help simplifications to improve speed

florianhartig · Sep 8, 2020 · 212f594 · 212f594
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Showing 10 changed files with 20 additions and 46 deletions.
diff --git a/DHARMa/inst/examples/simulateResidualsHelp.R b/DHARMa/inst/examples/simulateResidualsHelp.R
@@ -1,6 +1,6 @@
 library(lme4)
 
-testData = createData(sampleSize = 200, overdispersion = 0.5, family = poisson())
+testData = createData(sampleSize = 100, overdispersion = 0.5, family = poisson())
 fittedModel <- glmer(observedResponse ~ Environment1 + (1|group), 
                      family = "poisson", data = testData)
 
@@ -18,14 +18,9 @@ residuals(simulationOutput)
 # transform residuals to other pdf, see ?residuals.DHARMa for details
 residuals(simulationOutput, quantileFunction = qnorm, outlierValues = c(-7,7))
 
-# calculating summaries per group
+# calculating residuals per group
 simulationOutput = recalculateResiduals(simulationOutput, group = testData$group)
 plot(simulationOutput, quantreg = FALSE)
 
-# create residuals with refitting, see ?simulateResiduals for details
-# n=10 is very low, set higher when using this for real
-simulationOutput <- simulateResiduals(fittedModel = fittedModel, 
-                                      n = 10, refit = TRUE)
-plot(simulationOutput, quantreg = FALSE)
 
 
diff --git a/DHARMa/inst/examples/testsHelp.R b/DHARMa/inst/examples/testsHelp.R
@@ -1,4 +1,4 @@
-testData = createData(sampleSize = 200, overdispersion = 0.5, randomEffectVariance = 0)
+testData = createData(sampleSize = 100, overdispersion = 0.5, randomEffectVariance = 0)
 fittedModel <- glm(observedResponse ~ Environment1 , family = "poisson", data = testData)
 simulationOutput <- simulateResiduals(fittedModel = fittedModel)
 
@@ -7,7 +7,7 @@ simulationOutput <- simulateResiduals(fittedModel = fittedModel)
 plot(simulationOutput, quantreg = TRUE)
 
 # testResiduals tests distribution, dispersion and outliers
-testResiduals(simulationOutput)
+# testResiduals(simulationOutput)
 
 ####### Individual tests #######
 
@@ -17,7 +17,6 @@ testUniformity(simulationOutput)
 # Dispersion test
 testDispersion(simulationOutput) # tests under and overdispersion
 testDispersion(simulationOutput, alternative = "less") # only underdispersion
-testDispersion(simulationOutput, alternative = "less") # only underdispersion
 
 # if model is refitted, a different test will be called
 simulationOutput2 <- simulateResiduals(fittedModel = fittedModel, refit = TRUE, seed = 12)

diff --git a/DHARMa/man/recalculateResiduals.Rd b/DHARMa/man/recalculateResiduals.Rd
diff --git a/DHARMa/man/residuals.DHARMa.Rd b/DHARMa/man/residuals.DHARMa.Rd
diff --git a/DHARMa/man/simulateResiduals.Rd b/DHARMa/man/simulateResiduals.Rd
diff --git a/DHARMa/man/testDispersion.Rd b/DHARMa/man/testDispersion.Rd
diff --git a/DHARMa/man/testGeneric.Rd b/DHARMa/man/testGeneric.Rd
diff --git a/DHARMa/man/testResiduals.Rd b/DHARMa/man/testResiduals.Rd
diff --git a/DHARMa/man/testUniformity.Rd b/DHARMa/man/testUniformity.Rd
diff --git a/DHARMa/man/testZeroInflation.Rd b/DHARMa/man/testZeroInflation.Rd