testUniformity: Test for overall uniformity

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

Test for overall uniformity

Description

This function tests the overall uniformity of the simulated residuals in a DHARMa object

Usage

testUniformity(simulationOutput, alternative = c("two.sided", "less",
  "greater"), 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.
alternative	a character string specifying whether the test should test if observations are "greater", "less" or "two.sided" compared to the simulated null hypothesis. See stats::ks.test for details
plot	if TRUE, plots calls plotQQunif as well

Details

The function applies a stats::ks.test for uniformity on the simulated residuals.

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.