Thierry Chambert, David A. W. Miller, and James D. Nichols. 2015. Modeling false positive detections in species occurrence data under different study designs. Ecology 96:332339. http://dx.doi.org/10.1890/14-1507.1


Supplement

R and BUGS code to fit the three different false positive occupancy models.
Ecological Archives E096-034-S1.

Copyright


Authors
File list (downloads)
Description


Author(s)

Thierry Chambert
Department of Ecosystem Science and Management
Pennsylvania State University
12100 Beech Forest Road, G2
Laurel, MD 20708
E-mail: thierry.chambert@gmail.com

David A. W. Miller
Department of Ecosystem Science and Management
Pennsylvania State University
411 Forest Resources Building
University Park, PA 16802

James D. Nichols
Patuxent Wildlife Research Center
U.S. Geological Survey
12100 Beech Forest Road, G2
Laurel, MD 20708


File list

BUGS-Models.bug (MD5: bbc0c6df0dc6e68ff25a3172ad349f07)

FormatData_forBUGS.r (MD5: cb618b5c9dae1c6a5c19730541f8a74a)

Likelihoods.r (MD5: 0e56760d67549e4e6efc587d94097907)

SimulateData_Calibration.r (MD5: cf2a083f6a73bdb71db9d6c4966d8976)

SimulateData_ObservationConf.r (MD5: a08687fcc8a826dbebb64b7e57647b78)

SimulateData_SiteConf-MM.r (MD5: 885ee8cb22dea9bee08ea53d7cacaede)

SimulateData_SiteConf-MS.r (MD5: f826d94e8c110481c544696e94d5cf60 )

Description

The Four files named as SimulateData_xxx.r are used to simulate data for each of the four corresponding study design described in the text. Note that the site confirmation design has two variants: (1) the Multiple-Method design (MM) and (2) the Multiple-State design (MS). The file Likelihoods.r contains the likelihoods for the four models, and it can be run in R, as is. To run the Bayesian models in OpenBUGS (or WinBUGS), run the script FormatData_forBUGS first. It will transform the simulated data in the appropriate from for BUGS. Then, you can use the code in BUGS-Models.bug to run each of the four models presented in the paper.