# R Interface to HDF5

## Documentation for package ‘rhdf5’ version 2.54.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

C H L R S misc

## -- C --

c-method | An S4 class representing H5 references.

## -- H --

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 | Open an attribute for an HDF5 object
H5Aopen_by_idx | Open an attribute for an HDF5 object
H5Aopen_by_name | Open an attribute for an HDF5 object
H5Aread | Read data from an HDF5 attribute
H5Awrite | Write data to an HDF5 attribute
H5close | HDF5 General Library Functions
h5closeAll | Close open HDF5 handles
h5const | HDF5 library constants.
h5constants | HDF5 library constants.
h5constType | HDF5 library constants.
h5createAttribute | Create HDF5 attribute
h5createDataset | Create HDF5 dataset
h5createFile | Create HDF5 file
h5createGroup | Create HDF5 group
H5Dchunk_dims | Additional functions for finding details of dataset chunking.
H5Dclose | Close an open HDF5 dataset
H5Dcreate | Create a new HDF5 dataset
h5default | HDF5 library constants.
h5delete | Delete objects within a HDF5 file
h5deleteAttribute | Delete attribute
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
h5disableFileLocking | Test and set file locking for HDF5
H5Dis_chunked | Additional functions for finding details of dataset chunking.
H5Dopen | Open an existing HDF5 dataset
H5Dread | Read from an HDF5 dataset
H5Dset_extent | Change the dimensions of an HDF5 dataset
h5dump | Dump the content of an HDF5 file.
H5Dwrite | Write data to dataset
H5D_extras | Additional functions for finding details of dataset chunking.
h5enableFileLocking | Test and set file locking for HDF5
h5errorHandling | Set how HDF5 error messages are displayed
H5Fclose | Close access to an HDF5 file
H5Fcreate | Create an HDF5 file
H5Fflush | Flush all buffers associated with a file to disk
H5Fget_access_plist | Get property lists associated with an HDF5 file
H5Fget_create_plist | Get property lists associated with an HDF5 file
H5Fget_filesize | Find the size of an open HDF5 file
H5Fget_intent | Retermine 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_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
H5functions | HDF5 General Library Functions
H5garbage_collect | HDF5 General Library Functions
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
H5get_libversion | HDF5 General Library Functions
H5Gget_info | Retrieve information about a group
H5Gget_info_by_idx | Retrieve information about a group
H5Gget_info_by_name | Retrieve information about a group
H5Gopen | Open a specified group
H5IdComponent-class | 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
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
h5listIdentifier | List all open HDF5 objects.
h5listObjects | List all open HDF5 objects.
H5Lmove | Move a link within an HDF5 file
h5ls | List the content of an HDF5 file.
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 | Find the number of attributes associated with an HDF5 object
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
H5open | HDF5 General Library Functions
H5Pall_filters_avail | Query dataset filter properties.
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
H5Pfill_value_defined | Determine whether a property list has a fill value defined
H5Pget_chunk | Get and set the size of the chunks used to store a chunked layout dataset
H5Pget_class | Return the property list class identifier for a property list
H5Pget_create_intermediate_group | Get and set whether to create missing intermediate groups
H5Pget_fill_time | Set the time when fill values are written to a dataset
H5Pget_filter | Query dataset filter properties.
H5Pget_istore_k | Get and set the 1/2 rank of an indexed storage B-tree
H5Pget_layout | Get and set the type of storage used to store the raw data for a dataset
H5Pget_libver_bounds | Control the range of HDF5 library versions that will be compatible with a file.
H5Pget_nfilters | Query dataset filter properties.
H5Pget_obj_track_times | Set whether to record timestamps for operations performed on an HDF5 object.
H5Pget_shared_mesg_index | Get and set shared object header message index properties
H5Pget_shared_mesg_nindexes | Get and set the number of object header message indexes
H5Pget_shared_mesg_phase_change | Get and set threshold values for storage of shared object header message indexes
H5Pget_sizes | Get and set the sizes of offsets and lengths used in an HDF5 file
H5Pget_sym_k | Get and set the size of the symbol table B-tree 1/2 rank and the leaf node 1/2 size
H5Pget_userblock | Get and set the user block size
H5Pget_version | Get version information for objects in a file creation property list
H5Pobject_track_times | Set whether to record timestamps for operations performed on an HDF5 object.
H5Pset_blosc | Add the BLOSC filter to the chunk processing pipeline.
H5Pset_bzip2 | Add the BZIP2 filter to the chunk processing pipeline.
H5Pset_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_create_intermediate_group | Get and set whether to create missing intermediate groups
H5Pset_deflate | Add the deflate compression filter to the chunk processing pipeline.
H5Pset_fapl_ros3 | Set the read-only S3 virtual file driver
H5Pset_fill_time | Set the time when fill values are written to a dataset
H5Pset_fill_value | Set the fill value for an HDF5 dataset
H5Pset_filter | Add a filter to the dataset filter pipeline.
H5Pset_istore_k | Get and set the 1/2 rank of an indexed storage B-tree
H5Pset_layout | Get and set the type of storage used to store the raw data for a dataset
H5Pset_libver_bounds | Control the range of HDF5 library versions that will be compatible with a file.
H5Pset_lzf | Add the LZF filter to the chunk processing pipeline.
H5Pset_nbit | Add the N-Bit filter to the chunk processing pipeline.
H5Pset_obj_track_times | Set whether to record timestamps for operations performed on an HDF5 object.
H5Pset_shared_mesg_index | Get and set shared object header message index properties
H5Pset_shared_mesg_nindexes | Get and set the number of object header message indexes
H5Pset_shared_mesg_phase_change | Get and set threshold values for storage of shared object header message indexes
H5Pset_shuffle | Add the shuffle filter to the chunk processing pipeline.
H5Pset_sizes | Get and set the sizes of offsets and lengths used in an HDF5 file
H5Pset_sym_k | Get and set the size of the symbol table B-tree 1/2 rank and the leaf node 1/2 size
H5Pset_szip | Add the SZIP compression filter to the chunk processing pipeline.
H5Pset_userblock | Get and set the user block size
H5P_chunk | Get and set the size of the chunks used to store a chunked layout dataset
H5P_chunk_cache | Set parameters for the raw data chunk cache
H5P_create_intermediate_group | Get and set whether to create missing intermediate groups
H5P_fill_time | Set the time when fill values are written to a dataset
H5P_fill_value | Set the fill value for an HDF5 dataset
H5P_layout | Get and set the type of storage used to store the raw data for a dataset
H5P_libver_bounds | Control the range of HDF5 library versions that will be compatible with a file.
H5R | H5R - References to objects and regions
H5Rcreate | Create a reference
H5Rdereference | Open a reference object.
h5read | Reads and write object in HDF5 files
h5readAttributes | Read all attributes from a given location in an HDF5 file
h5readTimestamps | Read the time stamps associated with an HDF5 group or dataset.
H5Ref-class | 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
h5save | Saves a one or more objects to an HDF5 file.
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
h5set_extent | Set a new dataset extension
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
H5Tcopy | Copy an existing datatype
H5Tenum_create | Create or modify an HDF5 enum datatype
H5Tenum_insert | Create or modify an HDF5 enum datatype
h5testFileLocking | Test and set file locking for HDF5
H5Tget_class | Get details of HDF5 data types
H5Tget_cset | Retrieve or set the character set to be used in a string datatype.
H5Tget_nmembers | Get details of HDF5 data types
H5Tget_precision | Retrieve or set the precision of an HDF5 datatype
H5Tget_size | Retrieve or set the type of padding used by string datatype
H5Tget_strpad | Retrieve or set the type of padding used by string datatype
H5Tis_variable_str | Determine whether a datatype is a variable length string
H5Tset_cset | Retrieve or set the character set to be used in a string datatype.
H5Tset_precision | Retrieve or set the precision of an HDF5 datatype
H5Tset_size | Retrieve or set the type of padding used by string datatype
H5Tset_strpad | Retrieve or set the type of padding used by string datatype
H5T_cset | Retrieve or set the character set to be used in a string datatype.
H5T_enum | Create or modify an HDF5 enum datatype
H5T_ops | Get details of HDF5 data types
H5T_precision | Retrieve or set the precision of an HDF5 datatype
H5T_size | Retrieve or set the type of padding used by string datatype
H5T_strpad | Retrieve or set the type of padding used by string datatype
h5validObjects | List all open HDF5 objects.
h5version | Print the rhdf5 and libhdf5 version numbers
h5write | Write object to an HDF5 file.
h5write.default | Write object to an HDF5 file.
h5writeAttribute | Write an R object as an HDF5 attribute
h5writeAttribute.array | Write an R object as an HDF5 attribute
h5writeDataset | Write object to an HDF5 file.
h5writeDataset.array | Write object to an HDF5 file.
h5writeDataset.data.frame | Write object to an HDF5 file.
H5Zfilter_avail | Determine whether a filter is available on this system
h5_createAttribute | Create HDF5 attribute
h5_createDataset | Create HDF5 dataset
h5_createFile | Create HDF5 file
h5_createGroup | Create HDF5 group
h5_delete | Delete objects within a HDF5 file
h5_deleteAttribute | Delete attribute
h5_dump | Dump the content of an HDF5 file.
h5_errorHandling | Set how HDF5 error messages are displayed
h5_FileLocking | Test and set file locking for HDF5
h5_read | Reads and write object in HDF5 files
h5_readAttributes | Read all attributes from a given location in an HDF5 file
h5_save | Saves a one or more objects to an HDF5 file.
h5_set_extent | Set a new dataset extension
h5_write | Write object to an HDF5 file.
h5_writeAttribute | Write an R object as an HDF5 attribute

## -- L --

length-method | An S4 class representing H5 references.

## -- R --

rhdf5 | rhdf5: An interface between HDF5 and R

## -- S --

show-method | An S4 class representing an H5 object
show-method | An S4 class representing H5 references.

## -- misc --

$-method | An S4 class representing an H5 object
$<--method | An S4 class representing an H5 object
&-method | An S4 class representing an H5 object
[-method | An S4 class representing an H5 object
[-method | An S4 class representing H5 references.
[<--method | An S4 class representing an H5 object