Changelog

Add integrated distance sampling model function (IDS)
Improved simulation and power analysis tools based on unmarkedFrame input
Deprecated old simulation and power analysis methods, and imputeMissing function
Fix noRemap issue reported by CRAN

Added count-data occupancy model (occuCOP)
Added multi-scale occupancy model (goccu)
Added ZIP support to gdistsamp, gmultmix, and gpcount
Fixed bug in TMB engine for occu that resulted in incorrect detection coefficient estimates when there were many interspersed NAs in the encounter history

Add gdistremoval function to fit distance/removal models, see Amundson et al. 2014
Add power analysis tools (powerAnalysis)
Simulate datasets from scratch for any model type using simulate()
Add penalized likelihood option to occuMulti, see Clipp et al. 2021
Experimental random effects support for distsamp, multinomPois, and gdistremoval using TMB
Improvements to predict() speed and better error messages
Add vignettes for occuMulti, power analysis, simulation, and random effects
Overhaul package tests and move to testthat
New package website using pkgdown
Move raster package from imports to suggests
Fix assorted compilation warnings with newer versions of compilers on CRAN
Remove call in TMB code to deprecated DOUBLE_XMIN
Many bugfixes

Add nmixTTD fitting function
Add experimental random effects support and TMB engine to occu and pcount
Add openMP support to some fitting functions (occuRN, gdistsamp, gmultmix, gpcount) for calculating likelihood in parallel
Define STRICT_R_HEADERS in C++ code for compatibility with future Rcpp update
Many bugfixes mainly related to predict()

New functions ‘distsampOpen’ and ‘multmixOpen’ - open population versions of distsamp/gdistsamp and multinomPois/gmultmix
Add ‘predict’ method for output from ‘ranef’, for generating posterior samples of the random effects and running a function on them
Predict now correctly handles formulas containing functions and newdata with invalid factor levels
Remove reshape2 dependency
Bugfixes

New ‘occuMS’ function added for fitting multi-state occupancy models (single-season and dynamic)
New ‘occuTTD’ function for fitting continuous time-to-detection occupancy models (single season and dynamic). Thanks to Jonathan Cohen for help with this
New ‘crossVal’ function for doing cross-validation on fitted unmarked models and fitLists
New ‘vif’ function for calculating variance inflation factors for fitted unmarked models
Add ability to use complimentary-log-log link function in occu
Add built-in dependent double observer pi function
New C++ engines for gmultmix, gdistsamp, multinomPois, occuRN
Approximate integrals in C++ engines with trapezoidal rule function instead of using Rdqags
Misc minor bugfixes

Fixed mistake in turnover calculations in colext vignette (thanks to Giacomo Tavecchia)
added pcount.spHDS from AHM book.
updated predict method for pcount to include ZIP model
Adam Smith added some parallel capabilities to the parboot functionality
Adam Smith fixed formatMult conversion of julian date to factor
Auriel Fournier fixed formatDistData to pad data with NA
fixed error in obsToY for custom pi function

Andy Royle is the new maintainer
Added Rebecca Hutchinson’s penalized likelihood function occuPEN (experimental)
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)
Changed variable ‘ufp’ to ‘ufc’ in ovenbird data and related functions.
Removed constraint in pcountOpen that lambdaformula==omegaformula
Fixed bug in gdistsamp that caused error when NAs were present in half-normal model
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)
Fixed bug in pcountOpen that occurred when covariates were time varying but not varying among sites

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

Added importFrom(“plyr”, “ldply”) to NAMESPACE because “reshape” no longer depends on “plyr”

RcppArmadillo was moved from “Depends” section of DESCRIPTION file to “LinkingTo”

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

Fixed NA handling in occuFP()
Fixed integration setting in C++ code that were causing segfaults when calling distsamp
Replace raster:::layerNames() with raster:::names()
distsamp() and gdistsamp() should be faster and more stable for some keyfun/survey combinations

unmarked 1.4.32024-09-01