evonet

0th

Percentile

Evolutionary Networks

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

Keywords
manip, hplot
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':
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, ...)
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.

See Also

as.networx in package phangorn

Aliases
Examples
tr <- rcoal(5)
(x <- evonet(tr, 6:7, 8:9))
plot(x)
Documentation reproduced from package ape, version 3.0-2, License: GPL (>= 2)

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