read.cep: Reads a CEP (Canoco) data file

Description Usage Arguments Details Value Note Author(s) References Examples


read.cep reads a file formatted with relaxed strict CEP format used in Canoco software, among others.


read.cep(file, positive=TRUE)



File name (character variable).


Only positive entries, like in community data.


Cornell Ecology Programs (CEP) introduced several data formats designed for punched cards. One of these was the ‘condensed strict’ format which was adopted by popular software DECORANA and TWINSPAN. A relaxed variant of this format was later adopted in Canoco software (ter Braak 1984). Function read.cep reads legacy files written in this format.

The condensed CEP and CANOCO formats have:

With option positive = TRUE the function removes all rows and columns with zero or negative marginal sums. In community data with only positive entries, this removes empty sites and species. If data entries can be negative, this ruins data, and such data sets should be read in with option positive = FALSE.


Returns a data frame, where columns are species and rows are sites. Column and row names are taken from the CEP file, and changed into unique R names by make.names after stripping the blanks.


Function read.cep used Fortran to read data in vegan 2.4-5 and earlier, but Fortran I/O is no longer allowed in CRAN packages, and the function was re-written in R. The original Fortran code was more robust, and there are several legacy data sets that may fail with the current version, but could be read with the previous Fortran version. Github package cepreader makes available the original Fortran-based code. The cepreader package can also read ‘free’ and ‘open’ Canoco formats that are not handled in this function.

The function is based on read.fortran. If the REAL format defines a decimal part for species abundances (such as F5.1), read.fortran divides the input with the corresponding power of 10 even when the input data had explicit decimal separator. With F5.1, 100 would become 10, and 0.1 become 0.01. Function read.cep tries to undo this division, but you should check the scaling of results after reading the data, and if necessary, multiply results to the original scale.


Jari Oksanen


ter Braak, C.J.F. (1984–): CANOCO – a FORTRAN program for canonical community ordination by [partial] [detrended] [canonical] correspondence analysis, principal components analysis and redundancy analysis. TNO Inst. of Applied Computer Sci., Stat. Dept. Wageningen, The Netherlands.


## Provided that you have the file `dune.spe'
## Not run: 
theclassic <- read.cep("dune.spe")
## End(Not run)

vegan documentation built on Jan. 25, 2018, 9:45 a.m.