Profiles of temperature made along a ship track, originally made available by US NOAA NODC.
The data were merged from 29 input files named gtspp_103799_xb_111.nc
till gtspp_103827_xb_111.nc.
These data were acquired from the US NOAA National Oceanographic Data Center
(NODC) on 9/06/2012 from http://www.nodc.noaa.gov/gtspp/.
Usage
data(TrackProf)
Format
list with
meta, a data.frame with the metadata, containing for each of the
29 profiles the following:
station, the number of the station (part of the original filename).
filename, the original name of the NetCDF file.
date, the date of sampling.
time, the time of sampling, a number relative to 1-1-1900 0 hours.
longitude, dg E.
latitutde, dg N.
temp, the seawater temperature, at the depth of the
measurement in dg C. A matrix of dimension (29, 93) for the
29 profiles and (at most) 93 depth values; NA means no measurement.
depth, the depth of the measurement in temp, in metres,
positive downward. A matrix of dimension (29, 93) for the
29 profiles and (at most) 93 depth values; NA means no measurement.
U.S. National Oceanographic Data Center: Global Temperature-Salinity Profile Programme.
June 2006. U.S. Department of Commerce, National Oceanic and Atmosphere Administration,
National Oceanographic Data Center, Silver Spring, Maryland, 20910. Date of Access: 9/06/2012.
See Also
image2D for plotting images, package plot3D.
ImageOcean for an image of the ocean bathymetry, package plot3D.
scatter2D for making scatterplots, package plot3D.
Oxsat for a 3-D data set, package plot3D.
Examples
# save plotting parameters
pm <- par(mfrow = c(2, 2))
mar <- par("mar")
## =============================================================================
## show the metadata
## =============================================================================
print(TrackProf$meta)
## =============================================================================
## display the cruisetrack on the Ocean Bathymetry data
## =============================================================================
# 1. plots the ocean's bathymetry and add sampling positions
ImageOcean(xlim = c(-50, 50), ylim = c(-50, 50),
main = "cruise track")
points(TrackProf$meta$longitude, TrackProf$meta$latitude, pch = "+")
# mark starting point
points(TrackProf$meta$longitude[1], TrackProf$meta$latitude[1],
pch = 18, cex = 2, col = "purple")
## =============================================================================
## image plots of raw data
## =============================================================================
image2D(z = TrackProf$depth, main = "raw depth values",
xlab = "station nr", ylab = "sample nr", clab = "depth")
image2D(z = TrackProf$temp, main = "raw temperature values",
xlab = "station nr", ylab = "sample nr", clab = "dgC")
## =============================================================================
## image plots of temperatures at correct depth
## =============================================================================
# water depths to which data set is interpolated
depth <- 0 : 809
# map from "sigma" to "depth" coordinates
Temp_Depth <- mapsigma (TrackProf$temp, sigma = TrackProf$depth,
depth = depth)$var
# image with depth increasing downward and increased resolution (resfac)
image2D(z = Temp_Depth, main = "Temperature-depth",
ylim = c(809, 0), y = depth, NAcol ="black", resfac = 2,
xlab = "station nr", ylab = "depth, m", clab = "dgC")
## =============================================================================
## scatterplot of surface values on ocean bathymetry
## =============================================================================
par(mar = mar + c(0, 0, 0, 2))
par(mfrow = c(1, 1))
# No colors, but add contours
ImageOcean(xlim = c(-30, 30), ylim = c(-40, 40),
main = "cruise track", col = "white", contour = TRUE)
# use data set TrackProf to add measured temperature, with color key
with (TrackProf,
scatter2D(colvar = temp[,1], x = meta[ ,"longitude"],
y = meta[ ,"latitude"], clab = "temp",
add = TRUE, pch = 18, cex = 2))
# reset plotting parameters
par(mar = mar)
par(mfrow = pm)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(OceanView)
Loading required package: plot3D
Loading required package: plot3Drgl
Loading required package: rgl
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/OceanView/TempTraject.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Profile data set
> ### Title: Temperature profiles made along a ship track.
> ### Aliases: TrackProf
> ### Keywords: datasets
>
> ### ** Examples
>
> # save plotting parameters
> pm <- par(mfrow = c(2, 2))
> mar <- par("mar")
>
> ## =============================================================================
> ## show the metadata
> ## =============================================================================
> print(TrackProf$meta)
station filename date time longitude latitude
1 103799 gtspp_103799_xb_111.nc 3/05/1990 32996.50 11.2333 -19.7167
2 103800 gtspp_103800_xb_111.nc 3/05/1990 32996.74 9.8667 -18.3333
3 103801 gtspp_103801_xb_111.nc 4/05/1990 32997.00 8.6000 -17.0833
4 103802 gtspp_103802_xb_111.nc 4/05/1990 32997.24 7.3667 -15.8333
5 103803 gtspp_103803_xb_111.nc 4/05/1990 32997.50 6.0000 -14.4500
6 103804 gtspp_103804_xb_111.nc 4/05/1990 32997.74 4.7333 -13.1000
7 103805 gtspp_103805_xb_111.nc 5/05/1990 32998.00 3.4333 -11.8167
8 103806 gtspp_103806_xb_111.nc 5/05/1990 32998.24 2.2167 -10.5167
9 103807 gtspp_103807_xb_111.nc 5/05/1990 32998.50 0.9333 -9.1167
10 103808 gtspp_103808_xb_111.nc 5/05/1990 32998.74 -0.3000 -7.8333
11 103809 gtspp_103809_xb_111.nc 6/05/1990 32999.00 -1.4667 -6.5833
12 103810 gtspp_103810_xb_111.nc 6/05/1990 32999.24 -2.6500 -5.3167
13 103811 gtspp_103811_xb_111.nc 6/05/1990 32999.52 -4.0333 -3.8000
14 103812 gtspp_103812_xb_111.nc 6/05/1990 32999.76 -5.2333 -2.5333
15 103813 gtspp_103813_xb_111.nc 7/05/1990 33000.00 -6.4833 -1.2167
16 103814 gtspp_103814_xb_111.nc 7/05/1990 33000.25 -7.6333 0.1000
17 103815 gtspp_103815_xb_111.nc 7/05/1990 33000.50 -8.8667 1.4833
18 103816 gtspp_103816_xb_111.nc 7/05/1990 33000.75 -10.1500 2.9000
19 103817 gtspp_103817_xb_111.nc 8/05/1990 33001.00 -11.3333 4.2667
20 103818 gtspp_103818_xb_111.nc 8/05/1990 33001.24 -12.3833 5.4500
21 103819 gtspp_103819_xb_111.nc 8/05/1990 33001.53 -13.7500 6.8167
22 103820 gtspp_103820_xb_111.nc 8/05/1990 33001.75 -14.7833 7.9167
23 103821 gtspp_103821_xb_111.nc 9/05/1990 33002.00 -15.9333 9.2333
24 103822 gtspp_103822_xb_111.nc 9/05/1990 33002.25 -17.0167 10.5500
25 103823 gtspp_103823_xb_111.nc 9/05/1990 33002.50 -17.6333 12.0833
26 103824 gtspp_103824_xb_111.nc 9/05/1990 33002.75 -17.7000 13.5333
27 103825 gtspp_103825_xb_111.nc 10/05/1990 33003.00 -17.7667 15.0833
28 103826 gtspp_103826_xb_111.nc 10/05/1990 33003.25 -17.7167 16.5333
29 103827 gtspp_103827_xb_111.nc 10/05/1990 33003.51 -17.7333 18.1000
>
> ## =============================================================================
> ## display the cruisetrack on the Ocean Bathymetry data
> ## =============================================================================
> # 1. plots the ocean's bathymetry and add sampling positions
> ImageOcean(xlim = c(-50, 50), ylim = c(-50, 50),
+ main = "cruise track")
> points(TrackProf$meta$longitude, TrackProf$meta$latitude, pch = "+")
>
> # mark starting point
> points(TrackProf$meta$longitude[1], TrackProf$meta$latitude[1],
+ pch = 18, cex = 2, col = "purple")
>
> ## =============================================================================
> ## image plots of raw data
> ## =============================================================================
>
> image2D(z = TrackProf$depth, main = "raw depth values",
+ xlab = "station nr", ylab = "sample nr", clab = "depth")
> image2D(z = TrackProf$temp, main = "raw temperature values",
+ xlab = "station nr", ylab = "sample nr", clab = "dgC")
>
> ## =============================================================================
> ## image plots of temperatures at correct depth
> ## =============================================================================
>
> # water depths to which data set is interpolated
> depth <- 0 : 809
>
> # map from "sigma" to "depth" coordinates
> Temp_Depth <- mapsigma (TrackProf$temp, sigma = TrackProf$depth,
+ depth = depth)$var
>
> # image with depth increasing downward and increased resolution (resfac)
> image2D(z = Temp_Depth, main = "Temperature-depth",
+ ylim = c(809, 0), y = depth, NAcol ="black", resfac = 2,
+ xlab = "station nr", ylab = "depth, m", clab = "dgC")
>
> ## =============================================================================
> ## scatterplot of surface values on ocean bathymetry
> ## =============================================================================
>
> par(mar = mar + c(0, 0, 0, 2))
> par(mfrow = c(1, 1))
>
> # No colors, but add contours
> ImageOcean(xlim = c(-30, 30), ylim = c(-40, 40),
+ main = "cruise track", col = "white", contour = TRUE)
>
> # use data set TrackProf to add measured temperature, with color key
> with (TrackProf,
+ scatter2D(colvar = temp[,1], x = meta[ ,"longitude"],
+ y = meta[ ,"latitude"], clab = "temp",
+ add = TRUE, pch = 18, cex = 2))
>
> # reset plotting parameters
> par(mar = mar)
> par(mfrow = pm)
>
>
>
>
>
> dev.off()
null device
1
>