read.nexus.splits: Function to import and export splits and networks

Description

read.nexus.splits, write.nexus.splits, read.nexus.networx, write.nexus.networx can be used to import and export splits and networks with nexus format and allow to exchange these object with other software like SplitsTree. write.splits returns a human readable output.

Usage

read.nexus.splits(file)
write.nexus.splits(obj, file = "", weights = NULL, taxa = TRUE,
  append = FALSE)
write.nexus.networx(obj, file = "", taxa = TRUE, splits = TRUE,
  append = FALSE)
read.nexus.networx(file, splits = TRUE)
write.splits(x, file = "", zero.print = ".", one.print = "|",
  print.labels = TRUE, ...)

Value

write.nexus.splits and write.nexus.networx write out the splits and networx object to read with other software like SplitsTree. read.nexus.splits and read.nexus.networx return an splits and networx object.

Arguments

file: a file name.
obj: An object of class splits.
weights: Edge weights.
taxa: logical. If TRUE a taxa block is added
append: logical. If TRUE the nexus blocks will be added to a file.
splits: logical. If TRUE the nexus blocks will be added to a file.
x: An object of class splits.
zero.print: character which should be printed for zeros.
one.print: character which should be printed for ones.
print.labels: logical. If TRUE labels are printed.
...: Further arguments passed to or from other methods.
labels: names of taxa.

Author

Klaus Schliep klaus.schliep@gmail.com

Examples

Run this code


(sp <- as.splits(rtree(5)))
write.nexus.splits(sp)
spl <- allCircularSplits(5)
plot(as.networx(spl))
write.splits(spl, print.labels = FALSE)