library("maps")
library("mapdata")
library("mapproj")
library("Rgooglemaps")
library("Rgooglemap")
library("RgoogleMaps")
map("state", "washington", fill=T, col="palegreen3", boundary=F, fill=terrain.colors)
map("state", "washington", fill=T, boundary=F, fill=terrain.colors)
map("state", "washington", fill=terrain.colors, boundary=F)
map("state", "washington", fill="terrain.colors", boundary=F)
?map
map("state", "washington", fill=T,col=terrain.colors, boundary=F)
map("state", "washington", fill=T,col="terrain.colors", boundary=F)
library("GEOmaps")
library("GEOmap")
library("geomapdata")
library("RPMG")
library("akima")
library("splancs")
library("sp")
library("splancs")
?GEOmap
x<-c(-122.753796, -122.827754, -122.852089, -123.052859, -122.361794, -122.65349, -122.63235, -122.38929)
y<-c(48.976076, 47.597041, 47.436205, 48.706982, 47.599821, 47.542182, 47.138708, 47.276488)
BASICTOPOMAP(x,y,DOIMG=T, DOCONT=F)
?basictopomap
library("maps")
library("mapdata")
library("mapproj")
?map
map("county", regions=c("king", "whatcom"))
map("state", "washington", regions=c("whatcom", "king"))
map("county", "washington")
map("usa", "washington", fill=T, boundary=F, col="palegreen3")
map("state", "washington", fill=T, boundary=F, col="palegreen3")
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F)
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F, interior=F)
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F, interior=F, resolution=0)
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F, add=T, col="white")
text(-122.4, 48.9, expression(bold("Drayton Harbor")))
text(-122.4, 48.9, expression(bold("Drayton Harbor"), cex=0.5))
?text
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F, add=T, col="white")
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F)
text(-122.4, 48.9, expression(bold("Drayton Harbor")), cex=0.5)
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F)
text(-122.4, 48.9, expression(bold("Drayton Harbor")), cex=0.5, offset=1)
text(-122.4, 48.9, expression(bold("Drayton Harbor")), cex=0.5, offset=2)
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F)
text(-122.4, 48.9, expression(bold("Drayton Harbor")), cex=0.5, offset=2)
text(-123.2, 47.597041, expression(bold("Big Beef Creek")), cex=0.5)
text(-122.1, 47.599821, expression(bold("Elliot Bay")), cex=0.5)
text(-122.9, 47.542182, expression(bold("Sinclair Inlet")), cex=0.5)
text(-122.3, 47.138708, expression(bold("Solo Point")), cex=0.5)
text(-121.9, 47.276488, expression(bold("Hylebos Waterway")), cex=0.5)
points(x,y)
x1<-c(-122.753796, -122.827754, -122.361794, -122.65349, -122.63235, -122.38929)
y1<-c(48.976076, 47.597041, 47.599821, 47.542182, 47.138708, 47.276488)
points(x,y)
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F)
points(x1,y1)
points(x1,y1, cex=3)
?points
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F)
points(x1,y1, bg="black")
?points
points(x1,y1, pch=21:25, bg="black")
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F)
points(x1,y1, pch=21, bg="black")
text(-123.2, 47.597041, expression(bold("Big Beef Creek")), cex=0.5)#
text(-122.1, 47.599821, expression(bold("Elliot Bay")), cex=0.5)#
text(-122.9, 47.542182, expression(bold("Sinclair Inlet")), cex=0.5)#
text(-122.3, 47.138708, expression(bold("Solo Point")), cex=0.5)#
text(-121.9, 47.276488, expression(bold("Hylebos Waterway")), cex=0.5)
text(-122.4, 48.9, expression(bold("Drayton Harbor")), cex=0.5, offset=2)
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F)
points(x1,y1, pch=21, bg="firebrickred")
points(x1,y1, pch=21, bg="firebrickred3")
points(x1,y1, pch=21, bg="red")
text(-122.4, 48.9, expression(bold("Drayton Harbor")), cex=0.5, offset=2)#
text(-123.2, 47.597041, expression(bold("Big Beef Creek")), cex=0.5)#
text(-122.1, 47.599821, expression(bold("Elliot Bay")), cex=0.5)#
text(-122.9, 47.542182, expression(bold("Sinclair Inlet")), cex=0.5)#
text(-122.3, 47.138708, expression(bold("Solo Point")), cex=0.5)#
text(-121.9, 47.276488, expression(bold("Hylebos Waterway")), cex=0.5)
library("maps")
library("mapdata")
library("mapproj")
map("state", "washington", fill=T, col="palegreen3", boundary=F)
x<-c(-122.753796, -122.827754, -122.852089, -123.052859, -122.361794, -122.65349, -122.63235, -122.38929)
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F)
x1<-c(-122.753796, -122.827754, -122.361794, -122.65349, -122.63235, -122.38929)#
y1<-c(48.976076, 47.597041, 47.599821, 47.542182, 47.138708, 47.276488)
points(x1,y1, pch=21, bg="red")
text(-122.4, 48.9, expression(bold("Drayton Harbor")), cex=0.5, offset=2)#
text(-123.2, 47.597041, expression(bold("Big Beef Creek")), cex=0.5)#
text(-122.1, 47.599821, expression(bold("Elliot Bay")), cex=0.5)#
text(-122.9, 47.542182, expression(bold("Sinclair Inlet")), cex=0.5)#
text(-122.3, 47.138708, expression(bold("Solo Point")), cex=0.5)#
text(-121.9, 47.276488, expression(bold("Hylebos Waterway")), cex=0.5)
?merge
library(affy)
?edge
library(edgeR)
?edgeR
edgeR
edge
?edge
?seacarb
?pgas
library(seacarb)
?seacarb
?pgas
setwd("/Users/emmatimminsschiffman/Documents/Dissertation/Summer 2010")#
development<-read.csv("OADev1.csv", sep=",", header=T)#
raw.dev<-read.csv("OADev counts.csv", sep=",", header=T)
T1380<-development$Percent[1]#
T1840<-development$Percent[2]#
T2380<-development$Percent[3]#
T2840<-development$Percent[4]#
T3380<-development$Percent[5]#
T3840<-development$Percent[6]#
T4380<-development$Percent[7]#
T4840<-development$Percent[8]#
T5380<-development$Percent[9]#
T5840<-development$Percent[10]
error.bar<-function(x,y,upper, lower=upper, length=0.1)#
{if(length(x) !=length(y)|length(y) !=length(lower)|length(lower) !=length(upper))#
	stop("vectors must be same length")#
	arrows(x,y+upper, x, y-lower, angle=90, code=3, length=length)#
	}
cleav.mat<-matrix(data=c(T1380, T2380,T1840, T2840), ncol=2, nrow=2, byrow=T)
plot.cleav<-c(T1380, T2380,T1840, T2840)
bar.clv<-barplot(plot.cleav,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.names=1.2, cex.lab=1.5,ylim=c(0,.6))
plot.cleav<-c(T1380, T2380,T1840, T2840)
bar.clv<-barplot(plot.cleav,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.names=1.2, cex.lab=1.5,ylim=c(0,.6))
T1380<-development$Percent[1]
development<-read.csv("OADev1.csv", sep=",", header=T)
setwd("/Users/emmatimminsschiffman/Documents/Dissertation/Summer 2010")
getwd()
setwd("/Users/emmatimminsschiffman/Documents/Dissertation/Summer 2010")
getwd()
setwd("/Users/emmatimminsschiffman/Documents/Dissertation/Summer 2010")
development<-read.csv("OADev1.csv", sep=",", header=T)
raw.dev<-read.csv("OADev counts.csv", sep=",", header=T)
T1380<-development$Percent[1]#
T1840<-development$Percent[2]#
T2380<-development$Percent[3]#
T2840<-development$Percent[4]#
T3380<-development$Percent[5]#
T3840<-development$Percent[6]#
T4380<-development$Percent[7]#
T4840<-development$Percent[8]#
T5380<-development$Percent[9]#
T5840<-development$Percent[10]
error.bar<-function(x,y,upper, lower=upper, length=0.1)#
{if(length(x) !=length(y)|length(y) !=length(lower)|length(lower) !=length(upper))#
	stop("vectors must be same length")#
	arrows(x,y+upper, x, y-lower, angle=90, code=3, length=length)#
	}
cleav.mat<-matrix(data=c(T1380, T2380,T1840, T2840), ncol=2, nrow=2, byrow=T)
plot.cleav<-c(T1380, T2380,T1840, T2840)
bar.clv<-barplot(plot.cleav,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.names=1.2, cex.lab=1.5,ylim=c(0,.6))
T1380
T1840
T2380
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.names=1.2, cex.lab=1.5,ylim=c(0,.6))
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.names=1.15, cex.lab=1.5,ylim=c(0,.6))
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.names=1.1, cex.lab=1.5,ylim=c(0,.6))
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.names=1.05, cex.lab=1.5,ylim=c(0,.6))
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.lab=1.5,ylim=c(0,.6))
setwd("/Users/emmatimminsschiffman/Documents/Dissertation/Summer 2010")
raw.dev<-read.csv("OADev counts.csv", sep=",", header=T)
y.err.cleav<-c(sd(raw.dev$development[1:3]),sd(raw.dev$development[4:6]),sd(raw.dev$development[7:9]),sd(raw.dev$development[10:12]) )
error.bar(bar.clv,plot.cleav,y.err.cleav)
error.bar(bar.clv,cleav.mat,y.err.cleav)
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.lab=1.5,ylim=c(0,.6))
error.bar(bar.clv,cleav.mat,y.err.cleav)
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.lab=1.5,ylim=c(0,.62))
error.bar(bar.clv,cleav.mat,y.err.cleav)
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.lab=1.5,ylim=c(0,.65))
error.bar(bar.clv,cleav.mat,y.err.cleav)
hatch.dat<-c(T3380, T3840, T4380,T4840, T5380,T5840)
bar.hatch<-barplot(hatch.dat, beside=T,space=c(0.1,0.5), width=0.5, col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization (Hours)", ylab="Proportion Hatched", names.arg=c("5", "5", "17", "17", "24","24"), cex.names=1.5,cex.lab=1.5,ylim=c(0,1.1))
T3380
T3840
T4380
T4840
bar.hatch<-barplot(hatch.dat, beside=T,space=c(0,0,1,0,1,0,1), width=0.5, col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization (Hours)", ylab="Proportion Hatched", names.arg=c("5", "5", "17", "17", "24","24"), cex.names=1.5,cex.lab=1.5,ylim=c(0,1.1))
bar.hatch<-barplot(hatch.dat, beside=T,space=c(0,0,1,0,1,0), width=0.5, col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization (Hours)", ylab="Proportion Hatched", names.arg=c("5", "5", "17", "17", "24","24"), cex.names=1.5,cex.lab=1.5,ylim=c(0,1.1))
y.err.hatch<-c(sd(raw.dev$development[13:15]),sd(raw.dev$development[6:18]),sd(raw.dev$development[19:21]),sd(raw.dev$development[22:24]),sd(raw.dev$development[25:27]),sd(raw.dev$development[28:30]))
error.bar(bar.hatch,hatch.dat,y.err.hatch)
setwd("/Users/emmatimminsschiffman/Documents/Dissertation/Summer 2010")
development<-read.csv("OADev1.csv", sep=",", header=T)
T1380<-development$Percent[1]#
T1840<-development$Percent[2]#
T2380<-development$Percent[3]#
T2840<-development$Percent[4]#
T3380<-development$Percent[5]#
T3840<-development$Percent[6]#
T4380<-development$Percent[7]#
T4840<-development$Percent[8]#
T5380<-development$Percent[9]#
T5840<-development$Percent[10]
cleav.mat<-matrix(data=c(T1380, T2380,T1840, T2840), ncol=2, nrow=2, byrow=T)
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.lab=1.5,ylim=c(0,.65))
?setwd
library(seacarb)
c(1,2,3,4,5)
1:5
help(package='seacarb')
?seacarb
amp(s=35,T=25)
amp(S=35,T=25)
?alkalinity
alkalinity
data(alkalinity)
p2fCO2(T=16, 860)
p2fCO2(T=16, pCO2=860)
library(seacarb)
p2fCO2
f2pCO2
bjerrum
library(seacarb)
p2fCO2
f2pCO2
amp
buffer
carb
library(seacarb)
p2fCO2(T=25, pCO2=380)
p2fCO2
alkalinit
alkalinity
bjerrum
amp
p2fco2
p2fCO2
?aov
?TukeyHSD
?aov
?model.aov
?model
?ordi.monte
source("/Users/emmatimminsschiffman/Documents/Autumn 2010/Multivariate Stats/biostats.R")
ordi.monte
setwd('/Users/emmatimminsschiffman/Documents/Dissertation/Larvae/FHL 2011')
counts.dat<-read.csv('fixedlarvae.csv', header=T, na.strings='na')
density.dat<-read.csv('treatmentdensity.csv', header=T)
size3<-read.csv('size3.csv', header=T)
plot(size3$hinge, size3$height, pch=c(rep(16,14), rep(17,11), rep(18,16), rep(1,14), rep(2,23), rep(5,12)), col=c(rep('black',41), rep('black',49)), cex=1.5, ylab='Shell Height (µm)', xlab='Hinge Length (µm)', ylim=c(25,80), xlim=c(25,80))
abline(27.4677,0.6459) #solid line
abline(15.7575,0.8224, lty=3) #dotted
abline(37.0987,0.3625, lty=5) #dashed
?legend
legend(65, 35, legend=c('Ambient', 'MidCO2', 'HighCO2'), pch=c(16, 17, 18))
legend(65, 35, legend=c('Ambient', 'MidCO2', 'HighCO2'), pch=c(16, 17, 18), lty=c(1, 3, 5))
plot(size3$hinge, size3$height, pch=c(rep(16,14), rep(17,11), rep(18,16), rep(1,14), rep(2,23), rep(5,12)), col=c(rep('black',41), rep('black',49)), cex=1.5, ylab='Shell Height (µm)', xlab='Hinge Length (µm)', ylim=c(25,80), xlim=c(25,80))
legend(65, 35, legend=c('Ambient', 'MidCO2', 'HighCO2'), pch=c(16, 17, 18), lty=c(1, 3, 5))
abline(27.4677,0.6459) #solid line
abline(15.7575,0.8224, lty=3) #dotted
abline(37.0987,0.3625, lty=5) #dashed
par(mfrow=c(1,3))
hinge.Control<-data.frame(size.dat[,1],size.dat[,5])
size.dat<-read.csv('size.csv', header=T, na.strings='na')
hinge.plot<-data.frame(size.dat[,1],size.dat[,5], size.dat[,2], size.dat[,6], size.dat[,3], size.dat[,7])
boxplot(hinge.plot, names=c('Ambient', 'Ambient', 'MidCO2', 'MidCO2', 'HighCO2', 'HighCO2'), main='Hinge Length by Treatment and Day', ylab='Hinge Length (µm)', xlab='Day and pCO2', col=c('white','white', 'gray71', 'gray71', 'gray28', 'gray28'), cex.main=2, cex.lab=1.5, border=c('gray59', 'black'))
par(mfrow=c(1,3))
hinge.Control<-data.frame(size.dat[,1],size.dat[,5])
boxplot(hinge.Control, col=c('white', 'gray28'), names=c('Day 1', 'Day 3'), main='A', ylab='Hinge Length (µm)', ylim=c(20,75), cex.lab=1.5, cex.main=2, cex.axis=1.5)
hinge.midco2<-data.frame(size.dat[,2], size.dat[,6])
boxplot(hinge.midco2, col=c('white', 'gray28'), names=c('Day 1', 'Day 3'), main='B',ylim=c(20,75), cex.main=2, cex.axis=1.5)
hinge.highco2<-data.frame(size.dat[,3], size.dat[,7])
boxplot(hinge.highco2, col=c('white', 'gray28'), names=c('Day 1', 'Day 3'), main='C',ylim=c(20,75), cex.main=2, cex.axis=1.5)
par(mfrow=c(1,3))
par(mfrow=c(1,3))
boxplot(hinge.Control, col=c('white', 'gray28'), names=c('Day 1', 'Day 3'), main='Ambient', ylab='Hinge Length (µm)', ylim=c(20,75), cex.lab=1.5, cex.main=2, cex.axis=1.5)
boxplot(hinge.midco2, col=c('white', 'gray28'), names=c('Day 1', 'Day 3'), main='MidCO2',ylim=c(20,75), cex.main=2, cex.axis=1.5)
boxplot(hinge.highco2, col=c('white', 'gray28'), names=c('Day 1', 'Day 3'), main='HighCO2',ylim=c(20,75), cex.main=2, cex.axis=1.5)
par(mfrow=c(1,3))
height.Control<-data.frame(size.dat[,9],size.dat[,13])
boxplot(height.Control, col=c('white', 'gray28'), names=c('Day 1', 'Day 3'), main='Ambient', ylab='Shell Height (µm)', ylim=c(30,82), cex.main=2, cex.axis=1.5, cex.lab=1.5)
height.midco2<-data.frame(size.dat[,10], size.dat[,14])
boxplot(height.midco2, col=c('white', 'gray28'), names=c('Day 1', 'Day 3'), main='MidCO2',ylim=c(30,82), cex.main=2, cex.axis=1.5)
height.highco2<-data.frame(size.dat[,11], size.dat[,15])
boxplot(height.highco2, col=c('white', 'gray28'), names=c('Day 1', 'Day 3'), main='HighCO2',ylim=c(30,82), cex.main=2, cex.axis=1.5)
setwd('/Users/emmatimminsschiffman/Documents/Dissertation/Larvae/FHL 2011')
setwd('/Users/emmatimminsschiffman/Documents/Dissertation/Larvae/FHL 2011/controller logs')
T103a<-read.csv('103a.csv', header=T)
T103b<-read.csv('103b.csv', header=T)
T105a<-read.csv('105a.csv', header=T)
plot(T103a$Day2[1:5754], T103a$pH[1:5754], ylim=c(7.2,8.3), col='gray71',  xlab='Day', ylab='pH', cex.lab=1.5, cex.main=2, xaxp=c(0,3,3))
abline(7.75,0, col='gray71', lwd=3)
points(T103b$Day2[1:5754], T103b$pH[1:5754], col='gray28')
abline(7.66,0, col='gray28', lwd=3)
points(T105a$Day2[1:5754], T105a$pH[1:5754], pch=1)
abline(7.99,0,col='black', lwd=3)
pH.leg<-c('Ambient', 'MidCO2', 'HighCO2')
legend(0,7.3, pH.leg,pch=1, cex=1.5, col=c('black', 'gray71', 'gray28'))
legend(0,7.3, pH.leg,pch=1, col=c('black', 'gray71', 'gray28'))
legend(0,7.35, pH.leg,pch=1, col=c('black', 'gray71', 'gray28'))
plot(T103a$Day2[1:5754], T103a$pH[1:5754], ylim=c(7.2,8.3), col='gray71',  xlab='Day', ylab='pH', cex.lab=1.5, cex.main=2, xaxp=c(0,3,3))#
#avg 103a pH = 7.75#
abline(7.75,0, col='gray71', lwd=3)#
points(T103b$Day2[1:5754], T103b$pH[1:5754], col='gray28')#
abline(7.66,0, col='gray28', lwd=3)#
points(T105a$Day2[1:5754], T105a$pH[1:5754], pch=1)#
abline(7.99,0,col='black', lwd=3)#
pH.leg<-c('Ambient', 'MidCO2', 'HighCO2')#
legend(0,7.35, pH.leg,pch=1, col=c('black', 'gray71', 'gray28'))