Package index • rhdf5

About rhdf5

rhdf5: rhdf5: An interface between HDF5 and R

High level functions

Wrappers around several low-level functions

h5testFileLocking() h5disableFileLocking() h5enableFileLocking(): Test and set file locking for HDF5
h5createFile(): Create HDF5 file
h5createGroup(): Create HDF5 group
h5delete(): Delete objects within a HDF5 file
h5deleteAttribute(): Delete attribute
h5dump(): Dump the content of an HDF5 file.
h5errorHandling(): Set how HDF5 error messages are displayed
h5read(): Reads and write object in HDF5 files
h5readAttributes(): Read all attributes from a given location in an HDF5 file
h5save(): Saves a one or more objects to an HDF5 file.
h5set_extent(): Set a new dataset extension
h5write() h5writeDataset(): Write object to an HDF5 file.
h5writeAttribute(): Write an R object as an HDF5 attribute
h5closeAll(): Close open HDF5 handles
h5const() h5constType() h5default(): HDF5 library constants.
h5createAttribute(): Create HDF5 attribute
h5createDataset(): Create HDF5 dataset
h5listIdentifier() h5validObjects(): List all open HDF5 objects.
h5ls(): List the content of an HDF5 file.
h5readTimestamps(): Read the time stamps associated with an HDF5 group or dataset.
h5version(): Print the rhdf5 and libhdf5 version numbers

HDF5 Files

Functions for working with HDF5 Files

H5Fclose(): Close access to an HDF5 file
H5Fcreate(): Create an HDF5 file
H5Fflush(): Flush all buffers associated with a file to disk
H5Fget_filesize(): Find the size of an open HDF5 file
H5Fget_intent(): Determine the read only or read/write status of an open file handle.
H5Fget_name(): Retrieve the name of the file to which an object belongs
H5Fget_create_plist() H5Fget_access_plist(): Get property lists associated with an HDF5 file
H5Fis_hdf5(): Determine whether a file is in the HDF5 format
H5Fopen(): Open an existing HDF5 file

HDF5 Groups

Functions for working with HDF5 Groups

H5Gclose(): Close a specified group
H5Gcreate(): Create a new HDF5 group and link it to a location in a file
H5Gcreate_anon(): Create a new HDF5 group without linking it into a file
H5Gget_info() H5Gget_info_by_name() H5Gget_info_by_idx(): Retrieve information about a group
H5Gopen(): Open a specified group

HDF5 Datasets

Functions for working with HDF5 Datasets

H5Dchunk_dims() H5Dis_chunked(): Additional functions for finding details of dataset chunking.
H5Dclose(): Close an open HDF5 dataset
H5Dcreate(): Create a new HDF5 dataset
H5Dget_create_plist(): Return a copy of the dataset creation property list for a dataset
H5Dget_num_chunks(): Get the number of chunks in a dataset
H5Dget_space(): Return a copy of the HDF5 dataspace for a dataset
H5Dget_storage_size(): Find the amount of storage allocated for a dataset
H5Dget_type(): Return a copy of the HDF5 datatype for a dataset
H5Dopen(): Open an existing HDF5 dataset
H5Dread(): Read from an HDF5 dataset
H5Dset_extent(): Change the dimensions of an HDF5 dataset
H5Dwrite(): Write data to dataset

HDF5 Dataspaces

Functions for working with HDF5 Dataspaces

H5Sclose(): Close and release a dataspace
H5Scombine_hyperslab(): Perform operation between an existing selection and an another hyperslab definition.
H5Scombine_select(): Combine two selections
H5Scopy(): Create a copy of a dataspace
H5Screate(): Create a new dataspace of a specified type
H5Screate_simple(): Create a simple dataspace
H5Sget_select_npoints(): Find the number of elements in a dataspace selection
H5Sget_simple_extent_dims(): Find the size of a dataspace
H5Sis_simple(): Determine whether a dataspace is a simple dataspace
H5Sselect_all(): Set the selection region of a dataspace to include all elements
H5Sselect_hyperslab(): Perform operation between an existing selection and an another hyperslab definition.
H5Sselect_index(): Select elements of a dataspace using R-style indexing
H5Sselect_none(): Set the selection region of a dataspace to include no elements
H5Sselect_valid(): Check that a selection is valid
H5Sset_extent_simple(): Set the size of a dataspace
H5Sunlimited(): Retrieve value for H5S_UNLIMITED constant

HDF5 Attributes

Functions for working with HDF5 Attributes

H5Aclose(): Close an HDF5 attribute
H5Acreate(): Create an attribute for an HDF5 object
H5Adelete(): Delete an specified attribute of an HDF5 object
H5Aexists(): Check whether an specific attribute exists for an HDF5 object
H5Aget_name(): Get the name of an HDF5 attribute object
H5Aget_space(): Get a copy of the attribute dataspace
H5Aget_type(): Get a copy of the attribute datatype
H5Aopen() H5Aopen_by_name() H5Aopen_by_idx(): Open an attribute for an HDF5 object
H5Aread(): Read data from an HDF5 attribute
H5Awrite(): Write data to an HDF5 attribute

HDF5 Objects

Functions for working with HDF5 Objects

H5Oclose(): Close an HDF5 object
H5Ocopy(): Copies an HDF5 object
H5Oget_info(): Retrieves the metadata for an HDF5 object specified by an identifier.
H5Oget_num_attrs() H5Oget_num_attrs_by_name(): Find the number of attributes associated with an HDF5 object
H5Olink(): Create a hard link to an object in an HDF5 file
H5Oopen(): Open an object in an HDF5 file

HDF5 Links

Functions for working with HDF5 Links

H5Lcopy(): Copy a link from one location to another
H5Lcreate_external(): Create a link to an object in a different HDF5 file
H5Ldelete(): Remove a link from a group
H5Lexists(): Confirm existence of a link
H5Lget_info(): Find information about a link
H5Lmove(): Move a link within an HDF5 file

HDF5 Identifiers

Functions for working with HDF5 Identifiers

show(<H5IdComponent>) `&`(<H5IdComponent>,<character>) `$`(<H5IdComponent>) `$<-`(<H5IdComponent>) `[`(<H5IdComponent>) `[<-`(<H5IdComponent>): An S4 class representing an H5 object
H5Iget_name(): Retrieve the name of an object from a given identifier
H5Iget_type(): Find the type of an object
H5Iis_valid(): Determine whether an identifier is valid

HDF5 Datatypes

Functions for working with HDF5 Datatypes

H5Tset_cset() H5Tget_cset(): Retrieve or set the character set to be used in a string datatype.
H5Tenum_create() H5Tenum_insert(): Create or modify an HDF5 enum datatype
H5Tget_class() H5Tget_nmembers(): Get details of HDF5 data types
H5Tset_precision() H5Tget_precision(): Retrieve or set the precision of an HDF5 datatype
H5Tset_size() H5Tget_size(): Retrieve or set the type of padding used by string datatype
H5Tset_strpad() H5Tget_strpad(): Retrieve or set the type of padding used by string datatype
H5Tcopy(): Copy an existing datatype
H5Tis_variable_str(): Determine whether a datatype is a variable length string

HDF5 Property Lists

File Creation Properties

H5Pget_version(): Get version information for objects in a file creation property list
H5Pset_shared_mesg_nindexes() H5Pget_shared_mesg_nindexes(): Get and set the number of object header message indexes
H5Pset_shared_mesg_phase_change() H5Pget_shared_mesg_phase_change(): Get and set threshold values for storage of shared object header message indexes
H5Pset_istore_k() H5Pget_istore_k(): Get and set the 1/2 rank of an indexed storage B-tree
H5Pset_shared_mesg_index() H5Pget_shared_mesg_index(): Get and set shared object header message index properties
H5Pset_sizes() H5Pget_sizes(): Get and set the sizes of offsets and lengths used in an HDF5 file
H5Pset_sym_k() H5Pget_sym_k(): Get and set the size of the symbol table B-tree 1/2 rank and the leaf node 1/2 size
H5Pset_userblock() H5Pget_userblock(): Get and set the user block size

File Access Properties

H5Pset_libver_bounds() H5Pget_libver_bounds(): Control the range of HDF5 library versions that will be compatible with a file.
H5Pset_fapl_ros3(): Set the read-only S3 virtual file driver

Group Creation Properties

H5Pset_create_intermediate_group() H5Pget_create_intermediate_group(): Get and set whether to create missing intermediate groups

Object Creation Properties

H5Pset_obj_track_times() H5Pget_obj_track_times(): Set whether to record timestamps for operations performed on an HDF5 object.

Dataset Creation Properties

H5Pall_filters_avail() H5Pget_nfilters() H5Pget_filter(): Query dataset filter properties.
H5Pset_shuffle(): Add the shuffle filter to the chunk processing pipeline.
H5Pset_nbit(): Add the N-Bit filter to the chunk processing pipeline.
H5Pset_deflate(): Add the deflate compression filter to the chunk processing pipeline.
H5Pset_szip(): Add the SZIP compression filter to the chunk processing pipeline.
H5Pset_bzip2(): Add the BZIP2 filter to the chunk processing pipeline.
H5Pset_blosc(): Add the BLOSC filter to the chunk processing pipeline.
H5Pset_lzf(): Add the LZF filter to the chunk processing pipeline.
H5Pset_filter(): Add a filter to the dataset filter pipeline.
H5Pset_chunk() H5Pget_chunk(): Get and set the size of the chunks used to store a chunked layout dataset
H5Pset_chunk_cache(): Set parameters for the raw data chunk cache
H5Pset_layout() H5Pget_layout(): Get and set the type of storage used to store the raw data for a dataset
H5Pclose(): Close and release a property list
H5Pcopy(): Copy an existing property list to create a new property list
H5Pcreate(): Create a new HDF5 property list
H5Pget_class(): Return the property list class identifier for a property list
H5Pset_fill_value(): Set the fill value for an HDF5 dataset
H5Pset_fill_time() H5Pget_fill_time(): Set the time when fill values are written to a dataset
H5Pfill_value_defined(): Determine whether a property list has a fill value defined
H5Pset_fapl_ros3(): Set the read-only S3 virtual file driver

HDF5 References

H5R: H5R - References to objects and regions
H5Rcreate(): Create a reference
H5Rdereference(): Open a reference object.
show(<H5Ref>) length(<H5Ref>) c(<H5Ref>) `[`(<H5Ref>): An S4 class representing H5 references.
H5Rget_name(): Return the name of the object that a reference points to
H5Rget_obj_type(): Identify the type of object that a reference points to
H5Rget_region(): Return selection for a reference to dataset region

HDF5 Filters

H5Zfilter_avail(): Determine whether a filter is available on this system

H5 Library Functions

H5open() H5close() H5garbage_collect() H5get_libversion(): HDF5 General Library Functions