What is cepreader?

Cornell Ecology Programs (CEP) introduced a popular data file format for ecological community data, and this format was later adopted by CANOCO software with small modifications. Many legacy data sets are still written in these formats. The cepreader package provides function readCEP() to read these data files into R as a data.frame or a sparse Matrix. The function does not handle all possible CEP formats, but it handles transposed condensed format which was the most popular one plus some other popular formats.

Why a Package?

The package has only function readCEP(). This function was earlier included in the vegan package. However, the function is written in FORTRAN, and FORTRAN input can interfere with other compiled code, in particular in Windows. To minimize the risk of conflicts, reading of CEP files was moved to a separate package. The CEP format can save data in flexible forms as defined by a FORTRAN format specification in the file, and this format is best interpreted using FORTRAN code. The vegan package has function read.cep() that uses only R code and can read many files written in transposed condensed format, but this package is more versatile and robust and can handle a wider array of CEP formats.