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Thursday, September 18, 2014 09:41AM

PRESENCE 6.9 - 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.

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


book cover image MacKenzie, D. I., J. D. Nichols, J. A. Royle, K. H. Pollock, L.L. Bailey, and J. E. Hines. 2005. Occupancy Estimation and Modeling - Inferring Patterns and Dynamics of Species Occurrence. Elsevier Publishing.
ecology image 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
ecology image 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.


view user manual buttonPRESENCE user-manual

view user manual buttonWorked Examples and Exercises in PRESENCE

view user manual buttonGENPRES user-manual


Download PRESENCE 6.9 (last modified:) Thursday, 04-Sep-2014 07:58:51 EDT

Download Genpres (last modified:) Friday, 01-Aug-2014 11:50:26 EDT

Recent Modifications

Ver 6.9 (1Aug2014) - fixed corr.det. models
Ver 6.8 (30Jul2014) - fixed MS corr.det. and stag.ent. models
Ver 6.7 (18Jul2014) - fixed MS stag.ent. model
Ver 6.6 (15Jul2014) - Added 2-sp-corr-det model
Ver 6.5 (27Jun2014) - fixed retrieve model for ms w/ het
Ver 6.4 (27Mar2014) - modified des.mat. for ms 4th parm model
Ver 6.3 (27Mar2014) - fixed link for rho in 2sp model
Ver 6.2 (14Jan2014) - fixed SE's and in R/N model
Ver 6.1 (27Oct2013) - renamed spatial-correlation model to correlated-detections
Ver 6.1 (28Aug2013) - Added gof for pre-defined model
Ver 6.0 (26Aug2013) - Added model: multi-season staggered-entry
Ver 5.9 (08Jul2013) - fixed bug in read csv routine
Ver 5.8 (14Mar2013) - fixed bugs in Multi-state, FalsePos models
Ver 5.7 (28Jan2013) - fixed problem with filenames starting with
Ver 5.6 (18Dec2012) - fixed error R/N std. errors
Ver 5.5 (06Dec2012) - fixed filename error in model averaging routine
Ver 5.4 (31Oct2012) - fixed conf. interval for cond. psi's in single-season model
Ver 5.3 (26Oct2012) - fixed bug in multi-season model
Ver 5.2 (12Oct2012) - fixed bug in spatial-dep model
Ver 5.1 (19Sep2012) - fixed extra param in design matrix 3 for single season model
Ver 5.0 (18Sep2012) - corrected spatial-dep gof and time-specific thetas
Ver 4.9 (26Aug2012) - fixed read-from-file bug
Ver 4.9 (24Aug2012) - fixed gof for spatial dependency model
Ver 4.8 (22Aug2012) - fixed output of conditional psi (derived parameter) in single-season model
Ver 4.7 (15Aug2012) - fixed bugs in multi-season, multi-state model
Ver 4.6 (27July2012) - fixed error in output w/ covars
Ver 4.5 (27July2012) - fixed input of site covar file, changed desmat to names instead of numbers
Ver 4.4 (15May2012) - fixed multi-season-multi-state general parm. model
Ver 4.3 (13Apr2012) - Modified spatial-correlation model to allow robust design
Ver 4.2 (17Feb2012) - added parameters to 2 species multi-season model
Ver 4.1 (07Feb2012) - fixed output for multi-season model w/ combined DM
Ver 4.1 (09Jan2012) - fixed conf. interval in Royle/Nichols output
Ver 4.0 (06Oct2011) - Added models: multi-season-het, multi-season-2species
Ver 3.1 (14Oct2010) - Added model: single-season-false-positive-detections
Ver 3.0 (27Jan2010) - changed results file structure...

PRESENCE workshops

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