DHARMa

Diagnostics for HierArchical Regession Models

View the Project on GitHub florianhartig/DHARMa

Project Status: Active – The project has reached a stable, usable state and is being actively developed. License: AGPL v3 CRAN_Status_Badge minimal R version

DHARMa - Residual Diagnostics for HierARchical Models

The ‘DHARMa’ package uses a simulation-based approach to create readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed models. Currently supported are linear and generalized linear (mixed) models from ‘lme4’ (classes ‘lmerMod’, ‘glmerMod’), ‘glmmTMB’ and ‘spaMM’, generalized additive models (‘gam’ from ‘mgcv’), ‘glm’ (including ‘negbin’ from ‘MASS’, but excluding quasi-distributions) and ‘lm’ model classes. Moreover, 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.

Getting DHARMa

From CRAN

DHARMa is on CRAN. So, to install the latest CRAN release, just run

install.packages("DHARMa")

To get an overview about its functionality once the package is installed, run

library(DHARMa)
?DHARMa
vignette("DHARMa", package="DHARMa")

The vignette, which can also be read online here, provides many exampless about how to use the package function for the supported regression models. To cite the package, run

citation("DHARMa")

To fit a model (from any package supported by DHARMa), run

testData = createData(sampleSize = 200, family = poisson())
m1 <- glm(observedResponse ~ Environment1, 
                     family = "poisson", data = testData)

res <- simulateResiduals(m1, plot = T)

and read to help of ?simulateResiduals and the vignette to understand what you can do with the object res.

Development release

If you want to install the current (development) version from this repository, run

devtools::install_github(repo = "florianhartig/DHARMa", subdir = "DHARMa", 
dependencies = T, build_vignettes = T)

Below the status of the automatic Travis CI tests on the master branch (if this doesn’t load see here)

Build Status

Development branches / older releases

To install a specific (older) release, or a particular branch, decide for the version number that you want to install in https://github.com/florianhartig/DHARMa/releases (version numbering corresponds to CRAN, but there may be smaller releases that were not pushed to CRAN), or branch and run

devtools::install_github(repo = "florianhartig/DHARMa", subdir = "DHARMa", 
ref = "v0.0.2.1", dependencies = T, build_vignettes = T)

with the appropriate version number / branch as argument to ref.

Acknowledgements

A question by Catalina Gutiérrez Chacón provided me with the motivation write the first version of DHARMa. Thanks for useful suggestions to improve DHARMa by Jochen Fründ, Tomer J. Czaczkes, Luis Cayuela Delgado, Alexandre Courtiol, Jim Thorson, Lukas Lohse and many other people that made comments on GitHub, Crossvalidated or via email.