Function reference • 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
`h5createAttribute()`	Create HDF5 attribute
`h5createDataset()`	Create HDF5 dataset
`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 all open HDF5 handles
`h5const()` `h5constType()` `h5default()`	HDF5 library constants.
`h5listIdentifier()` `h5validObjects()`	List all open HDF5 objects.
`h5ls()`	List the content of an HDF5 file.
`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_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()`	Return the dimensions of a dataset chunk
`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_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
`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.
`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
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_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

Reference

About rhdf5

High level functions

HDF5 Files

HDF5 Groups

HDF5 Datasets

HDF5 Dataspaces

HDF5 Attributes

HDF5 Objects

HDF5 Links

HDF5 Identifiers

HDF5 Datatypes

HDF5 Property Lists

File Creation Properties

File Access Properties

Object Creation Properties

Dataset Creation Properties

HDF5 References

HDF5 Filters

H5 Library Functions