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Accessing netCDF/OPeNDAP data with R

Get R, which includes several netCDF4 packages.

require(ncdf)
  1. Go to an OPeNDAP server (e.g. http://opendap.deltares.nl) and pick a netCDF file by copying the contents of the Data URL box. Because the netcdf packages for windows are not yet opendap-enabled, download them.
  2. Define the associated url you just copied.
    url_grid <-
    "http://opendap.deltares.nl/thredds/fileServer/opendap/rijkswaterstaat/vaklodingen/vaklodingenKB116_4544.nc" # note: netcdf4 does not work on windows R
    
    url_time <-
    "http://opendap.deltares.nl/thredds/fileServer/opendap/rijkswaterstaat/waterbase/concentration_of_suspended_matter_in_sea_water/id410-DELFZBTHVN.nc"
    
    download.file(url_grid, "vaklodingenKB116_4544.nc", method = "auto",
    quiet = FALSE, mode="wb", cacheOK = TRUE)
    
    download.file(url_time, "id410-DELFZBTHVN.nc", method = "auto",
    quiet = FALSE, mode="wb", cacheOK = TRUE)
    
    A complete linux image with the R netcdf package compiled with OPeNDAP is available upon request from ""adaguc "at" knmi.nl"".
  3. Extract the data.
    grid.nc <- open.ncdf("vaklodingenKB116_4544.nc")
    
    # look what's in there...
    grid.nc
    
    # Get grid data
    G.x <- get.var.ncdf(grid.nc,'x')
    G.y <- get.var.ncdf(grid.nc,'y')
    
    # get only first timestep
    G.z <- get.var.ncdf(grid.nc,'z')[,,1]
    
    # to get a black background, and set the scale of depth values to start from 0.
    G.z[G.z == -9999] <- 0
    
    # image.plot needs sorted x- and y-values;
    # as y-values are descending, the order is reversed here...
    G.y <- rev(G.y)
    G.z <- G.z[,length(G.y):1]
    
    time.nc <- open.ncdf("id410-DELFZBTHVN.nc")
    # look what's in there...
    time.nc
    
    T.t <- get.var.ncdf(time.nc,'time')
    T.eta <-
    get.var.ncdf(time.nc,'concentration_of_suspended_matter_in_sea_water')
    
  4. plot ...
    # R-package fields provides nice image facilities and color schemes
    par (mfrow = c(1,2))
    library(fields)
    image.plot(G.x,G.y,as.matrix(G.z),
            col = c(tim.colors(),"black"),
            xlab = "x [m]", ylab = "y [m]")
    
    plot(as.Date(T.t, origin="1970-01-01"), T.eta, type = "l", ylab = "spm
    [mg/l]")
    
  5. et voila

Download the code of this R example (repos,manual download), which was provided by Karline Soetaert and Tom van Engeland.

See also: Accessing netCDF/OPeNDAP data with python, Accessing netCDF/OPeNDAP data with Matlab, PostgreSQL access with R, OPeNDAP subsetting with R