ape: evonet – R documentation

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evonet

Evolutionary Networks

Description

evonet builds a network from a tree of class "phylo". There are print, plot, and reorder methods as well as a few conversion functions.

Usage

evonet(phy, from, to = NULL)
## S3 method for class 'evonet'
print(x, ...)
## S3 method for class 'evonet'
plot(x, col = "blue", lty = 1, lwd = 1, alpha = 0.5,
              arrows = 0, arrow.type = "classical", ...)
## S3 method for class 'evonet'
Nedge(phy)
## S3 method for class 'evonet'
reorder(x, order = "cladewise", index.only = FALSE, ...)
## S3 method for class 'evonet'
as.phylo(x, ...)
## S3 method for class 'evonet'
as.networx(x, weight = NA, ...)
## S3 method for class 'evonet'
as.network(x, directed = TRUE, ...)
## S3 method for class 'evonet'
as.igraph(x, directed = TRUE, use.labels = TRUE, ...)

as.evonet(x, ...)
## S3 method for class 'phylo'
as.evonet(x, ...)

read.evonet(file = "", text = NULL, comment.char = "", ...)
write.evonet(x, file = "", ...)

Arguments

`phy`	an object of class `"phylo"`.
`x`	an object of class `"evonet"`.
`from`	a vector (or a matrix if `to = NULL`) giving the node or tip numbers involved in the reticulations.
`to`	a vector of the same length than `from`.
`col, lty, lwd`	colors, line type and width of the reticulations (recycled if necessary).
`alpha`	a value between 0 and 1 specifying the transparency of the reticulations.
`arrows, arrow.type`	see `fancyarrows`.
`order, index.only`	see `reorder.phylo`.
`weight`	a numeric vector giving the weights for the reticulations when converting to the class `"networx"` (recycled or shortened if needed).
`directed`	a logical: should the network be considered as directed? `TRUE` by default.
`use.labels`	a logical specifying whether to use the tip and node labels when building the network of class `"igraph"`.
`file, text, comment.char`	see `read.tree`.
`...`	arguments passed to other methods.

Details

evonet is a constructor function that checks the arguments.

The classes "networx", "network", and "igraph" are defined in the packages phangorn, network, and igraph, respectively.

read.evonet reads networks from files in extended newick format (Cardona et al. 2008).

Value

an object of class c("evonet", "phylo") which is made of an object of class "phylo" plus an element reticulation coding additional edges among nodes and uses the same coding rules than the edge matrix.

The conversion functions return an object of the appropriate class.

Author(s)

Emmanuel Paradis, Klaus Schliep

References

Cardona, G., Rossell, F., and Valiente, G. (2008) Extended Newick: it is time for a standard representation of phylogenetic networks. BMC Bioinformatics, 9, 532.

Examples

tr <- rcoal(5)
(x <- evonet(tr, 6:7, 8:9))
plot(x)
## simple example of extended Newick format:
(enet <- read.evonet(text = "((a:2,(b:1)#H1:1):1,(#H1,c:1):2);"))
plot(enet, arrows=1)
## from Fig. 2 in Cardona et al. 2008:
z <- read.evonet(text =
"((1,((2,(3,(4)Y#H1)g)e,(((Y#H1, 5)h,6)f)X#H2)c)a,((X#H2,7)d,8)b)r;")
z
plot(z)
## Not run: 
if (require(igraph)) {
    plot(as.igraph(z))
}
## 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