DHARMa: Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models
Version 0.1.5

The 'DHARMa' package uses a simulation-based approach to create readily interpretable scaled (quantile) residuals for fitted generalized linear mixed models. Currently supported are generalized linear mixed models from 'lme4' (classes 'lmerMod', 'glmerMod'), generalized additive models ('gam' from 'mgcv'), '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 problems, such as over/underdispersion, zero-inflation, and residual spatial and temporal autocorrelation.

Browse man pages Browse package API and functions Browse package files

AuthorFlorian Hartig [aut, cre]
Date of publication2017-03-11 00:03:57
MaintainerFlorian Hartig <florian.hartig@biologie.uni-regensburg.de>
LicenseGPL (>= 3)
Version0.1.5
URL http://florianhartig.github.io/DHARMa/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("DHARMa")

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 /...
fitted.gam: This function overwrites the standard fitted function for GAM
if-predictor-is-a-factor-a-boxplot-will-be-plotted-instead-of-a-scatter-plot.: Generic residual plot with either spline or quantile...
plotConventionalResiduals: Conventional residual plot
plot.DHARMa: Plot simulated residuals
plotSimulatedResiduals: DHARMa standard residual plots
print.DHARMa: Print simulated residuals
simulateResiduals: Create simulated residuals
testOverdispersion: Test for over/underdispersion
testOverdispersionParametric: Parametric overdispersion test
testSimulatedResiduals: Residual tests
testSpatialAutocorrelation: Test for spatial autocorrelation
testTemporalAutocorrelation: Test for temporal autocorrelation
testUniformity: Test for overall uniformity
testZeroInflation: Tests for zero-inflation

Functions

DHARMa Man page
DHARMa-package Man page
benchmarkOverdispersion Man page Source code
benchmarkP Man page Source code
benchmarkUniformity Man page Source code
checkModel Source code
createDHARMa Man page Source code
createData Man page Source code
fitted.gam Man page Source code
generateGenerator Source code
getPossibleModels Source code
if predictor is a factor, a boxplot will be plotted instead of a Man page
od.point Source code
od.point2 Source code
plot.DHARMa Man page Source code
plotConventionalResiduals Man page Source code
plotResiduals Man page Source code
plotSimulatedResiduals Man page Source code
print.DHARMa Man page Source code
simulateResiduals Man page Source code
testOverdispersion Man page Source code
testOverdispersionParametric Man page Source code
testSimulatedResiduals Man page Source code
testSpatialAutocorrelation Man page Source code
testTemporalAutocorrelation Man page Source code
testUniformity Man page Source code
testZeroInflation Man page Source code

Files

inst
inst/examples
inst/examples/simulateResidualsHelp.R
inst/examples/createDataHelp.R
inst/examples/benchmarkUniformityHelp.R
inst/doc
inst/doc/DHARMa.html
inst/doc/DHARMa.R
inst/doc/DHARMa.Rmd
tests
tests/manualTests
tests/manualTests/PowerBias.Rmd
tests/testthat.R
tests/testthat
tests/testthat/testModelTypes.R
NAMESPACE
NEWS
R
R/benchmarkPvalues.R
R/plotResiduals.R
R/benchmarkOverdispersion.R
R/testsParametric.R
R/DHARMa.R
R/benchmarkUniformity.R
R/testsResiduals.R
R/simulateResiduals.R
R/compatibility.R
R/createData.R
vignettes
vignettes/ECDFmotivation.pdf
vignettes/overdispersion.png
vignettes/DHARMa.Rmd
vignettes/ECDFmotivation.png
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/DHARMa.Rd
man/testZeroInflation.Rd
man/benchmarkOverdispersion.Rd
man/testUniformity.Rd
man/createDHARMa.Rd
man/fitted.gam.Rd
man/print.DHARMa.Rd
man/benchmarkP.Rd
man/simulateResiduals.Rd
man/plot.DHARMa.Rd
man/testOverdispersionParametric.Rd
man/plotSimulatedResiduals.Rd
man/benchmarkUniformity.Rd
man/testTemporalAutocorrelation.Rd
man/createData.Rd
man/testSpatialAutocorrelation.Rd
man/plotConventionalResiduals.Rd
man/if-predictor-is-a-factor-a-boxplot-will-be-plotted-instead-of-a-scatter-plot..Rd
man/testOverdispersion.Rd
man/testSimulatedResiduals.Rd
DHARMa documentation built on May 19, 2017, 7:58 a.m.