DHARMa 0.5.0

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

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

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

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 0.4.3.1

reintroduced glmmTMB

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

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 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