Reads a CEP (Canoco) data file
read.cep reads a file formatted by relaxed strict CEP format
Canoco software, among others.
File name (character variable).
Maximum number of non-zero entries.
Only positive entries, like in community data.
Run function, even if R refuses first.
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
TWINSPAN. Later, Cajo ter Braak wrote
DECORANA, where he adopted the format, but relaxed it
somewhat (that's why I call it a ‘relaxed strict’ format). Further, he
introduced a more ordinary ‘free’ format, and allowed the use of
classical Fortran style ‘open’ format with fixed field widths. This
function should be able to deal with all these
whereas it cannot read many of the traditional CEP alternatives.
All variants of CEP formats have:
Two or three title cards, most importantly specifying the format (or word
FREE) and the number of items per record (number of species and sites for
Data in one of three accepted formats:
Condensed format: First number on the line is the site identifier, and it is followed by pairs (‘couplets’) of numbers identifying the species and its abundance (an integer and a floating point number).
Open Fortran format, where the first number on the line must be the site number, followed by abundance values in fields of fixed widths. Empty fields are interpreted as zeros.
‘Free’ format, where the numbers are interpreted as abundance values. These numbers must be separated by blank space, and zeros must be written as zeros.
Species and site names, given in Fortran format
(10A8): Ten names per line, eight columns for each.
positive = TRUE the function removes all lines 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.
The function relies on smooth linking of Fortran file IO in R session. This is not guaranteed to work, and therefore the function may not work in your system, but it can crash the R session. Therefore the default is that the function does not run. If you still want to try:
Save your session
If you transfer files between operating systems or platforms, you
should always check that your file is formatted to your current
platform. For instance, if you transfer files from Windows to Linux,
you should change the files to
unix format, or your session may
crash when Fortran program tries to read the invisible characters that
Windows uses at the end of each line.
If you compiled
gfortran, the input is
probably corrupted. You either should compile
vegan with other
FORTRAN compilers or not to use
read.cep. The problems still
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.
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