TrackReconstruction (version 1.1)

bathymetry: Bathymetry data for the Eastern Bering Sea

Description

Bathymetry data for the Eastern Bering Sea at a resolution of 30 arc seconds downloaded from http://www.gebco.net

Usage

data(bathymetry)

Format

A data frame with 1814400 observations on the following 3 variables.

Long

a numeric vector

Lat

a numeric vector

Depth

a numeric vector

Details

If you want to do color graphing of the tracks within R I have provided a Mapper function to do this but it requires gridded bathymetric data to create the background map. The source for this example data set comes from the General Bathymetric Chart of the Oceans or GEBCO at http://www.gebco.net.

You will need to get their GridViewer software and data, currently there is a link to get it at http://www.gebco.net/data_and_products/grid_display_software/

which at the time of writing sent me to https://www.bodc.ac.uk/products/software_products/gebco_grid_display/

There are currently two options for the world data file, a 1 arc min or 30 arc sec file. The bathymetry data set is from the GEBCO_08 Grid a global 30 arc-second grid which is the larger and more detailed data. If you have a very wide ranging animal (albatross, elephant seal etc.), the smaller data set will probably be easier for R to handle and adequate for viewing the entire track, but you might want the more detailed data set to map portions of the track. Some experimentation by you may be necessary here.

This is fairly easy to use, just open the grid viewer and choose whatever way to select the portion of the globe you want to see, I used the "Exact Area" section in the Area tab. This then produces a map of the data you selected and you can then export the data that made that map in an ascii (*.asc) file. In order to import this into R as a data frame you might need to edit the file, such as deleting the header, but especially make sure the delimiters between columns are consistent, in my files I get multiple spaces between one column and a single space between the other column. R may have a way to deal with this when importing files but I typically open these files up in a text editor such as TextPad, view "Visible Spaces" and then do a find and replace to make the column delimiters either tab or comma.

Examples

# NOT RUN {
data(bathymetry)
str(bathymetry)
head(bathymetry);tail(bathymetry)
bathymetryBogs<-subset(bathymetry,Long<=(-166) & Long >=(-169)
	& Lat<= 54.5 & Lat >=53,select=Long:Depth)

image.xyz=tapply(bathymetryBogs$Depth, list(bathymetryBogs$Long, bathymetryBogs$Lat), unique)
#create palette for depth colors
Bathymetry.palette<-colorRampPalette(brewer.pal(9, "Blues"),bias=3)
#Plot the background map image
image.plot(image.xyz,
	col=c(rev(Bathymetry.palette(200)),terrain.colors(100)),#gray(0:20/20),
	breaks=round(c(seq(from=min(image.xyz),to=0,length.out=201),seq(from=max(image.xyz)/101
	,to=max(image.xyz),length.out=100)))
	#,smallplot=2 #plots legend off x axis
	)
# }
# NOT RUN {
#If you want to map the entire bathymetry file, it takes a while
image.xyz=tapply(bathymetry$Depth, list(bathymetry$Long, bathymetry$Lat), unique)
#create palette for depth colors
Bathymetry.palette<-colorRampPalette(brewer.pal(9, "Blues"),bias=3)
#Plot the background map image
image.plot(image.xyz,
	col=c(rev(Bathymetry.palette(200)),terrain.colors(100)),#gray(0:20/20),
	breaks=round(c(seq(from=min(image.xyz),to=0,length.out=201),seq(from=max(image.xyz)/101
	,to=max(image.xyz),length.out=100)))
	#,smallplot=2 #plots legend off x axis
	)
# }