Read from or write to existing netCDF format files, or create new ones.
David W. Pierce dpierce@ucsd.edu
More information on this package, including detailed installation instructions, can be found at http://dwpierce.com/software.
The netCDF data file format from Unidata is a platform-independent, binary file that also contains metadata describing the contents and format of the data in the file. Version 4 of the netcdf library stores data in HDF5 format files; earlier versions stored data in a custom format. The R package ncdf4 can read either format.
NetCDF files contain one or more variables, which are usually structured as regular N-dimensional arrays. For example, you might have a variable named "Temperature" that is a function of longitude, latitude, and height. NetCDF files also contain dimensions, which describe the extent of the variables' arrays. In our Temperature example, the dimensions are "longitude", "latitude", and "height". Data can be read from or written to variables in arbitrary hyperslabs (for example, you can read or write all the Temperature values at a given height, or at a given latitude).
The R package 'ncdf4' allows reading from, writing to, and creation of netCDF files, either netCDF version 3 or (optionally) netCDF version 4. If you choose to create version 4 output files, be aware that older netcdf software might only be able to read version 3 files.
Note that both the netCDF library and the HDF5 library must already be installed on your machine for this R interface to the library to work.
If you are new to netCDF files, they can be a little overwhelming, so here is a brief sketch of what documentation you need to read next.
If you want to READ data
from an already-existing netCDF file, first call nc_open
to open the file, then call ncvar_get to read the data
from a variable in the file.
If you want to WRITE data to a new netCDF file, the procedure is
to first define the dimensions your data array has, then define the
variable, then create the file. So, first call
ncdim_def to define the dimensions that your data
exists along (for example, latitude, longitude, and time). Then call
ncvar_def to define a variable
that uses those dimensions, and will hold your data.
Then call nc_create
to create the netCDF file.
Finally, call ncvar_put
to write your data to the newly created netCDF file,
and nc_close when you are done.
Not all features of netcdf-4 are supported yet. This version supports compression, chunking, groups, vlen strings, and multiple unlimited dimensions. User-defined types and vlen data arrays (variable-length arrays) are not supported yet.
http://dwpierce.com/software
print.ncdf4,
nc_open,
nc_close,
nc_create,
ncdim_def,
ncvar_def,
ncvar_get,
ncvar_put,
ncvar_change_missval,
ncatt_get,
ncatt_put,
nc_sync,
nc_redef.