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

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The 'DHARMa' package uses a simulation-based approach to create readily interpretable scaled (quantile) residuals from fitted generalized linear mixed models. Currently supported are all 'merMod' classes from 'lme4' ('lmerMod', 'glmerMod'), 'glm' (including 'negbin' from 'MASS', but excluding quasi-distributions) and 'lm' model classes. Alternatively, externally created simulations, e.g. posterior predictive simulations from Bayesian software such as 'JAGS', 'STAN', or 'BUGS' can be processed as well. The resulting residuals are standardized to values between 0 and 1 and can be interpreted as intuitively as residuals from a linear regression. The package also provides a number of plot and test functions for typical model misspecification problem, such as over/underdispersion, zero-inflation, and residual spatial and temporal autocorrelation.

Author
Florian Hartig [aut, cre]
Date of publication
2016-11-19 18:44:40
Maintainer
Florian Hartig <florian.hartig@biologie.uni-regensburg.de>
License
GPL (>= 3)
Version
0.1.2
URLs

View on CRAN

Man pages

benchmarkOverdispersion
Overdispersion benchmarks
benchmarkP
General Type I/II benchmarks
benchmarkUniformity
Uniformity benchmarks
createData
Simulate test data
createDHARMa
Convert simulated residuals to a DHARMa object
DHARMa
DHARMa - Residual Diagnostics for HierArchical (Multi-level /...
plotConventionalResiduals
Conventional residual plot
plot.DHARMa
Plot simulated residuals
plotResiduals
Generic residual plot with either spline or quantile...
plotSimulatedResiduals
DHARMa standard residual plots
print.DHARMa
Print simulated residuals
simulateResiduals
Create simulated residuals
testOverdispersion
Test for over/underdispersion
testOverdispersionParametric
Parametric overdipersion test
testSimulatedResiduals
Residual tests
testSpatialAutocorrelation
Test for spatial autocorrelation
testTemporalAutocorrelation
Test for temporal autocorrelation
testUniformity
Test for overall uniformity
testZeroInflation
Tests for zero-inflation

Files in this package

DHARMa
DHARMa/inst
DHARMa/inst/examples
DHARMa/inst/examples/simulateResidualsHelp.R
DHARMa/inst/examples/createDataHelp.R
DHARMa/inst/examples/benchmarkUniformityHelp.R
DHARMa/inst/doc
DHARMa/inst/doc/DHARMa.html
DHARMa/inst/doc/DHARMa.R
DHARMa/inst/doc/DHARMa.Rmd
DHARMa/tests
DHARMa/tests/manualTests
DHARMa/tests/manualTests/PowerBias.Rmd
DHARMa/tests/testthat.R
DHARMa/tests/testthat
DHARMa/tests/testthat/Rplots.pdf
DHARMa/tests/testthat/testModelTypes.R
DHARMa/NAMESPACE
DHARMa/NEWS
DHARMa/R
DHARMa/R/benchmarkPvalues.R
DHARMa/R/plotResiduals.R
DHARMa/R/benchmarkOverdispersion.R
DHARMa/R/testsParametric.R
DHARMa/R/DHARMa.R
DHARMa/R/benchmarkUniformity.R
DHARMa/R/testsResiduals.R
DHARMa/R/simulateResiduals.R
DHARMa/R/createData.R
DHARMa/vignettes
DHARMa/vignettes/Overdispersion.png
DHARMa/vignettes/ECDFmotivation.pdf
DHARMa/vignettes/DHARMa.Rmd
DHARMa/vignettes/ECDFmotivation.png
DHARMa/README.md
DHARMa/MD5
DHARMa/build
DHARMa/build/vignette.rds
DHARMa/DESCRIPTION
DHARMa/man
DHARMa/man/DHARMa.Rd
DHARMa/man/testZeroInflation.Rd
DHARMa/man/plotResiduals.Rd
DHARMa/man/benchmarkOverdispersion.Rd
DHARMa/man/testUniformity.Rd
DHARMa/man/createDHARMa.Rd
DHARMa/man/print.DHARMa.Rd
DHARMa/man/benchmarkP.Rd
DHARMa/man/simulateResiduals.Rd
DHARMa/man/plot.DHARMa.Rd
DHARMa/man/testOverdispersionParametric.Rd
DHARMa/man/plotSimulatedResiduals.Rd
DHARMa/man/benchmarkUniformity.Rd
DHARMa/man/testTemporalAutocorrelation.Rd
DHARMa/man/createData.Rd
DHARMa/man/testSpatialAutocorrelation.Rd
DHARMa/man/plotConventionalResiduals.Rd
DHARMa/man/testOverdispersion.Rd
DHARMa/man/testSimulatedResiduals.Rd