Files and Groups

Objects representing HDF5 Files and Groups

H5File-class

Class for interacting with HDF5 files.

is_hdf5()

Check if a file is an HDF5 file

H5Group-class

Class for representing HDF5 groups

`[[`(<H5Group>) `[[`(<H5File>) `[[<-`(<H5Group>) `[[<-`(<H5File>)

Retrieve object from a group of file

names(<H5Group>) names(<H5File>)

Get the names of the items in the group or at the / root of the file

Spaces and Datasets

Objects representing HDF5 Datasets and Spaces

H5D-class

Class for representing HDF5 datasets

H5S-class

Class for representing HDF5 spaces

subset_h5.H5S() `[`(<H5S>) subset_h5.H5D() `[`(<H5D>) subset_assign_h5.H5D() `[<-`(<H5D>)

Selecting and assigning subsets of HDF5-Spaces and HDF5-Datasets

create_empty()

Create an empty R-object according to a given HDF5 datatype

guess_chunks()

Guess the dimension of a chunk

guess_nelem() guess_dim() guess_dtype()

Guess the HDF5 datatype of an R object

guess_space()

Guess the dataspace of an object

list.groups() list.datasets() list.objects()

List Groups and Datasets in object

HDF5 Datatypes

Objects representing HDF5 Datatypes

h5types

These are all types that are used in HDF5

H5T-class

Class for HDF5 datatypes.

H5T_ARRAY-class

Class for HDF5 array datatypes.

H5T_COMPLEX-class

Class for HDF5 complex datatypes

H5T_COMPOUND-class

Class for HDF5 compound datatypes.

H5T_ENUM-class

Class for HDF5 enumeration datatypes.

H5T_FLOAT-class

Class for HDF5 floating point datatypes.

H5T_INTEGER-class

Class for HDF5 integer-datatypes.

H5T_LOGICAL-class

Class for HDF5 logical datatypes. This is an enum with the 3 values FALSE, TRUE and NA mapped on values 0, 1 and 2. Is transparently mapped onto a logical variable

H5T_STRING-class

Class for HDF5 string datatypes.

H5T_VLEN-class

Class for HDF5 variable-length datatypes.

text_to_dtype()

Convert a text description to a datatype

HDF5 Attributes

h5attributes() h5attr_names() h5attr() `h5attr<-`()

Interface for HDF5 attributes

H5A-class

Class for representing HDF5 attributes

HDF5 Reference objects

H5R-class

Class for HDF5 Reference datatypes.

H5R_DATASET_REGION-class

Class for HDF5 dataset-region references.

H5R_OBJECT-class

Class for HDF5 Object-references.

is.H5R() is.H5R_OBJECT() is.H5R_DATASET_REGION() names(<H5R>) length(<H5R>) `[`(<H5R>) `[<-`(<H5R>) c(<H5R>) dim(<H5R>) `dim<-`(<H5R>) t(<H5R>) dimnames(<H5R>) `dimnames<-`(<H5R>) cbind(<H5R>) rbind(<H5R>) print(<H5R>) format(<H5R>) as.data.frame(<H5R>) as.vector(<H5R>)

Various functions for H5R objects

HDF5 Property lists

H5P-class

Class for HDF5 property lists.

H5P_ATTRIBUTE_CREATE-class

Class for HDF5 property list for attribute creation

H5P_CLASS-class

Class for HDF5 property list classes (not HDF5 property lists)

H5P_DATASET_ACCESS-class

Class for HDF5 property list for dataset access

H5P_DATASET_CREATE-class

Class for HDF5 property list for dataset creation

H5P_DATASET_XFER-class

Class for HDF5 property list for dataset transfer

H5P_FILE_ACCESS-class

Class for HDF5 property list for file creation

H5P_FILE_CREATE-class

Class for HDF5 property list for file creation

H5P_LINK_ACCESS-class

Class for HDF5 property list for link access

H5P_LINK_CREATE-class

Class for HDF5 property list for link creation

H5P_OBJECT_COPY-class

Class for HDF5 property list for object copying

H5P_OBJECT_CREATE-class

Class for HDF5 property list for object creation

Helpers

h5const

All constants used in HDF5

`$`(<types_env>) `[[`(<types_env>)

Retrieving a copy of a type

h5file() createGroup() openLocation() openGroup() createDataSet() readDataSet() h5close() h5flush() existsGroup() is.h5file() extendDataSet() rbind(<H5D>) cbind(<H5D>) c(<H5D>) h5unlink() list.attributes()

Wrapper functions to provide an h5 compatible interface.

h5version()

Return the version of the HDF5-API

h5garbage_collect()

Trigger the HDF5 garbage collection

H5RefClass-class

Base class that tracks the ids and allows for closing an id

as_hex()

Convert a double or integer to hex

flatten_df()

Flatten a nested data.frame

print(<data.frame_ext>)

Print a data frame with extended factor objects

Extended factors

factor_ext()

Create an extended factor

values() as.character(<factor_ext>) `[[`(<factor_ext>) `[[<-`(<factor_ext>) `[`(<factor_ext>) `[<-`(<factor_ext>) is.factor_ext() coercible_to_factor() coerce_to_factor() print(<factor_ext>) `==`(<factor_ext>) `!=`(<factor_ext>) c(<factor_ext>)

Various functions for factor_ext objects

Package description

hdf5r-package

hdf5r: A package to provide an interface to hdf5 from R