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traj_compOcMod.r
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rm(list=ls())
############################# get bathymetry #################################
nc <- nc_open("C:/Users/mkarnauskas/Desktop/RS_FATEproject/GEBCO_GOM_SATL.nc") # open netcdf file from GEBCO
v1 <- nc$var[[1]]
z <-ncvar_get(nc, v1)
x <- v1$dim[[1]]$vals
y <- v1$dim[[2]]$vals
nc_close(nc)
z[z>0] <- 100
z[z< (-800)] <- -800
cols <- rainbow(100, start=0.55, end=0.62)[100:1]
cols[100] <- "white"
######################### GET HYCOM TRAJECTORIES ############################
setwd("C://Users/mkarnauskas/Desktop/RS_FATEproject/compOcMod/HYCOM")
lona <- c()
lata <- c()
depa <- c()
coda <- c()
dat1 <- c()
for (m in 1:7) {
nam <- paste("traj_file_", m, ".nc", sep="")
nc <- nc_open(nam, write=FALSE, readunlim=TRUE, verbose=FALSE)
v2 <- nc$var[[2]]
lon <- ncvar_get(nc, v2)
lon[which(lon>10000)] <- NA
v3 <- nc$var[[3]]
lat <- ncvar_get(nc, v3)
lat[which(lat>10000)] <- NA
v4 <- nc$var[[4]]
dep <- ncvar_get(nc, v4)
dep[which(dep>10000)] <- NA
v6 <- nc$var[[6]]
cod <- ncvar_get(nc, v6)
cod[which(cod>10000)] <- NA # 0 can still move; -1 left area; -2 close to land; -3 dead; -4 settled; -5 no oceanographic data
v7 <- nc$var[[7]]
dat <- ncvar_get(nc, v7)
lona <- cbind(lona, lon)
lata <- cbind(lata, lat)
depa <- cbind(depa, dep)
coda <- c(coda, cod)
dat1 <- c(dat1, dat)
nc_close(nc) }
brks <- seq(2453000-365, 2453000+365*12, 365)
plot(dat1)
dcut1 <- as.numeric(cut(dat1, brks))
########################## GET SABGOM TRAJECTORIES ##########################
setwd("C://Users/mkarnauskas/Desktop/RS_FATEproject/compOcMod/SABGOM")
setwd("C://Users/mkarnauskas/Desktop/RS_FATEproject/initial_run2")
lonb <- c()
latb <- c()
depb <- c()
codb <- c()
dat2 <- c()
intb <- c()
for (m in 1:6) {
nam <- paste("traj_file_", m, ".nc", sep="")
nc <- nc_open(nam, write=FALSE, readunlim=TRUE, verbose=FALSE)
v1 <- nc$var[[1]]
int <- ncvar_get(nc, v1)
v2 <- nc$var[[2]]
lon <- ncvar_get(nc, v2)
lon[which(lon>10000)] <- NA
v3 <- nc$var[[3]]
lat <- ncvar_get(nc, v3)
lat[which(lat>10000)] <- NA
v4 <- nc$var[[4]]
dep <- ncvar_get(nc, v4)
dep[which(dep>10000)] <- NA
v6 <- nc$var[[6]]
cod <- ncvar_get(nc, v6)
cod[which(cod>10000)] <- NA # 0 can still move; -1 left area; -2 close to land; -3 dead; -4 settled; -5 no oceanographic data
v7 <- nc$var[[7]]
dat <- ncvar_get(nc, v7)
lonb <- cbind(lonb, lon)
latb <- cbind(latb, lat)
depb <- cbind(depb, dep)
codb <- c(codb, cod)
dat2 <- c(dat2, dat)
intb <- c(intb, int)
nc_close(nc) }
plot(dat2)
dcut2 <- as.numeric(cut(dat2, brks))
############################ PLOT TRAJECTORIES #############################
cols <- gray(seq(0.6, 0.999, length.out=100))
cols[100] <- "black"
#cols[1:99] <- "white"
cols2 <- rainbow(31, start=0.01, end=0.8, alpha=0.20)
par(mfrow=c(3, 2), mex=0.4)
yrs <- 2003:2010
m <- 2
for (m in 2:7) {
map('usa', xlim=c(-98, -85), ylim=c(23.8,31), col=0)
image(x,y,z, col=cols, axes=T, xlab="", ylab="", add=T); box(); axis(1, cex=1.2); axis(2, las=2, cex=1.2)
legend(-98.7, 31.2, paste(yrs[m]), cex=1.5, text.font=2, bty="n", text.col="white")
i <- which(dcut2 == m) # & coda != (-4))
k <- i[seq(1, length(i), length.out=200)]
for (j in k) {
lines(lonb[,j]-360, latb[,j], col="#FF000040") # SABGOM
points(lona[1,j]-360, lata[1,j], col="#00000060", pch=19, cex=0.8) }
i <- which(dcut1 == m) # & coda != (-4))
k <- i[seq(1, length(i), length.out=200)]
for (j in k) {
lines(lona[,j]-360, lata[,j], col="#0000FF15") # HYCOM
points(lona[1,j]-360, lata[1,j], col="#00000060", pch=19, cex=0.8) }
legend("bottomright", c("HYCOM", "SABGOM"), col=c("#0000FF80", "#FF000080"), lty=1, lwd=2, bty="n")
}
cols2 <- rainbow(31, start=0.01, end=0.8, alpha=0.20)
xloc <- seq(-92,-86, length.out=31)
cols3 <- rainbow(31, start=0.01, end=0.8, alpha=0.80)
###################### PLOT TRAJECTORIES BY MODEL ###########################
### SABGOM
par(mfrow=c(3, 2), mex=0.4)
for (m in 2:7) {
map('usa', xlim=c(-98, -85), ylim=c(23.8,31), col=0)
image(x,y,z, col=cols, axes=T, xlab="", ylab="", add=T); box(); axis(1, cex=1.2); axis(2, las=2, cex=1.2)
legend(-98.7, 31.2, paste("SABGOM", yrs[m]), cex=1.2, text.font=2, bty="n", text.col="white")
i <- which(dcut2 == m) # & coda != (-4))
k <- i[seq(1, length(i), length.out=500)]
for (j in k) {
points(lonb[1,j]-360, latb[1,j], col="#00000060", pch=19, cex=0.7)
for (f in 2:length(lona[,1])) {
lines(lonb[(f-1):f,j]-360, latb[(f-1):f,j], col=cols2[f]) } }
for (j in 1:31) { polygon(c(xloc[j], xloc[j+1],xloc[j+1], xloc[j]), c(24.35, 24.35, 24.7, 24.7), col=cols3[j], border=NA) }
text(-89, 25.1, "days after release", cex=1)
text(xloc[seq(4,30,4)], 24.1, seq(4,30,4), cex=1)
}
### HYCOM
par(mfrow=c(3, 2), mex=0.4)
for (m in 2:7) {
map('usa', xlim=c(-98, -85), ylim=c(23.8,31), col=0)
image(x,y,z, col=cols, axes=T, xlab="", ylab="", add=T); box(); axis(1, cex=1.2); axis(2, las=2, cex=1.2)
legend(-98.7, 31.2, paste("HYCOM", yrs[m]), cex=1.2, text.font=2, bty="n", text.col="white")
i <- which(dcut1 == m) # & coda != (-4))
k <- i[seq(1, length(i), length.out=500)]
for (j in k) {
points(lona[1,j]-360, lata[1,j], col="#00000060", pch=19, cex=0.7)
for (f in 2:length(lona[,1])) {
lines(lona[(f-1):f,j]-360, lata[(f-1):f,j], col=cols2[f]) } }
for (j in 1:31) { polygon(c(xloc[j], xloc[j+1],xloc[j+1], xloc[j]), c(24.35, 24.35, 24.7, 24.7), col=cols3[j], border=NA) }
text(-89, 25.1, "days after release", cex=1)
text(xloc[seq(4,30,4)], 24.1, seq(4,30,4), cex=1)
}
################################################################################
rm(list=ls())
setwd("C://Users/mkarnauskas/Desktop/RS_FATEproject/compOcMod")
nc <- nc_open("C:/Users/mkarnauskas/Desktop/RS_FATEproject/GEBCO_GOM_SATL.nc") # open netcdf file from GEBCO
v1 <- nc$var[[1]]
z <-ncvar_get(nc, v1)
x <- v1$dim[[1]]$vals
y <- v1$dim[[2]]$vals
nc_close(nc)
z[z>0] <- 100
z[z< (-800)] <- -800
cols <- rainbow(100, start=0.55, end=0.62)[100:1]
cols[100] <- "white"
nam <- "traj_file_diff5.nc"
nc <- nc_open(nam, write=FALSE, readunlim=TRUE, verbose=FALSE)
v1 <- nc$var[[1]]
int <- ncvar_get(nc, v1)
v2 <- nc$var[[2]]
lon <- ncvar_get(nc, v2)
lon[which(lon>10000)] <- NA
v3 <- nc$var[[3]]
lat <- ncvar_get(nc, v3)
lat[which(lat>10000)] <- NA
v4 <- nc$var[[4]]
dep <- ncvar_get(nc, v4)
dep[which(dep>10000)] <- NA
v6 <- nc$var[[6]]
cod <- ncvar_get(nc, v6)
cod[which(cod>10000)] <- NA # 0 can still move; -1 left area; -2 close to land; -3 dead; -4 settled; -5 no oceanographic data
v7 <- nc$var[[7]]
dat <- ncvar_get(nc, v7)
nc_close(nc)
brks <- seq(2453000-365, 2453000+365*12, 365)
plot(dat)
dcut1 <- as.numeric(cut(dat, brks))
nam <- "traj_file_diff25.nc"
nc <- nc_open(nam, write=FALSE, readunlim=TRUE, verbose=FALSE)
v1 <- nc$var[[1]]
inta <- ncvar_get(nc, v1)
v2 <- nc$var[[2]]
lona <- ncvar_get(nc, v2)
lona[which(lona>10000)] <- NA
v3 <- nc$var[[3]]
lata <- ncvar_get(nc, v3)
lata[which(lata>10000)] <- NA
v4 <- nc$var[[4]]
depa <- ncvar_get(nc, v4)
depa[which(depa>10000)] <- NA
v6 <- nc$var[[6]]
coda <- ncvar_get(nc, v6)
coda[which(coda>10000)] <- NA # 0 can still move; -1 left area; -2 close to land; -3 dead; -4 settled; -5 no oceanographic data
v7 <- nc$var[[7]]
dat2 <- ncvar_get(nc, v7)
nc_close(nc)
plot(dat2)
dcut2 <- as.numeric(cut(dat2, brks))
cols <- gray(seq(0.6, 0.999, length.out=100))
cols[100] <- "black"
cols2 <- rainbow(31, start=0.01, end=0.8, alpha=0.20)
xloc <- seq(-92,-86, length.out=31)
cols3 <- rainbow(31, start=0.01, end=0.8, alpha=0.80)
yrs <- 2003:2010
### diff 25
par(mfrow=c(5, 2), mex=0.4)
for (m in 2:6) {
map('usa', xlim=c(-98, -85), ylim=c(23.8,31), col=0)
image(x,y,z, col=cols, axes=T, xlab="", ylab="", add=T); box(); axis(1, cex=1.2); axis(2, las=2, cex=1.2)
legend(-98.7, 31.2, paste(yrs[m], "diffusivity = 5"), cex=1.2, text.font=2, bty="n", text.col="white")
i <- which(dcut1 == m) # & cod != (-4))
k <- i[seq(1, length(i), length.out=500)]
for (j in k) {
points(lon[1,j]-360, lat[1,j], col="#00000060", pch=19, cex=0.7)
for (f in 2:length(lon[,1])) {
lines(lon[(f-1):f,j]-360, lat[(f-1):f,j], col=cols2[f]) } }
for (j in 1:31) { polygon(c(xloc[j], xloc[j+1],xloc[j+1], xloc[j]), c(24.35, 24.35, 24.7, 24.7), col=cols3[j], border=NA) }
text(-89, 25.1, "days after release", cex=1)
text(xloc[seq(4,30,4)], 24.1, seq(4,30,4), cex=1)
map('usa', xlim=c(-98, -85), ylim=c(23.8,31), col=0)
image(x,y,z, col=cols, axes=T, xlab="", ylab="", add=T); box(); axis(1, cex=1.2); axis(2, las=2, cex=1.2)
legend(-98.7, 31.2, paste(yrs[m], "diffusivity = 25"), cex=1.2, text.font=2, bty="n", text.col="white")
i <- which(dcut2 == m) # & coda != (-4))
k <- i[seq(1, length(i), length.out=500)]
for (j in k) {
points(lona[1,j]-360, lata[1,j], col="#00000060", pch=19, cex=0.7)
for (f in 2:length(lona[,1])) {
lines(lona[(f-1):f,j]-360, lata[(f-1):f,j], col=cols2[f]) } }
for (j in 1:31) { polygon(c(xloc[j], xloc[j+1],xloc[j+1], xloc[j]), c(24.35, 24.35, 24.7, 24.7), col=cols3[j], border=NA) }
text(-89, 25.1, "days after release", cex=1)
text(xloc[seq(4,30,4)], 24.1, seq(4,30,4), cex=1)
}
setwd("C://Users/mkarnauskas/Desktop/RS_FATEproject/GoM_Atl_conn_lores_byyear")
lonb <- c()
latb <- c()
depb <- c()
codb <- c()
dat2 <- c()
intb <- c()
for (m in 1:7) {
nam <- paste("traj_file_", m, ".nc", sep="")
nc <- nc_open(nam, write=FALSE, readunlim=TRUE, verbose=FALSE)
v1 <- nc$var[[1]]
int <- ncvar_get(nc, v1)
v2 <- nc$var[[2]]
lon <- ncvar_get(nc, v2)
lon[which(lon>10000)] <- NA
v3 <- nc$var[[3]]
lat <- ncvar_get(nc, v3)
lat[which(lat>10000)] <- NA
v4 <- nc$var[[4]]
dep <- ncvar_get(nc, v4)
dep[which(dep>10000)] <- NA
v6 <- nc$var[[6]]
cod <- ncvar_get(nc, v6)
cod[which(cod>10000)] <- NA # 0 can still move; -1 left area; -2 close to land; -3 dead; -4 settled; -5 no oceanographic data
v7 <- nc$var[[7]]
dat <- ncvar_get(nc, v7)
lonb <- cbind(lonb, lon)
latb <- cbind(latb, lat)
depb <- cbind(depb, dep)
codb <- c(codb, cod)
dat2 <- c(dat2, dat)
intb <- c(intb, int)
nc_close(nc) }
plot(dat2)
dcut2 <- as.numeric(cut(dat2, brks))
map('usa', xlim=c(-82, -78), ylim=c(27,33), col=0)
image(x,y,z, col=cols, axes=T, xlab="", ylab="", add=T); box(); axis(1, cex=1.2); axis(2, las=2, cex=1.2)
legend(-98.7, 31.2, paste("SABGOM", yrs[m]), cex=1.2, text.font=2, bty="n", text.col="white")
i <- which(dcut2 == 2) # & coda != (-4))
k <- i[seq(1, length(i), length.out=500)]
for (j in k) {
if (lonb[1,j]-360 > (-81.5)) {
points(lonb[1,j]-360, latb[1,j], col="#00000060", pch=19, cex=0.7)
for (f in 2:length(lona[,1])) {
lines(lonb[(f-1):f,j]-360, latb[(f-1):f,j], col=cols2[f]) } } }
xloc <- seq(-81,-79, length.out=31)
for (j in 1:31) { polygon(c(xloc[j], xloc[j+1],xloc[j+1], xloc[j]), c(27.2, 27.2, 27.3, 27.3), col=cols3[j], border=NA) }
text(-80, 27.4, "days after release", cex=1)
text(xloc[seq(4,30,4)], 27.1, seq(4,30,4), cex=1)
mtext(side=3, line=2, "SABGOM trajectories", cex=1.1, font=2)