ape: write.nexus.data – R documentation

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write.nexus.data

Write Character Data in NEXUS Format

Description

This function writes in a file a list of data in the NEXUS format. The names of the vectors of the list are used as taxon names.

For the moment, only sequence data (DNA or protein) are supported.

Usage

write.nexus.data(x, file, format = "dna", datablock = TRUE,
                 interleaved = TRUE, charsperline = NULL,
                 gap = NULL, missing = NULL)

Arguments

`x`	a matrix or a list of data each made of a single vector of mode character where each element is a character state (e.g., “A”, “C”, ...) Objects of class of “DNAbin” are accepted.
`file`	a file name specified by either a variable of mode character, or a double-quoted string.
`format`	a character string specifying the format of the sequences. Four choices are possible: `"dna"` (the default) `"protein"`, `"standard"` or `"continuous"` or any unambiguous abbreviation of these (case insensitive).
`datablock`	a logical, if `TRUE` the data are written in a single DATA block. If `FALSE`, the data are written in TAXA and CHARACTER blocks. Default is `TRUE`.
`interleaved`	a logical, if `TRUE` the data is written in interleaved format with number of characters per line as specified with `charsperline = numerical_value`. If `FALSE`, the data are written in sequential format. Default is `TRUE`.
`charsperline`	a numeric value specifying the number of characters per line when used with `interleaved = TRUE`. Default is 80.
`gap`	a character specifying the symbol for gap. Default is “`-`”.
`missing`	a character specifying the symbol for missing data. Default is “`?`”.

Details

If the sequences have no names, then they are given “1”, “2”, ..., as names in the file.

Sequences must be all of the same length.

Value

None (invisible ‘NULL’).

Author(s)

Johan Nylander nylander@scs.fsu.edu and Thomas Guillerme

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

## Not run: 
## Write interleaved DNA data with 100 characters per line in a DATA block
data(woodmouse)
write.nexus.data(woodmouse, file= "wood.ex.nex", interleaved = TRUE, charsperline = 100)
## Write sequential DNA data in TAXA and CHARACTERS blocks
data(cynipids)
write.nexus.data(cynipids, file = "cyn.ex.nex", format = "protein",
                 datablock = FALSE, interleaved = FALSE)
unlink(c("wood.ex.nex", "cyn.ex.nex"))

## End(Not run)

ape

Analyses of Phylogenetics and Evolution

v5.5

GPL-2 | GPL-3

Authors

Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>), Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>), Joseph Brown [aut, cph] (<https://orcid.org/0000-0002-3835-8062>), Santiago Claramunt [aut, cph] (<https://orcid.org/0000-0002-8926-5974>), Julien Claude [aut, cph] (<https://orcid.org/0000-0002-9267-1228>), Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph] (<https://orcid.org/0000-0003-0596-9112>), Benoit Durand [aut, cph], Julien Dutheil [aut, cph] (<https://orcid.org/0000-0001-7753-4121>), RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme [aut, cph] (<https://orcid.org/0000-0003-4325-1275>), Christoph Heibl [aut, cph] (<https://orcid.org/0000-0002-7655-3299>), Anthony Ives [aut, cph] (<https://orcid.org/0000-0001-9375-9523>), Bradley Jones [aut, cph] (<https://orcid.org/0000-0003-4498-1069>), Franz Krah [aut, cph] (<https://orcid.org/0000-0001-7866-7508>), Daniel Lawson [aut, cph] (<https://orcid.org/0000-0002-5311-6213>), Vincent Lefort [aut, cph], Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>), Jim Lemon [aut, cph], Guillaume Louvel [aut, cph] (<https://orcid.org/0000-0002-7745-0785>), Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>), Rosemary McCloskey [aut, cph] (<https://orcid.org/0000-0002-9772-8553>), Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Korbinian Strimmer [aut, cph] (<https://orcid.org/0000-0001-7917-2056>), Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)

Initial release

2021-04-24