[Rd] HDF5 compound data types and h5r/hdf5 R packages

From: Jeremy Reeve <jeremy.reeve1_at_gmail.com>
Date: Thu, 01 Dec 2011 19:22:01 +1300

ink1">ink1">Hi there,

I have a Java process that writes HDF5 files with the following approximate structure:

group "xxx" {

    group "yyy" {

        dataset {}
        dataset {}


    group "zzz" {

        dataset {}
        dataset {}



where dataset is a rank one dataspace having a compound datatype defined as:

H5T_UNIX_TIME, float, float, float, float

I have tried R packages h5r and hdf5 in an attempt to read the file but examining the source of h5r and reading documentation for hdf5 here: http://xweb.geos.ed.ac.uk/~hcp/Rhdf5.html leads me to believe that compound datatypes are not supported by these packages. My guess is that mapping arbitrary type definitions in HDF5 to available types in R might be somewhat tricky. Incidentally, h5dump has trouble displaying the data in the dataset but I think this is to do with the time 'field':

      DATASPACE  SIMPLE { ( 33 ) / ( H5S_UNLIMITED ) }
      DATA {
         h5dump error: unable to print data

Since I am new to both HDF5 and R I wonder if there are better approaches to storing the information I have that will allow me to use either h5r or hdf5 packages unmodified. I expect I can contribute changes to either of the packages that will allow me to do what I describe but fall short of general compound datatype support.

Any comments or advice gratefully received.


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