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unmarked 1.4.0
- 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
- Modernize some Cpp code to pass new LTO checks
unmarked 1.3.1
- 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
- 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
- Fix address sanitizer problems with multmixOpen
unmarked 1.1.0
- 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
- Fix LTO mismatches
- Automatically convert characters to factors in unmarkedFrames
- Many bugfixes, mainly related to predict()
unmarked 1.0.0
- 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
- Fixes for compatibility with R 4.0
unmarked 0.13-0
- 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
- New ‘occuMulti’ function added by Ken Kellner
unmarked 0.12-0
- 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
- 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
- Fixed bug in C++ code that was causing problems on Solaris
unmarked 0.10-5
- Added new models of population dynamics to pcountOpen. Most changes contributed by Jeff Hostetler.
unmarked 0.10-4
- Added importFrom(“plyr”, “ldply”) to NAMESPACE because “reshape” no longer depends on “plyr”
unmarked 0.10-3
- RcppArmadillo was moved from “Depends” section of DESCRIPTION file to “LinkingTo”
unmarked 0.10-2
- 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
- Doc fixes requested by CRAN
unmarked 0.10-0
- 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
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