Changelog

Source: NEWS.md

unmarked 1.2.4 Unreleased

  • 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