ape (version 5.5)

read.caic: Read Tree File in CAIC Format

Description

This function reads one tree from a CAIC file. A second file containing branch lengths values may also be passed (experimental).

Usage

read.caic(file, brlen = NULL, skip = 0, comment.char = "#", ...)

Arguments

file

a file name specified by either a variable of mode character, or a double-quoted string.

brlen

a file name for the branch lengths file.

skip

the number of lines of the input file to skip before beginning to read data (this is passed directly to scan()).

comment.char

a single character, the remaining of the line after this character is ignored (this is passed directly to scan()).

…

Further arguments to be passed to scan().

Value

an object of class "phylo".

Warning

The branch length support is still experimental and was not fully tested.

Details

Read a tree from a file in the format used by the CAIC and MacroCAIc program.

References

Purvis, A. and Rambaut, A. (1995) Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data. CABIOS, 11 :241--251.

See Also

read.tree, read.nexus

Examples

# NOT RUN {
### The same example than in read.tree, without branch lengths.
### An extract from Sibley and Ahlquist (1990)
cat("AAA","Strix_aluco","AAB","Asio_otus",
   "AB","Athene_noctua","B","Tyto_alba",
   file = "ex.tre", sep = "\n")
tree.owls <- read.caic("ex.tre")
plot(tree.owls)
tree.owls
unlink("ex.tre") # delete the file "ex.tre"
# }