phangorn: writeDist – R documentation

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writeDist

Writing and reading distances in phylip and nexus format

Description

readDist, writeDist and write.nexus.dist are useful to exchange distance matrices with other phylogenetic programs.

Usage

writeDist(x, file = "", format = "phylip", ...)

write.nexus.dist(x, file = "", append = FALSE, upper = FALSE,
  diag = TRUE, digits = getOption("digits"), taxa = !append)

readDist(file, format = "phylip")

read.nexus.dist(file)

## S3 method for class 'dist'
unique(x, incomparables, ...)

Arguments

`x`	A `dist` object.
`file`	A file name.
`format`	file format, default is "phylip", only other option so far is "nexus".
`...`	Further arguments passed to or from other methods.
`append`	logical. If TRUE the nexus blocks will be added to a file.
`upper`	logical value indicating whether the upper triangle of the distance matrix should be printed.
`diag`	logical value indicating whether the diagonal of the distance matrix should be printed.
`digits`	passed to format inside of `write.nexus.dist`.
`taxa`	logical. If TRUE a taxa block is added.
`incomparables`	Not used so far.

Value

an object of class dist

Author(s)

Klaus Schliep klaus.schliep@gmail.com

References

Maddison, D. R., Swofford, D. L. and Maddison, W. P. (1997) NEXUS: an extensible file format for systematic information. Systematic Biology, 46, 590–621.

Examples

data(yeast)
dm <- dist.ml(yeast)
writeDist(dm)
write.nexus.dist(dm)

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