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