NEWS

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unmarked 1.4.3 (2024-09-01)

• 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

unmarked 1.4.1 (2024-01-09)

• 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

unmarked 1.3.3

• Increase required R version to 4.0

unmarked 1.3.2 (2023-07-08)

• Modernize some Cpp code to pass new LTO checks

unmarked 1.3.1 (2023-06-29)

• Remove log.grad function to pass CRAN checks

unmarked 1.3.0

• Add support for terra package rasters
• Add plotEffects function for plotting marginal effects
• Better default names in fitLists
• Optional Shiny app for power analysis
• parboot now more robust to errors
• Add back temporarily removed occuMulti and colext vignettes
• Remove dependency on plyr package and move methods to imports
• Expand powerAnalysis vignette
• Many small bugfixes

unmarked 1.2.4

• Convert vignettes to use rmarkdown
• Handle suggested packages in vignettes
• Remove occuMulti vignette due to AHMbook being temporarily off CRAN

unmarked 1.2.3 (2022-04-26)

• 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

unmarked 1.1.1 (2021-05-27)

• Fix address sanitizer problems with multmixOpen

unmarked 1.1.0 (2021-05-06)

• 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()

unmarked 1.0.1 (2020-07-02)

• Fix LTO mismatches
• Automatically convert characters to factors in unmarkedFrames
• Many bugfixes, mainly related to predict()

unmarked 1.0.0 (2020-05-04)

• 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

unmarked 0.13-1 (2019-12-16)

• Fixes for compatibility with R 4.0

unmarked 0.13-0 (2019-11-12)

• 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

unmarked 0.12-3 (2019-02-05)

• New 'occuMulti' function added by Ken Kellner

unmarked 0.12-0 (2017-04-16)

• 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

unmarked 0.11-0 (2015-09-03)

• 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

unmarked 0.10-6 (2015-01-27)

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

unmarked 0.10-5 (2015-01-23)

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

unmarked 0.10-4 (2014-04-28)

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

unmarked 0.10-3 (2014-01-14)

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

unmarked 0.10-2 (2013-08-07)

• 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.

unmarked 0.10-1 (2013-06-12)

• Doc fixes requested by CRAN

unmarked 0.10-0 (2013-04-16)

• 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