setwd('C:/Users/NSG/Research/2011 - Flower Insect Manipulation/R') alldata<-read.csv('Soper_Gorden_Adler_AJB_2018_Flower_Insect_Interactions_Processed_Data.csv',header=TRUE) #####loading needed libraries##### library(nortest) library(MVN) library(car) library(lme4) library(doBy) library(lsmeans) library(vegan) library(fields) library(scatterplot3d) library(ellipse) library(mgcv) library(akima) library(energy) #####Running PCA on Flower Size##### morpho <- alldata[16:19] morpho$plot <- alldata$Plot str(morpho) morpho$Flower_Spur_Length <- (morpho$Flower_Spur_Length)^2 #transforming for normality# morpho$Flower_Length <- (morpho$Flower_Length)^3 #transforming for normality# morpho2<-(morpho[,-1]) #removing plot number# morpho2<-data.stand(morpho2, method='standardize', margin='column', plot=FALSE) #standardizing data# morpho.pca <- prcomp(morpho2, scale=TRUE) morpho.pca$x pca.eigenval(morpho.pca) #####Testing MANCOVAs##### ##Start over by re-uploading dataset before each test## #growth MANCOVA# alldata <- (alldata[-c(161),]) #removing a known outlier# veggrow.man <- lm(cbind(Maximum_Plant_Height, Maximum_Number_of_Nodes, Average_Leaf_Area) ~ Florivory * Pollination * Robbing + Julian_Date_of_First_CH_Flower, data=alldata, contrasts=list(topic=contr.sum, sys=contr.sum), type=3) Manova(veggrow.man, type=3) veggrow.man summary.aov(veggrow.man) #flower traits MANCOVA# flow.man <-lm(cbind(Change_in_Anthocyanins, Change_in_Condensed_Tannins, Flower_Size_PC1) ~ Florivory * Pollination * Robbing + Julian_Date_of_First_CH_Flower, data=alldata, contrasts=list(topic=contr.sum, sys=contr.sum), type=3) Manova(flow.man, type=3) flow.man summary.aov(flow.man) #nectar ANCOVA# alldata$ul.nectarL <- log1p(alldata$Average_Nectar_Volume) #transforming for normality# nec.man <- Anova(aov(alldata$Average_Nectar_Volume ~ Florivory * Pollination * Robbing + Julian_Date_of_First_CH_Flower, data=alldata, contrasts=list(topic=contr.sum, sys=contr.sum), type=3)) nec.man #reproduction MANCOVA# alldata$CH.FlowersL <- (alldata$Total_CH_Flower_Production)^(1/2) #transforming for normality# alldata$CH.fruitsL <- log(alldata$Average_CH_Fruits_Per_Day + 2) #transforming for normality# alldata$CL.fruitL <- log1p(alldata$Average_CL_Fruits_Per_Day) #transforming for normality# alldata$CH.to.CLL <- log(alldata$Ratio_of_CH_to_CL_Fruits + .5) #transforming for normality# fruit.man <- lm(cbind(CH.fruitsL, CL.fruitL, CH.to.CLL, CH.FlowersL) ~ Florivory * Pollination * Robbing + Julian_Date_of_First_Flower + Maximum_Plant_Height, data=alldata, contrasts=list(topic=contr.sum, sys=contr.sum), type=3) Manova(fruit.man, type=3) fruit.man summary.aov(fruit.man) #seed MANCOVA# alldata$CL.seedsL <- log1p(alldata$Average_Seeds_Per_CL_Fruit) #transforming for normality# alldata$CL.massL <- log(alldata$Average_CL_Seed_Mass+0.001) #transforming for normality# seed.man <- lm(cbind(Average_Seeds_Per_CH_Fruit, CL.seedsL, Average_CH_Seed_Mass, CL.massL) ~ Florivory * Pollination * Robbing + Julian_Date_of_First_Flower + Maximum_Plant_Height, data=alldata, contrasts=list(topic=contr.sum, sys=contr.sum), type=3) Manova(seed.man, type=3) seed.man summary.aov(seed.man) #herbivory MANCOVA# alldata <- (alldata[-c(48,49),]) #removing known outliers# alldata$DamageL <- log(alldata$Average_Percent_Leaf_Damage+0.15) #transforming for normality# alldata$DensityL <- log(alldata$Average_Herbivore_Density + 3) #transforming for normality# herb.man <- lm(cbind(DamageL, DensityL, Average_Herbivore_Richness) ~ Florivory * Pollination * Robbing + Julian_Date_of_First_Flower, data=alldata, contrasts=list(topic=contr.sum, sys=contr.sum), type=3) Manova(herb.man, type=3) herb.man summary.aov(herb.man) #####Testing GLIMs##### #pollinators# test.poll<-glm(Pollinators_Per_Hour ~ Robbing * Florivory * Pollination + Julian_Date_of_First_CH_Flower, family=poisson, data=alldata) summary(test.poll) #nectar robbers# test.rob<-glm(Robbers_Per_Hour ~ Robbing * Florivory * Pollination + Julian_Date_of_First_CH_Flower, family=poisson, data=alldata) summary(test.rob) #nectar thieves) test.thv<-glm(Thieves_Per_Hour ~ Robbing * Florivory * Pollination + Julian_Date_of_First_CH_Flower, family=poisson, data=alldata) summary(test.thv) #Florivory# test.flor<-glm(Average_Percent_Florivory ~ Robbing * Florivory * Pollination + Julian_Date_of_First_CH_Flower, family=poisson, data=alldata) summary(test.flor) #flower color# test.red<-glm(Change_in_Flower_Redness ~ Robbing * Florivory * Pollination + Julian_Date_of_First_CH_Flower, family=gaussian, data=alldata) summary(test.red) #nectar# alldata$nectar<-alldata$Average_Nectar_Volume * 1000 #converting to ml# test.nec<-glm(nectar ~ Robbing * Florivory * Pollination + Julian_Date_of_First_CH_Flower, family=quasipoisson, data=alldata) summary(test.nec)