Recent Releases of DHARMa
DHARMa - 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.
- R
Published by melina-leite over 1 year ago
DHARMa - 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
- R
Published by florianhartig almost 4 years ago
DHARMa - 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
- R
Published by florianhartig over 4 years ago
DHARMa - 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
- R
Published by florianhartig over 4 years ago
DHARMa - DHARMa 0.4.3
Bugfixes
- Removed glmmTMB completely, see #289
- R
Published by florianhartig almost 5 years ago
DHARMa - 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
- R
Published by florianhartig almost 5 years ago
DHARMa - 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
- R
Published by florianhartig almost 5 years ago
DHARMa - 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
- R
Published by florianhartig about 5 years ago
DHARMa - 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
- R
Published by florianhartig about 5 years ago
DHARMa - DHARMa 0.3.3.2
This is a pre-release for 0.3.4, containing all the important changes, in particular the overdispersion branch
- R
Published by florianhartig over 5 years ago
DHARMa - DHARMa 0.3.3.1
Support for GLMMadaptive added
- R
Published by florianhartig over 5 years ago
DHARMa - 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
- R
Published by florianhartig almost 6 years ago
DHARMa - DHARMa 0.3.1.1
pre-release with updated outlier test
- R
Published by florianhartig about 6 years ago
DHARMa - 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
- R
Published by florianhartig about 6 years ago
DHARMa - 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
- R
Published by florianhartig over 6 years ago
DHARMa - DHARMa 0.2.5
Minor changes
- several smaller corrections to help
- R
Published by florianhartig over 6 years ago
DHARMa - 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
- R
Published by florianhartig over 7 years ago
DHARMa - 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
- R
Published by florianhartig over 7 years ago
DHARMa - DHARMa 0.2.0.3
- spaMM support
- outlier detection
https://github.com/florianhartig/DHARMa/pull/100
- R
Published by florianhartig over 7 years ago
DHARMa - DHARMa 0.2.0.1
a number of smaller updates, mostly to help files fixes #82 / Bug in recalculateResiduals
- R
Published by florianhartig almost 8 years ago
DHARMa - DHARMa 0.2.0
Changes since 0.1.6
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
- R
Published by florianhartig about 8 years ago
DHARMa - DHARMa 0.1.6.6
pre-release for 0.2.0 / various smaller bugfixes
- R
Published by florianhartig about 8 years ago
DHARMa - DHARMa 0.1.6.5
- bugfixes
- grouping option implemented
- R
Published by florianhartig about 8 years ago
DHARMa - DHARMa 0.1.6.4
remodeled dispersion tests, addresses https://github.com/florianhartig/DHARMa/issues/62 and linked issues
- R
Published by florianhartig about 8 years ago
DHARMa - DHARMa 0.1.6.3
- remodeled runBenchmarks options
- switched glmmTMB to CRAN
- R
Published by florianhartig about 8 years ago
DHARMa - 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
- R
Published by florianhartig over 8 years ago
DHARMa - 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.
- R
Published by florianhartig over 9 years ago
DHARMa - 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
- R
Published by florianhartig over 9 years ago
DHARMa - DHARMa 0.1.3
Minor update to CRAN version 0.1.3
Important 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
- R
Published by florianhartig over 9 years ago
DHARMa - 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.
- R
Published by florianhartig over 9 years ago
DHARMa - DHARMa 0.1.1
Minor update to CRAN version 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 simulations, for example for Bayesian predictive simulations
- R
Published by florianhartig over 9 years ago
DHARMa - DHARMa 0.1
Stable version of the package sent to CRAN
Compared to 0.0.3 mostly bugfixes (a few of them important) and updates of the help
- R
Published by florianhartig almost 10 years ago
DHARMa - DHARMa 0.0.3.0
create data updates / added options test updates --> Morans I on space Simulations and Help added
- R
Published by florianhartig almost 10 years ago
DHARMa - DHARMa 0.0.2.3
Bugfixes - in the options for the parametric bootstrap - For CRAN
- R
Published by florianhartig almost 10 years ago
DHARMa - DHARMa 0.0.2.1
Bugfixes in the test function
- R
Published by florianhartig almost 10 years ago
DHARMa - DHARMa 0.0.1.3 alpha
added spatial / temporal tests
- R
Published by florianhartig almost 10 years ago
DHARMa - DHARMa 0.0.1.1 alpha
Included KS test Added quantile gams
- R
Published by florianhartig almost 10 years ago