phangorn: read.nexus.splits – R documentation

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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, ...)

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

Examples

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

phangorn

Phylogenetic Reconstruction and Analysis

v2.7.0

GPL (>= 2)

Authors

Klaus Schliep [aut, cre] (<https://orcid.org/0000-0003-2941-0161>), Emmanuel Paradis [aut] (<https://orcid.org/0000-0003-3092-2199>), Leonardo de Oliveira Martins [aut] (<https://orcid.org/0000-0001-5247-1320>), Alastair Potts [aut], Tim W. White [aut], Cyrill Stachniss [ctb], Michelle Kendall [ctb], Keren Halabi [ctb], Richel Bilderbeek [ctb], Kristin Winchell [ctb], Liam Revell [ctb], Mike Gilchrist [ctb], Jeremy Beaulieu [ctb], Brian O'Meara [ctb], Long Qu [ctb]

Initial release