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

DHARMa 0.4.6

New Features

• new function benchmarkRuntime() for checking runtime of functions
• new function simulatedLRT() to generate a simulated likelihood ratio test

Bugfixes

• fixed issue with parallelization in runBenchmarks
• various minor bugfixed and help improvements

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