Question

I have a netcdf file that I would like to just visualize the soil depth map

   [1] "file C:\\Users\\SoilDepth-gswp.nc has 3 dimensions:"
     [1] "x   Size: 360"
     [1] "y   Size: 150"
     [1] "land   Size: 15238"
     [1] "------------------------"
     [1] "file C:\\SoilDepth-gswp.nc has 3 variables:"
     [1] "float nav_lon[x,y]  Longname:Longitude Missval:1e+30"
     [1] "float nav_lat[x,y]  Longname:Latitude Missval:1e+30"
     [1] "float SoilDepth[land]  Longname:Soil depth Missval:1.00000002004088e+20"

It seems that I have to connect the latitudes with longitudes as well as the land points to get a map of the soil depth.I am really confused .Can anyone help me with this kind of data.

Answer 1

library(ncdf)
# I'm assuming this is the netcdf file you are working with:
download.file("http://dods.ipsl.jussieu.fr/gswp/Fixed/SoilDepth.nc", destfile="SoilDepth.nc")
soil <- open.ncdf("SoilDepth.nc")
#The way to extract a variable is as following:
soil$var[[3]] -> var3 # here, as shown in your question, SoilDepth is the 3rd variable
get.var.ncdf(soil, var3) -> SoilDepth

dim(SoilDepth)
[1] 15238

As was said in the summary for your netcdf file, the variable SoilDepth depends on dimension land only and not on x and y so I’m not sure where does that leave you when it comes to plotting this dataset.

Edit

It turns out there is a key that links x, y and land:

download.file("http://dods.ipsl.jussieu.fr/gswp/Fixed/landmask_gswp.nc", destfile="landmask.nc")
landmask <- open.ncdf("landmask.nc")
landmask$var[[3]] -> varland
get.var.ncdf(landmask, varland) -> land
sum(land==1)
[1] 15238

So in order to plot:

# The values where stored in an expected order, hence the transpose
land = t(land)
land[land==1] <- SoilDepth
land[land==0] <- NA
land = t(land)
image(land)