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When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

#install.packages("dplyr")
#install.packages("tidyr")
#install.packages("ggplot2")
#install.packages("leaflet")
#install.packages("gsw")
library(tidyr)
library(dplyr)
## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
library(ggplot2)
library(gsw)
library(leaflet)
#cd /Users/w5/Mast467/Code 
#./Hw3code
#ls -la output.dat

omg <- read.csv(file="/Users/w5/Mast467/Code/output.dat",sep=" ")
ggplot(omg,aes(x=depth,y=temp)) +
  geom_path() +
  ylab("Temperature, C") +
  xlab("Depth, m") +
  coord_flip(expand=FALSE)

ggplot(omg,aes(x=depth,y=Sal)) +
  geom_path() +
  ylab("Salinity, PPT") +
  xlab("Depth, m") +
  coord_flip(expand=FALSE)

ggplot(omg,aes(x=Sal,y=temp)) +
  geom_path() +
  ylab("Temperature, C") +
  xlab("Salinity, PPT") +
  coord_flip(expand=FALSE)

ggplot(omg,aes(x=Sal,y=temp,color=depth)) +
  geom_path() +
  ylab("Temperature, C") +
  xlab("Salinity, PPT") +
  scale_color_viridis_c(guide=guide_colorbar(barheight=16.5)) +
  coord_flip(expand=FALSE)

ggplot(omg,aes(x=depth,y=temp,color=Sal)) +
  geom_path() +
  ylab("Temperature, C") +
  xlab("Depth, m") +
  scale_color_viridis_c(guide=guide_colorbar(barheight=16.5)) +
  coord_flip(expand=FALSE)

ggplot(omg,aes(x=depth,y=Sal,color=temp)) +
  geom_path() +
  ylab("Salinity, PPT") +
  xlab("Depth, m") +
  scale_color_viridis_c(guide=guide_colorbar(barheight=16.5)) +
  coord_flip(expand=FALSE)

ggplot(omg,aes(x=depth,y=Sal,color=temp)) +
  geom_path() +
  ylab("Salinity, PPT") +
  xlab("Depth, m") +
  ylim(32,35) +
  xlim(-750,0) +
  scale_color_viridis_c(guide=guide_colorbar(barheight=16.5)) +
  coord_flip(expand=FALSE)
## Warning: Removed 234 row(s) containing missing values (geom_path).

depth <- omg$depth
Sal <- omg$Sal
temp <- omg$temp
z=depth

p=gsw_p_from_z(z,70)
s=Sal
latitude=70.
longitude=-35.
SA=gsw_SA_from_SP(s,p,latitude,longitude)
t=temp
pt=gsw_pt_from_t(SA,t,p,0)
CT=gsw_CT_from_t(SA,t,p)
r0=gsw_sigma0(SA,CT)
r1=gsw_sigma1(SA,CT)
tf=gsw_CT_freezing(SA,p,1)
omg1 <- data.frame (pt,r0,r1,s,SA,t,tf,z,CT,depth,temp,Sal,p)
#library(dplyr)
#vector(mode = "logical", length = 0)
depth <- omg$depth
Sal <- omg$Sal
temp <- omg$temp
pt <- omg1$pt
r0 <- omg1$r0
r1 <- omg1$r1
s <- omg1$s
SA <- omg1$SA
t <- omg1$t
tf <- omg1$tf
z <- omg1$z
CT <- omg1$CT
depth <- omg1$depth
temp <- omg1$temp
Sal <- omg1$Sal
p <- omg1$p
#as.vector(x, mode = "")
#mutate(omg, depth=)
ggplot(omg1,aes(x=SA,y=z)) +
  geom_path() +
  ylab("Depth, m") +
  xlab("Absolute Salinity, PSU") +
  ylim(-750,0) +
  xlim(25,35)
## Warning: Removed 2677 row(s) containing missing values (geom_path).

ggplot(omg1,aes(x=temp,y=pt)) +
  geom_path() +
  ylab("Potential Temperature, C") +
  xlab("Temperature, c") +
  ylim(-2.5,6) +
  xlim(-2.5,6)

ggplot(omg1,aes(x=SA,y=r1)) +
  geom_path() +
  ylab("Potential density, kg/m^3 +1000") +
  xlab("Absolute Salinity, PSU") +
  ylim(23,33) +
  xlim(25,35)
## Warning: Removed 2677 row(s) containing missing values (geom_path).

ggplot(omg1,aes(x=r1,y=SA,)) +
  geom_path() +
  ylab("Absolute Salinity, PPT") +
  xlab("Potential Density, kg/m^3+1000") +
  ylim(23,35) +
  xlim(23,35)
## Warning: Removed 2677 row(s) containing missing values (geom_path).

ggplot(omg1,aes(x=CT,y=SA,)) +
  geom_path() +
  ylab("Absolute Salinity, PPT") +
  xlab("Conservative Temperature, C") +
  ylim(23,35) +
  xlim(-1,5) +
  coord_flip(expand=FALSE)
## Warning: Removed 2677 row(s) containing missing values (geom_path).

#install.packages("matrixStats")
library(matrixStats)
## 
## Attaching package: 'matrixStats'
## The following object is masked from 'package:dplyr':
## 
##     count
for (i in 49:50)
   { data <- filter(omg,cast == 1)
     #if (head(depth, n >=10))
      print(i)
        

depth <- as.numeric(data[,3])
temp <- as.numeric(data[,4])
Sal <- as.numeric(data[,5])

maxdepth <- as.integer(tail(depth,i))
     print(maxdepth)
       #dmax=0
         #if(maxdepth >= dmax)
            #{ dmax = maxdepth}
#bindepth <- seq(-2,maxdepth,1)
#binSal <- binMeans(Sal,x=depth,bx=bindepth,na.rm=TRUE)
#bintemp <- binMeans(temp,x=depth,bx=bindepth,na.rm=TRUE)
#BinMetrics <- data.frame(bindepth[-2:maxdepth],binSal[-2:maxdepth],bintemp[-2:maxdepth])
}
## [1] 49
## integer(0)
## [1] 50
## integer(0)

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