read.nexus.partitions {phangorn} | R Documentation |
Function to import partitioned data from nexus files
Description
read.nexus.partitions
reads in sequences in NEXUS format and splits
the data according to the charsets given in the SETS block.
Usage
read.nexus.partitions(file, return = "list", ...)
Arguments
file |
a file name. |
return |
either returns a list where each element is a 'phyDat' object or an object of class 'multiphyDat' |
... |
Further arguments passed to or from other methods. |
Value
a list where each element is a 'phyDat' object or an object of class 'multiphyDat'.
Author(s)
Klaus Schliep klaus.schliep@gmail.com
See Also
Examples
tree <- rtree(10)
dat <- simSeq(tree, l=24)
fcat <- function(..., file = zz) cat(..., file=file, sep="", append=TRUE)
zz <- tempfile(pattern="file", tmpdir=tempdir(), fileext=".nex")
write.phyDat(dat, file=zz, format="nexus")
fcat("BEGIN SETS;\n")
fcat(" Charset codon1 = 1-12/3;\n")
fcat(" Charset codon2 = 2-12/3;\n")
fcat(" Charset codon3 = 3-12/3;\n")
fcat(" Charset range = 16-18;\n")
fcat(" Charset range2 = 13-15 19-21;\n")
fcat(" Charset singles = 22 23 24;\n")
fcat("END;\n")
tmp <- read.nexus.partitions(zz)
tmp
unlink(zz)
[Package phangorn version 2.12.1 Index]