inst/examples/createDharmaHelp.R

In DHARMa: Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models

## READING IN HAND-CODED SIMULATIONS

testData = createData(sampleSize = 50, randomEffectVariance = 0)
fittedModel <- glm(observedResponse ~ Environment1, data = testData, family = "poisson")

# in DHARMA, using the simulate.glm function of glm 
sims = simulateResiduals(fittedModel)
plot(sims, quantreg = FALSE)

# Doing the same with a handcoded simulate function. 
# of course this code will only work with a 1-par glm model
simulateMyfit <- function(n=10, fittedModel){
  int = coef(fittedModel)[1]
  slo = coef(fittedModel)[2]
  pred = exp(int + slo * testData$Environment1)
  predSim = replicate(n, rpois(length(pred), pred))
  return(predSim)
}

sims = simulateMyfit(250, fittedModel)

dharmaRes <- createDHARMa(simulatedResponse = sims, 
                          observedResponse = testData$observedResponse, 
                          fittedPredictedResponse = predict(fittedModel, type = "response"), 
                          integer = TRUE)
plot(dharmaRes, quantreg = FALSE)