Changelog • DHARMa

DHARMa 0.5.0

CRAN release: 2026-06-01

Major changes

For hierarchical models (GLMMs), we changed the default simulations from the supported model’s default (mostly unconditional) to conditional simulations (for most of the supported models and packages). This represents a major change in the calculated scaled residuals and is implemented to ensure higher power in dispersion and other tests. We expect different results for calculated residuals using this or older DHARMa versions. For compatibility, you can use the argument simulateREs = "user-specified" to change back to the model’s default (older DHARMa versions). See package vignette for more details.
In plotResiduals, we increased the threshold for the automatic change from quantile regression lines to the spline: from 2,000 to 10,000 data points. When it happens, a message is displayed to warn users. Also, when quantreg = F, the color of the spline was changed to black because there is no test associated with the line (as there is for quantile regression).
In plotResiduals, the argument form has a new functionality. Beyond the syntax data$predictor, it allows now to use the formula structure ~predictor, ~predictor1+predictor2, ~., ~predictor|group and ~predictor|group == "group_level" to plot the residuals against specific/all predictors and grouping variables/levels. This works for most of the supported model functions. It solves problems with NAs in datasets that were excluded by the model. #407 / #425
In testCategorical, recalculateResiduals, testQuantiles, testSpatialAutocorrelation and testTemporalAutocorrelation, additional predictors (catPred, group, sel, predictor, time, x,y- respectively) can now be specified as a formula (similar to plotResiduals). This handles rows with NAs that were excluded by the model automatically.
brms is now supported by DHARMa for simple models, i.e. models that could also be fit using glmmTMB (no multi-response, multinomial or structural equation models).

Bugfixes

Fixing error in runBenchmarks.
Fixing inconsistency in testQuantiles() #465. Including rankTransform() help function.

Minor changes

Using 95% confidence intervals for confidence bands in plots for testQuantiles(). Before, we were using standard errors (~ 68% CI).
Vectorize randomization of residuals to improve speed - PR#493 contributed by StaffanBetner.
Adding color legend to testSpatialAutocorrelation().
New function plotResidualsAll() to plot residuals against multiple predictors/all predictors of the model via plotResiduals().
New function getPredictorNames() extracts names of fixed and random effects (predictors) from a model.
testCategorical() now allows additional arguments to boxplot via …, mainly to allow for appropriate x-axis labels when running plotResidualsAll().
Improved appearance of user-specified titles via “main” in plotResiduals().

DHARMa 0.4.7

CRAN release: 2024-10-18

New Features

Includes support for the package phylolm.
New function for testing residual phylogenetic autocorrelation testPylogeneticAutocorrelation().

Major change

New optional argument ‘rotation’ in simulateResiduals() for the rotation of the residual space prior to calculating the quantile residuals to account for residual covariance as created by temporal, spatial or phylogenetic autocorrelation.

Minor changes

Residual plots: Option to change the red color for significant results to any color of preference through options(DHARMaSignalColor = “red”). This is a good option for color-blind friendly plots.
Documentation: improved help files and vignette.

DHARMa 0.4.6

CRAN release: 2022-09-08

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

CRAN release: 2022-01-16

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

CRAN release: 2021-09-28

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 could 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

CRAN release: 2021-07-07

Bugfixes

Removed glmmTMB completely, see #289

DHARMa 0.4.2

CRAN release: 2021-07-05

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

CRAN release: 2021-04-08

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

CRAN release: 2021-03-28

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

CRAN release: 2021-03-23

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

CRAN release: 2020-05-12

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

CRAN release: 2020-04-20

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

CRAN release: 2020-02-06

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

CRAN release: 2019-11-26

Bugfixes

return of plotResiduals set to invisible

DHARMa 0.2.5

CRAN release: 2019-11-18

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

CRAN release: 2019-03-06

Bugfixes

corrected issues in the vignette
small corrections to help

DHARMa 0.2.3

CRAN release: 2019-02-12

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

CRAN release: 2019-01-20

Bugfixes

fixes bug in Vignette (header lost)

DHARMa 0.2.1

CRAN release: 2019-01-17

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

CRAN release: 2018-06-05

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

CRAN release: 2018-03-18

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

CRAN release: 2017-03-10

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

CRAN release: 2017-03-07

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

CRAN release: 2016-12-11

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

CRAN release: 2016-11-19

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

CRAN release: 2016-11-16

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

CRAN release: 2016-08-26

initial release, with support for lm, glm, lme4