R help - Jun 2009 - How to read a specific dataset, not the entire data, from HDF5?

Hi. Recently I am working for  a project to generate massive numeric data.
After storing them in HDF5 using PyTables, we are trying to use R for
data analysis and visualisation.
Surprising to me, however, I could not find a R package to allow the
reading of a specific dataset (or its slide) in a HDF5 file.
I found I can read and write only the entire data using hdf5 package
and I could not locate rhdf5 in bioconductor.
Each dataset is huge, so selecting a specific dataset is a mandatory
function for my project.
Could you give me a hint for the solution? Thanks.

-- 
DH

Hi DH

I recommend the rgdal package, which provides R bindings for the
Geospatial Data Abstraction Library (GDAL). This does handle HDF5,
according to the list at http://www.gdal.org/formats_list.html

I have not ever used HDF5 myself, but that it what I would try.

-Felix


2009/6/27 Daehyok Shin <sdhyok at gmail.com>:
> Hi. Recently I am working for  a project to generate massive numeric data.
> After storing them in HDF5 using PyTables, we are trying to use R for
> data analysis and visualisation.
> Surprising to me, however, I could not find a R package to allow the
> reading of a specific dataset (or its slide) in a HDF5 file.
> I found I can read and write only the entire data using hdf5 package
> and I could not locate rhdf5 in bioconductor.
> Each dataset is huge, so selecting a specific dataset is a mandatory
> function for my project.
> Could you give me a hint for the solution? Thanks.
>
> --
> DH
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
Felix Andrews / ???
Post-Doctoral Fellow
Integrated Catchment Assessment and Management (iCAM) Centre
Fenner School of Environment and Society [Bldg 48a]
The Australian National University
Canberra ACT 0200 Australia
M: +61 410 400 963
T: + 61 2 6125 1670
E: felix.andrews at anu.edu.au
CRICOS Provider No. 00120C
-- 
http://www.neurofractal.org/felix/

Thanks, Felix.
You are watching new questions here.
I will give a try to rgdal and let you know the result.
BTW, it is surprising to me that there seems no R package handling
HDF5 like PyTables does for Python community, considering HDF5 is as
popular as NetCDF as a file format for scientific data. I hope the gap
will be filled in near future.

Regards,

DH

2009/6/27 Felix Andrews <felix at nfrac.org>:
> Hi DH
>
> I recommend the rgdal package, which provides R bindings for the
> Geospatial Data Abstraction Library (GDAL). This does handle HDF5,
> according to the list at http://www.gdal.org/formats_list.html
>
> I have not ever used HDF5 myself, but that it what I would try.
>
> -Felix
>
>
> 2009/6/27 Daehyok Shin <sdhyok at gmail.com>:
>> Hi. Recently I am working for  a project to generate massive numeric
data.
>> After storing them in HDF5 using PyTables, we are trying to use R for
>> data analysis and visualisation.
>> Surprising to me, however, I could not find a R package to allow the
>> reading of a specific dataset (or its slide) in a HDF5 file.
>> I found I can read and write only the entire data using hdf5 package
>> and I could not locate rhdf5 in bioconductor.
>> Each dataset is huge, so selecting a specific dataset is a mandatory
>> function for my project.
>> Could you give me a hint for the solution? Thanks.
>>
>> --
>> DH
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
>
> --
> Felix Andrews / ???
> Post-Doctoral Fellow
> Integrated Catchment Assessment and Management (iCAM) Centre
> Fenner School of Environment and Society [Bldg 48a]
> The Australian National University
> Canberra ACT 0200 Australia
> M: +61 410 400 963
> T: + 61 2 6125 1670
> E: felix.andrews at anu.edu.au
> CRICOS Provider No. 00120C
> --
> http://www.neurofractal.org/felix/
>


-- 
Daehyok Shin, PhD
Geography Department
University of North Carolina-Chapel Hill
USA