testResiduals: DHARMa general residual test

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

DHARMa general residual test

Description

Calls uniformity, dispersion and outliers tests.

Usage

testResiduals(simulationOutput, plot = TRUE)

Arguments

simulationOutput	an object of class DHARMa, either created via simulateResiduals for supported models or by createDHARMa for simulations created outside DHARMa, or a supported model. Providing a supported model directly is discouraged, because simulation settings cannot be changed in this case.
plot	if TRUE, plots functions of the tests are called.

Details

This function is a wrapper for the various test functions implemented in DHARMa. Currently, this function calls the functions testUniformity, testDispersion, and testOutliers. All other tests (see list below) have to be called by hand.

Author(s)

Florian Hartig

See Also

testResiduals, testUniformity, testOutliers, testDispersion, testZeroInflation, testGeneric, testTemporalAutocorrelation, testSpatialAutocorrelation, testQuantiles, testCategorical

Examples

testData = createData(sampleSize = 100, overdispersion = 0.5, randomEffectVariance = 0)
fittedModel <- glm(observedResponse ~ Environment1 , family = "poisson", data = testData)
simulationOutput <- simulateResiduals(fittedModel = fittedModel)

# the plot function shows 2 plots and runs 4 tests
# i) KS test i) Dispersion test iii) Outlier test iv) quantile test
plot(simulationOutput, quantreg = TRUE)

# testResiduals tests distribution, dispersion and outliers
testResiduals(simulationOutput)

####### Individual tests #######

# KS test for correct distribution of residuals
testUniformity(simulationOutput)

# KS test for correct distribution within and between groups
testCategorical(simulationOutput, testData$group)

# Dispersion test - for details see ?testDispersion
testDispersion(simulationOutput) # tests under and overdispersion

# Outlier test (number of observations outside simulation envelope)
# Use type = "boostrap" for exact values, see ?testOutliers
testOutliers(simulationOutput, type = "binomial")

# testing zero inflation
testZeroInflation(simulationOutput)

# testing generic summaries
countOnes <- function(x) sum(x == 1)  # testing for number of 1s
testGeneric(simulationOutput, summary = countOnes) # 1-inflation
testGeneric(simulationOutput, summary = countOnes, alternative = "less") # 1-deficit

means <- function(x) mean(x) # testing if mean prediction fits
testGeneric(simulationOutput, summary = means)

spread <- function(x) sd(x) # testing if mean sd fits
testGeneric(simulationOutput, summary = spread)

DHARMa documentation built on Oct. 18, 2024, 5:09 p.m.