Ogata, and Stoyan (2008)
First proposed by Tanaka, Ogata, and Stoyan (2008), maximisation of the Palm likelihood can provide computationally efficient parameter estimation for point process models in situations where the full likelihood is intractable. This package contains functions to fit a variety of point process models, but is chiefly concerned with Neyman-Scott point processes (NSPPs).
The development of this package was motivated by the analysis of capture-recapture surveys on which individuals cannot be identified---the data from which can conceptually be seen as a NSPP (Fewster, Stevenson, and Borchers, 2016). As such, some of the functions in this package are specifically for the estimation of cetacean density from two-camera aerial surveys; see Stevenson, Borchers, and Fewster (in press).
This package can also fit void processes, which, along with NSPPs, have been fitted to patterns of colon cancer and stroma cell locations (Jones-Todd et al., in press).
The stable version of this package can be installed from CRAN:
Fewster, R. M., Stevenson, B. C., and Borchers, D. L. (2016) Trace-contrast methods for capture-recapture without capture histories. Statistical Science, 31: 245--258.
Jones-Todd, C. M., Caie, P., Illian, J. B., Stevenson, B. C., Savage, A., Harrison, D. J., and Bown, J. L. (in press). Identifying prognostic structural features in tissue sections of colon cancer patients using point pattern analysis. Statistics in Medicine.
Stevenson, B. C., Borchers, D. L., and Fewster, R. M. (in press) Cluster capture-recapture to account for identification uncertainty on aerial surveys of animal populations. Biometrics.
Tanaka, U., Ogata, Y., and Stoyan, D. (2008) Parameter estimation and model selection for Neyman-Scott point processes. Biometrical Journal, 50: 43--57.
Implemented multipattern model fitting, so a single process can be fitted to multiple independent patterns.
Minor bug fixes for void process fits.
Added the `use.bobyqa' argument to fit.ns(), allowing optimisation via the bobyqa() function from the minqa package.
Bug fix for bootstrap simulations with no generated children.
Added sim.twocamera() to simulate data from two-camera aerial surveys.
Added the `parents' argument to simulation functions, so that the user can specify their own parent locations.
Added a component containing parent locations to the output of sim.ns().
Bug fix for buffer edge correction with fit.twocamera().
Bug fix for user-specified parameter bounds with fit.void().
First release of palm, after the original project was named 'nspp'.
Includes functions to fit Neyman-Scott point processes (including Thomas process and Matern process variants) and void processes.
Includes a function to estimate cetacean density from two-camera aerial surveys.
Includes functions to simulate from all of the above models.