data<-read.csv("Visitation_sequence_Data.csv",header=T) Eye<-read.csv("Eye_Length.csv", header=T) data$Bee_ID_No<-as.factor(data$Bee_ID_No) data2<-subset(data,!data$Look=="L") library(glmmML) time<-read.csv("Time.csv",header=T) ##test of eye length between experiments oneway.test(Eye$Comp_Length~Eye$set2) ##test of eye length between experiments ##plots for Figure3 Model<-aggregate(data2$Mo1_O0,list(data2$Stage,data2$Bee_ID_No,data2$Ex_Set,data2$Ex_Type),sum) Alternative<-aggregate(data2$Al1_O0,list(data2$Stage,data2$Bee_ID_No,data2$Ex_Set,data2$Ex_Type),sum) Mimic<-aggregate(data2$Mi1_O0,list(data2$Stage,data2$Bee_ID_No,data2$Ex_Set,data2$Ex_Type),sum) ag_data<-data.frame(st=Model$Group.1,ID=Model$Group.2,Set=Model$Group.3,Type=Model$Group.4) ag_data$Model<-Model$x ag_data$Alternative<-Alternative$x ag_data$Mimic<-Mimic$x relat_ag_d<-ag_data relat_ag_d[,8]<-apply(relat_ag_d[,5:7],sum,MARGIN=1) relat_ag_d[,5:7]<-relat_ag_d[,5:7]/relat_ag_d[,8] relat_ag_d$stage2<-rep(c(25,75,150,300,600,1000,1400),54) Ex2_BI<-subset(relat_ag_d,relat_ag_d$Set=="Ex2"&relat_ag_d$Type=="BI") Ex2_BIY<-subset(relat_ag_d,relat_ag_d$Set=="Ex2"&relat_ag_d$Type=="BIY") Ex2_BY<-subset(relat_ag_d,relat_ag_d$Set=="Ex2"&relat_ag_d$Type=="BY") Ex1_BS<-subset(relat_ag_d,relat_ag_d$Set=="Ex1"&relat_ag_d$Type=="BS") Ex1_BSY<-subset(relat_ag_d,relat_ag_d$Set=="Ex1"&relat_ag_d$Type=="BSY") Ex1_BY<-subset(relat_ag_d,relat_ag_d$Set=="Ex1"&relat_ag_d$Type=="BY") #Ex1_MoMi id<-unique(Ex1_BS$ID) id<-id[drop=TRUE] Ex1_BS$ID<-Ex1_BS$ID[drop=TRUE] plot(relat_ag_d$stage2,relat_ag_d$Mimic,xlim=c(0,1600),ylim=c(0,1),type="n") for(i in id){ dfi<-subset(Ex1_BS,Ex1_BS$ID==i) lines(dfi$stage2+10,dfi$Mimic,lty=3,lwd=0.01,col=rgb(0,0,1,60,maxColorValue=255)) lines(dfi$stage2,dfi$Model,lwd=0.01,col=rgb(0,0,1,60,maxColorValue=255)) points(dfi$stage2+10,dfi$Mimic,pch=16,cex=1.3,col=rgb(0,0,1,maxColorValue=255)) points(dfi$stage2+10,dfi$Mimic,pch=16,cex=0.8,col=rgb(255,255,255,maxColorValue=255)) points(dfi$stage2,dfi$Model,pch=16,cex=1.3,col=rgb(0,0,1,maxColorValue=255)) } #Ex1_MoMiAl id<-unique(Ex1_BSY$ID) id<-id[drop=TRUE] Ex1_BSY$ID<-Ex1_BSY$ID[drop=TRUE] plot(relat_ag_d$stage2,relat_ag_d$Mimic,xlim=c(0,1600),ylim=c(0,0.66),type="n") for(i in id){ dfi<-subset(Ex1_BSY,Ex1_BSY$ID==i) lines(dfi$stage2+10,dfi$Mimic,lty=3,lwd=0.01,col=rgb(0,0,1,60,maxColorValue=255)) lines(dfi$stage2,dfi$Model,lwd=0.01,col=rgb(0,0,1,60,maxColorValue=255)) lines(dfi$stage2-10,dfi$Alternative,lwd=0.01,col=rgb(206,206,206,160,maxColorValue=255)) points(dfi$stage2-10,dfi$Alternative,pch=16,cex=1.3,col=rgb(206,206,206,maxColorValue=255)) points(dfi$stage2+10,dfi$Mimic,pch=16,cex=1.3,col=rgb(0,0,1,maxColorValue=255)) points(dfi$stage2+10,dfi$Mimic,pch=16,cex=0.8,col=rgb(255,255,255,maxColorValue=255)) points(dfi$stage2,dfi$Model,pch=16,cex=1.3,col=rgb(0,0,1,maxColorValue=255)) } #Ex1_MoAl id<-unique(Ex1_BY$ID) id<-id[drop=TRUE] Ex1_BY$ID<-Ex1_BY$ID[drop=TRUE] plot(relat_ag_d$stage2,relat_ag_d$Mimic,xlim=c(0,1600),ylim=c(0,1),type="n") for(i in id){ dfi<-subset(Ex1_BY,Ex1_BY$ID==i) lines(dfi$stage2,dfi$Model,lwd=0.01,col=rgb(0,0,1,60,maxColorValue=255)) lines(dfi$stage2-10,dfi$Alternative,lwd=0.01,col=rgb(206,206,206,160,maxColorValue=255)) points(dfi$stage2-10,dfi$Alternative,pch=16,cex=1.3,col=rgb(206,206,206,maxColorValue=255)) points(dfi$stage2,dfi$Model,pch=16,cex=1.3,col=rgb(0,0,1,maxColorValue=255)) } #Ex2_MoMi id<-unique(Ex2_BI$ID) id<-id[drop=TRUE] Ex2_BI$ID<-Ex2_BI$ID[drop=TRUE] plot(relat_ag_d$stage2,relat_ag_d$Mimic,xlim=c(0,1600),ylim=c(0,1),type="n") for(i in id){ dfi<-subset(Ex2_BI,Ex2_BI$ID==i) lines(dfi$stage2+10,dfi$Mimic,lty=3,lwd=0.01,col=rgb(0,0,1,60,maxColorValue=255)) lines(dfi$stage2,dfi$Model,lwd=0.01,col=rgb(0,0,1,60,maxColorValue=255)) points(dfi$stage2+10,dfi$Mimic,pch=16,cex=1.3,col=rgb(0,0,1,maxColorValue=255)) points(dfi$stage2+10,dfi$Mimic,pch=16,cex=0.8,col=rgb(255,255,255,maxColorValue=255)) points(dfi$stage2,dfi$Model,pch=16,cex=1.3,col=rgb(0,0,1,maxColorValue=255)) } #Ex2_MoMiAl id<-unique(Ex2_BIY$ID) id<-id[drop=TRUE] Ex2_BIY$ID<-Ex2_BIY$ID[drop=TRUE] plot(relat_ag_d$stage2,relat_ag_d$Mimic,xlim=c(0,1600),ylim=c(0,0.66),type="n") for(i in id){ dfi<-subset(Ex2_BIY,Ex2_BIY$ID==i) lines(dfi$stage2+10,dfi$Mimic,lty=3,lwd=0.01,col=rgb(0,0,1,60,maxColorValue=255)) lines(dfi$stage2,dfi$Model,lwd=0.01,col=rgb(0,0,1,60,maxColorValue=255)) lines(dfi$stage2-10,dfi$Alternative,lwd=0.01,col=rgb(206,206,206,160,maxColorValue=255)) points(dfi$stage2-10,dfi$Alternative,pch=16,cex=1.3,col=rgb(206,206,206,maxColorValue=255)) points(dfi$stage2+10,dfi$Mimic,pch=16,cex=1.3,col=rgb(0,0,1,maxColorValue=255)) points(dfi$stage2+10,dfi$Mimic,pch=16,cex=0.8,col=rgb(255,255,255,maxColorValue=255)) points(dfi$stage2,dfi$Model,pch=16,cex=1.3,col=rgb(0,0,1,maxColorValue=255)) } #Ex2_MoAl id<-unique(Ex2_BY$ID) id<-id[drop=TRUE] Ex2_BY$ID<-Ex2_BY$ID[drop=TRUE] plot(relat_ag_d$stage2,relat_ag_d$Mimic,xlim=c(0,1600),ylim=c(0,1),type="n") for(i in id){ dfi<-subset(Ex2_BY,Ex2_BY$ID==i) lines(dfi$stage2,dfi$Model,lwd=0.01,col=rgb(0,0,1,60,maxColorValue=255)) lines(dfi$stage2-10,dfi$Alternative,lwd=0.01,col=rgb(206,206,206,160,maxColorValue=255)) points(dfi$stage2-10,dfi$Alternative,pch=16,cex=1.3,col=rgb(206,206,206,maxColorValue=255)) points(dfi$stage2,dfi$Model,pch=16,cex=1.3,col=rgb(0,0,1,maxColorValue=255)) } ##plots for Figure3 ##tests for Figure4 ##Analysis for visits to mimics ##Figure4a lastst<-subset(data2,data2$Stage>=5) summary(lastst) lastst<-subset(lastst,!lastst$Ex_Type=="BY") Ex1_MoMi_Ex1_MoMiAl<-subset(lastst,lastst$Ex_Type=="BS"|lastst$Ex_Type=="BSY") Ex1_MoMi_Ex2_MoMi<-subset(lastst,lastst$Ex_Type=="BS"|lastst$Ex_Type=="BI") Ex1_MoMi_Ex2_MoMiAl<-subset(lastst,lastst$Ex_Type=="BS"|lastst$Ex_Type=="BIY") Ex1_MoMiAl_Ex2_MoMi<-subset(lastst,lastst$Ex_Type=="BSY"|lastst$Ex_Type=="BI") Ex1_MoMiAl_Ex2_MoMiAl<-subset(lastst,lastst$Ex_Type=="BSY"|lastst$Ex_Type=="BIY") Ex2_MoMi_Ex2_MoMiAl<-subset(lastst,lastst$Ex_Type=="BI"|lastst$Ex_Type=="BIY") Ex1_MoMi_Ex1_MoMiAl$Ex_Type<-Ex1_MoMi_Ex1_MoMiAl$Ex_Type[drop=T] Ex1_MoMi_Ex2_MoMi$Ex_Type<-Ex1_MoMi_Ex2_MoMi$Ex_Type[drop=T] Ex1_MoMi_Ex2_MoMiAl$Ex_Type<-Ex1_MoMi_Ex2_MoMiAl$Ex_Type[drop=T] Ex1_MoMiAl_Ex2_MoMi$Ex_Type<-Ex1_MoMiAl_Ex2_MoMi$Ex_Type[drop=T] Ex1_MoMiAl_Ex2_MoMiAl$Ex_Type<-Ex1_MoMiAl_Ex2_MoMiAl$Ex_Type[drop=T] Ex2_MoMi_Ex2_MoMiAl$Ex_Type<-Ex2_MoMi_Ex2_MoMiAl$Ex_Type[drop=T] a<-glmmML(Mi1_O0~Ex_Type,cluster=Bee_ID_No,data=Ex1_MoMi_Ex1_MoMiAl,family=binomial) summary(a,digit=5) a<-glmmML(Mi1_O0~Ex_Type,cluster=Bee_ID_No,data=Ex1_MoMi_Ex2_MoMi,family=binomial,start.sigma=1) summary(a,digit=5) a<-glmmML(Mi1_O0~Ex_Type,cluster=Bee_ID_No,data=Ex1_MoMi_Ex2_MoMiAl,family=binomial,start.sigma=1) summary(a,digit=5) a<-glmmML(Mi1_O0~Ex_Type,cluster=Bee_ID_No,data=Ex1_MoMiAl_Ex2_MoMi,family=binomial,start.sigma=1) summary(a,digit=5) a<-glmmML(Mi1_O0~Ex_Type,cluster=Bee_ID_No,data=Ex1_MoMiAl_Ex2_MoMiAl,family=binomial,start.sigma=1) summary(a,digit=5) a<-glmmML(Mi1_O0~Ex_Type,cluster=Bee_ID_No,data=Ex2_MoMi_Ex2_MoMiAl,family=binomial,start.sigma=1) summary(a,digit=5) ##Figure4a ##Figure4b #Ex2_MoMi vs Ex2_MoMiAl latter_st<-subset(data2,data2$Stage=="5"|data2$Stage=="6"|data2$Stage=="7") latter_st_2MoMi_2MoMiAl<-subset(latter_st,latter_st$Ex_Type=="BI"|latter_st$Ex_Type=="BIY") latter_st_2MoMi_2MoMiAl<-subset(latter_st_2MoMi_2MoMiAl,!latter_st_2MoMi_2MoMiAl$Flower_Color=="y") latter_st_2MoMi_2MoMiAl$Ex_Type<-latter_st_2MoMi_2MoMiAl$Ex_Type[drop=T] a<-glmmML(Mi1_O0~Ex_Type,cluster=Bee_ID_No,data=latter_st_2MoMi_2MoMiAl,start.sigma=1,control=list(maxit=500)) summary(a,digit=5) #Ex1_MoMiAl vs Ex2_MoMi latter_st<-subset(data2,data2$Stage=="5"|data2$Stage=="6"|data2$Stage=="7") latter_st_2MoMi_1MoMiAl<-subset(latter_st,latter_st$Ex_Type=="BI"|latter_st$Ex_Type=="BSY") latter_st_2MoMi_1MoMiAl<-subset(latter_st_2MoMi_1MoMiAl,!latter_st_2MoMi_1MoMiAl$Flower_Color=="y") latter_st_2MoMi_1MoMiAl$Ex_Type<-latter_st_2MoMi_1MoMiAl$Ex_Type[drop=T] a<-glmmML(Mi1_O0~Ex_Type,cluster=Bee_ID_No,data=latter_st_2MoMi_1MoMiAl,start.sigma=1,control=list(maxit=500)) summary(a,digit=5) #Ex1_MoMi vs Ex2_MoMi latter_st<-subset(data2,data2$Stage=="5"|data2$Stage=="6"|data2$Stage=="7") latter_st_1MoMi_2MoMi<-subset(latter_st,latter_st$Ex_Type=="BI"|latter_st$Ex_Type=="BS") latter_st_1MoMi_2MoMi<-subset(latter_st_1MoMi_2MoMi,!latter_st_1MoMi_2MoMi$Flower_Color=="y") latter_st_1MoMi_2MoMi$Ex_Type<-latter_st_1MoMi_2MoMi$Ex_Type[drop=T] a<-glmmML(Mi1_O0~Ex_Type,cluster=Bee_ID_No,data=latter_st_1MoMi_2MoMi,start.sigma=1,control=list(maxit=500)) summary(a,digit=5) #Ex1_MoMi vs Ex2_MoMiAl latter_st<-subset(data2,data2$Stage=="5"|data2$Stage=="6"|data2$Stage=="7") latter_st_1MoMiAl_2MoMi<-subset(latter_st,latter_st$Ex_Type=="BIY"|latter_st$Ex_Type=="BS") latter_st_1MoMiAl_2MoMi<-subset(latter_st_1MoMiAl_2MoMi,!latter_st_1MoMiAl_2MoMi$Flower_Color=="y") latter_st_1MoMiAl_2MoMi$Ex_Type<-latter_st_1MoMiAl_2MoMi$Ex_Type[drop=T] a<-glmmML(Mi1_O0~Ex_Type,cluster=Bee_ID_No,data=latter_st_1MoMiAl_2MoMi,start.sigma=1,control=list(maxit=500)) summary(a,digit=5) summary(latter_st_1MoMi_2MoMi) summary(latter_st_1MoMiAl_2MoMi) #Ex1_MoMiAl vs Ex2_MoMiAl latter_st<-subset(data2,data2$Stage=="5"|data2$Stage=="6"|data2$Stage=="7") latter_st_1MoMiAl_2MoMiAl<-subset(latter_st,latter_st$Ex_Type=="BIY"|latter_st$Ex_Type=="BSY") latter_st_1MoMiAl_2MoMiAl<-subset(latter_st_1MoMiAl_2MoMiAl,!latter_st_1MoMiAl_2MoMiAl$Flower_Color=="y") latter_st_1MoMiAl_2MoMiAl$Ex_Type<-latter_st_1MoMiAl_2MoMiAl$Ex_Type[drop=T] a<-glmmML(Mi1_O0~Ex_Type,cluster=Bee_ID_No,data=latter_st_1MoMiAl_2MoMiAl,start.sigma=1,control=list(maxit=500)) summary(a,digit=5) #Ex1_MoMi vs Ex1_MoMiAl latter_st<-subset(data2,data2$Stage=="5"|data2$Stage=="6"|data2$Stage=="7") latter_st_1MoMi_1MoMiAl<-subset(latter_st,latter_st$Ex_Type=="BS"|latter_st$Ex_Type=="BSY") latter_st_1MoMi_1MoMiAl<-subset(latter_st_1MoMi_1MoMiAl,!latter_st_1MoMi_1MoMiAl$Flower_Color=="y") latter_st_1MoMi_1MoMiAl$Ex_Type<-latter_st_1MoMi_1MoMiAl$Ex_Type[drop=T] a<-glmmML(Mi1_O0~Ex_Type,cluster=Bee_ID_No,data=latter_st_1MoMi_1MoMiAl,start.sigma=1,control=list(maxit=500)) summary(a,digit=5) ##Figure4b ##Figure4c #Ex2_MoAl vs Ex2_MoMiAl latter_st<-subset(data2,data2$Stage=="5"|data2$Stage=="6"|data2$Stage=="7") latter_st_2MoAl_2MoMiAl<-subset(latter_st,latter_st$Ex_Type=="BY"|latter_st$Ex_Type=="BIY") latter_st_2MoAl_2MoMiAl<-subset(latter_st_2MoAl_2MoMiAl,!latter_st_2MoAl_2MoMiAl$Ex_Set=="Ex1") latter_st_2MoAl_2MoMiAl<-subset(latter_st_2MoAl_2MoMiAl,!(latter_st_2MoAl_2MoMiAl$Flower_Color=="i"|latter_st_2MoAl_2MoMiAl$Flower_Color=="s")) latter_st_2MoAl_2MoMiAl$Ex_Type<-latter_st_2MoAl_2MoMiAl$Ex_Type[drop=T] a<-glmmML(Al1_O0~Ex_Type,cluster=Bee_ID_No,data=latter_st_2MoAl_2MoMiAl,start.sigma=1,control=list(maxit=500)) summary(a,digit=5) #Ex1_MoAl vs Ex2_MoAl latter_st<-subset(data2,data2$Stage=="5"|data2$Stage=="6"|data2$Stage=="7") latter_st_2MoAl_1MoAl<-subset(latter_st,latter_st$Ex_Type=="BY") latter_st_2MoAl_1MoAl<-subset(latter_st_2MoAl_1MoAl,!(latter_st_2MoAl_1MoAl$Flower_Color=="i"|latter_st_2MoAl_1MoAl$Flower_Color=="s")) latter_st_2MoAl_1MoAl$Ex_Type<-latter_st_2MoAl_1MoAl$Ex_Type[drop=T] a<-glmmML(Al1_O0~Ex_Set,cluster=Bee_ID_No,data=latter_st_2MoAl_1MoAl,start.sigma=1,control=list(maxit=500)) summary(a,digit=5) #Ex1_MoMiAl vs Ex2_MoAl latter_st<-subset(data2,data2$Stage=="5"|data2$Stage=="6"|data2$Stage=="7") latter_st_2MoAl_1MoMiAl<-subset(latter_st,latter_st$Ex_Type=="BY"|latter_st$Ex_Type=="BSY") latter_st_2MoAl_1MoMiAl<-subset(latter_st_2MoAl_1MoMiAl,!(latter_st_2MoAl_1MoMiAl$Ex_Type=="BY"&latter_st_2MoAl_1MoMiAl$Ex_Set=="Ex1")) latter_st_2MoAl_1MoMiAl<-subset(latter_st_2MoAl_1MoMiAl,!(latter_st_2MoAl_1MoMiAl$Flower_Color=="i"|latter_st_2MoAl_1MoMiAl$Flower_Color=="s")) latter_st_2MoAl_1MoMiAl$Ex_Type<-latter_st_2MoAl_1MoMiAl$Ex_Type[drop=T] a<-glmmML(Al1_O0~Ex_Type,cluster=Bee_ID_No,data=latter_st_2MoAl_1MoMiAl,start.sigma=1,control=list(maxit=500)) summary(a,digit=5) #Ex1_MoAl vs Ex2_MoMiAl latter_st<-subset(data2,data2$Stage=="5"|data2$Stage=="6"|data2$Stage=="7") latter_st_2MoMiAl_1MoAl<-subset(latter_st,latter_st$Ex_Type=="BIY"|latter_st$Ex_Type=="BY") latter_st_2MoMiAl_1MoAl<-subset(latter_st_2MoMiAl_1MoAl,!(latter_st_2MoMiAl_1MoAl$Ex_Type=="BY"&latter_st_2MoMiAl_1MoAl$Ex_Set=="Ex2")) latter_st_2MoMiAl_1MoAl<-subset(latter_st_2MoMiAl_1MoAl,!(latter_st_2MoMiAl_1MoAl$Flower_Color=="i"|latter_st_2MoMiAl_1MoAl$Flower_Color=="s")) latter_st_2MoMiAl_1MoAl$Ex_Type<-latter_st_2MoMiAl_1MoAl$Ex_Type[drop=T] a<-glmmML(Al1_O0~Ex_Type,cluster=Bee_ID_No,data=latter_st_2MoMiAl_1MoAl,start.sigma=1,control=list(maxit=500)) summary(a,digit=5) #Ex1_MoMiAl vs Ex2_MoMiAl latter_st<-subset(data2,data2$Stage=="5"|data2$Stage=="6"|data2$Stage=="7") latter_st_2MoMiAl_1MoMiAl<-subset(latter_st,latter_st$Ex_Type=="BIY"|latter_st$Ex_Type=="BSY") latter_st_2MoMiAl_1MoMiAl<-subset(latter_st_2MoMiAl_1MoMiAl,!(latter_st_2MoMiAl_1MoMiAl$Flower_Color=="i"|latter_st_2MoMiAl_1MoMiAl$Flower_Color=="s")) latter_st_2MoMiAl_1MoMiAl$Ex_Type<-latter_st_2MoMiAl_1MoMiAl$Ex_Type[drop=T] a<-glmmML(Al1_O0~Ex_Type,cluster=Bee_ID_No,data=latter_st_2MoMiAl_1MoMiAl,start.sigma=1,control=list(maxit=500)) summary(a,digit=5) #Ex1_MoMiAl vs Ex1_MoAl latter_st<-subset(data2,data2$Stage=="5"|data2$Stage=="6"|data2$Stage=="7") latter_st_1MoAl_1MoMiAl<-subset(latter_st,latter_st$Ex_Type=="BSY"|latter_st$Ex_Type=="BY") latter_st_1MoAl_1MoMiAl<-subset(latter_st_1MoAl_1MoMiAl,!(latter_st_1MoAl_1MoMiAl$Ex_Type=="BY"&latter_st_1MoAl_1MoMiAl$Ex_Set=="Ex2")) latter_st_1MoAl_1MoMiAl<-subset(latter_st_1MoAl_1MoMiAl,!(latter_st_1MoAl_1MoMiAl$Flower_Color=="i"|latter_st_1MoAl_1MoMiAl$Flower_Color=="s")) latter_st_1MoAl_1MoMiAl$Ex_Type<-latter_st_1MoAl_1MoMiAl$Ex_Type[drop=T] a<-glmmML(Al1_O0~Ex_Type,cluster=Bee_ID_No,data=latter_st_1MoAl_1MoMiAl,start.sigma=1,control=list(maxit=500)) summary(a,digit=5) ##Figure4c ##tests for Figure4 ##plots for Figure4 ##Plot for visits to mimics(Figure4a) ag_st<-aggregate(lastst$Mi1_O0,list(st=lastst$Stage,Ex_Type=lastst$Ex_Type,ID=lastst$Bee_ID_No),mean) for(i in 1:nrow(ag_st)){ if(ag_st$Ex_Type[i]=="BS"){ ag_st$type2[i]<-1 }else{ if(ag_st$Ex_Type[i]=="BSY"){ ag_st$type2[i]<-2 }else{ if(ag_st$Ex_Type[i]=="BI"){ ag_st$type2[i]<-3 }else{ if(ag_st$Ex_Type[i]=="BIY"){ ag_st$type2[i]<-4 }else{ ag_st$type2[i]<-5 }}}}} boxplot(x~type2,data=ag_st) ##Plot for visits to mimics(Figure4a) #Mimic relative to Blue shades (Figure4b) latter_st<-subset(data2,data2$Stage=="5"|data2$Stage=="6"|data2$Stage=="7") Mimic_Plot_latter_st<-subset(latter_st,!(latter_st$Ex_Type=="BY"|latter_st$Flower_Color=="y")) ag_st<-aggregate(Mimic_Plot_latter_st$Mi1_O0,list(st=Mimic_Plot_latter_st$Stage,Ex_Type=Mimic_Plot_latter_st$Ex_Type,ID=Mimic_Plot_latter_st$Bee_ID_No),mean) for(i in 1:nrow(ag_st)){ if(ag_st$Ex_Type[i]=="BS"){ ag_st$type2[i]<-1 }else{ if(ag_st$Ex_Type[i]=="BSY"){ ag_st$type2[i]<-2 }else{ if(ag_st$Ex_Type[i]=="BI"){ ag_st$type2[i]<-3 }else{ if(ag_st$Ex_Type[i]=="BIY"){ ag_st$type2[i]<-4 }else{ ag_st$type2[i]<-5 }}}}} boxplot(x~type2,data=ag_st) #Mimic relative to Blue shades (Figure4b) #Alternative relative to reward (Figure4c) latter_st<-subset(data2,data2$Stage=="5"|data2$Stage=="6"|data2$Stage=="7") Mimic_Plot_latter_st<-subset(latter_st,!(latter_st$Flower_Color=="i"|latter_st$Flower_Color=="s"|latter_st$Ex_Type=="BI"|latter_st$Ex_Type=="BS")) ag_st<-aggregate(Mimic_Plot_latter_st$Al1_O0,list(st=Mimic_Plot_latter_st$Stage,set=Mimic_Plot_latter_st$Ex_Set,Ex_Type=Mimic_Plot_latter_st$Ex_Type,ID=Mimic_Plot_latter_st$Bee_ID_No),mean) for(i in 1:nrow(ag_st)){ if(ag_st$Ex_Type[i]=="BY"&ag_st$set[i]=="Ex2"){ ag_st$type2[i]<-3 }else{ if(ag_st$Ex_Type[i]=="BIY"){ ag_st$type2[i]<-4 }else{ if(ag_st$Ex_Type[i]=="BY"&ag_st$set[i]=="Ex1"){ ag_st$type2[i]<-1 }else{ if(ag_st$Ex_Type[i]=="BSY"){ ag_st$type2[i]<-2 }else{ ag_st$type2[i]<-5 }}}}} boxplot(x~type2,data=ag_st) #Alternative relative to reward (Figure4c) ##plots for Figure4 ##plots for Figure5 reject<-aggregate(data$Look1_Visit0,list(st=data$Stage,ID=data$Bee_ID_No,Set=data$Ex_Set,Type=data$Ex_Type,Color=data$Flower_Color),mean) reject$stage2<-rep(c(25,75,150,300,600,1000,1400),126) Ex1_BS<-subset(reject,reject$Set=="Ex1"&reject$Type=="BS") Ex1_BSY<-subset(reject,reject$Set=="Ex1"&reject$Type=="BSY") Ex1_BY<-subset(reject,reject$Set=="Ex1"&reject$Type=="BY") Ex2_BI<-subset(reject,reject$Set=="Ex2"&reject$Type=="BI") Ex2_BIY<-subset(reject,reject$Set=="Ex2"&reject$Type=="BIY") Ex2_BY<-subset(reject,reject$Set=="Ex2"&reject$Type=="BY") Ex1_BS_b<-subset(Ex1_BS,Ex1_BS$Color=="b") Ex1_BS_s<-subset(Ex1_BS,Ex1_BS$Color=="s") colnames(Ex1_BS_b)<-c("st","ID","Set","Type","Color","B","stage2") Ex1_BS_b$S<-Ex1_BS_s$x Ex1_BSY_b<-subset(Ex1_BSY,Ex1_BSY$Color=="b") Ex1_BSY_s<-subset(Ex1_BSY,Ex1_BSY$Color=="s") Ex1_BSY_y<-subset(Ex1_BSY,Ex1_BSY$Color=="y") colnames(Ex1_BSY_b)<-c("st","ID","Set","Type","Color","B","stage2") Ex1_BSY_b$S<-Ex1_BSY_s$x Ex1_BSY_b$Y<-Ex1_BSY_y$x Ex1_BY_b<-subset(Ex1_BY,Ex1_BY$Color=="b") Ex1_BY_y<-subset(Ex1_BY,Ex1_BY$Color=="y") colnames(Ex1_BY_b)<-c("st","ID","Set","Type","Color","B","stage2") Ex1_BY_b$Y<-Ex1_BY_y$x Ex2_BI_b<-subset(Ex2_BI,Ex2_BI$Color=="b") Ex2_BI_i<-subset(Ex2_BI,Ex2_BI$Color=="i") colnames(Ex2_BI_b)<-c("st","ID","Set","Type","Color","B","stage2") Ex2_BI_b$I<-Ex2_BI_i$x Ex2_BIY_b<-subset(Ex2_BIY,Ex2_BIY$Color=="b") Ex2_BIY_i<-subset(Ex2_BIY,Ex2_BIY$Color=="i") Ex2_BIY_y<-subset(Ex2_BIY,Ex2_BIY$Color=="y") colnames(Ex2_BIY_b)<-c("st","ID","Set","Type","Color","B","stage2") Ex2_BIY_b$I<-Ex2_BIY_i$x Ex2_BIY_b$Y<-Ex2_BIY_y$x Ex2_BY_b<-subset(Ex2_BY,Ex2_BY$Color=="b") Ex2_BY_y<-subset(Ex2_BY,Ex2_BY$Color=="y") colnames(Ex2_BY_b)<-c("st","ID","Set","Type","Color","B","stage2") Ex2_BY_b$Y<-Ex2_BY_y$x #Ex1_MoMi id<-unique(Ex1_BS_b$ID) id<-id[drop=TRUE] Ex1_BS_b$ID<-Ex1_BS_b$ID[drop=TRUE] plot(Ex1_BS_b$stage2,Ex1_BS_b$B,xlim=c(0,1600),ylim=c(0,1),type="n") for(i in id){ dfi<-subset(Ex1_BS_b,Ex1_BS_b$ID==i) lines(dfi$stage2+10,dfi$S,lty=3,lwd=0.01,col=rgb(0,0,1,60,maxColorValue=255)) lines(dfi$stage2,dfi$B,lwd=0.01,col=rgb(0,0,1,60,maxColorValue=255)) points(dfi$stage2+10,dfi$S,pch=16,cex=1.3,col=rgb(0,0,1,maxColorValue=255)) points(dfi$stage2+10,dfi$S,pch=16,cex=0.8,col=rgb(255,255,255,maxColorValue=255)) points(dfi$stage2,dfi$B,pch=16,cex=1.3,col=rgb(0,0,1,maxColorValue=255)) } #Ex1_MoMiAl id<-unique(Ex1_BSY_b$ID) id<-id[drop=TRUE] Ex1_BSY_b$ID<-Ex1_BSY_b$ID[drop=TRUE] plot(Ex1_BSY_b$stage2,Ex1_BSY_b$B,xlim=c(0,1600),ylim=c(0,1),type="n") for(i in id){ dfi<-subset(Ex1_BSY_b,Ex1_BSY_b$ID==i) lines(dfi$stage2+10,dfi$S,lty=3,lwd=0.01,col=rgb(0,0,1,60,maxColorValue=255)) lines(dfi$stage2,dfi$B,lwd=0.01,col=rgb(0,0,1,60,maxColorValue=255)) lines(dfi$stage2-10,dfi$Y,lwd=0.01,col=rgb(206,206,206,160,maxColorValue=255)) points(dfi$stage2-10,dfi$Y,pch=16,cex=1.3,col=rgb(206,206,206,maxColorValue=255)) points(dfi$stage2+10,dfi$S,pch=16,cex=1.3,col=rgb(0,0,1,maxColorValue=255)) points(dfi$stage2+10,dfi$S,pch=16,cex=0.8,col=rgb(255,255,255,maxColorValue=255)) points(dfi$stage2,dfi$B,pch=16,cex=1.3,col=rgb(0,0,1,maxColorValue=255)) } #Ex1_MoAl id<-unique(Ex1_BY_b$ID) id<-id[drop=TRUE] Ex1_BY_b$ID<-Ex1_BY_b$ID[drop=TRUE] plot(Ex1_BY_b$stage2,Ex1_BY_b$B,xlim=c(0,1600),ylim=c(0,1),type="n") for(i in id){ dfi<-subset(Ex1_BY_b,Ex1_BY_b$ID==i) lines(dfi$stage2,dfi$B,lwd=0.01,col=rgb(0,0,1,60,maxColorValue=255)) lines(dfi$stage2-10,dfi$Y,lwd=0.01,col=rgb(206,206,206,160,maxColorValue=255)) points(dfi$stage2-10,dfi$Y,pch=16,cex=1.3,col=rgb(206,206,206,maxColorValue=255)) points(dfi$stage2,dfi$B,pch=16,cex=1.3,col=rgb(0,0,1,maxColorValue=255)) } #Ex2_MoMi id<-unique(Ex2_BI_b$ID) id<-id[drop=TRUE] Ex2_BI_b$ID<-Ex2_BI_b$ID[drop=TRUE] plot(Ex2_BI_b$stage2,Ex2_BI_b$B,xlim=c(0,1600),ylim=c(0,1),type="n") for(i in id){ dfi<-subset(Ex2_BI_b,Ex2_BI_b$ID==i) lines(dfi$stage2+10,dfi$I,lty=3,lwd=0.01,col=rgb(0,0,1,60,maxColorValue=255)) lines(dfi$stage2,dfi$B,lwd=0.01,col=rgb(0,0,1,60,maxColorValue=255)) points(dfi$stage2+10,dfi$I,pch=16,cex=1.3,col=rgb(0,0,1,maxColorValue=255)) points(dfi$stage2+10,dfi$I,pch=16,cex=0.8,col=rgb(255,255,255,maxColorValue=255)) points(dfi$stage2,dfi$B,pch=16,cex=1.3,col=rgb(0,0,1,maxColorValue=255)) } #Ex2_MoMiAl id<-unique(Ex2_BIY_b$ID) id<-id[drop=TRUE] Ex2_BIY_b$ID<-Ex2_BIY_b$ID[drop=TRUE] plot(Ex2_BIY_b$stage2,Ex2_BIY_b$B,xlim=c(0,1600),ylim=c(0,1),type="n") for(i in id){ dfi<-subset(Ex2_BIY_b,Ex2_BIY_b$ID==i) lines(dfi$stage2+10,dfi$I,lty=3,lwd=0.01,col=rgb(0,0,1,60,maxColorValue=255)) lines(dfi$stage2,dfi$B,lwd=0.01,col=rgb(0,0,1,60,maxColorValue=255)) lines(dfi$stage2-10,dfi$Y,lwd=0.01,col=rgb(206,206,206,160,maxColorValue=255)) points(dfi$stage2-10,dfi$Y,pch=16,cex=1.3,col=rgb(206,206,206,maxColorValue=255)) points(dfi$stage2+10,dfi$I,pch=16,cex=1.3,col=rgb(0,0,1,maxColorValue=255)) points(dfi$stage2+10,dfi$I,pch=16,cex=0.8,col=rgb(255,255,255,maxColorValue=255)) points(dfi$stage2,dfi$B,pch=16,cex=1.3,col=rgb(0,0,1,maxColorValue=255)) } #Ex2_MoAl id<-unique(Ex2_BY_b$ID) id<-id[drop=TRUE] Ex2_BY_b$ID<-Ex2_BY_b$ID[drop=TRUE] plot(Ex2_BY_b$stage2,Ex2_BY_b$B,xlim=c(0,1600),ylim=c(0,1),type="n") for(i in id){ dfi<-subset(Ex2_BY_b,Ex2_BY_b$ID==i) lines(dfi$stage2,dfi$B,lwd=0.01,col=rgb(0,0,1,60,maxColorValue=255)) lines(dfi$stage2-10,dfi$Y,lwd=0.01,col=rgb(206,206,206,160,maxColorValue=255)) points(dfi$stage2-10,dfi$Y,pch=16,cex=1.3,col=rgb(206,206,206,maxColorValue=255)) points(dfi$stage2,dfi$B,pch=16,cex=1.3,col=rgb(0,0,1,maxColorValue=255)) } ##plots for Figure5 ##tests for Figure6 latter_reject<-subset(data,data$Stage<=7&data$Stage>=5) #Ex2_MoMi vs Ex2_MoMiAl Mi_reject<-subset(latter_reject,latter_reject$Ex_Type=="BI"|latter_reject$Ex_Type=="BIY") Mi_reject<-subset(Mi_reject,Mi_reject$Flower_Color=="i") Mi_reject$Ex_Type<-Mi_reject$Ex_Type[drop=T] a<-glmmML(Look1_Visit0~Ex_Type,cluster=Bee_ID_No,data=Mi_reject,control=list(maxit=500)) summary(a,digit=5) #Ex1_MoMi vs Ex2_Momi Mi_reject<-subset(latter_reject,latter_reject$Ex_Type=="BI"|latter_reject$Ex_Type=="BS") Mi_reject<-subset(Mi_reject,Mi_reject$Flower_Color=="s"|Mi_reject$Flower_Color=="i") Mi_reject$Ex_Type<-Mi_reject$Ex_Type[drop=T] a<-glmmML(Look1_Visit0~Ex_Type,cluster=Bee_ID_No,data=Mi_reject,control=list(maxit=500)) summary(a,digit=5) #Ex1_MoMiAl vs Ex2_Momi Mi_reject<-subset(latter_reject,latter_reject$Ex_Type=="BI"|latter_reject$Ex_Type=="BSY") Mi_reject<-subset(Mi_reject,Mi_reject$Flower_Color=="s"|Mi_reject$Flower_Color=="i") Mi_reject$Ex_Type<-Mi_reject$Ex_Type[drop=T] a<-glmmML(Look1_Visit0~Ex_Type,cluster=Bee_ID_No,data=Mi_reject,start.sigma=1,control=list(maxit=500)) summary(a,digit=5) #Ex1_MoMi vs Ex2_MoMiAl Mi_reject<-subset(latter_reject,latter_reject$Ex_Type=="BIY"|latter_reject$Ex_Type=="BS") Mi_reject<-subset(Mi_reject,Mi_reject$Flower_Color=="s"|Mi_reject$Flower_Color=="i") Mi_reject$Ex_Type<-Mi_reject$Ex_Type[drop=T] a<-glmmML(Look1_Visit0~Ex_Type,cluster=Bee_ID_No,data=Mi_reject,start.sigma=1,control=list(maxit=500)) summary(a,digit=5) #Ex1_MoMiAl vs Ex2_MoMiAl Mi_reject<-subset(latter_reject,latter_reject$Ex_Type=="BIY"|latter_reject$Ex_Type=="BSY") Mi_reject<-subset(Mi_reject,Mi_reject$Flower_Color=="s"|Mi_reject$Flower_Color=="i") Mi_reject$Ex_Type<-Mi_reject$Ex_Type[drop=T] a<-glmmML(Look1_Visit0~Ex_Type,cluster=Bee_ID_No,data=Mi_reject,start.sigma=1,control=list(maxit=500)) summary(a,digit=5) #Ex1_MoMi vs Ex1_MoMiAl Mi_reject<-subset(latter_reject,latter_reject$Ex_Type=="BS"|latter_reject$Ex_Type=="BSY") Mi_reject<-subset(Mi_reject,Mi_reject$Flower_Color=="s") Mi_reject$Ex_Type<-Mi_reject$Ex_Type[drop=T] a<-glmmML(Look1_Visit0~Ex_Type,cluster=Bee_ID_No,data=Mi_reject,start.sigma=1,control=list(maxit=500)) summary(a,digit=5) ##tests for Figure6 ##plots for Figure6 summary(data) latter_reject<-subset(data,data$Stage<=7&data$Stage>=5) Mi_reject<-subset(latter_reject,latter_reject$Flower_Color=="s"|latter_reject$Flower_Color=="i") Mi_reject$Ex_Type<-Mi_reject$Ex_Type[drop=T] Mi_reject_means_st57<-aggregate(Mi_reject$Look1_Visit0,list(ID=Mi_reject$Bee_ID_No,Ex_Type=Mi_reject$Ex_Type),mean) Mi_reject_means_st57$Ex_Type<-factor(Mi_reject_means_st57$Ex_Type,levels=c("BS","BSY","BI","BIY"),labels=c("BS","BSY","BI","BIY")) boxplot(split(Mi_reject_means_st57$x,list(Mi_reject_means_st57$Ex_Type))) ##plots for Figure6 ##Analysis for time for 1600 visits summary(time) min(time$Time) max(time$Time) mean(time$Time) sd(time$Time) time$Set_Type<-as.factor(paste(time$Set,time$Type)) kruskal.test(Time~Set_Type,data=time) ##Analysis for time for 1600 visits ##Analysis for foraging time time2<-read.csv("time2.csv",header=T) summary(time2) a<-aov(time~Type+Set,data=time2) summary(a) ##Analysis for foraging time