PRESENCE

PRESENCE  - Estimates patch occupancy rates and related parameters. This work is in collaboration with Darryl MacKenzie, and is largely funded by the Amphibian Research and Monitoring Initiative (ARMI). Contact Darryl if you would like to learn more about this project.

RPresence - Provides an R interface for running occupancy models available in Program PRESENCE plus some additional helpful routines.

GENPRES - Generates patch occupancy data and analyzes using program PRESENCE.

OccPower.xlsx - Spreadsheet to compute power to detect difference in 2 independent occupancy estimates using asymptotic approximations described in Guillera-Arroita et. al. (2012).

References

• MacKenzie, D. I., J. Nichols, J. A. Royle, K. Pollock, L. Bailey, and J. Hines.  2018.  Occupancy Estimation and Modeling : Inferring Patterns and Dynamics of Species Occurrence.  2nd edition.   Academic Press, San Diego.  xxiii, 648 pp.  Abstract
• Guillera-Arroita, G. and J.J. Lahoz-Monfort. 2012. Designing studies to detect differences in species occupancy: power analysis under imperfect detection. Methods in Ecology and Evolution 5(3): 860-869. doi:10.1111/j.2041-210X.2012.00225.x
• Bailey, L. L., J. E. Hines, and J. D. Nichols.  2007.  Sampling design trade-offs in occupancy studies with imperfect detection:  examples and software.  Ecological Applications 17(1):281-290.  doi:10.1890/1051-0761(2007)017[0281:SDTIOS]2.0.CO;2
• MacKenzie, D. I., J. D. Nichols, J. E. Hines, M. G. Knutson, and A. B. Franklin.  2003.  Estimating site occupancy, colonization, and local extinction when a species is detected imperfectly.  Ecology 84(8):2200-2207.  doi:10.1890/02-3090
• MacKenzie, D. I., J. D. Nichols, G. B. Lachman, S. Droege, J. A. Royle, and C. A. Langtimm.  2002.  Estimating site occupancy rates when detection probabilities are less than one.  Ecology 83(8):2248-2255. doi: 10.1890/0012-9658(2002)083[2248:ESORWD]2.0.CO;2

Documentation

• PRESENCE user-manual
• Worked Examples and Exercises in PRESENCE
• GENPRES user-manual

Downloads

• PRESENCE
• PRESENCE (no install/setup program)
• RPresence binary package for Windows
• RPresence source package for OSX/Linux
• OccPower.xlsx

Information about upcoming workshops on the use of Occupancy modeling using PRESENCE can be found at:

• www.proteus.co.nz/courses.php
• www.mbr-pwrc.usgs.gov/workshops