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appendixFigures.Rmd
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appendixFigures.Rmd
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---
title: "Appendix Figures"
author: "Sara Stoudt"
date: "May 3, 2017"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
Figure 1
```{r,eval=F}
load(file="~/Desktop/DS421_summerProject/GAM_weightedReg_comparison/shiny/data/delt_map.RData")
plot(delt_map)
points(longitude,latitude,pch=19)
points(sfei$Longitude,sfei$Latitude,col="red",cex=2)
setwd("~/UC_Berkeley/Semester_4/timeSeries")
D10<-read.csv("D10data.csv",stringsAsFactors=F)
D12<-read.csv("D12data.csv",stringsAsFactors=F)
D22<-read.csv("D22data.csv",stringsAsFactors=F)
D26<-read.csv("D26data.csv",stringsAsFactors=F)
D4<-read.csv("D4data.csv",stringsAsFactors=F)
stationNames<-c("D10","D12","D22","D26","D4")
D10=cbind(D10,rep("D10",nrow(D10)))
D12=cbind(D12,rep("D12",nrow(D11)))
D22=cbind(D22,rep("D22",nrow(D22)))
D26=cbind(D26,rep("D26",nrow(D26)))
D4=cbind(D4,rep("D4",nrow(D4)))
D10n=D10[,c(1:13,ncol(D10))]
D12n=D12[,c(1:13,ncol(D12))]
D22n=D22[,c(1:13,ncol(D22))]
D26n=D26[,c(1:13,ncol(D26))]
D4n=D4[,c(1:13,ncol(D4))]
names(D10n)[14]=names(D12n)[14]=names(D22n)[14]=names(D26n)[14]=names(D4n)[14]="station"
D10[,14]=as.character(D10[,14])
D12[,14]=as.character(D12[,14])
D22[,14]=as.character(D22[,14])
D26[,14]=as.character(D26[,14])
D4[,14]=as.character(D4[,14])
sfei=rbind(D10n, D12n, D22n, D26n, D4n)
require(ggplot2)
g1=ggplot(sfei, aes(x=date_dec, y=chl, colour=as.factor(Station)))+geom_line()+xlim(2000,2015)+ labs(colour = "Station")+xlab("Date")
g2=ggplot(sfei, aes(x=date_dec, y=pheo, colour=as.factor(Station)))+geom_line()+xlim(2000,2015)+ labs(colour = "Station") +xlab("Date")
g3=ggplot(sfei, aes(x=date_dec, y=temp, colour=as.factor(Station)))+geom_line()+xlim(2000,2015)+ labs(colour = "Station") +xlab("Date")
g4=ggplot(sfei, aes(x=date_dec, y=sal, colour=as.factor(Station)))+geom_line()+xlim(2000,2015)+ labs(colour = "Station") +xlab("Date")
g5=ggplot(sfei, aes(x=date_dec, y=do, colour=as.factor(Station)))+geom_line()+xlim(2000,2015)+ labs(colour = "Station") +xlab("Date")
library(gridExtra)
grid.arrange(g1,g2,g3,g4,g5, ncol=1, nrow =5)
```
Figure 2
```{r,eval=F}
par(mfrow=c(3,1))
plot(D10$chl,type="l",main="Seasonal Component D10",xlab="Date",ylab="chl")
lines(D10$predGAMchl,col="red")
legend("topleft",lty=1,lwd=2,col=c("black","red"),c("orig","GAM fitted"),bty="n")
plot(D4$pheo,type="l",main="Seasonal Component D4",xlab="Date",ylab="pheo")
lines(D4$predGAMpheo,col="red")
legend("topleft",lty=1,lwd=2,col=c("black","red"),c("orig","GAM fitted"),bty="n")
plot(D22$do,type="l",main="Seasonal Component D22",xlab="Date",ylab="do")
lines(D22$predGAMdo,col="red")
legend("topleft",lty=1,lwd=2,col=c("black","red"),c("orig","GAM fitted"),bty="n")
par(mfrow=c(3,1))
plot(D26$residGAMpheo,type="l",xlab="Date",ylab="Resid Pheo D26",main="Variance Stabilization")
lines(D26$residGAMpheoTransform,col="red")
legend("topleft",lty=1,lwd=2,col=c("black","red"),c("orig","log transform"),bty="n")
plot(D4$residGAMchl,type="l",xlab="Date",ylab="Resid Chl D4",main="Variance Stabilization")
lines(D4$residGAMchlTransform,col="red")
legend("topleft",lty=1,lwd=2,col=c("black","red"),c("orig","log transform"),bty="n")
plot(D12$residGAMsal,type="l",main="Transform Doesn't Help",xlab="Date",ylab="Resid Sal D12")
lines(log(D12$residGAMsal+abs(min(D12$residGAMsal))),col="red")
legend("topleft",lty=1,lwd=2,col=c("black","red"),c("orig","log transform"),bty="n")
```
Figure 3
```{r,eval=F}
par(mfrow=c(3,1))
plot(D12$residGAMdo,D12$residGAMtemp,xlab="resid do",ylab="resid temp",main="D12")
test=ccf(D12$residGAMdo,D12$residGAMtemp,lag.max=12,plot=T,main="")
station1Data=station2Data=D12
varName="do"
varName2="temp"
empP<-c()
for(i in 2:nrow(station2Data) ){
test1=station2Data[c((i):nrow(station2Data),1:(i-1)),varName2]
test=ccf(station1Data[,varName],test1,lag.max=12,plot=F)
ccfOfInterest=test$acf[14:25]
empP<-c( empP,ccfOfInterest[which.max(abs(ccfOfInterest))] )
# print(i)
}
test=ccf(station1Data[,varName],station2Data[,varName2],lag.max=12,plot=F)
ccfOfInterest=test$acf[14:25]
hist(empP,xlab="Max Absolute Cross Correlation",main="Empirical Distribution from Rotation Test")
abline(v=ccfOfInterest[which.max(ccfOfInterest)],col="red")
##
par(mfrow=c(4,1))
test=spectrum( cbind(D12[,"residGAMdo"],D12[,"residGAMtemp"]),taper=.2,log="no",spans=c(2,2),demean=T,detrend=F,plot=F)
plot(test,plot.type = "coherency",sub=c("Window = 2"))
f=qf(0.95,2,test$df-2)
C = f/(test$df/2-1+f)
## test$df is 2L
abline(h=C,col="red")
test=spectrum( cbind(D12[,"residGAMdo"],D12[,"residGAMtemp"]),taper=.2,log="no",spans=c(8,8),demean=T,detrend=F,plot=F)
plot(test,plot.type = "coherency",sub=c("Window = 8"))
f=qf(0.95,2,test$df-2)
C = f/(test$df/2-1+f)
## test$df is 2L
abline(h=C,col="red")
test=spectrum( cbind(D12[,"residGAMdo"],D12[,"residGAMtemp"]),taper=.2,log="no",spans=c(16,16),demean=T,detrend=F,plot=F)
plot(test,plot.type = "coherency",sub=c("Window = 16"))
f=qf(0.95,2,test$df-2)
C = f/(test$df/2-1+f)
## test$df is 2L
abline(h=C,col="red")
test=spectrum( cbind(D12[,"residGAMdo"],D12[,"residGAMtemp"]),taper=.2,log="no",spans=c(20,20),demean=T,detrend=F,plot=F)
plot(test,plot.type = "coherency",sub=c("Window = 20"))
f=qf(0.95,2,test$df-2)
C = f/(test$df/2-1+f)
## test$df is 2L
abline(h=C,col="red")
```
Figure 4
```{r,eval=F}
longitude=c(-121.2647, -121.5205, -121.9183, -121.8063, -121.6148, -121.7391, -121.5669, -121.5730, -121.8205,
-122.3729, -122.1177,-122.0397, -121.9900, -121.4199, -121.3823)
latitude=c(37.67934, 38.36771, 38.04631, 38.02161, 38.04376, 38.08453, 38.07664, 37.97048, 38.06248, 38.03022,
38.04436, 38.11714, 38.05992, 38.04226, 37.97817)
sigToPlot=acrossStationSameVar[which(p.adjust(acrossStationSameVarResults$pVal, method = "BY") <0.05),]
resToPlot=acrossStationSameVarResults[which(p.adjust(acrossStationSameVarResults$pVal, method = "BY") <0.05),]
sigToPlot$station1=as.character(sigToPlot$station1)
sigToPlot$station2=as.character(sigToPlot$station2)
plot(longitude,latitude,main="Across Stations, Same Nutrient")
points(lonSub,latSub,col="red",pch=19)
arrows(lonSub[sigToPlot$station1],latSub[sigToPlot$station1],
lonSub[sigToPlot$station2],latSub[sigToPlot$station2],length=0)
text(-121.8,38.1,paste(sigToPlot$var1[1],resToPlot$maxLag[1],sep=" "),col="dodgerblue")
text(-121.65,38.1,paste(sigToPlot$var1[2],resToPlot$maxLag[2],sep=" "),col="dodgerblue")
text(-121.7,38.05,paste(sigToPlot$var1[3],resToPlot$maxLag[3],sep=" "),col="dodgerblue")
##
sigToPlot=acrossStationDiffVar[which(p.adjust(acrossStationDiffVarResults$pVal, method = "BY") <0.05),]
resToPlot=acrossStationDiffVarResults[which(p.adjust(acrossStationDiffVarResults$pVal, method = "BY") <0.05),]
plot(longitude,latitude,main="Across Stations, Different Nutrients",xlim=c(-122.2,-121.4),ylim=c(37.95,38.12))
points(lonSub,latSub,col="red",pch=19)
arrows(lonSub[sigToPlot$station1],latSub[sigToPlot$station1],
lonSub[sigToPlot$station2],latSub[sigToPlot$station2],length=0)
text(jitter(lonSub,10),jitter(latSub,10),stationNameSub)
##
toPrint=cbind(sigToPlot,resToPlot$maxLag)
row.names(toPrint)=NULL
names(toPrint)=c("Station 1", "Station 2", "Nutrient 1", "Nutrient 2", "Lag Max")
toPrint
library(gridExtra)
pdf("acrossStationsDiffNutrientTab.pdf", height=6, width=6)
grid.table(toPrint)
dev.off()
```
Figure 5
```{r,eval=F}
toPrint=acrossStationSameVar[which(!p.adjust(acrossStationSameVarResults$pVal, method = "BY") <0.05),]
row.names(toPrint)=NULL
names(toPrint)=c("Station 1", "Station 2", "Nutrient 1", "Nutrient 2")
library(gridExtra)
pdf("acrossStationsSameNutrientFREQTab.pdf", height=6, width=6)
grid.table(toPrint)
dev.off()
##
lonSub=c(D4$Longitude[1],D10$Longitude[1],D12$Longitude[1],D22$Longitude[1],D26$Longitude[1])
latSub=c(D4$Latitude[1], D10$Latitude[1], D12$Latitude[1],D22$Latitude[1],D26$Latitude[1])
stationNameSub=c("D4","D10","D12","D22","D26")
names(lonSub)=names(latSub)=stationNameSub
longitude=c(-121.2647, -121.5205, -121.9183, -121.8063, -121.6148, -121.7391, -121.5669, -121.5730, -121.8205,
-122.3729, -122.1177,-122.0397, -121.9900, -121.4199, -121.3823)
latitude=c(37.67934, 38.36771, 38.04631, 38.02161, 38.04376, 38.08453, 38.07664, 37.97048, 38.06248, 38.03022,
38.04436, 38.11714, 38.05992, 38.04226, 37.97817)
plot(longitude,latitude,cex=4)
points(lonSub,latSub,col="red",cex=4)
text(lonSub,latSub,stationNameSub)
##
par(mfrow=c(2,1))
hist(acrossStationSameVarResults[which(p.adjust(acrossStationSameVarResults$pVal, method = "BY") <0.05),"maxPhase"],
main="Distribution of Phase for Significant Pairs",xlab="phase for maximum cross coherence")
hist(acrossStationSameVarResults[which(p.adjust(acrossStationSameVarResults$pVal, method = "BY") <0.05),"maxFreq"],
main="Distribution of Frequency for Significant Pairs",xlab="frequency for maximum cross coherence",breaks=seq(0,200,by=1))
abline(v=12,col="red")
```
Figure 6
```{r,eval=F}
toPrint=acrossStationDiffVar[which(p.adjust(acrossStationDiffVarResults$pVal, method = "BY") <0.05),]
toPrint[order(toPrint[,1],toPrint[,2]),]
toPrint$statstat=paste(toPrint$station1,toPrint$station2,sep="_")
tt=table(toPrint$statstat)[order(table(toPrint$statstat),decreasing=T)]
toPrint=as.data.frame(cbind(row.names(tt),unname(tt)))
names(toPrint)=c("Station Combination","Number of Significant Pairs")
row.names(toPrint)=NULL
pdf("acrossStationsDiffNutComboSTab.pdf", height=8, width=6)
grid.table(toPrint)
dev.off()
##
toPrint=acrossStationDiffVar[which(p.adjust(acrossStationDiffVarResults$pVal, method = "BY") <0.05),]
toPrint[order(toPrint$station1),]
row.names(toPrint)=NULL
toPrint$nutnut=paste(toPrint$var1,toPrint$var2,sep="_")
table(toPrint$nutnut)
tt=table(toPrint$nutnut)[order(table(toPrint$nutnut),decreasing=T)]
toPrint=as.data.frame(cbind(row.names(tt),unname(tt)))
names(toPrint)=c("Nutrient Combination","Number of Significant Pairs")
row.names(toPrint)=NULL
library(gridExtra)
pdf("acrossStationsDiffNutrientComboTab.pdf", height=8, width=6)
grid.table(toPrint)
dev.off()
##
par(mfrow=c(2,1))
hist(acrossStationDiffVarResults[which(p.adjust(acrossStationDiffVarResults$pVal, method = "BY") <0.05),"maxPhase"],
main="Distribution of Phase for Significant Pairs",xlab="phase for maximum cross coherence")
hist(acrossStationDiffVarResults[which(p.adjust(acrossStationDiffVarResults$pVal, method = "BY") <0.05),"maxFreq"],
main="Distribution of Frequency for Significant Pairs",xlab="frequency for maximum cross coherence",breaks=seq(0,200,by=1))
abline(v=12,col="red")
```
More Tables Referenced in the Paper
```{r,echo=F}
stationNames<-c("D10","D12","D22","D26","D4")
varNames<-c("chl","do","pheo","sal","temp")
allCombo=expand.grid(stationNames,stationNames,varNames,varNames)
dim(allCombo)
head(allCombo)
names(allCombo)=c("station1","station2","var1","var2")
withinStation=allCombo[which(allCombo$station1==allCombo$station2),]
dim(withinStation) ## 125
withinStation[,1]=as.character(withinStation[,1])
withinStation[,2]=as.character(withinStation[,2])
withinStation[,3]=as.character(withinStation[,3])
withinStation[,4]=as.character(withinStation[,4])
withinStationSameVar=withinStation[which(withinStation$var1==withinStation$var2),]
dim(withinStationSameVar) ## 25
withinStationSameVar[,1]=as.character(withinStationSameVar[,1])
withinStationSameVar[,2]=as.character(withinStationSameVar[,2])
withinStationSameVar[,3]=as.character(withinStationSameVar[,3])
withinStationSameVar[,4]=as.character(withinStationSameVar[,4])
withinStationDiffVar=withinStation[which(withinStation$var1!=withinStation$var2),]
dim(withinStationDiffVar) ## 100
withinStationDiffVar[,1]=as.character(withinStationDiffVar[,1])
withinStationDiffVar[,2]=as.character(withinStationDiffVar[,2])
withinStationDiffVar[,3]=as.character(withinStationDiffVar[,3])
withinStationDiffVar[,4]=as.character(withinStationDiffVar[,4])
leftOver=allCombo[-which(allCombo$station1==allCombo$station2),]
acrossStationSameVar=leftOver[which(leftOver$var1==leftOver$var2),]
dim(acrossStationSameVar) ## 100
acrossStationSameVar[,1]=as.character(acrossStationSameVar[,1])
acrossStationSameVar[,2]=as.character(acrossStationSameVar[,2])
acrossStationSameVar[,3]=as.character(acrossStationSameVar[,3])
acrossStationSameVar[,4]=as.character(acrossStationSameVar[,4])
leftOver2=leftOver[-which(leftOver$var1==leftOver$var2),]
dim(leftOver2)
acrossStationDiffVar=leftOver2[which(leftOver2$var1!=leftOver2$var2),]
dim(acrossStationDiffVar) ## 400 same as leftOver2 as expected
acrossStationDiffVar[,1]=as.character(acrossStationDiffVar[,1])
acrossStationDiffVar[,2]=as.character(acrossStationDiffVar[,2])
acrossStationDiffVar[,3]=as.character(acrossStationDiffVar[,3])
acrossStationDiffVar[,4]=as.character(acrossStationDiffVar[,4])
```
```{r}
setwd("~/UC_Berkeley/Semester_4/timeSeries")
withinStationDiffVarResults<-read.csv("withinStationDiffVarResultsFreq.csv",stringsAsFactors=F)
names(withinStationDiffVarResults)=c("maxPhase","maxCoh","maxFreq","pVal")
sigToPlot=withinStationDiffVar[which(p.adjust(withinStationDiffVarResults$pVal, method = "BY") <0.05),]
resToPlot=withinStationDiffVarResults[which(p.adjust(withinStationDiffVarResults$pVal, method = "BY") <0.05),]
sigToPlot
resToPlot
```
```{r}
setwd("~/UC_Berkeley/Semester_4/timeSeries")
acrossStationSameVarResults<-read.csv("acrossStationSameVarResultsFreq.csv",stringsAsFactors=F)
names(acrossStationSameVarResults)=c("maxPhase","maxCoh","maxFreq","pVal")
toPrint=acrossStationSameVar[which(p.adjust(acrossStationSameVarResults$pVal,method="BY")<0.05),][which(acrossStationSameVarResults[which(p.adjust(acrossStationSameVarResults$pVal, method = "BY") <0.05),"maxFreq"]<12),]
row.names(toPrint)=NULL
names(toPrint)=c("Station 1", "Station 2", "Nutrient 1", "Nutrient 2")
toPrint
```