Dear All, I have data in HDF file format and would like to read it into R. I have tried the package hdf5 without success. Any ideas and suggestions?? Kind regards, Katrin -- Katrin Fleischer Vrije Universiteit Amsterdam Faculty of Earth and Life Sciences Subdepartment Hydrolgy and Geo-Environmental Sciences Room E-360 De Boelelaan 1085 1081 HV AMSTERDAM Tel: +31 20 59 87391
Hi, On Thu, Sep 23, 2010 at 7:13 AM, Katrin Fleischer <katrin.fleischer at falw.vu.nl> wrote:> Dear All, > > I have data in HDF file format and would like to read it into R. > I have tried the package hdf5 without success.What type of errors are you getting?> Any ideas and suggestions??Sure, from: http://cran.r-project.org/doc/manuals/R-data.html "Packages hdf5, RNetCDF and ncdf on CRAN provide interfaces to NASA's HDF5 ..." I'm not familiar with the differences between hdf5 and netCDF, but perhaps those other packages can help (I see that they've been more recently updated, anyway ...). -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
Hi Katrin, (don't forget to reply-all to R-help messages -- by default they are only sent to the recipient, and not back to the list). On Thu, Sep 23, 2010 at 10:03 AM, Katrin Fleischer <katrin.fleischer at falw.vu.nl> wrote:> The error message is > > Error in hdf5load("Jan2006.HDF") : unable to open HDF file: Jan2006.HDFDumb question, but is that the correct path to the file? If you call `dir()` in your R session, is "Jan2006.HDF" one of the elements returned? Maybe try the absolute path to the file if not.> I have also seen these other packages, but Im afraid that the data I have > might be in hdf4 (thats would be an explanation to why "hdf5load" isnt > working), so I was wondering whether there is a package for R dealing with > hdf4 files..Perhaps you could try converting it to hdf5 format, if that's the case. It looks like there is a utility you can use to do so here: http://www.hdfgroup.org/h4toh5/ -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact