Changes in version 1.5.1 (2025-09-26) - Rewrite colext likelihood in TMB to improve speed and fix missing values bugs - Internal refactoring to facilitate long term maintenance. Saved model objects (e.g., in an .Rdata file) for certain model types will no longer work with some methods. - Informative error when a user attempts to use nested formula functions such as I(scale()) - Better generation of random effects for simulated datasets - Fix deprecated arma::is_finite warnings from CRAN - Remove some deprecated simulate/power analysis functions - Minor bugfixes Changes in version 1.5.0 (2025-02-10) - Add community occupancy model (occuComm) - Add hazard key function support to IDS - Large overhaul of unmarkedFit methods including getP, fitted, residuals, ranef, nonparboot, parboot, simulate etc. Most important change was to standardize missing value handling; sites with all missing values are no longer silently dropped in output - Improve and standardize documentation for these methods - More tests for these methods - Use reformulas package instead of lme4 for random effects formula handling - Fix likelihood bug in goccu when primary periods were missing - Fix bug in occuMulti getP method Changes in version 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 Changes in version 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 Changes in version 1.3.3 - Increase required R version to 4.0 Changes in version 1.3.2 (2023-07-08) - Modernize some Cpp code to pass new LTO checks Changes in version 1.3.1 (2023-06-29) - Remove log.grad function to pass CRAN checks Changes in version 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 Changes in version 1.2.4 - Convert vignettes to use rmarkdown - Handle suggested packages in vignettes - Remove occuMulti vignette due to AHMbook being temporarily off CRAN Changes in version 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 Changes in version 1.1.1 (2021-05-27) - Fix address sanitizer problems with multmixOpen Changes in version 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() Changes in version 1.0.1 (2020-07-02) - Fix LTO mismatches - Automatically convert characters to factors in unmarkedFrames - Many bugfixes, mainly related to predict() Changes in version 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 Changes in version 0.13-1 (2019-12-16) - Fixes for compatibility with R 4.0 Changes in version 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 Changes in version 0.12-3 (2019-02-05) - New 'occuMulti' function added by Ken Kellner Changes in version 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 Changes in version 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 Changes in version 0.10-6 (2015-01-27) - Fixed bug in C++ code that was causing problems on Solaris Changes in version 0.10-5 (2015-01-23) - Added new models of population dynamics to pcountOpen. Most changes contributed by Jeff Hostetler. Changes in version 0.10-4 (2014-04-28) - Added importFrom("plyr", "ldply") to NAMESPACE because "reshape" no longer depends on "plyr" Changes in version 0.10-3 (2014-01-14) - RcppArmadillo was moved from "Depends" section of DESCRIPTION file to "LinkingTo" Changes in version 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. Changes in version 0.10-1 (2013-06-12) - Doc fixes requested by CRAN Changes in version 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