Murray G. Efford and Deanna K. Dawson. 2012. Occupancy in continuous habitat. Ecosphere 3:art32. http://dx.doi.org/10.1890/ES11-00308.1

Supplement

R package for conducting the simulations described in the main text.
Ecological Archives C003-004-S1.

Copyright

Authors
File list (downloads)
Description

Author(s)

Murray G. Efford
Department of Zoology
University of Otago
PO Box 56, Dunedin 9054 New Zealand
E-mail: murray.efford@otago.ac.nz

Deanna K. Dawson
USGS Patuxent Wildlife Research Center
12100 Beech Forest Road
Laurel, Maryland 20708, USA
E-mail: ddawson@usgs.gov

File list

simpsi_1.1.tar.gz -- (MD5: 33f82ba813a98b6cc5b0bf56d6b276bd)

simpsi_1.1.zip -- (MD5: 895ccf64f96d49978c32b468bd686999)

simpsi-manual.pdf -- (MD5: da0a009057855112950fd1851a5329c6)

Description

Code to conduct the simulations underlying Figs. 3–6 in the main text is provided as an R package. The source code for this package is in simpsi_1.1.tar.gz and a Windows binary is in simpsi_1.1.zip (note that the latter should be installed as a package in R using the “Install package(s) from local zip files” menu option). The source code in simpsi_1.1.tar.gz comprises files circle.square.overlap.R,  occpsi.R, runsimDDD.R, runsimHRDD.R, runsimRPSD.R, and runsimSR.R. Details of usage are provided in the help (.Rd) files, collated in simpsi-manual.pdf. Each group of simulations has its own ‘runsim’ function, as indicated on Page 2 of the manual. Actual code to perform the simulations is given as “Not run” code in each Examples section (“Not run” is used to skip these lines during automatic checking, to save time). Source code for each function may be viewed from within R once the package has been installed.

The R code uses the other R packages ‘secr’, ‘abind’, and ‘spatstat’; these should be downloaded from the CRAN website (http://cran.r-project.org).