Lampe Speiser R file

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require(ggplot2)

  1. library(directlabels)

library(RColorBrewer)

setwd("/Users/oakley/Dropbox/Road Work/euphPredation/") source(file="myFluc.R")

  1. Read Data

allTrials<-read.csv("EuphilomedesPredationTrials.csv") maleTrials<-subset(allTrials,allTrials$Sex=="male") chupaTable<-read.table("Chupa_Pred_Summary.csv",header=TRUE, sep = ",")


          • FLUCTUATIONS PLOT MALES

source(file="myFluc.R") #customize style a little source(file="myFluc2.R") #divides by 2 for morini sample size


  1. chupacabra ggfluctuations plot

chupamatrix<-matrix(c(100, 112, 113, 20,8,7), byrow = FALSE, 3, 2) colnames(chupamatrix)<-c("Survivors","Lost") rownames(chupamatrix)<-c("Blindfolded","Control","Unaltered") chupaTable <- as.table(chupamatrix) p1<-myFluc(chupaTable)

  1. morini ggfluctuations plot

mormatrix<-matrix(c(8, 14, 45, 52, 46, 15), byrow = FALSE, 3, 2)

  1. scale morini divide by 2

colnames(mormatrix)<-c("Survivors","Lost") rownames(mormatrix)<-c("Blindfolded","Control","Unaltered") morTable <- as.table(mormatrix, ceiling=120) p2<-myFluc2(morTable)

  1. print both species next to each other

pushViewport(viewport(x = 0.25,y = 0.6, width = 0.5, height = 0.8, 

   angle = 0, name = "topleftvp"))

print(p1, vp = "topleftvp") pushViewport(viewport(x = 0.7,y = 0.6, width = 0.5, height = 0.8, 

   angle = 0, name = "botleftvp"))

print(p2, vp = "botleftvp")

  2. FLUCTUATIONS PLOT MALES M v F = FIGURE

source(file="myFluc.R") #customize style a little source(file="myFluc2.R") #divides by 2 for morini sample size

  1. Male versus Female morini ggfluctuations plot

MFmatrix<-matrix(c(58, 97, 157, 53), byrow = FALSE, 2, 2) colnames(MFmatrix)<-c("Survivors","Lost") rownames(MFmatrix)<-c("Male","Female") MFTable <- as.table(MFmatrix) MF <- myFluc(MFTable) MF


  2. SIMPLE BAR CHARTS
  3. Plot chupacabra results

chupaTrials<-subset(allTrials,allTrials$Species=="chupacabra") chupasums<-aggregate(chupaTrials$finish, by=list(Category=chupaTrials$Treatment), FUN=sum) chupatotal<-sum(chupaTrials$start/3)

c <- ggplot(chupasums, aes(x = reorder(Category, -x, mean), y = x)) + geom_bar(stat = 'identity') + xlab(expression(plain("Experimental Treatment"))) + ylab(expression(italic("E. chupacabra"))) + theme_bw(base_family="sans") chupabar <- c + geom_bar()

  1. plot morini results

moriniAllTrials<-subset(allTrials,allTrials$Species=="morini") moriniTrials<-subset(moriniAllTrials,moriniAllTrials$artifact=="no") moriniMaleTrials<-subset(moriniTrials, moriniTrials$Sex=="male") moriniFemaleTrials<-subset(moriniTrials, moriniTrials$Sex=="female") morinisums <- aggregate(moriniMaleTrials$finish, by=list(Category=moriniMaleTrials$Treatment), FUN=sum)

m <- ggplot(morinisums, aes(x = reorder(Category, -x, mean), y = x)) + geom_bar(stat = 'identity') + xlab(expression(plain("Experimental Treatment"))) + ylab(expression(italic("E. morini"))) + theme_bw(base_family="sans") morinibar <- m + geom_bar()

  1. print both species next to each other

pushViewport(viewport(x = 0.25,y = 0.6, width = 0.5, height = 0.8, 

   angle = 0, name = "topleftvp"))

print(chupabar, vp = "topleftvp") pushViewport(viewport(x = 0.7,y = 0.6, width = 0.5, height = 0.8, 

   angle = 0, name = "botleftvp"))

print(morinibar, vp = "botleftvp")

  2. Box Plot of porportions in each trial

par(mfrow=c(1,2)) boxplot(ratio~Treatment, data=chupaTrials,xlab=expression(plain("Experimental Treatment")),ylab=c("Proportion", "E. chupacabra Recovered"))

boxplot(ratio~Treatment, data=moriniMaleTrials,xlab=expression(plain("Experimental Treatment")),ylab=c("Proportion", "E. morini Recovered"))


  2. Bar charts with bar as stacks of trials -- Color

moriniStacks <- qplot(Treatment, data=moriniMaleTrials, geom="bar", weight=finish, fill=factor(Trial), ylab="E. morini recovered", xlab="", ymax=120) + theme_bw() + scale_fill_brewer(type="div", na.colour = "grey80") + labs(fill = "Trial") chupaStacks <- qplot(Treatment, data=chupaTrials, geom="bar", weight=finish, fill=factor(Trial), ylab="E. chupacabra recovered", xlab="", ymax=120) + theme_bw() + scale_fill_hue(h=c(20,275), l=50, c=70) + labs(fill = "Trial")

  1. print both species next to each other

pushViewport(viewport(x = 0.25,y = 0.6, width = 0.5, height = 0.8, 

   angle = 0, name = "topleftvp"))

print(chupaStacks, vp = "topleftvp") pushViewport(viewport(x = 0.7,y = 0.6, width = 0.5, height = 0.8, 

   angle = 0, name = "botleftvp"))

print(moriniStacks, vp = "botleftvp")

  2. Bar charts Male Predation with bar as stacks of trials -- BW

moriniStacks <- qplot(Treatment, data=moriniMaleTrials, geom="bar", weight=finish, fill=factor(Trial), ylab="E. morini (Male) Recovered", xlab="", ymax=120) + theme_bw() + scale_fill_grey() + labs(fill = "") +opts(legend.position="none") chupaStacks <- qplot(Treatment, data=chupaTrials, geom="bar", weight=finish, fill=factor(Trial), ylab="E. chupacabra (Male) Recovered", xlab="", ymax=120) + theme_bw() + scale_fill_grey() + labs(fill = "") +opts(legend.position="none")

  1. print both species next to each other

pushViewport(viewport(x = 0.25,y = 0.6, width = 0.5, height = 0.8, 

   angle = 0, name = "topleftvp"))

print(chupaStacks, vp = "topleftvp") pushViewport(viewport(x = 0.75,y = 0.6, width = 0.5, height = 0.8, 

   angle = 0, name = "botleftvp"))

print(moriniStacks, vp = "botleftvp")

  2. Bar charts Female Predation with bar as stacks of trials -- BW

moriniFStacks <- qplot(Treatment, data=moriniFemaleTrials, geom="bar", weight=finish, fill=factor(Trial), ylab="E. morini (Female) Recovered", xlab="", ymax=120) + theme_bw() + scale_fill_grey() + labs(fill = "") +opts(legend.position="none")

moriniFStacks

  2. Bar charts Female Predation with bar as stacks of trials -- Color

moriniFStacks <- qplot(Treatment, data=moriniFemaleTrials, geom="bar", weight=finish, fill=factor(Trial), ylab="E. morini (Female) Recovered", xlab="", ymax=120) + theme_bw() + scale_fill_brewer(type="qual", palette="Accent") + labs(fill = "") + opts(legend.position="none") moriniFStacks


  1. Figure5
  2. print both species next to each other

pushViewport(viewport(x = 0.2,y = 0.6, width = 0.3, height = 0.8, 

   angle = 0, name = "leftvp"))

print(chupaStacks, vp = "leftvp") pushViewport(viewport(x = 0.5,y = 0.6, width = 0.3, height = 0.8, 

   angle = 0, name = "midvp"))

print(moriniStacks, vp = "midvp") pushViewport(viewport(x = 0.8,y = 0.6, width = 0.3, height = 0.8, 

   angle = 0, name = "rightvp"))

print(moriniFStacks, vp = "rightvp")

  1. Figure for talk


  1. TESTING
  2. chupacabra ggfluctuations plot

chupamatrix<-matrix(c(100, 112, 113, 8,14,45,20,8,7,52,46,15), byrow = FALSE, 3, 4) colnames(chupamatrix)<-c("C Survivors","C Lost","M Survivors","M Lost") rownames(chupamatrix)<-c("Blindfolded","Control","Unaltered") chupaTable <- as.table(chupamatrix) myFluc(chupaTable)


ggplot(diamonds, aes(x=cut, y=price, group=cut))+ geom_boxplot(aes(fill=cut))+scale_fill_brewer(palette="OrRd")


  1. morini ggfluctuations plot

mormatrix<-matrix(c(8, 14, 45, 52, 46, 15), byrow = FALSE, 3, 2) colnames(mormatrix)<-c("Survivors","Lost") rownames(mormatrix)<-c("Blindfolded","Control","Unaltered") morTable <- as.table(mormatrix, ceiling=max(10)) p2<-myFluc(morTable)

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