| read.nexus.splits {phangorn} | R Documentation |
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 klaus.schliep@gmail.com
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)