[R] [ncdf] programmatically copying a netCDF file

[Tom Roche]

How to programmatically (i.e., without no or minimal handcoding) copy
a netCDF file? (Without calling

> system("cp whatever wherever")

:-) Why I ask:

I need to "do surgery" on a large netCDF file (technically an I/O API
file which uses netCDF). My group believes a data-assimilation error
caused a data variable to be corrupted in a certain way, so I'm going
to "decorrupt" it so we can compare values with the raw data. Thanks
to help from this list,

* I understand that, generally, R wants value semantics (though
  mechanisms like package=proto allow reference semantics). Therefore,
  ISTM, rather than attempting to modify a (copy of a) file in-place,
  I should instead [copy the bits I want to keep from the source file
  to the new/target file, read the one data variable I want to modify
  from the source file, write the one modified datavar to the target
  file]. (Please correct me if wrong!)

* I have a routine that (I believe) does the desired modification of
  the one datavar.

And from reading `help(*ncdf)` and

http://www.image.ucar.edu/Software/Netcdf/

I believe (ICBW :-) I understand the definition, get, and put steps
that are involved in reading and writing netCDF. However,

* the file I'm working with is large and complex

* the examples above hand-craft their output files

So I'm wondering, can anyone point me to, or provide, code that copies
a netCDF file both

* completely: all coordinate variables, all data variables and their
  attributes, and all global attributes, such that

$ diff -wB  <( ncdump -h source.nc ) <( ncdump -h target.nc ) | wc -l
0

* programmatically: no or minimal hand-coding of, e.g., attribute
  names and values, missing-value value.

? If not, can this be done in principle, or are there steps that must
(at least currently) necessarily be hand-coded?

TIA, Tom Roche <Tom_Roche at pobox.com>