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
unmarked 1.5.0
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
unmarked 1.4.3
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
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