PRESENCE 12.32 - 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).


book cover image 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.
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.
ecological Applications image 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.
methods in ecology and evolution image 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.


view user manual buttonPRESENCE user-manual

view user manual buttonWorked Examples and Exercises in PRESENCE

view user manual buttonGENPRES user-manual


PRESENCE 12.32 (last modified:) Monday, 29-Jul-2019 11:51:54 EDT
PRESENCE 12.32 (no install/setup program) (last modified:) Saturday, 23-Nov-2019 09:38:01 EST
RPresence binary package for Windows (last modified:) Thursday, 11-Jul-2019 21:00:28 EDT
RPresence source package for OSX/Linux (last modified:) Thursday, 11-Jul-2019 21:01:28 EDT
OccPower.xlsx (last modified:) Friday, 19-Dec-2014 08:01:45 EST

Recent Modifications

Ver 12.32 (11Jul2019) = fix bug output of p for missing data
Ver 12.31 (21May2019) = fix bug dynamic 2sp output (gamma)
Ver 12.29 (15Apr2019) = fix bug in gof test
Ver 12.28 (09Apr2019) = fix import func in RPresence, add multi-threading in Presence
Ver 12.26 (16Mar2019) - fix bugs mod-avg, import-proj

Ver 12.25 (09Nov2018) - fix bug w/ memory error in SS model

Ver 12.24 (09Nov2018) - fix bug w/ naive occ computation in 2sp model

Ver 12.22 (02Oct2018) - fix bug output w/ fixed values

Ver 12.21 (18Aug2018) - fix bug in single-season multi-method model

Ver 12.20 (18Aug2018) - modify 2sp model to allow 1sp to have missing detections

Ver 12.19 (19Jul2018) - fix "fixed value" bug in RPresence

Ver 12.18 (02Jul2018) - more fixing covariates in multi-state model in RPresence

Ver 12.17 (02Jul2018) - fixed covariates in multi-state model in RPresence

Ver 12.16 (27Jun2018) - allow survey-specific covar on theta in multi-method model in RPresence
Ver 12.15 (19Jun2018) - fixed beta.coeff data.frame in RPresence
Ver 12.14 (01Jun2018) - fixed multi-state psi/R parm. in RPresence
Ver 12.13 (29May2018) - recompiled for R version 3.5.0
Ver 12.12 (11May2018) - New model, 2-sp false-pos added.
Ver 12.10 (23Feb2018) - fix predict function in RPresence
Ver 12.9 (16Feb2018) - fix model averaging bug
Ver 12.8 (02Feb2018) - added multi-season false-positive model to RPresence
Ver 12.6 (08Aug2017) - no change - update ver number to match RPresence
Ver 12.5 (22Jun2017) - added random initial values option
Ver 12.4 (22Jun2017) - fix multi-season multi-state, general parameterization,
Ver 12.3 (22Jun2017) - no change, just matching version number with RPrersence
Ver 12.2 (22Jun2017) - fix mod. avg. output
Ver 12.1 (08Jun2017) - fix 2-sp real param output
Ver 12.0 (23May2017) - changed VarCov output options
Ver 11.9 (06Mar2017) - fix un-init of output real parms
Ver 11.8 (23Jan2017) - fix multiseason 4th parameterization model w/ RPresence
Ver 11.7 (01Dec2016) - fix mod.avg. derived parm. output
Ver 11.6 (08Nov2016) - fix derived parm. output in multi-season models
Ver 11.5 (16Sep2016) - re-package with zip/unzip w/o msys.dll
Ver 11.4 (26Aug2016) - fix int. habitat model select
Ver 11.3 (18Aug2016) - recompile presence.exe for 32-bit
Ver 11.2 (25Jul2016) - fix betaname output bug
Ver 11.1 (11Jul2016) - fix mod. avg. w/ 2sp output
Ver 11.0 (10Jun2016) - fix mod. avg., mods to make easier to work with RPRESENCE
Ver 10.9 (20Apr2016) - truncate sitenames >= 32 chars. and print warning
Ver 10.8 (18Apr2016) - fix output of duplicate estimates.
Ver 10.7 (22Mar2016) - fix run-from-file bug.
Ver 10.6 (10Mar2016) - fix msSD memory error bug.
Ver 10.5 (08Feb2016) - fix pre-def 2grp mod and mod.avg bug.
Ver 10.4 (08Feb2016) - fix mult-season corr.det. derived parm output.
Ver 10.3 (08Feb2016) - fix mult-season derived parm output.
Ver 10.2 (10Dec2015) - fix mod. avg. bug
Ver 10.1 (03Dec2015) - fix run from file error #2.
Ver 10.0 (22Nov2015) - fix output of derived parms in mseasn mod.
Ver 9.9 (09Nov2015) - fix run from file error.
Ver 9.8 (04Nov2015) - allow paste single col. in samp. covar.
Ver 9.7 (14Aug2015) - fix multi-season-multi-state bug
Ver 9.6 (14Aug2015) - fix combined design matrix problem
Ver 9.5 (22Jul2015) - fix Open project, Run/simulations, and int-hab model bugs.
Ver 9.4 (16Jul2015) - fix multimethod model bug.
Ver 9.3 (14May2015) - fix paste data/des.mat.
Ver 9.2 (14May2015) - fix stag.entry model
Ver 9.1 (08May2015) - add zero-inflated poisson to Royle point count model
Ver 9.0 (04May2015) - fix misc small bugs
Ver 8.9 (23Apr2015) - fix mod.avg. w/ derived parameters
Ver 8.8 (09Apr2015) - fix mod.avg. w/ missing real parms
Ver 8.7 (03Apr2015) - fix csv input, fix mod-avg tool
Ver 8.4 (13Mar2015) - added Nichols-Het. Neg. binomial model
Ver 8.3 (21Jan2015) - fix input multiseason/alt parm bug
Ver 8.2 (21Jan2015) - fix input error (nmeth) bug
Ver 8.1 (21Jan2015) - added Royle neg. binomial model
Ver 8.0 (12Dec2014) - added MSMM model, fix multi-season bug

PRESENCE workshops

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