rhdf5: Package overview

In rhdf5: R Interface to HDF5

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, [e-mail] EMBL - European Molecular Biology Laboratory Heidelberg Germany

The package contains the HDF5 library (https://portal.hdfgroup.org/display/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))

Example output

[1] TRUE
[1] TRUE
[1] TRUE
  group   name       otype dclass       dim
0     /    foo   H5I_GROUP                 
1  /foo      B H5I_DATASET  FLOAT 5 x 2 x 2
2  /foo foobaa   H5I_GROUP                 
[1] TRUE
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,]    1    0    0    0    0    0    0    0
[2,]    2    0    0    0    0    0    0    0
[3,]    3    0    0    0    0    0    0    0
[4,]    4    0    0    0    0    0    0    0
[5,]    5    0    0    0    0    0    0    0
     [,1] [,2]
[1,]    0    0
[2,]    0    0

rhdf5 documentation built on Nov. 8, 2020, 6:56 p.m.