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

Description Usage Arguments Value Note Author(s) See Also Examples

View source: R/read.nexus.splits.R

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

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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 klaus.schliep@gmail.com

See Also

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

Examples

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(sp <- as.splits(rtree(5)))
write.nexus.splits(sp)
spl <- allCircularSplits(5)
plot(as.networx(spl), "2D")
write.splits(spl, print.labels = FALSE)

phangorn documentation built on May 3, 2021, 5:07 p.m.