NOTE: for more news about the package, see https://github.com/florianhartig/DHARMa/releases

DHARMa 0.4.5
============

Minor changes

- included option to simulate mgcv models using the functions implemented in mgcViz which should improve mgcv compatibility with DHARMa

- Added option to include plot title in plot() #320

Bugfixes

- fixed issues with plotting, see #313 and #274

DHARMa 0.4.4
============

Major changes

- remodelled tests so that all tested packages can be used conditionally

Minor changes

- re-introduced glmmTMB to suggests
- phyr moved to enhances
- re-modelled package unit tests
- added RStan, CmdStanR, rjags, BayesianTools to enhances, as they coudld be used with DHARMa
- moved parallel calculations in runBenchmark to R native parallel functions

New features

- Added rotation option to all functions that create residuals (simulateResiduals, recalculateResiduals, createDHARMa)

Documentation

- Added help comments about autocorrelation structures, in particular in simulateResiduals, testSpatialAutocorrelation, testTemporalAutocorrelation
- Added example about the use of rotation in testTemporalAutocorrelation
- Improved help of dispersion test

DHARMa 0.4.3
============

Bugfixes

- Removed glmmTMB completely, see #289

DHARMa 0.4.2
============

Bugfixes

- Moved glmmTMB from suggest to import because this package is used in the vignette, see #289

Minor changes

- Added hurricane dataset
- Help and vignette updates
- phyr added in suggests


DHARMa 0.4.1
============

Bugfixes

- Force method = traditional for refit = T, as it turns out that the PIT method is not a good idea on the residuals, see #272


DHARMa 0.4.0
============

This is actually a bugfix release for 0.3.4, but on reflection I decided that 0.4.0 should have been a minor release, so I pushed the version number up to 0.4.0

Bugfixes

- bugfix in getResiduals, which had consequences for quantile residual calculations with refit = T


DHARMa 0.3.4
============

0.3.4 is a relatively important release with various minor improvements a smaller new features, most noteworthy the support of glmmAdaptive

New features

- added parametric dispersion test in testDispersion (0.3.3.2)
- support for glmmAdaptive (0.3.3.1)
- new plot for categorical predictors
- new plots for result of runBenchmarks

Major changes

-

Minor changes

- changed test statistics in standard dispersion test to standardized variance, to be more in line with standard dispersion parameters
- defaults for plot function unified
- removed option to provide no x,y / time in the correlation tests
- recalculateResiduals now allows subsetting #246
- better input checking in correlation tests #190

Bugfixes

- bugfix in runBenchmarks included in https://github.com/florianhartig/DHARMa/pull/247
- bugfix in testQuantiles https://github.com/florianhartig/DHARMa/pull/261
- bugfix in getRandomState https://github.com/florianhartig/DHARMa/issues/254


DHARMa 0.3.3
============

Bugfixes

- bugfix in testOutliers, see https://github.com/florianhartig/DHARMa/issues/197
- bugfix in the ecdf / PIT residual function, see https://github.com/florianhartig/DHARMa/issues/195

DHARMa 0.3.2
============

Bugfixes

- bugfix in testOutliers, see https://github.com/florianhartig/DHARMa/issues/182


DHARMa 0.3.1
============

Major changes

- added PIT quantile calculations based on suggestion in #168. For details see ?getQuantiles

Bugfixes

- bugfix for passing on parameters to plot.default through plotR.DHARMa and plotResiduals

Minor changes

- added checks / warnings for models fit with weights


DHARMa 0.3.0
============

New features

- quantile regressions switched to qgam, which also calculates p-values on the quantile estimates
- new testQuantiles function, based on the qgam quantile regressions

Changes

- syntax change for plotResiduals, see ?plotResiduals
- transformQuantiles is deprecated, functionality included in residuals()
- nearly all functions can now also be called directly with a fitted model (for computational efficiency, however, it is still recommended to calculate the residuals first)
- qqPlot now shows disribution, dispersion and outlier test

Bugfixes

- bugfix #158 for fitting glmmTMB binomial with proportions


DHARMa 0.2.7
============

New features

- added smooth scatter in plotResiduals https://github.com/florianhartig/DHARMa/commit/da01d8c7a9a74558817e4a73fe826084164cf05d

- glmmTMB now fully supported through new compulsory version 1.0 of glmmTMB, which includes the re.form argument in the simulations required by DHARMa https://github.com/florianhartig/DHARMa/pull/140


DHARMa 0.2.6
============

Bugfixes

- return of plotResiduals set to invisible


DHARMa 0.2.5
============

New features

- transformQuantiles function added to transform uniform DHARMa residuals to normal or other residuals

Minor changes

- several smaller corrections to help


DHARMa 0.2.4
============

Bugfixes

- corrected issues in the vignette
- small corrections to help

DHARMa 0.2.3
============

Bugfixes

- added missing distributions https://github.com/florianhartig/DHARMa/pull/104
- bugfix in simulate residuals https://github.com/florianhartig/DHARMa/issues/107

DHARMa 0.2.2
============

Bugfixes

- fixes bug in Vignette (header lost)

DHARMa 0.2.1
============

New features

- Outlier highlighting (in plots) and formal outlier test, implemented in https://github.com/florianhartig/DHARMa/pull/99
- Supporting now also models fit with the spaMM package

Major changes

- Remodelled createDHARMa function - option to directly provide scaled residuals was removed
- Rewrote ecdf function for DHARMa to get fully balanced scale, in the course of https://github.com/florianhartig/DHARMa/pull/99

Minor changes

- a number of smaller updates, mostly to help files

Bugfixes

- fixes #82 / Bug in recalculateResiduals


DHARMa 0.2.0
============

New features

- support for glmmTMB https://github.com/florianhartig/DHARMa/issues/16, implemented since https://github.com/florianhartig/DHARMa/releases/tag/v0.1.6.2
- support for grouping of residuals, see https://github.com/florianhartig/DHARMa/issues/22
- residual function for DHARMa


Major changes

- remodeled benchmarks functions in https://github.com/florianhartig/DHARMa/releases/tag/v0.1.6.3
- remodeled dispersion testsin https://github.com/florianhartig/DHARMa/releases/tag/v0.1.6.4, adresses https://github.com/florianhartig/DHARMa/issues/62

Minor changes

- changed plot function names in https://github.com/florianhartig/DHARMa/releases/tag/v0.1.6.1

Bugfixes

- fixed bug with zeroinflation test for k/n binomial data https://github.com/florianhartig/DHARMa/issues/55
- fixed bug with p-value calculation via ecdf https://github.com/florianhartig/DHARMa/issues/55


DHARMa 0.1.6
============

New features

- option to apply rank tranformation of x values in plotResiduals, see https://github.com/florianhartig/DHARMa/issues/44
- option to convert predictor to factor
- random seed is fixed, random state is recorded

Minor changes

- changed syntax in tests for sptial / temporal autocorrlation - null provides now random. Also, custom distance matrices can be provided to testSpatialAutocorrelation
- slight changes to plot layout

Bugfixes

- error catching for crashes in plot function https://github.com/florianhartig/DHARMa/issues/42
- bugfix for glmer.nb parametricOverdispersinTest https://github.com/florianhartig/DHARMa/issues/47

DHARMa 0.1.5

Minor changes

- fixes a bug in version 0.1.4 that occurred when running simulateResiduals with refit = T. Apologies for any inconvenience.


DHARMa 0.1.4
============

Major changes

- new experimental non-parametric dispersion test on simulated residuals. Extended simulations to compare dispersion tests

Minor changes

- supports for binomial with response coded as factor
- error catching for refit procedure https://github.com/florianhartig/DHARMa/issues/18
- warnings in case the refit procedure fails or produces identical parameter values https://github.com/florianhartig/DHARMa/issues/20

DHARMa 0.1.3
============

Major changes

- includes support for model class 'gam' from package 'mgcv'. Required overwriting the 'fitted' function for gam, see https://github.com/florianhartig/DHARMa/issues/12

Minor changes

- plotResiduals includes support for factors

- updates to the help

DHARMa 0.1.2
============

- This bugfix release fixes an issue with backwards compatibility introduced in the 0.1.1 release, which used the 'startsWith' function that is only available in R base since 3.3.0. In 0.1.2, all occurences of 'startsWith' were replaced with 'grepl', which restores the compatibility with older R versions.

DHARMa 0.1.1
============

- including now the negative binomial models from MASS and lme4, as well as the possibility to create synthetic data from the negative binomial family

- includes a createDHARMa function that allows using the plot functions of DHARMa also with externally created simualtions, for example for Bayesian predictive simulations

DHARMA 0.1.0
============

- initial release, with support for lm, glm, lme4
