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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: 2.13.43

• 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

install.packages('RPresence', repo='https://www.mbr-pwrc.usgs.gov/mbrCRAN')

Ver 13.43 (26Oct2022) - add derived parms for 2sp model
Ver 13.35 (06May2022) - fix output when constraints are specifiedIn RPresence, del beta cols in DM all=0
Ver 13.27 (18Mar2022) - In RPresence, del beta cols in DM all=0
Ver 13.20 (20Jan2022) - cleaned up unnecessary files in setup file
Ver 13.19 (11Jan2022) - added derived parm output to 2sp model

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