PRESENCE

Release Date:

PRESENCE 12.17 - 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

Downloads

Recent Modifications

  • 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 here.