## T&E.figures.R File	Name:	T&E.figures.R
Author:	Abt	Associates	Inc. Created:	5/27/2010 Updated:	2/5/2013 Purpose:	R	script	to	create	the	ECDF	plots	found	in	the	T&E	chapter	of	the	BA

setwd("~/Desktop/I&E/T&E Overlaps/T&E Tables/")

#library(countreg)

facs=read.csv("facilities.csv") # CBI list of facilities with overlap facs$region[is.na(facs$region)] <

- "NA" facs[is.na(facs)] <

- 0 spp=read.csv("species.csv") # CBI list of species coun t by facility overlaps

## 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 Overlaps per Facility",ylab="Cumulative Proportion of Facilities",xlim=c(

- .05,35),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="Facility Overlaps per Impacted Species",ylab="Cumulative Proportion of Species",xlim=c(

- .05,2200), main="",family="serif",cex.lab=1.2,cex=1.1,cex.axis=1.1) dev.off()

## ecdf plot of all facilities by species png(file="facility.all.crithab.ecdf.png",width=768,height=768,pointsize=24) par(mfrow=c(1,1)) plot(ecdf(facs$crithab[facs$crithab>0]),verticals=TRUE,xlab="Critical Habitat Overlaps per Facility",ylab="Cumulative Proportion of Facilities",xlim=c(

- .05,10),ma in="",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.crithab.ecdf.png",width=768,height=768,pointsize=24) par(mfrow=c(1,1)) plot(ecdf(spp$crithab[spp$crithab>0]),verticals=TRUE,xlab ="Facility Overlaps per Species' Critical Habitat",ylab="Cumulative Proportion of Species",xlim=c(

- .05,60),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 =1152,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$group=="m")$facilities),verticals=TRUE,xlab="Facilitie s per Impacted Species",ylab="Cumulative Proportion of Species",xlim=c(

-

. 05,105),main="",family="serif",cex.lab=1.2,cex=1.1,cex.axis=1.1,ylim=c(0,1.1), xaxt ="n") mtext("Freshwater Mussels (53)",line=

- 1.5,family="serif") axis(3,family="serif"); mtext("Proportion of Species",side=2,line=2.5,cex=1.2,family="serif",at=

- .08)

plot( ecdf(subset(spp,spp$group=="a")$facilities),verticals=TRUE,xlab="Facilitie s per Impacted Species",ylab="Cumulative Proportion of Species",xlim=c(

- .05,105),main="",family="serif",cex.lab=1.2,cex=1.1,cex.axis=1.1,ylim=c(0,1.1), xaxt = "n", yaxt = "n") mtext( "Anadromous Fish (12)",line=

- 1.5,family="serif") axis(3,family="serif"); axis(4,family="serif")

plot.new()

plot(ecdf(subset(spp,spp$group=="s")$facilities),verticals=TRUE,xlab="Facilitie s per Impacted Species",ylab="Cumulative Proportion of Species",xlim =c(

- .05,105),main="",family="serif",cex.lab=1.2,cex=1.1,cex.axis=1.1,ylim=c(0,1.1)) mtext("Snails (7)",line=

- 1.5,family="serif")

plot(ecdf(subset(spp,spp$group=="t")$facilities),verticals=TRUE,xlab="Facilitie s per Impacted Species",ylab="Cumulative Proportion of Species",xlim=c(

- .05,105),main="",family="serif",cex.lab=1.2,cex=1.1,cex.axis=1.1,ylim=c(0,1.1), yaxt="n") mtext("Sea Turtl es (6)",line=

- 1.5,family="serif") mtext("Facilities per Species",side=1,line=2.5,cex=1.2,family="serif", at = 50)

plot(ecdf(subset(spp,spp$group=="o")$facilities),verticals=TRUE,xlab="Facilitie s 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,ylim=c(0,1.1),ya xt="n") mtext("Freshwater Fish* (21)",line=

- 1.5,family="serif") axis(4,family="serif")

dev.off()

## ecdf plots of all species within regions png(file="regions.ecdf.p ng",width=1024,height=1024,pointsize=24) facs$regs <

- as.factor(facs$regs) regs=levels(facs$regs) regs[regs=="Inland"]="Inland*" regs[regs=="West Coast"]="California"

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(21, 50, 22, 566, 46, 21, 12) table(facs$regs)for(i in c(1,6,5,7,3,2,4)){ if(i== 5 | i==3) plot(1, type="n", axes=F, xlab="", ylab="") if (i == 1 | i == 5 | i == 3) plot(ecdf(subset(facs,facs$regs==levels(facs$regs)[i])$all),verticals=TRUE,xlab ="Number of Species per Facility",ylab="Cumulative Proportion of Facilities",xlim=c(

- .05,9),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 == 6 | i == 7 | i == 2) 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(

- .05,9),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",yli m=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(

- .05,30),main="",family="serif",cex.lab=1.2,cex=1.1,cex.axis=1.1,yaxt="n",xaxt=" n", ylim=c(0,1.1)) mtext(paste(regs[i]," (",reg.count[i],")",sep=""),line=

- 1.3,family="serif") if(i == 4) axis(1,family="serif",cex=1.3) if(i == 3 | i == 2) axis(1,family="serif",cex=1.3) if(i==1 | i == 5 | i ==3) 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) 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==2) mtext("Species per Facility",side=1,line=2. 5,cex=1.2,family="serif") } dev.off()