Residual Diagnostics for Hierarchical (Multi-Level / Mixed)
Regression Models
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Documentation for package ‘DHARMa’ version 0.5.0
Help Pages
| DHARMa-package | DHARMa: Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models |
| benchmarkRuntime | Benchmark runtimes of several functions |
| 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 |
| getData | Get model data |
| getData.brmsfit | Get model data |
| getData.default | Get model data |
| getData.merMod | Get model data |
| 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.brmsfit | 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.brmsfit | 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.brms | Get Pearson residuals |
| getPearsonResiduals.default | Get Pearson residuals |
| getPearsonResiduals.gam | Get Pearson residuals |
| getPredictorNames | Get predictor names |
| getPredictorNames.default | Get predictor names |
| getPredictorNames.MixMod | Get predictor names |
| getQuantile | Calculate Residual Quantiles |
| getRandomState | Record and restore a random state |
| getRefit | Get model refit |
| getRefit.brmsfit | 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.brmsfit | Get model residuals |
| getResiduals.default | Get model residuals |
| getResiduals.MixMod | Get model residuals |
| getSimulations | Get model simulations |
| getSimulations.brmsfit | Get model simulations |
| getSimulations.default | Get model simulations |
| getSimulations.gam | Get model simulations |
| getSimulations.glmmTMB | Get model simulations |
| getSimulations.HLfit | Get model simulations |
| getSimulations.merMod | 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 |
| plotResidualsAll | Create multiple residual plots simultaneously. |
| plotSimulatedResiduals | DHARMa standard residual plots (deprecated) |
| 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 (deprecated) |
| testOverdispersionParametric | Parametric overdisperstion tests (deprecated) |
| 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) |