Christopher T Rota, Christopher K. Wikle, Roland W. Kays, Tavis D. Forrester, William
J. McShea, Arielle W. Parsons, and Joshua J. Millspaugh. Year of publication. A twospecies occupancy model accommodating simultaneous spatial and interspecific
dependence. Ecology VOL:pp–pp.
Supplement
Data and code for fitting the 2-species spatial occupancy model.
Ecological Archives A/E/M000-000-S1.
Copyright
Christopher T. Rota
University of Missouri, Department of Fisheries and Wildlife Sciences
302 Anheuser-Busch Natural Resources Building
Columbia, MO 65203
Email: rotact@missouri.edu
Christopher K. Wikle
University of Missouri, Department of Statistics
146 Middlebush Hall
Columbia, MO 65211
Roland W. Kays
North Carolina Museum of Natural Sciences
11 West Jones Street
Raleigh, NC 27601
Tavis D. Forrester
Smithsonian Conservation Biology Institute
1500 Remount Road
Front Royal, VA 22630
William J. McShea
Smithsonian Conservation Biology Institute
1500 Remount Road
Front Royal, VA 22630
Arielle W. Parsons
North Carolina Museum of Natural Sciences
11 West Jones Street
Raleigh, NC 27601
Joshua J. Millspaugh
University of Missouri, Department of Fisheries and Wildlife Sciences
302 Anheuser-Busch Natural Resources Building
Columbia, MO 65203
File List
Directions for fitting the model.pdf
Adaptive Function.R
countdown.R
Coyote.csv
Format Data.R
Gibbs Sampler.R
Knot Alt.csv
Model.R
p covariates.csv
psi covariates.csv
Red Fox.csv
Training Logical.csv
Description
Directions for fitting the model.pdf – describes the order in which .R
files should be opened and executed
Adaptive Function.R – a function for tuning the parameters of the proposal
distribution necessary in the Metropolis Hastings step
countdown.R – a function to indicate how much time remains to run the Gibbs
sampler
Coyote.csv – detection / non-detection data of Coyote at all sites. Each row is a site
and each column is a detection / non-detection survey. Values of 0 indicate nondetection, values of 1 indicate detection, and blank cells indicate no survey was
conducted.
Format Data.R – a script to read and format data to be subsequently supplied to the
Gibbs sampler
Gibbs Sampler.R – executes the Gibbs sampler as described in Appendix B
Knot Alt.csv – indicates which sites are treated as knots. Each row corresponds to a
site. Values of TRUE indicate a site is treated as a knot, values of FALSE indicate a site
is not treated as a knot.
Model.R – reads and executes all of the functions, determine how many simulations to
conduct, and prepare posterior simulations for post-processing
p covariates.csv – site-specific covariates for the detection model. Each row is a
site. Column “Camsite” is a unique identifier; “Latitude” and “Longitude” are latitude
and longitude in decimal degrees / 100; “Park_ID” identifies the park or protected are a
camera is located in; “Det_dist” is the maximum detection distance in meters of the
camera trap.
psi covariates – site-specific covariates for occupancy model. Each row is a site.
Column “Camsite” is a unique identifier; “Latitude” and “Longitude” are latitude and
longitude in decimal degrees / 100; “HDens_5k” is the housing density within a 5km
radius, in units of houses × km-2; “Trail” is an indicator of whether a camera is on (=1) or
off (=0) a trail; “Park_ID” identifies the park or protected are a camera is located in;
“Hunting” in an indicator of whether a camera is located in a park or protected area that
allows hunting; “People_site” is the total number of people detected at a site / 1,000.
Red Fox.csv – detection / non-detection data of Red Fox at all sites. Each row is a
site and each column is a detection / non-detection survey. Values of 0 indicate nondetection, values of 1 indicate detection, and blank cells indicate no survey was
conducted.
Training Logical.csv – Each row corresponds to a site. Values of TRUE
indicate a site is a training site, values of FALSE indicate a site is a validation site.