residuals.DHARMa {DHARMa} | R Documentation |
Return residuals of a DHARMa simulation
## S3 method for class 'DHARMa'
residuals(object, quantileFunction = NULL,
outlierValues = NULL, ...)
object |
an object with simulated residuals created by |
quantileFunction |
optional - a quantile function to transform the uniform 0/1 scaling of DHARMa to another distribution |
outlierValues |
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 $scaledResiduals in a fitted DHARMa object, and optionally transforms the standard DHARMa quantile residuals (which have a uniform distribution) to a particular pdf.
some of the papers on simulated quantile residuals transforming the residuals (which are natively uniform) back to a normal distribution. I presume this is because of the larger familiarity of most users with normal residuals. Personally, I never considered this desirable, for the reasons explained in https://github.com/florianhartig/DHARMa/issues/39, but with this function, I wanted to give users the option to plot normal residuals if they so wish.
library(lme4)
testData = createData(sampleSize = 100, overdispersion = 0.5, family = poisson())
fittedModel <- glmer(observedResponse ~ Environment1 + (1|group),
family = "poisson", data = testData)
simulationOutput <- simulateResiduals(fittedModel = fittedModel)
# standard plot
plot(simulationOutput)
# one of the possible test, for other options see ?testResiduals / vignette
testDispersion(simulationOutput)
# the calculated residuals can be accessed via
residuals(simulationOutput)
# transform residuals to other pdf, see ?residuals.DHARMa for details
residuals(simulationOutput, quantileFunction = qnorm, outlierValues = c(-7,7))
# get residuals that are outside the simulation envelope
outliers(simulationOutput)
# calculating aggregated residuals per group
simulationOutput2 = recalculateResiduals(simulationOutput, group = testData$group)
plot(simulationOutput2, quantreg = FALSE)
# calculating residuals only for subset of the data
simulationOutput3 = recalculateResiduals(simulationOutput, sel = testData$group == 1 )
plot(simulationOutput3, quantreg = FALSE)