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

In phangorn: Phylogenetic Reconstruction and Analysis

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, ...)

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.

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.

Note

read.nexus.splits reads in the splits block of a nexus file. It assumes that different co-variables are tab delimited and the bipartition are separated with white-space. Comments in square brackets are ignored.

Author(s)

Klaus Schliep [e-mail]

See Also

prop.part, lento, as.splits, as.networx

Examples

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

phangorn documentation built on Sept. 17, 2024, 5:08 p.m.