Search Search

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.

Current Version: 13.6

• 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. D. Nichols, J. A. Royle, K. H. Pollock, L.L. Bailey, and J. E. Hines. 2018. Occupancy Estimation and Modeling - Inferring Patterns and Dynamics of Species Occurrence. 2nd Edition. Elsevier Publishing.
	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		MacKenzie, D. I., J. D. Nichols, J. E. Hines, M. G. Knutson and A. B. Franklin. 2003. Estimating site occupancy, colonization and local extinction probabilities when a species is detected imperfectly. Ecology 84(8) 2200-2207.
	Bailey, L. L., J.D. Nichols and J.E. Hines. 2007. Exploring Sampling Design Trade-Offs In Occupancy Studies With imperfect detection: examples and software. Ecological Applications, 17(1). pp. 281-290.		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 2012, 3, 860-869.

• PDF documents can be viewed using a PDF reader program ( Adobe, Foxit, SumatraPDF...)

Documentation

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

Ver 13.5 (05Jun2020) - fix error in seasonal covariates for p1,p2 in RPresence
Ver 13.4 (05Jun2020) - fix error in seasonal covariates for Cpsi,CR in RPresence
Ver 13.1 (14May2020) - recompile RPrsence for R 4.0.0
Ver 12.43 (21Apr2020) - fix Nichols/Royal models in Presence GUI
Ver 12.42 (14Apr2020) - fix do.4 model in RPresence
Ver 12.41 (07Apr2020) - minor misc updates
Ver 12.40 (31Mar2020) - modified limit on warnings about missing det/cov data
Ver 12.39 (05Mar2020) - modified do.ms.2 model in RPresence, fix bug in cpsi output for mult-season model.
Ver 12.38 (07Feb2020) - add seasonal cpsi to multi-season model.
Ver 12.37 (03Jan2020) - fix MS/DO RPres model.
PRESENCE workshops
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