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

## Documentation for package ‘DHARMa’ version 0.4.7

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

benchmarkRuntime | Benchmark runtimes of several functions
createData | Simulate test data
createDHARMa | Create a DHARMa object from hand-coded simulations or Bayesian posterior predictive simulations.
getFamily | Get model family
getFamily.default | Get model family
getFamily.phyloglm | Get model family
getFamily.phylolm | Get model family
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
getFitted.phyloglm | Get fitted/predicted values
getFitted.phylolm | Get fitted/predicted values
getFixedEffects | Extract fixed effects of a supported model
getFixedEffects.default | 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
getObservedResponse.phyloglm | Get model response
getObservedResponse.phylolm | Get model response
getPearsonResiduals | Get Pearson residuals
getPearsonResiduals.default | Get Pearson residuals
getPearsonResiduals.gam | Get Pearson residuals
getQuantile | Calculate Residual 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
getRefit.phyloglm | Get model refit
getRefit.phylolm | Get model refit
getResiduals | Get model residuals
getResiduals.default | Get model residuals
getResiduals.MixMod | Get model residuals
getSimulations | Get model simulations
getSimulations.default | Get model simulations
getSimulations.gam | 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
getSimulations.phyloglm | Get model simulations
getSimulations.phylolm | Get model simulations
hist.DHARMa | Histogram of DHARMa residuals
hurricanes | Hurricanes
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
simulateLRT | Simulated likelihood ratio tests for (generalized) linear mixed models
simulateResiduals | Create simulated residuals
testCategorical | Test for categorical dependencies
testDispersion | DHARMa dispersion tests
testGeneric | Test for a generic summary statistic based on simulated data
testOutliers | Test for outliers
testOverdispersion | Simulated overdisperstion tests
testOverdispersionParametric | Parametric overdisperstion tests
testPDistribution | Plot distribution of p-values.
testPhylogeneticAutocorrelation | Test for phylogenetic autocorrelation
testQuantiles | Test for quantiles
testResiduals | DHARMa general residual test
testSimulatedResiduals | Residual tests
testSpatialAutocorrelation | Test for distance-based spatial (or similar type) autocorrelation
testTemporalAutocorrelation | Test for temporal autocorrelation
testUniformity | Test for overall uniformity
testZeroInflation | Tests for zero-inflation
transformQuantiles | Transform quantiles to pdf (deprecated)