rhdf5: HDF5 interface to R

This R/Bioconductor package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("rhdf5")
AuthorBernd Fischer, Gregoire Pau
Bioconductor views DataImport Infrastructure
Date of publicationNone
MaintainerMike Smith <mike.smith@embl.de>
LicenseArtistic-2.0
Version2.20.0

View on Bioconductor

Functions

H5 Man page
H5A Man page
H5Aclose Man page
H5Acreate Man page
H5Adelete Man page
H5Aexists Man page
H5Aget_name Man page
H5Aget_space Man page
H5Aget_type Man page
H5Aopen Man page
H5Aopen_by_idx Man page
H5Aopen_by_name Man page
H5Aread Man page
H5Awrite Man page
H5close Man page
h5const Man page
h5constType Man page
h5createAttribute Man page
h5createDataset Man page
h5createFile Man page
h5createGroup Man page
H5D Man page
H5Dclose Man page
H5Dcreate Man page
h5default Man page
H5Dget_create_plist Man page
H5Dget_space Man page
H5Dget_storage_size Man page
H5Dget_type Man page
H5Dopen Man page
H5Dread Man page
H5Dset_extent Man page
h5dump Man page
H5Dwrite Man page
h5errorHandling Man page
H5F Man page
H5Fclose Man page
H5Fcreate Man page
H5Fflush Man page
H5Fget_access_plist Man page
H5Fget_create_plist Man page
H5Fget_filesize Man page
H5Fget_name Man page
H5Fis_hdf5 Man page
H5Fopen Man page
H5G Man page
H5garbage_collect Man page
H5Gclose Man page
H5Gcreate Man page
H5Gcreate_anon Man page
H5get_libversion Man page
H5Gget_info Man page
H5Gget_info_by_idx Man page
H5Gget_info_by_name Man page
H5Gopen Man page
H5I Man page
H5IdComponent Man page
&,H5IdComponent,ANY-method Man page
H5IdComponent-class Man page
[<-,H5IdComponent-method Man page
[,H5IdComponent-method Man page
$<-,H5IdComponent-method Man page
$,H5IdComponent-method Man page
H5Iget_name Man page
H5Iget_type Man page
H5Iis_valid Man page
H5L Man page
H5Lcreate_external Man page
H5Lexists Man page
H5Lget_info Man page
h5listIdentifier Man page
h5ls Man page
H5O Man page
H5Oclose Man page
H5Oget_info Man page
H5Oget_info_by_name Man page
H5Oget_num_attrs Man page
H5Oget_num_attrs_by_name Man page
H5Oopen Man page
H5open Man page
H5P Man page
H5Pall_filters_avail Man page
H5Pclose Man page
H5Pclose_class Man page
H5Pcopy Man page
H5Pcreate Man page
H5P_DATASET_ACCESS Man page
H5P_DATASET_CREATE Man page
H5Pequal Man page
H5Pfill_value_defined Man page
H5Pget_alloc_time Man page
H5Pget_char_encoding Man page
H5Pget_chunk Man page
H5Pget_chunk_cache Man page
H5Pget_class Man page
H5Pget_create_intermediate_group Man page
H5Pget_external Man page
H5Pget_external_count Man page
H5Pget_fill_time Man page
H5Pget_fill_value Man page
H5Pget_filter1 Man page
H5Pget_filter2 Man page
H5Pget_filter_by_id1 Man page
H5Pget_filter_by_id2 Man page
H5Pget_layout Man page
H5Pget_libver_bounds Man page
H5Pget_nfilters Man page
H5P_LINK_CREATE Man page
H5Pmodify_filter Man page
H5Premove_filter Man page
H5Pset_alloc_time Man page
H5Pset_char_encoding Man page
H5Pset_chunk Man page
H5Pset_chunk_cache Man page
H5Pset_create_intermediate_group Man page
H5Pset_deflate Man page
H5Pset_external Man page
H5Pset_fill_time Man page
H5Pset_fill_value Man page
H5Pset_filter Man page
H5Pset_fletcher32 Man page
H5Pset_layout Man page
H5Pset_libver_bounds Man page
H5Pset_nbit Man page
H5Pset_scaleoffset Man page
H5Pset_shuffle Man page
H5Pset_szip Man page
h5r Man page
h5read Man page
h5readAttributes Man page
H5S Man page
h5save Man page
H5Sclose Man page
H5Scopy Man page
H5Screate Man page
H5Screate_simple Man page
h5set_extent Man page
H5Sget_simple_extent_dims Man page
H5Sis_simple Man page
H5Sselect_hyperslab Man page
H5Sselect_index Man page
H5Sset_extent_simple Man page
H5T Man page
H5Tcopy Man page
H5Tset_size Man page
h5validObjects Man page
h5version Man page
h5write Man page
h5writeAttribute Man page
h5writeAttribute.array Man page
h5writeAttribute.character Man page
h5writeAttribute.double Man page
h5writeAttribute.integer Man page
h5writeAttribute.logical Man page
h5writeAttribute.matrix Man page
h5writeDataset Man page
h5writeDataset.array Man page
h5writeDataset.character Man page
h5writeDataset.data.frame Man page
h5writeDataset.double Man page
h5writeDataset.integer Man page
h5writeDataset.list Man page
h5writeDataset.logical Man page
h5writeDataset.matrix Man page
h5write.default Man page
hdf5 Man page
HDF5 Man page
rhdf5 Man page
show,H5IdComponent-method Man page

Files

BinaryFiles
CHANGES
DESCRIPTION
NAMESPACE
R
R/AllClass.R R/AllMethods.R R/H5.R R/H5A.R R/H5D.R R/H5F.R R/H5G.R R/H5I.R R/H5L.R R/H5O.R R/H5P.R R/H5S.R R/H5T.R R/H5constants.R R/Rhdf5.R R/h5checktype.R R/h5create.R R/h5dump.R R/h5errorHandling.R R/h5ls.R R/h5modifier.R R/h5read.R R/h5readAttributes.R R/h5save.R R/h5write.R R/h5writeAttr.R R/zzz.R
TODO
build
build/vignette.rds
cleanup
cleanup.win
inst
inst/NEWS.Rd
inst/demoChunkSize
inst/demoChunkSize/chunksize.pdf
inst/demoChunkSize/demoChunkSize.R
inst/doc
inst/doc/rhdf5.R
inst/doc/rhdf5.Rnw
inst/doc/rhdf5.pdf
inst/downloadHDF5
inst/downloadHDF5/README.txt
inst/downloadHDF5/downloadHDF5.sh
inst/downloadHDF5/replacestr.R
man
man/H5.Rd man/H5A.Rd man/H5D.Rd man/H5F.Rd man/H5G.Rd man/H5I.Rd man/H5IdComponent-class.Rd man/H5L.Rd man/H5O.Rd man/H5P.Rd man/H5P_DATASET_ACCESS.Rd man/H5P_DATASET_CREATE.Rd man/H5P_LINK_CREATE.Rd man/H5S.Rd man/H5T.Rd man/h5const.Rd man/h5createAttribute.Rd man/h5createDataset.Rd man/h5createFile.Rd man/h5createGroup.Rd man/h5errorHandling.Rd man/h5listIdentifier.Rd man/h5ls.Rd man/h5save.Rd man/h5set_extent.Rd man/h5version.Rd man/h5write.Rd man/methods-And.Rd man/methods-Dollar1.Rd man/methods-Dollar2.Rd man/methods-subset1.Rd man/methods-subset2.Rd man/rhdf5.Rd
src
src/H5.c
src/H5.h
src/H5A.c
src/H5A.h
src/H5D.c
src/H5D.h
src/H5E.c
src/H5E.h
src/H5F.c
src/H5F.h
src/H5G.c
src/H5G.h
src/H5I.c
src/H5I.h
src/H5L.c
src/H5L.h
src/H5O.c
src/H5O.h
src/H5P.c
src/H5P.h
src/H5S.c
src/H5S.h
src/H5T.c
src/H5T.h
src/H5constants.c
src/H5constants.h
src/HandleList.cpp
src/HandleList.h
src/HandleList2.h
src/HandleListWrap.c
src/HandleListcpp.h
src/Makevars
src/Makevars.win
src/h5dump.c
src/h5dump.h
src/h5ls.c
src/h5ls.h
src/h5writeDataFrame.c
src/h5writeDataFrame.h
src/hdf5source
src/hdf5source/hdf5small.tgz
src/includeWin
src/includeWin/i386
src/includeWin/i386/H5ACpkg.h
src/includeWin/i386/H5ACprivate.h
src/includeWin/i386/H5ACpublic.h
src/includeWin/i386/H5Apkg.h
src/includeWin/i386/H5Aprivate.h
src/includeWin/i386/H5Apublic.h
src/includeWin/i386/H5B2pkg.h
src/includeWin/i386/H5B2private.h
src/includeWin/i386/H5B2public.h
src/includeWin/i386/H5Bpkg.h
src/includeWin/i386/H5Bprivate.h
src/includeWin/i386/H5Bpublic.h
src/includeWin/i386/H5CSprivate.h
src/includeWin/i386/H5Cpkg.h
src/includeWin/i386/H5Cprivate.h
src/includeWin/i386/H5Cpublic.h
src/includeWin/i386/H5Dpkg.h
src/includeWin/i386/H5Dprivate.h
src/includeWin/i386/H5Dpublic.h
src/includeWin/i386/H5Edefin.h
src/includeWin/i386/H5Einit.h
src/includeWin/i386/H5Epkg.h
src/includeWin/i386/H5Eprivate.h
src/includeWin/i386/H5Epubgen.h
src/includeWin/i386/H5Epublic.h
src/includeWin/i386/H5Eterm.h
src/includeWin/i386/H5FDcore.h
src/includeWin/i386/H5FDdirect.h
src/includeWin/i386/H5FDfamily.h
src/includeWin/i386/H5FDlog.h
src/includeWin/i386/H5FDmpi.h
src/includeWin/i386/H5FDmpio.h
src/includeWin/i386/H5FDmpiposix.h
src/includeWin/i386/H5FDmulti.h
src/includeWin/i386/H5FDpkg.h
src/includeWin/i386/H5FDprivate.h
src/includeWin/i386/H5FDpublic.h
src/includeWin/i386/H5FDsec2.h
src/includeWin/i386/H5FDstdio.h
src/includeWin/i386/H5FDwindows.h
src/includeWin/i386/H5FLprivate.h
src/includeWin/i386/H5FOprivate.h
src/includeWin/i386/H5FSpkg.h
src/includeWin/i386/H5FSprivate.h
src/includeWin/i386/H5FSpublic.h
src/includeWin/i386/H5Fpkg.h
src/includeWin/i386/H5Fprivate.h
src/includeWin/i386/H5Fpublic.h
src/includeWin/i386/H5Gpkg.h
src/includeWin/i386/H5Gprivate.h
src/includeWin/i386/H5Gpublic.h
src/includeWin/i386/H5HFpkg.h
src/includeWin/i386/H5HFprivate.h
src/includeWin/i386/H5HFpublic.h
src/includeWin/i386/H5HGpkg.h
src/includeWin/i386/H5HGprivate.h
src/includeWin/i386/H5HGpublic.h
src/includeWin/i386/H5HLpkg.h
src/includeWin/i386/H5HLprivate.h
src/includeWin/i386/H5HLpublic.h
src/includeWin/i386/H5HPprivate.h
src/includeWin/i386/H5Ipkg.h
src/includeWin/i386/H5Iprivate.h
src/includeWin/i386/H5Ipublic.h
src/includeWin/i386/H5Lpkg.h
src/includeWin/i386/H5Lprivate.h
src/includeWin/i386/H5Lpublic.h
src/includeWin/i386/H5MFpkg.h
src/includeWin/i386/H5MFprivate.h
src/includeWin/i386/H5MMprivate.h
src/includeWin/i386/H5MMpublic.h
src/includeWin/i386/H5MPpkg.h
src/includeWin/i386/H5MPprivate.h
src/includeWin/i386/H5Opkg.h
src/includeWin/i386/H5Oprivate.h
src/includeWin/i386/H5Opublic.h
src/includeWin/i386/H5Oshared.h
src/includeWin/i386/H5Ppkg.h
src/includeWin/i386/H5Pprivate.h
src/includeWin/i386/H5Ppublic.h
src/includeWin/i386/H5RCprivate.h
src/includeWin/i386/H5RSprivate.h
src/includeWin/i386/H5Rpkg.h
src/includeWin/i386/H5Rprivate.h
src/includeWin/i386/H5Rpublic.h
src/includeWin/i386/H5SLprivate.h
src/includeWin/i386/H5SMpkg.h
src/includeWin/i386/H5SMprivate.h
src/includeWin/i386/H5STprivate.h
src/includeWin/i386/H5Spkg.h
src/includeWin/i386/H5Sprivate.h
src/includeWin/i386/H5Spublic.h
src/includeWin/i386/H5TSprivate.h
src/includeWin/i386/H5Tpkg.h
src/includeWin/i386/H5Tprivate.h
src/includeWin/i386/H5Tpublic.h
src/includeWin/i386/H5Vprivate.h
src/includeWin/i386/H5WBprivate.h
src/includeWin/i386/H5Zpkg.h
src/includeWin/i386/H5Zprivate.h
src/includeWin/i386/H5Zpublic.h
src/includeWin/i386/H5api_adpt.h
src/includeWin/i386/H5config.h
src/includeWin/i386/H5overflow.h
src/includeWin/i386/H5private.h
src/includeWin/i386/H5pubconf.h
src/includeWin/i386/H5public.h
src/includeWin/i386/H5version.h
src/includeWin/i386/H5win32defs.h
src/includeWin/i386/SZconfig.h
src/includeWin/i386/hdf5.h
src/includeWin/i386/rice.h
src/includeWin/i386/ricehdf.h
src/includeWin/i386/szip_adpt.h
src/includeWin/x64
src/includeWin/x64/H5ACpkg.h
src/includeWin/x64/H5ACprivate.h
src/includeWin/x64/H5ACpublic.h
src/includeWin/x64/H5Apkg.h
src/includeWin/x64/H5Aprivate.h
src/includeWin/x64/H5Apublic.h
src/includeWin/x64/H5B2pkg.h
src/includeWin/x64/H5B2private.h
src/includeWin/x64/H5B2public.h
src/includeWin/x64/H5Bpkg.h
src/includeWin/x64/H5Bprivate.h
src/includeWin/x64/H5Bpublic.h
src/includeWin/x64/H5CSprivate.h
src/includeWin/x64/H5Cpkg.h
src/includeWin/x64/H5Cprivate.h
src/includeWin/x64/H5Cpublic.h
src/includeWin/x64/H5Dpkg.h
src/includeWin/x64/H5Dprivate.h
src/includeWin/x64/H5Dpublic.h
src/includeWin/x64/H5Edefin.h
src/includeWin/x64/H5Einit.h
src/includeWin/x64/H5Epkg.h
src/includeWin/x64/H5Eprivate.h
src/includeWin/x64/H5Epubgen.h
src/includeWin/x64/H5Epublic.h
src/includeWin/x64/H5Eterm.h
src/includeWin/x64/H5FDcore.h
src/includeWin/x64/H5FDdirect.h
src/includeWin/x64/H5FDfamily.h
src/includeWin/x64/H5FDlog.h
src/includeWin/x64/H5FDmpi.h
src/includeWin/x64/H5FDmpio.h
src/includeWin/x64/H5FDmpiposix.h
src/includeWin/x64/H5FDmulti.h
src/includeWin/x64/H5FDpkg.h
src/includeWin/x64/H5FDprivate.h
src/includeWin/x64/H5FDpublic.h
src/includeWin/x64/H5FDsec2.h
src/includeWin/x64/H5FDstdio.h
src/includeWin/x64/H5FDwindows.h
src/includeWin/x64/H5FLprivate.h
src/includeWin/x64/H5FOprivate.h
src/includeWin/x64/H5FSpkg.h
src/includeWin/x64/H5FSprivate.h
src/includeWin/x64/H5FSpublic.h
src/includeWin/x64/H5Fpkg.h
src/includeWin/x64/H5Fprivate.h
src/includeWin/x64/H5Fpublic.h
src/includeWin/x64/H5Gpkg.h
src/includeWin/x64/H5Gprivate.h
src/includeWin/x64/H5Gpublic.h
src/includeWin/x64/H5HFpkg.h
src/includeWin/x64/H5HFprivate.h
src/includeWin/x64/H5HFpublic.h
src/includeWin/x64/H5HGpkg.h
src/includeWin/x64/H5HGprivate.h
src/includeWin/x64/H5HGpublic.h
src/includeWin/x64/H5HLpkg.h
src/includeWin/x64/H5HLprivate.h
src/includeWin/x64/H5HLpublic.h
src/includeWin/x64/H5HPprivate.h
src/includeWin/x64/H5Ipkg.h
src/includeWin/x64/H5Iprivate.h
src/includeWin/x64/H5Ipublic.h
src/includeWin/x64/H5Lpkg.h
src/includeWin/x64/H5Lprivate.h
src/includeWin/x64/H5Lpublic.h
src/includeWin/x64/H5MFpkg.h
src/includeWin/x64/H5MFprivate.h
src/includeWin/x64/H5MMprivate.h
src/includeWin/x64/H5MMpublic.h
src/includeWin/x64/H5MPpkg.h
src/includeWin/x64/H5MPprivate.h
src/includeWin/x64/H5Opkg.h
src/includeWin/x64/H5Oprivate.h
src/includeWin/x64/H5Opublic.h
src/includeWin/x64/H5Oshared.h
src/includeWin/x64/H5Ppkg.h
src/includeWin/x64/H5Pprivate.h
src/includeWin/x64/H5Ppublic.h
src/includeWin/x64/H5RCprivate.h
src/includeWin/x64/H5RSprivate.h
src/includeWin/x64/H5Rpkg.h
src/includeWin/x64/H5Rprivate.h
src/includeWin/x64/H5Rpublic.h
src/includeWin/x64/H5SLprivate.h
src/includeWin/x64/H5SMpkg.h
src/includeWin/x64/H5SMprivate.h
src/includeWin/x64/H5STprivate.h
src/includeWin/x64/H5Spkg.h
src/includeWin/x64/H5Sprivate.h
src/includeWin/x64/H5Spublic.h
src/includeWin/x64/H5TSprivate.h
src/includeWin/x64/H5Tpkg.h
src/includeWin/x64/H5Tprivate.h
src/includeWin/x64/H5Tpublic.h
src/includeWin/x64/H5Vprivate.h
src/includeWin/x64/H5WBprivate.h
src/includeWin/x64/H5Zpkg.h
src/includeWin/x64/H5Zprivate.h
src/includeWin/x64/H5Zpublic.h
src/includeWin/x64/H5api_adpt.h
src/includeWin/x64/H5config.h
src/includeWin/x64/H5overflow.h
src/includeWin/x64/H5private.h
src/includeWin/x64/H5pubconf.h
src/includeWin/x64/H5public.h
src/includeWin/x64/H5version.h
src/includeWin/x64/H5win32defs.h
src/includeWin/x64/SZconfig.h
src/includeWin/x64/hdf5.h
src/includeWin/x64/rice.h
src/includeWin/x64/ricehdf.h
src/includeWin/x64/szip_adpt.h
src/includeWin/x64/szlib.h
src/libwin
src/libwin/i386
src/libwin/i386/libhdf5ForBioC-7.dll
src/libwin/i386/libsz-2.dll
src/libwin/x64
src/libwin/x64/libhdf5ForBioC-7.dll
src/libwin/x64/libsz-2.dll
src/myhdf5.h
src/printdatatype.c
src/printdatatype.h
src/wrap.c
vignettes
vignettes/rhdf5.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.