Package: hdf5r 1.3.12

hdf5r: Interface to the 'HDF5' Binary Data Format

'HDF5' is a data model, library and file format for storing and managing large amounts of data. This package provides a nearly feature complete, object oriented wrapper for the 'HDF5' API <https://support.hdfgroup.org/documentation/hdf5/latest/_r_m.html> using R6 classes. Additionally, functionality is added so that 'HDF5' objects behave very similar to their corresponding R counterparts.

Authors:Holger Hoefling [aut, cre], Mario Annau [aut], Novartis Institute for BioMedical Research [cph]

hdf5r_1.3.12.tar.gz
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hdf5r.pdf |hdf5r.html✨
hdf5r/json (API)
NEWS

# Install 'hdf5r' in R:
install.packages('hdf5r', repos = c('https://hhoeflin.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/hhoeflin/hdf5r/issues

Pkgdown site:https://hhoeflin.github.io

Uses libs:
  • hdf5– HDF5 High Level runtime files - serial version

On CRAN:

hdf5

12.09 score 82 stars 33 packages 996 scripts 15k downloads 76 exports 3 dependencies

Last updated 5 days agofrom:56a1519364. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 25 2025
R-4.5-win-x86_64OKJan 25 2025
R-4.5-linux-x86_64OKJan 25 2025
R-4.4-win-x86_64OKJan 25 2025
R-4.4-mac-x86_64OKJan 25 2025
R-4.4-mac-aarch64OKJan 25 2025
R-4.3-win-x86_64OKJan 25 2025
R-4.3-mac-x86_64OKJan 25 2025
R-4.3-mac-aarch64OKJan 25 2025

Exports:as_hexcoerce_to_factorcoercible_to_factorcreate_emptycreateDataSetcreateGroupexistsGroupextendDataSetfactor_extflatten_dfguess_chunksguess_dimguess_dtypeguess_nelemguess_spaceH5Ah5attrh5attr_namesh5attr<-h5attributesh5closeh5constH5Dh5fileH5Fileh5flushh5garbage_collectH5GroupH5PH5P_ATTRIBUTE_CREATEH5P_CLASSH5P_DATASET_ACCESSH5P_DATASET_CREATEH5P_DATASET_XFERH5P_FILE_ACCESSH5P_FILE_CREATEH5P_LINK_ACCESSH5P_LINK_CREATEH5P_OBJECT_COPYH5P_OBJECT_CREATEH5RH5R_DATASET_REGIONH5R_OBJECTH5RefClassH5SH5TH5T_ARRAYH5T_COMPLEXH5T_COMPOUNDH5T_ENUMH5T_FLOATH5T_INTEGERH5T_LOGICALH5T_STRINGH5T_VLENh5typesh5unlinkh5versionis_hdf5is.factor_extis.h5fileis.H5Ris.H5R_DATASET_REGIONis.H5R_OBJECTlist.attributeslist.datasetslist.groupslist.objectsopenGroupopenLocationreadDataSetsubset_assign_h5.H5Dsubset_h5.H5Dsubset_h5.H5Stext_to_dtypevalues

Dependencies:bitbit64R6

Introduction to the hdf5r package

Holger Hoefling

Rendered fromhdf5r.Rmdusingknitr::rmarkdownon Jan 25 2025.

Last update: 2025-01-25
Started: 2016-09-30

Readme and manuals

Help Manual

Help pageTopics
hdf5r: A package to provide an interface to hdf5 from Rhdf5r-package
Retrieving a copy of a type$.types_env [[.types_env
Convert a double or integer to hexas_hex
Create an empty R-object according to a given HDF5 datatypecreate_empty
Create an extended factorfactor_ext
Various functions for 'factor_ext' objects!=.factor_ext ==.factor_ext as.character.factor_ext c.factor_ext coerce_to_factor coercible_to_factor factor_ext_functions is.factor_ext print.factor_ext values values.default values.factor values.factor_ext [.factor_ext [<-.factor_ext [[.factor_ext [[<-.factor_ext
Flatten a nested data.frameflatten_df
Guess the dimension of a chunkguess_chunks
Guess the HDF5 datatype of an R objectguess_dim guess_dtype guess_nelem
Guess the dataspace of an objectguess_space
Wrapper functions to provide an 'h5' compatible interface.c.H5D cbind.H5D createDataSet createGroup existsGroup extendDataSet h5 h5-wrapper h5close h5file h5flush h5unlink is.h5file list.attributes openGroup openLocation rbind.H5D readDataSet
Class for representing HDF5 attributesH5A H5A-class
Interface for HDF5 attributesh5attr h5attr<- h5attributes h5attr_names
All constants used in HDF5h5const
Class for representing HDF5 datasetsH5D H5D-class
Class for interacting with HDF5 files.H5File H5File-class
Trigger the HDF5 garbage collectionh5garbage_collect
Retrieve object from a group of fileH5Group_access [[.H5File [[.H5Group [[<-.H5File [[<-.H5Group
Class for representing HDF5 groupsH5Group H5Group-class
Class for HDF5 property list for attribute creationH5P_ATTRIBUTE_CREATE H5P_ATTRIBUTE_CREATE-class
Class for HDF5 property list classes (not HDF5 property lists)H5P_CLASS H5P_CLASS-class
Class for HDF5 property list for dataset accessH5P_DATASET_ACCESS H5P_DATASET_ACCESS-class
Class for HDF5 property list for dataset creationH5P_DATASET_CREATE H5P_DATASET_CREATE-class
Class for HDF5 property list for dataset transferH5P_DATASET_XFER H5P_DATASET_XFER-class
Class for HDF5 property list for file creationH5P_FILE_ACCESS H5P_FILE_ACCESS-class
Class for HDF5 property list for file creationH5P_FILE_CREATE H5P_FILE_CREATE-class
Class for HDF5 property list for link accessH5P_LINK_ACCESS H5P_LINK_ACCESS-class
Class for HDF5 property list for link creationH5P_LINK_CREATE H5P_LINK_CREATE-class
Class for HDF5 property list for object copyingH5P_OBJECT_COPY H5P_OBJECT_COPY-class
Class for HDF5 property list for object creationH5P_OBJECT_CREATE H5P_OBJECT_CREATE-class
Class for HDF5 property lists.H5P H5P-class
Class for HDF5 dataset-region references.H5R_DATASET_REGION H5R_DATASET_REGION-class
Various functions for 'H5R' objectsas.data.frame.H5R as.vector.H5R c.H5R cbind.H5R dim.H5R dim<-.H5R dimnames.H5R dimnames<-.H5R format.H5R H5R_functions is.H5R is.H5R_DATASET_REGION is.H5R_OBJECT length.H5R names.H5R print.H5R rbind.H5R t.H5R [.H5R [<-.H5R
Class for HDF5 Object-references.H5R_OBJECT H5R_OBJECT-class
Class for HDF5 Reference datatypes.H5R H5R-class
Base class that tracks the ids and allows for closing an idH5RefClass H5RefClass-class
Selecting and assigning subsets of HDF5-Spaces and HDF5-DatasetsH5S_H5D_subset_assign subset_assign_h5.H5D subset_h5.H5D subset_h5.H5S [.H5D [.H5S [<-.H5D
Class for representing HDF5 spacesH5S H5S-class
Class for HDF5 array datatypes.H5T_ARRAY H5T_ARRAY-class
Class for HDF5 complex datatypesH5T_COMPLEX H5T_COMPLEX-class
Class for HDF5 compound datatypes.H5T_COMPOUND H5T_COMPOUND-class
Class for HDF5 enumeration datatypes.H5T_ENUM H5T_ENUM-class
Class for HDF5 floating point datatypes.H5T_FLOAT H5T_FLOAT-class
Class for HDF5 integer-datatypes.H5T_BITFIELD H5T_INTEGER H5T_INTEGER-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 variableH5T_LOGICAL H5T_LOGICAL-class
Class for HDF5 string datatypes.H5T_STRING H5T_STRING-class
Class for HDF5 variable-length datatypes.H5T_VLEN H5T_VLEN-class
Class for HDF5 datatypes.H5T H5T-class
These are all types that are used in HDF5h5types
Return the version of the HDF5-APIh5version
Check if a file is an HDF5 fileis_hdf5
List Groups and Datasets in objectlist-groups-datasets list.datasets list.groups list.objects
Get the names of the items in the group or at the '/' root of the filenames.H5File names.H5Group
Print a data frame with extended factor objectsprint.data.frame_ext
Convert a text description to a datatypetext_to_dtype