Models for Data from Unmarked Animals

Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates.


All changes can be found here: The following is just a summary.

Version 0.12-3

o New 'occuMulti' function added by Ken Kellner

Version 0.12-0

o Fixed mistake in turnover calculations in colext vignette (thanks to Giacomo Tavecchia)

o added pcount.spHDS from AHM book.

o updated predict method for pcount to include ZIP model

o Adam Smith added some parallel capabilities to the parboot functionality

o Adam Smith fixed formatMult conversion of julian date to factor

o Auriel Fournier fixed formatDistData to pad data with NA

o fixed error in obsToY for custom pi function

Version 0.11-0

o Andy Royle is the new maintainer

o Added Rebecca Hutchinson's penalized likelihood function occuPEN (experimental)

o fixed bug in gmultmix to accommodate mixed sampling protocols (NA in count frequency vector is not counted in the constraint that multinomial cell probabilities sum to 1)

o Changed variable 'ufp' to 'ufc' in ovenbird data and related functions.

o Removed constraint in pcountOpen that lambdaformula==omegaformula

o Fixed bug in gdistsamp that caused error when NAs were present in half-normal model

o Fixed bug in ranef (it was giving an error message for pcountOpen with the new dynamics options (Ricker and Gompertz) and working incorrectly for pcountOpen with immigration)

o Fixed bug in pcountOpen that occurred when covariates were time varying but not varying among sites

Version 0.10-6

o Fixed bug in C++ code that was causing problems on Solaris

Version 0.10-5

o Added new models of population dynamics to pcountOpen. Most changes contributed by Jeff Hostetler.

Version 0.10-4

o Added importFrom("plyr", "ldply") to NAMESPACE because "reshape" no longer depends on "plyr"

Version 0.10-3

o RcppArmadillo was moved from "Depends" section of DESCRIPTION file to "LinkingTo"

Version 0.10-2

Bug fixes

o Thanks for Dirk Eddelbuettel for patch to deal with change in Armadillo's in-place reshape function. Serious problems might occur if you use a recent version of RcppArmadillo and an old version of unmarked.

o Dave Miller added another NA handling fix in occuFP(). I forgot to add this one in the previous version.

Version 0.10-1

o Doc fixes requested by CRAN

Version 0.10-0

Bug fixes

o Fixed NA handling in occuFP()

o Fixed integration setting in C++ code that were causing segfaults when calling distsamp

o Replace raster:::layerNames() with raster:::names()

New features

o distsamp() and gdistsamp() should be faster and more stable for some keyfun/survey combinations

Version 0.12-0

Reference manual

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1.1.1 by Andy Royle, 8 months ago,,,

Report a bug at

Browse source code at

Authors: Richard Chandler [aut] , Ken Kellner [aut] , Ian Fiske [aut] , David Miller [aut] , Andy Royle [cre, aut] , Jeff Hostetler [aut] , Rebecca Hutchinson [aut] , Adam Smith [aut] , Marc Kery [ctb] , Mike Meredith [ctb] , Auriel Fournier [ctb] , Ariel Muldoon [ctb] , Chris Baker [ctb]

Documentation:   PDF Manual  

Task views: Analysis of Ecological and Environmental Data

GPL (>= 3) license

Imports graphics, lme4, MASS, Matrix, parallel, plyr, raster, Rcpp, stats, TMB, utils

Depends on methods, lattice

Linking to Rcpp, RcppArmadillo, TMB

System requirements: GNU make

Imported by AHMbook, AICcmodavg, AMModels, nmixgof.

Depended on by DiversityOccupancy, ubms.

Suggested by auk, camtrapR.

Enhanced by MuMIn.

See at CRAN