J. Andrew Royle, Richard B. Chandler, Kimberly D. Gazenski, Tabitha A. Graves. 2013. Spatial capture–recapture models for jointly estimating population density and landscape connectivity. Ecology 94:287–294. http://dx.doi.org/10.1890/12-0413.1

Supplement

R code for computing least-cost path distance and likelihood analysis of the spatial capture–recapture (SCR) model, for computing the marginal likelihood and obtaining the MLEs, and for simulation study, and a narrative walk-through in PDF format.
Ecological Archives E094-022-S1.

Copyright

Authors
File list (downloads)
Description

Author(s)

J. A. Royle
USGS Patuxent Wildlife Research Center
Laurel, MD
Email: aroyle@usgs.gov

Richard B. Chandler
USGS Patuxent Wildlife Research Center
Laurel, MD

Kimberly D. Gazenski
USGS Patuxent Wildlife Research Center
Laurel, MD

Tabitha A. Graves
Northern Arizona University
Flagstaff, AZ

File list

EDmanuscript-supplements.pdf (md5: 44eb27bf3d2ab768941365c6a9dc1d43) – R code in pdf form and extra explanation for supplement 1
leastcostpath.R (md5: f8d1a9c67e4ee10ed633937d82b68f3f) - R code for computing least-cost path distance and likelihood analysis of the SCR model
MLE.R (md5: 4a4f93a6aa444cb52f458e0dbdc80db5)- R code for computing the marginal likelihood and obtaining the MLEs
simstudy.R (md5: 1b05540b8556e498242191382ba37c1b) - R code for simulation study

Description

The supplement demonstrates the computation of least-cost path and its use in obtaining maximum likelihood estimates of model parameters. The file Leastcostpath.R is an R script which can be executed directly (narrative walk-through is provided by the PDF file EDmanuscript-supplements.pdf). The likelihood function (in the form of an R function) is provided in the R script MLE.R. Finally, the various pieces are put together to carry-out a simulation study in the R script simstudy.R.