DHARMa: residual diagnostics for hierarchical (multi-level/mixed) regression models

Florian Hartig, Theoretical Ecology, University of Regensburg website

2020-06-18

Abstract

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.

Motivation

The interpretation of conventional residuals for generalized linear (mixed) and other hierarchical statistical models is often problematic. As an example, here the result of conventional Deviance, Pearson and raw residuals for two Poisson GLMMs, one that is lacking a quadratic effect, and one that fits the data perfectly. Could you tell which is the correct model?

Just for completeness - it was the first one. But don’t get too excited if you got it right. Either you were lucky, or you noted that the first model seems a bit overdispersed (by the range of the Pearson residuals). But even so, would you have added a quadratic effect, instead of adding an overdispersion correction? The point here is that misspecifications in GL(M)Ms cannot reliably be diagnosed with standard residual plots, and thus GLMMs are often not as thoroughly checked as they should.

One reason why GL(M)Ms residuals are harder to interpret is that the expected distribution of the data (aka predictive distribution) changes with the fitted values. Reweighting with the expected dispersion, as done in Pearson residuals, or using deviance residuals, helps to some extent, but it does not lead to visually homogenous residuals, even if the model is correctly specified. As a result, standard residual plots, when interpreted in the same way as for linear models, seem to show all kind of problems, such as non-normality, heteroscedasticity, even if the model is correctly specified. Questions on the R mailing lists and forums show that practitioners are regularly confused about whether such patterns in GL(M)M residuals are a problem or not.

But even experienced statistical analysts currently have few options to diagnose misspecification problems in GLMMs. In my experience, the current standard practice is to eyeball the residual plots for major misspecifications, potentially have a look at the random effect distribution, and then run a test for overdispersion, which is usually positive, after which the model is modified towards an overdispersed / zero-inflated distribution. This approach, however, has a number of drawbacks, notably:

DHARMa aims at solving these problems by creating readily interpretable residuals for generalized linear (mixed) models that are standardized to values between 0 and 1, and that can be interpreted as intuitively as residuals for the linear model. This is achieved by a simulation-based approach, similar to the Bayesian p-value or the parametric bootstrap, that transforms the residuals to a standardized scale. The basic steps are:

  1. Simulate new data from the fitted model for each observation.

  2. For each observation, calculate the empirical cumulative density function for the simulated observations, which describes the possible values (and their probability) at the predictor combination of the observed value, assuming the fitted model is correct.

  3. The residual is then defined as the value of the empirical density function at the value of the observed data, so a residual of 0 means that all simulated values are larger than the observed value, and a residual of 0.5 means half of the simulated values are larger than the observed value.

These steps are visualized in the following figure

The key advantage of this definition is that the so-defined residuals always have the same, known distribution, independent of the model that is fit, if the model is correctly specified. To see this, note that, if the observed data was created from the same data-generating process that we simulate from, all values of the cumulative distribution should appear with equal probability. That means we expect the distribution of the residuals to be flat, regardless of the model structure (Poisson, binomial, random effects and so on).

I currently prepare a more exact statistical justification for the approach in an accompanying paper, but if you must provide a reference in the meantime, I would suggest citing

p.s.: DHARMa stands for “Diagnostics for HierArchical Regression Models” - which, strictly speaking, would make DHARM. But in German, Darm means intestines; plus, the meaning of DHARMa in Hinduism makes the current abbreviation so much more suitable for a package that tests whether your model is in harmony with your data:

From Wikipedia, 28/08/16: In Hinduism, dharma signifies behaviours that are considered to be in accord with rta, the order that makes life and universe possible, and includes duties, rights, laws, conduct, virtues and ‘right way of living’.

Workflow in DHARMa

Installing, loading and citing the package

If you haven’t installed the package yet, either run

install.packages("DHARMa")

Or follow the instructions on https://github.com/florianhartig/DHARMa to install a development version.

Loading and citation

library(DHARMa)
citation("DHARMa")
## 
## To cite package 'DHARMa' in publications use:
## 
##   Florian Hartig (2020). DHARMa: Residual Diagnostics for
##   Hierarchical (Multi-Level / Mixed) Regression Models. R package
##   version 0.3.2.0. http://florianhartig.github.io/DHARMa/
## 
## A BibTeX entry for LaTeX users is
## 
##   @Manual{,
##     title = {DHARMa: Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models},
##     author = {Florian Hartig},
##     year = {2020},
##     note = {R package version 0.3.2.0},
##     url = {http://florianhartig.github.io/DHARMa/},
##   }

Calculating scaled residuals

Let’s assume we have a fitted model that is supported by DHARMa.

testData = createData(sampleSize = 250)
fittedModel <- glmer(observedResponse ~ Environment1 + (1|group) , family = "poisson", data = testData)

Most functions in DHARMa could be calculated directly on the fitted model. So, for example, if you are only interested in testing dispersion, you could calculate

testDispersion(fittedModel)
## 
##  DHARMa nonparametric dispersion test via sd of residuals fitted
##  vs. simulated
## 
## data:  simulationOutput
## ratioObsSim = 0.86249, p-value = 0.952
## alternative hypothesis: two.sided

In this case, the randomized quantile residuals are calculated on the fly. However, residual calculation can take a while, and would have to be repeated by every other test you call. It is therefore highly recommended to first calculate the residuals once, using the simulateResiduals() function.

simulationOutput <- simulateResiduals(fittedModel = fittedModel, plot = T)

The function implements the algorithm discussed above, i.e. it a) creates n new synthetic datasets by simulating from the fitted model, b) calculates the cumulative distribution of simulated values for each observed value, and c) calculates the quantile (residual) value that corresponds to the observed value. Those quantiles are called “scaled residuals” in DHARMa. For example, a scaled residual value of 0.5 means that half of the simulated data are higher than the observed value, and half of them lower. A value of 0.99 would mean that nearly all simulated data are lower than the observed value. The minimum/maximum values for the residuals are 0 and 1. The function returns an object of class DHARMa, containing the simulations and the scaled residuals, which can then be passed on to all other plots and test functions. When specifying the optional argument plot = T, the standard DHARMa residual plot is displayed directly, which will be discussed below. The calculated residuals can be accesed via

residuals(simulationOutput)

Using the simulateResiduals function has the added benefit that you can modify the way in which residuals are calculated. For example, the default number of simulations to run is n = 250, which proved to be a reasonable compromise between computation time and precision, but if high precision is desired, n should be raised to 1000 at least.

As discussed above, for a correctly specified model we would expect assymptotically

Note: the expected uniform distribution is the only differences to the linear regression that one has to keep in mind when interpreting DHARMa residuals. If you cannot get used to this and you must have residuals that behave exactly like a linear regression, you can transform the uniform distribution to another distribution, for example normal, in the residual() function via

residuals(simulationOutput, quantileFunction = qnorm, outlierValues = c(-7,7))

These normal residuals will behave exactly like the residuals of a linear regression. However, for reasons of a) numeric stability with low number of simulations and b) my conviction that it is much easier to visually detect deviations from uniformity than normality, I would advice against using this transformation.

Plotting the scaled residuals

The main plot function for DHARMa residuals is the plot.DHARMa() function

plot(simulationOutput)

The plot function creates two plots, which can also be called separately

plotQQunif(simulationOutput) # left plot in plot.DHARMa()
plotResiduals(simulationOutput) # right plot in plot.DHARMa()

To provide a visual aid in detecting deviations from uniformity in y-direction, the plot function calculates an (optional) quantile regression, which compares the empirical 0.25, 0.5 and 0.75 quantiles in y direction (red solid lines) with the theoretical 0.25, 0.5 and 0.75 quantiles (dashed black line), and provides a p-value for the deviation from the expected quantile. The significance of the deviation to the expected quantiles is tested and displayed visually, and can be additionally extracted with the testQuantiles function.

If you want to plot the residuals against other predictors (highly recommend), you can use the function

plotResiduals(simulationOutput, YOURPREDICTOR)

You can also generate a histogram of the residuals via

hist(simulationOutput)

Goodness-of-fit tests on the scaled residuals

To support the visual inspection of the residuals, the DHARMa package provides a number of specialized goodness-of-fit tests on the simulated residuals:

See the help of the functions and further comments below for a more detailed description. The wrapper function testResiduals calculates the first three tests, including their graphical outputs

testResiduals(simulationOutput)

Simulation options

There are a few important technical details regarding how the simulations are performed, in particular regarding the treatments of random effects and integer responses. It is strongly recommended to read the help of

?simulateResiduals

Refit

simulationOutput <- simulateResiduals(fittedModel = fittedModel, refit = T)
  • if refit = F (default), new datasets are simulated from the fitted model, and residuals are calculated by comparing the observed data to the new data

  • if refit = T, a parametric bootstrap is performed, meaning that the model is refit to all new datasets, and residuals are created by comparing observed residuals against refitted residuals

The second option is much much slower, and also seemed to have lower power in some tests I ran. ** It is therefore not recommended for standard residual diagnostics!** I only recommend using it if you know what you are doing, and have particular reasons, for example if you estimate that the tested model is biased. A bias could, for example, arise in small data situations, or when estimating models with shrinkage estimators that include a purposeful bias, such as ridge/lasso, random effects or the splines in GAMs. My idea was then that simulated data would not fit to the observations, but that residuals for model fits on simulated data would have the same patterns/bias than model fits on the observed data.

Note also that refit = T can sometimes run into numerical problems, if the fitted model does not converge on the newly simulated data.

Random effect simulations

The second option is the treatment of the stochastic hierarchy. In a hierarchical model, several layers of stochasticity are placed on top of each other. Specifically, in a GLMM, we have a lower level stochastic process (random effect), whose result enters into a higher level (e.g. Poisson distribution). For other hierarchical models, such as state-space models, similar considerations apply, but the hierarchy can be more complex. When simulating, we have to decide if we want to re-simulate all stochastic levels, or only a subset of those. For example, in a GLMM, it is common to only simulate the last stochastic level (e.g. Poisson) conditional on the fitted random effects, meaning that the random effects are set on the fitted values.

For controlling how many levels should be re-simulated, the simulateResidual function allows to pass on parameters to the simulate function of the fitted model object. Please refer to the help of the different simulate functions (e.g. ?simulate.merMod) for details. For merMod (lme4) model objects, the relevant parameters are “use.u”, and “re.form”, as, e.g., in

simulationOutput <- simulateResiduals(fittedModel = fittedModel, n = 250, use.u = T)

If the model is correctly specified and the fitting procedure is unbiased (disclaimer: GLMM estimators are not always unbiased), the simulated residuals should be flat regardless how many hierarchical levels we re-simulate. The most thorough procedure would be therefore to test all possible options. If testing only one option, I would recommend to re-simulate all levels, because this essentially tests the model structure as a whole. This is the default setting in the DHARMa package. A potential drawback is that re-simulating the random effects creates more variability, which may reduce power for detecting problems in the upper-level stochastic processes.

Integer treatment / randomization

A third option is the treatment of integer responses. The background of this option is that, for integer-valued variables, some additional steps are necessary to make sure that the residual distribution becomes flat (essentially, we have to smoothen away the integer nature of the data). The idea is explained in

  • Dunn, K. P., and Smyth, G. K. (1996). Randomized quantile residuals. Journal of Computational and Graphical Statistics 5, 1-10.

The simulateResiduals function will automatically check if the family is integer valued, and apply randomization if that is the case. I see no reason why one would not want to randomize for an integer-valued function, so the parameter should usually not be changed.

Calculating residuals per group

In many situations, it can be useful to look at residuals per group, e.g. to see how much the model over / underpredicts per plot, year or subject. To do this, use the recalculateResiduals() function, together with a grouping variable

simulationOutput = recalculateResiduals(simulationOutput, group = testData$group)

you can keep using the simulation output as before. Note, hover, that items such as simulationOutput$scaledResiduals now have as many entries as you have groups, so if you perform plots by hand, you have to aggregate predictors in the same way. For the latter purpose, recalculateResiduals adds a function aggregateByGroup to the output.

Reproducibility notes, random seed and random state

As DHARMa uses simulations to calculate the residuals, a naive implementation of the algorithm would mean that residuals would look slightly different each time a DHARMa calculation is executed. This might both be confusing and bear the danger that a user would run the simulation several times and take the result that looks better (which would amount to multiple testing / p-hacking).

By default, DHARMa therefore fixes the random seed to the same value every time a simulation is run, and afterwards restores the random state to the old value. This means that you will get exactly the same residual plot each time. If you want to avoid this behavior, for example for simulation experiments on DHARMa, use seed = NULL -> no seed set, but random state will be restored, or seed = F -> no seed set, and random state will not be restored. Whether or not you fix the seed, the setting for the random seed and the random state are stored in

simulationOutput$randomState

If you want to reproduce simualtions for such a run, set the variable .Random.seed by hand, and simulate with seed = NULL.

Moreover (general advice), to ensure reproducibility, it’s advisable to add a set.seed() at the beginning, and a session.info() at the end of your script. The latter will list the version number of R and all loaded packages.

Interpreting residuals and recognizing misspecification problems

In all plots / tests that were shown so far, the model was correctly specified, resulting in “perfect” residual plots. In this section, we discuss how to recognize and interpret model misspecifications in the scaled residuals. Note, however, that

  1. The fact that none of the here-presented tests shows a misspecification problem doesn’t proof that the model is correctly specified. There are likely a large number of structural problems that will not show a pattern in the standard residual plots.

  2. Conversely, while a clear pattern in the residuals indicates with good reliability that the observed data would not be likely to originate from the fitted model, it doesn’t necessarily indicate that the model results are not useable. There are many cases where it is common practice to work “wrong models”. For example, random effect estimates (in particular in GLMMs) are often slightly biased, especially if the model is fit with MLE. For that reason, DHARMa will often show a slight pattern in the residuals even if the model is correctly specified, and tests for this can get significant for large sample sizes. Another example is data that is missing at random (MAR) (see here). It is known that this phenomenon does not createa bias on the fixed effect estimates, and it is therefore common practice to fit this data with mixed models. Nevertheless, DHARMa recognizes that the observed data looks different than what would be expected from the model assumptions, and flags the model as problematic

Important conclusion: DHARMa only flags a difference between the observed and expected data - the user has to decide whether this difference is actually a problem for the analysis!

Overdispersion / underdispersion

The most common concern for GLMMs is overdispersion, underdispersion and zero-inflation.

Over/underdispersion refers to the phenomenon that residual variance is larger/smaller than expected under the fitted model. Over/underdispersion can appear for any distributional family with fixed variance, in particular for Poisson and binomial models.

A few general rules of thumb

An example of overdispersion

This this is how overdispersion looks like in the DHARMa residuals

testData = createData(sampleSize = 200, overdispersion = 1.5, family = poisson())
fittedModel <- glm(observedResponse ~  Environment1 , family = "poisson", data = testData)

simulationOutput <- simulateResiduals(fittedModel = fittedModel)
plot(simulationOutput)

Note that we get more residuals around 0 and 1, which means that more residuals are in the tail of distribution than would be expected under the fitted model.

An example of underdispersion

This is an example of underdispersion

testData = createData(sampleSize = 500, intercept=0, fixedEffects = 2, overdispersion = 0, family = poisson(), roundPoissonVariance = 0.001, randomEffectVariance = 0)
fittedModel <- glmer(observedResponse ~ Environment1 + (1|group) , family = "poisson", data = testData)

simulationOutput <- simulateResiduals(fittedModel = fittedModel)
plot(simulationOutput)

Here, we get too many residuals around 0.5, which means that we are not getting as many residuals as we would expect in the tail of the distribution than expected from the fitted model.

Testing for over/underdispersion

Although, as discussed above, over/underdispersion will show up in the residuals, and it’s possible to detect it with the testUniformity function, simulations show that this test is less powerful than more targeted tests.

DHARMa therefore contains two overdispersion tests that compares the dispersion of simulated residuals to the observed residuals.

  1. A non-parametric test on the simulated residuals
  2. A non-parametric overdispersion test on the re-fitted residuals.

You can call these tests as follows:

# Option 2
testDispersion(simulationOutput)