Evolutionary Networks

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Description

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

Usage

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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'
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, ...)

Arguments

phy, x

an object of class "phylo" or "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

see fancyarrows.

arrow.type

idem.

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".

...

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.

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

See Also

as.networx in package phangorn

Examples

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tr <- rcoal(5)
(x <- evonet(tr, 6:7, 8:9))
plot(x)

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