Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models


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Documentation for package ‘DHARMa’ version 0.4.1

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createData Simulate test data
createDHARMa Create a DHARMa object from hand-coded simulations or Bayesian posterior predictive simulations
DHARMa DHARMa - Residual Diagnostics for HierArchical (Multi-level / Mixed) Regression Models
getFitted Get fitted / predicted values
getFitted.default Get fitted / predicted values
getFitted.gam Get fitted / predicted values
getFitted.HLfit Get fitted / predicted values
getFitted.MixMod Get fitted / predicted values
getFixedEffects Extract fixed effects of a supported model
getFixedEffects.MixMod Extract fixed effects of a supported model
getObservedResponse Get model response
getObservedResponse.default Get model response
getObservedResponse.HLfit Get model response
getQuantile calculate quantiles
getRandomState Record and restore a random state
getRefit Get model refit
getRefit.default Get model refit
getRefit.glmmTMB Get model refit
getRefit.HLfit Get model refit
getRefit.lm Get model refit
getRefit.MixMod Get model refit
getResiduals Get model residuals
getResiduals.default Get fitted / predicted values
getResiduals.MixMod Get model residuals
getSimulations Get model simulations
getSimulations.default Get model simulations
getSimulations.glmmTMB Get model simulations
getSimulations.HLfit Get model simulations
getSimulations.lmerMod Get model simulations
getSimulations.MixMod Get model simulations
getSimulations.negbin Get model simulations
hist.DHARMa Histogram of DHARMa residuals
outliers Return outliers
plot.DHARMa DHARMa standard residual plots
plot.DHARMaBenchmark Plots DHARMa benchmarks
plotConventionalResiduals Conventional residual plot
plotQQunif Quantile-quantile plot for a uniform distribution
plotResiduals Generic res ~ pred scatter plot with spline or quantile regression on top
plotSimulatedResiduals DHARMa standard residual plots
print.DHARMa Print simulated residuals
recalculateResiduals Recalculate residuals with grouping
residuals.DHARMa Return residuals of a DHARMa simulation
runBenchmarks Benchmark calculations
simulateResiduals Create simulated residuals
testCategorical Test for categorical dependencies
testDispersion DHARMa dispersion tests
testGeneric Generic simulation test of a summary statistic
testOutliers Test for outliers
testOverdispersion Simulated overdisperstion tests
testOverdispersionParametric Parametric overdisperstion tests
testPDistribution Plot distribution of p-values
testQuantiles Test for quantiles
testResiduals DHARMa general residual test
testSimulatedResiduals Residual tests
testSpatialAutocorrelation Test for distance-based (spatial, phylogenetic or similar) autocorrelation
testTemporalAutocorrelation Test for temporal autocorrelation
testUniformity Test for overall uniformity
testZeroInflation Tests for zero-inflation
transformQuantiles Transform quantiles to pdf (deprecated)