DHARMa (version 0.2.4)

residuals.DHARMa: Return residuals of a DHARMa simulation

Description

Return residuals of a DHARMa simulation

Usage

# S3 method for DHARMa
residuals(object, ...)

Arguments

object

an object with simulated residuals created by simulateResiduals

...

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

Details

the function accesses the slot $scaledResiduals in a fitted DHARMa object

Examples

# NOT RUN {
library(lme4)

testData = createData(sampleSize = 200, overdispersion = 0.5, family = poisson())
fittedModel <- glmer(observedResponse ~ Environment1 + (1|group), 
                     family = "poisson", data = testData,
                     control=glmerControl(optCtrl=list(maxfun=20000) ))

simulationOutput <- simulateResiduals(fittedModel = fittedModel)

# plot residuals, quantreg = T is better but costs more time
plot(simulationOutput, quantreg = FALSE)

# the calculated residuals can be accessed via 
residuals(simulationOutput)
simulationOutput$scaledResiduals

# calculating summaries per group
simulationOutput = recalculateResiduals(simulationOutput, group = testData$group)
plot(simulationOutput, quantreg = FALSE)

# create simulations with refitting, n=5 is very low, set higher when using this
simulationOutput <- simulateResiduals(fittedModel = fittedModel, 
                                      n = 10, refit = TRUE)
plot(simulationOutput, quantreg = FALSE)

# grouping per random effect group works as above
simulationOutput = recalculateResiduals(simulationOutput, group = testData$group)
plot(simulationOutput, quantreg = FALSE)

# }