residuals.DHARMa: Return residuals of a DHARMa simulation

View source: R/DHARMa.R

residuals.DHARMaR Documentation

Return residuals of a DHARMa simulation


Return residuals of a DHARMa simulation


## S3 method for class 'DHARMa'
residuals(object, quantileFunction = NULL,
  outlierValues = NULL, ...)



an object with simulated residuals created by simulateResiduals


optional - a quantile function to transform the uniform 0/1 scaling of DHARMa to another distribution


if a quantile function with infinite support (such as dnorm) is used, residuals that are 0/1 are mapped to -Inf / Inf. outlierValues allows to convert -Inf / Inf values to an optional min / max value.


optional arguments for compatibility with the generic function, no function implemented


the function accesses the slot $scaledResiduals in a fitted DHARMa object, and optionally transforms the standard DHARMa quantile residuals (which have a uniform distribution) to a particular pdf.


some of the papers on simulated quantile residuals transforming the residuals (which are natively uniform) back to a normal distribution. I presume this is because of the larger familiarity of most users with normal residuals. Personally, I never considered this desirable, for the reasons explained in, but with this function, I wanted to give users the option to plot normal residuals if they so wish.



testData = createData(sampleSize = 100, overdispersion = 0.5, family = poisson())
fittedModel <- glmer(observedResponse ~ Environment1 + (1|group), 
                     family = "poisson", data = testData)

simulationOutput <- simulateResiduals(fittedModel = fittedModel)

# standard plot 

# one of the possible test, for other options see ?testResiduals / vignette

# the calculated residuals can be accessed via 

# transform residuals to other pdf, see ?residuals.DHARMa for details
residuals(simulationOutput, quantileFunction = qnorm, outlierValues = c(-7,7))

# get residuals that are outside the simulation envelope

# calculating aggregated residuals per group
simulationOutput2 = recalculateResiduals(simulationOutput, group = testData$group)
plot(simulationOutput2, quantreg = FALSE)

# calculating residuals only for subset of the data
simulationOutput3 = recalculateResiduals(simulationOutput, sel = testData$group == 1 )
plot(simulationOutput3, quantreg = FALSE)

DHARMa documentation built on Sept. 9, 2022, 1:06 a.m.