Read from an HDF5 dataset — H5Dread • rhdf5

H5Dread() reads a (partial) dataset from an HDF5 file into the R session.

H5Dread(
  h5dataset,
  h5spaceFile = NULL,
  h5spaceMem = NULL,
  buf = NULL,
  compoundAsDataFrame = TRUE,
  bit64conversion = "int",
  drop = FALSE
)

Arguments

h5dataset: Object of class H5IdComponent representing an open HDF5 dataset.
h5spaceFile: An object of class H5IdComponent representing a HDF5 dataspace. See H5Dget_space(), H5Screate_simple(), H5Screate() to create an object of this kind.
h5spaceMem: An object of class H5IdComponent representing a HDF5 dataspace. See H5Dget_space(), H5Screate_simple(), H5Screate() to create an object of this kind. The dimensions of the dataset in the file and in memory. The dimensions in file and in memory are interpreted in an R-like manner. The first dimension is the fastest changing dimension. When reading the file with a C-program (e.g. HDFView) the order of dimensions will invert, because in C the fastest changing dimension is the last one.
buf: Buffer to hold the read data. The buffer size has to fit the size of the memory space h5spaceMem. No extra memory will be allocated for the data. A pointer to the same data is returned.
compoundAsDataFrame: Logical vector of length 1. If TRUE, a compound datatype will be coerced to a data.frame. This is not possible, if the dataset is multi-dimensional. Otherwise the compound datatype will be returned as a list. Nested compound data types will be returned as a nested list.
bit64conversion: Defines how 64-bit integers are converted. (See the details section for more information on these options.)
drop: Logical vector of length 1. If TRUE, the HDF5 object is read as a vector with NULL dim attributes. Default is FALSE.

Details

Internally, R does not support 64-bit integers. All integers in R are 32-bit integers. By setting bit64conversion='int', a coercing to 32-bit integers is enforced, with the risk of data loss, but with the insurance that numbers are represented as integers. bit64conversion='double' coerces the 64-bit integers to floating point numbers. doubles can represent integers with up to 54-bits, but they are not represented as integer values anymore. For larger numbers there is again a data loss. bit64conversion='bit64' is recommended way of coercing. It represents the 64-bit integers as objects of class 'integer64' as defined in the package 'bit64'. Make sure that you have installed 'bit64'. The datatype 'integer64' is not part of base R, but defined in an external package. This can produce unexpected behaviour when working with the data.