read.cep reads a file formatted with relaxed strict CEP format
used in Canoco software, among others.
read.cep(file, positive=TRUE)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.
File name (character variable).
Only positive entries, like in community data.
Jari Oksanen
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:
Two or three title cards, most importantly specifying the format and the number of items per record.
Data in condensed format: First number on the line is the site identifier (an integer), and it is followed by pairs (‘couplets’) of numbers identifying the species and its abundance (an integer and a floating point number).
Species and site names, given in Fortran format (10A8):
Ten names per line, eight columns for each.
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.
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"
if (FALSE) {
theclassic <- read.cep("dune.spe")}
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