Function to import partitioned data from nexus files

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'.

See also

read.nexus.data, read.phyDat

Author

Klaus Schliep klaus.schliep@gmail.com

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
#> $codon1
#> 10 sequences with 4 character and 4 different site patterns.
#> The states are a c g t 
#> 
#> $codon2
#> 10 sequences with 4 character and 4 different site patterns.
#> The states are a c g t 
#> 
#> $codon3
#> 10 sequences with 4 character and 4 different site patterns.
#> The states are a c g t 
#> 
#> $range
#> 10 sequences with 3 character and 3 different site patterns.
#> The states are a c g t 
#> 
#> $range2
#> 10 sequences with 6 character and 6 different site patterns.
#> The states are a c g t 
#> 
#> $singles
#> 10 sequences with 3 character and 3 different site patterns.
#> The states are a c g t 
#> 
unlink(zz)