Chapter 5 Binary files

Binary connections (Connections) are now the preferred way to handle binary files.

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5.1 Binary data formats

Packages h5, Bioconductor’s rhdf5, RNetCDF and ncdf4 on CRAN provide interfaces to NASA’s HDF5 (Hierarchical Data Format, see https://www.hdfgroup.org/HDF5/) and to UCAR’s netCDF data files (network Common Data Form, see http://www.unidata.ucar.edu/software/netcdf/).

Both of these are systems to store scientific data in array-oriented ways, including descriptions, labels, formats, units, …. HDF5 also allows groups of arrays, and the R interface maps lists to HDF5 groups, and can write numeric and character vectors and matrices.

NetCDF’s version 4 format (confusingly, implemented in netCDF 4.1.1 and later, but not in 4.0.1) includes the use of various HDF5 formats. This is handled by package ncdf4 whereas RNetCDF handles version 3 files.

The availability of software to support these formats is somewhat limited by platform, especially on Windows.

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5.2 dBase files (DBF)

dBase was a DOS program written by Ashton-Tate and later owned by Borland which has a binary flat-file format that became popular, with file extension .dbf. It has been adopted for the ’Xbase’ family of databases, covering dBase, Clipper, FoxPro and their Windows equivalents Visual dBase, Visual Objects and Visual FoxPro (see http://www.e-bachmann.dk/docs/xbase.htm). A dBase file contains a header and then a series of fields and so is most similar to an R data frame. The data itself is stored in text format, and can include character, logical and numeric fields, and other types in later versions (see for example http://www.digitalpreservation.gov/formats/fdd/fdd000325.shtml and http://www.clicketyclick.dk/databases/xbase/format/index.html).

Functions read.dbf and write.dbf provide ways to read and write basic DBF files on all R platforms. For Windows users odbcConnectDbase in package RODBC provides more comprehensive facilities to read DBF files via Microsoft’s dBase ODBC driver (and the Visual FoxPro driver can also be used via odbcDriverConnect).

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