T&E.figures.txt

File Name: T&E.figures.txt

Author: Abt Associates Inc.

Created: 5/27/2010

Updated: 12/15/2010

Purpose: R Script to create ECDF plots found in the T&E Chapter.

library(countreg)

facs=read.csv("facilities-no.california.csv")

spp=read.csv("species.csv")

## ecdf plot of all facilities by species

png(file="facility.all.ecdf.png",width=768,height=768,pointsize=24)

par(mfrow=c(1,1))

plot(ecdf(facs$all),verticals=TRUE,xlab="Species per Facility",ylab="Cumulative

Proportion of

Facilities",xlim=c(-.05,28),main="",family="serif",cex.lab=1.2,cex=1.1,cex.axis=1

.1)

dev.off()

## ecdf plot of all species by facility

png(file="species.all.ecdf.png",width=768,height=768,pointsize=24)

par(mfrow=c(1,1))

plot(ecdf(spp$facilities),verticals=TRUE,xlab="Facilities per Impacted

Species",ylab="Cumulative Proportion of

Species",xlim=c(-.05,160),main="",family="serif",cex.lab=1.2,cex=1.1,cex.axis=1.1

)

dev.off()

## ecdf plot of all species subsets by facility

png(file="species.ecdf.png",width=1024,height=768,pointsize=24)

par(mfrow=c(2,3))

par(oma=c(5,5,5,5)); par(mar=c(0.25,0.25,0.25,0.25))

plot(ecdf(subset(spp,spp$group=="o")$facilities),verticals=TRUE,xlab="Facilities

per Impacted Species",ylab="Cumulative Proportion of

Species",xlim=c(-.05,8),main="",family="serif",cex.lab=1.2,cex=1.1,cex.axis=1.1,y

lim=c(0,1.1),xaxt="n",yaxt="n")

mtext("Freshwater Fish (21)",line=-1.3,family="serif")

axis(3,family="serif");axis(2,family="serif")

mtext("Proportion of Species",side=2,line=2.5,cex=1.2,family="serif",at=-.08)

plot(ecdf(subset(spp,spp$group=="mar")$facilities),verticals=TRUE,xlab="Facilitie

s per Impacted Species",ylab="Cumulative Proportion of

Species",xlim=c(-.05,12),main="",family="serif",cex.lab=1.2,cex=1.1,cex.axis=1.1,

xaxt="n",yaxt="n",ylim=c(0,1.1))

mtext("Marine Fish (3)",line=-1.3,family="serif")

axis(3,family="serif")

plot(1, type="n", axes=F, xlab="", ylab="")

plot(ecdf(subset(spp,spp$group=="a")$facilities),verticals=TRUE,xlab="Facilities

per Impacted Species",ylab="Cumulative Proportion of

Species",xlim=c(-.05,65),main="",family="serif",cex.lab=1.2,cex=1.1,cex.axis=1.1,

ylim=c(0,1.1))

mtext("Anadromous Fish (13)",line=-1.3,family="serif")

plot(ecdf(subset(spp,spp$group=="m")$facilities),verticals=TRUE,xlab="Facilities

per Impacted Species",ylab="Cumulative Proportion of

Species",xlim=c(-.05,85),main="",family="serif",cex.lab=1.2,cex=1.1,cex.axis=1.1,

ylim=c(0,1.1),yaxt="n")

mtext("Freshwater Mussels (43)",line=-1.3,family="serif")

mtext("Facilities per Species",side=1,line=2.5,cex=1.2,family="serif")

plot(ecdf(subset(spp,spp$group=="t")$facilities),verticals=TRUE,xlab="Facilities

per Impacted Species",ylab="Cumulative Proportion of

Species",xlim=c(-.05,160),main="",family="serif",cex.lab=1.2,cex=1.1,cex.axis=1.1

,ylim=c(0,1.1),yaxt="n")

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T&E.figures.txt

mtext("Sea Turtles (6)",line=-1.3,family="serif")

dev.off()

## ecdf plots of all species within regions

png(file="regions.ecdf.png",width=1024,height=1024,pointsize=24)

regs=levels(facs$regs)

regs[4]="Inland*"

regs[9]="California"

facs$regs[which(facs$regs=="Hawaii")]="West Coast"

changes=read.csv("GL.changes.csv")

changes[,2]=as.character(changes[,2])

for(i in 1:dim(changes)[1]){

facs$regs[which(facs$surveyid==as.character(changes[i,1]))]=as.character(changes[

i,2])

}

par(mfrow=c(3,3))

par(cex.axis=1.3)

par(oma=c(5,5,5,5)); par(mar=c(0,0,0.25,0.25))

reg.count=c(67,30,0,669,54,26,17,0,8)

for(i in c(9,6,3,5,7,3,2,1,4)){

if(i!=4&i!=3)

plot(ecdf(subset(facs,facs$regs==levels(facs$regs)[i])$all),verticals=TRUE,xlab="

Number of Species per Facility",ylab="Cumulative Proportion of

Facilities",xlim=c(-.05,8),main="",family="serif",cex.lab=1.2,cex=1.1,cex.axis=1.

1,yaxt="n",xaxt="n",ylim=c(0,1.1))

if(i==3)plot(0,0,yaxt="n",xaxt="n",ylim=c(-2,-1),xlim=c(-4,-2),bty="n")

if(i==4)

plot(ecdf(subset(facs,facs$regs==levels(facs$regs)[i])$all),verticals=TRUE,xlab="

Number of Species per Facility",ylab="Cumulative Proportion of

Facilities",xlim=c(-.05,28),main="",family="serif",cex.lab=1.2,cex=1.1,cex.axis=1

.1,yaxt="n",xaxt="n",ylim=c(0,1.1))

if(i!=3) mtext(paste(regs[i],"

(",reg.count[i],")",sep=""),line=-1.3,family="serif")

#if(i>6) axis(1,family="serif",cex=1.3)

if(i==4|i==2|i==1) axis(1,family="serif",cex=1.3)

if(i==2|i==9|i==5)

axis(2,at=c(0,0.2,0.4,0.6,0.8,1.0),labels=TRUE,family="serif",cex=1.3)

if(i==6|i==7|i==4)

axis(4,at=c(0,0.2,0.4,0.6,0.8,1.0),labels=TRUE,family="serif",cex=1.3)

if(i==5) mtext("Proportion of Facilities",side=2,line=2.5,cex=1.2,family="serif")

if(i==1) mtext("Species per Facility",side=1,line=2.5,cex=1.2,family="serif")

}

dev.off()

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