The raster package isn't able to read the data from this "GMT-style"
NetCDF, since the structure of the variable is one-dimensional internally
and you are supposed to deal with that yourself. I would stick with the
ncdf4 package to read it, you'll have to scan into the "z" variable
manually to reconstruct it as a matrix, or subset it.

Note that you should have a large object size with "d", since the nc_open
function returns an index vector for each dimension (so one of them is
length 89784000, you must have sufficient memory to deal with that - I
would close/delete the "d" object once you read the "z", "dimension" and
other values).

I have code to read from these files, but I can't access it today - it's
not that difficult though, you can probably do something like matrix(z,
dimension[1], dimension[2]) but you'll have to fiddle to get the
orientation right.




On Fri, Mar 8, 2013 at 9:18 PM, Julian Burgos <julian@hafro.is> wrote:

> Dear list,
>
> I am having some troubles opening accessing a raster in the netCDF format.
>  The file is bathimetric data from GEBCO:
> http://www.gebco.net/data_and_products/gridded_bathymetry_data/
>
> If I use the ncdf4 package to open and access the data, I have no issues:
>
> library(ncdf4)
> > d <- nc_open("gebco_08_-82_37_63_80.nc")
> > z <- as.vector(ncvar_get(d,varid="z"))
> > head(z)
> [1] 19 40 61 83 106 128
>
>
> But if I try to use the raster package to access the file and create a
> raster object, I get the following error:
>
> bat <- raster(file="gebco_08_-82_37_63_80",varname="z")
> Error in .varName(nc, varname, warn = warn) :
>   varname: z does not exist in the file. Select one from:
>
> ... and no varnames are listed.
>
>
> If I do not define a variable name and let the raster package choose it, I
> get this:
>
> > bat <- raster(file="gebco_08_-82_37_63_80",varname="z")
> Error in .varName(nc, varname, warn = warn) :
>
> The description of the netCDF file is as following:
>
> > d
> [1] "File gebco_08_-82_37_63_80.nc (NC_FORMAT_CLASSIC):"
> [1] ""
> [1] "     6 variables:"
> [1] "        double x_range[side]   "
> [1] "            units: user_x_unit"
> [1] "        double y_range[side]   "
> [1] "            units: user_y_unit"
> [1] "        short z_range[side]   "
> [1] "            units: user_z_unit"
> [1] "        double spacing[side]   "
> [1] "        int dimension[side]   "
> [1] "        short z[xysize]   "
> [1] "            scale_factor: 1"
> [1] "            add_offset: 0"
> [1] "            node_offset: 1"
> [1] ""
> [1] "     2 dimensions:"
> [1] "        side  Size:2"
> [1] "        xysize  Size:89784000"
> [1] ""
> [1] "    2 global attributes:"
> [1] "        title: GEBCO_08 Grid"
> [1] "        source: 20100927"
>
> I am using R 15.2 on Linux (Fedora), raster 2.1-8, and ncdf4 version
> ncdf4_1.6.1_20120411.
> Any help will be welcomed!
>
> Julian
>
> --
> Julian Mariano Burgos, PhD
> Hafrannsóknastofnunin/Marine Research Institute
> Skúlagata 4, 121 Reykjavík, Iceland
> Sími/Telephone : +354-5752037
> Bréfsími/Telefax:  +354-5752001
> Netfang/Email: julian@hafro.is
>
> _______________________________________________
> R-sig-Geo mailing list
> R-sig-Geo@r-project.org
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>



-- 
Michael Sumner
Hobart, Australia
e-mail: mdsumner@gmail.com

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