Oakley: Created page with "require(ggplot2) #library(directlabels) library(RColorBrewer) setwd("/Users/oakley/Dropbox/Road Work/euphPredation/") source(file="myFluc.R") #Read Data allTrials<-read.csv("Eup…"

2011-11-19T07:29:25Z

Created page with "require(ggplot2) #library(directlabels) library(RColorBrewer) setwd("/Users/oakley/Dropbox/Road Work/euphPredation/") source(file="myFluc.R") #Read Data allTrials<-read.csv("Eup…"

New page

require(ggplot2)
#library(directlabels)
library(RColorBrewer)

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

#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)

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

#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")

#************************************
# 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

#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

#********************************************
#SIMPLE BAR CHARTS
#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()

#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()

#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")

#***************************************
#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"))

#**************************************
#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")

#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")

#**************************************
#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")

#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")

#**************************************
#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

#**************************************
#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

#Figure5
#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")

#Figure for talk

#TESTING
#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")

#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)

Lampe Speiser R file - Revision history

Oakley: Created page with "require(ggplot2) #library(directlabels) library(RColorBrewer) setwd("/Users/oakley/Dropbox/Road Work/euphPredation/") source(file="myFluc.R") #Read Data allTrials<-read.csv("Eup…"