rhdf5 (version 2.16.0)

rhdf5: Package overview

Description

rhdf5 is an interface to the HDF5 library. The R-package contains the complete HDF5 library, thus no further installation of external packages is necessary.

There are a number of high level R functions that provide a convinient way of accessing HDF5 file as well as R interfaces to a number of functions in the C-library.

Package content

HDF5 file, group, dataset creation

• h5createFile
• h5createGroup
• h5createDataset

HDF5 file content listing

• h5ls
• h5dump

Reading and writing data

• h5read, h5write
• h5dump, h5save

HDF5 constants

• h5const, h5default, h5constType

HDF5 version number

• h5version

Low level interface to HDF5 C-library (for expert users only!):

• general HDF5 functions (H5open / H5close / H5garbage_collect / H5get_libversion)
• HDF5 File Interface (H5Fcreate, H5Fopen / H5Fclose / H5Fflush)
• HDF5 Group Interface (H5Gcreate, H5Gcreate_anon, H5Gopen / H5Gclose / H5Gget_info, H5Gget_info_by_idx, H5Gget_info_by_name)
• HDF5 Link Interface (H5Lexists, H5Lget_info)
• HDF5 Object Interface (H5Oopen, H5Oclose, H5Oget_num_attrs, H5Oget_num_attrs_by_name)
• HDF5 Identifier Interface (H5Iget_type, H5Iget_name, H5Iis_valid)
• HDF5 Dataset Interface (H5Dcreate, H5Dopen / H5Dclose / H5Dget_space / H5Dread, H5Dwrite)
• HDF5 Attribute Interface (H5Acreate, H5Aopen, H5Aopen_by_idx, H5Aopen_by_name / H5Aclose, H5Adelete / H5Aexists / H5Aget_name, H5Aget_space, H5Aget_type / H5Aread, H5Awrite)
• HDF5 Dataspace Interface (H5Screate, H5Screate_simple, H5Scopy / H5Sclose / H5Sis_simple, H5Sget_simple_extent_dims / H5Sselect_hyperslab)
• HDF5 Datatype Interface (H5Tcopy, H5Tset_size)

Authors

R-interface by Bernd Fischer, EMBL - European Molecular Biology Laboratory Heidelberg Germany The package contains the HDF5 library (http://www.hdfgroup.org/HDF5).

Examples

h5createFile("ex_hdf5file.h5")

# create groups
h5createGroup("ex_hdf5file.h5","foo")
h5createGroup("ex_hdf5file.h5","foo/foobaa")

# write a matrix
B = array(seq(0.1,2.0,by=0.1),dim=c(5,2,2))
attr(B, "scale") <- "liter"
h5write(B, "ex_hdf5file.h5","foo/B")

# read a matrix
E = h5read("ex_hdf5file.h5","foo/B")

# list content of hdf5 file
h5ls("ex_hdf5file.h5")

# write and read submatrix
h5createDataset("ex_hdf5file.h5", "foo/S", c(5,8), storage.mode = "integer", chunk=c(5,1), level=7)
h5write(matrix(1:5,nr=5,nc=1), file="ex_hdf5file.h5", name="foo/S", index=list(NULL,1))
h5read("ex_hdf5file.h5", "foo/S")
h5read("ex_hdf5file.h5", "foo/S", index=list(2:3,2:3))