Merge branch 'master' of https://github.com/florianhartig/DHARMa

Code/DHARMaTeaching/roteiro_DHARMa_Port2024/roteiro_DHARMa-live.R

@@ -0,0 +1,98 @@
+# ISEC DHARMa skills showcase - script for live editing
+# During the skills showcase, please use Slack to interact, otherwise twitter @florianhartig
+
+library(DHARMa)
+library(lme4)
+library(glmmTMB)
+
+set.seed(123)
+testData = createData(sampleSize = 200, family = poisson())
+
+fittedModel <- glmer(observedResponse ~ Environment1 + (1 | group), 
+                     family = "poisson", data = testData)
+
+res <- simulateResiduals(fittedModel)
+plot(res)
+
+testDispersion(res)
+testUniformity(res)
+testOutliers(res)
+testQuantiles(res)
+
+testZeroInflation(res)
+testSpatialAutocorrelation(res)
+testTemporalAutocorrelation(res)
+
+testGeneric(res, summary=mean)
+
+res2 <- recalculateResiduals(res, group = testData$group)
+plot(res2)
+
+residuals(res)
+
+set.seed(123)
+testData = createData(sampleSize = 200, family = poisson())
+fittedModel <- glm(observedResponse ~ Environment1 , 
+                     family = "poisson", data = testData)
+res <- simulateResiduals(fittedModel)
+plot(res)
+
+
+set.seed(123)
+testData = createData(sampleSize = 200, family = poisson())
+fittedModel <- glmer(observedResponse ~ 1 + (1|group), 
+                   family = "poisson", data = testData)
+res <- simulateResiduals(fittedModel)
+plot(res)
+
+plotResiduals(res, form = testData$Environment1)
+
+
+plot(SiblingNegotiation ~ FoodTreatment, data = Owls)
+
+m1 <- glm(SiblingNegotiation ~ FoodTreatment*SexParent + 
+            offset(log(BroodSize)), data = Owls, family = poisson)
+
+res <- simulateResiduals(m1)
+plot(res)
+
+m2 <- glmer(SiblingNegotiation ~ FoodTreatment*SexParent + 
+            offset(log(BroodSize)) + (1|Nest), data = Owls, family = poisson)
+
+res <- simulateResiduals(m2)
+plot(res)
+
+
+m3 <- glmmTMB(SiblingNegotiation ~ FoodTreatment*SexParent + 
+              offset(log(BroodSize)) + (1|Nest), data = Owls, family = nbinom1)
+
+res <- simulateResiduals(m3)
+plot(res)
+
+plotResiduals(res, Owls$FoodTreatment)
+
+testDispersion(res)
+testZeroInflation(res)
+
+m4 <- glmmTMB(SiblingNegotiation ~ FoodTreatment*SexParent + 
+                offset(log(BroodSize)) + (1|Nest), 
+              ziformula = ~ FoodTreatment*SexParent,
+              data = Owls, family = nbinom1)
+
+res <- simulateResiduals(m4)
+plot(res)
+
+testDispersion(res)
+testZeroInflation(res)
+
+data(Salamanders)
+Salamanders$pres = Salamanders$count > 0
+
+mb1 = glm(pres ~ 0 + spp * cover, data = Salamanders, family = binomial)
+
+res<- simulateResiduals(mb1)
+plot(res)
+
+res2 <- recalculateResiduals(res, group = Salamanders$site)
+plot(res2)
+