evonet
builds a network from a tree of class
"phylo"
. There are print
and plot
methods as well
as a few conversion functions.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, ...)
"phylo"
or "evonet"
.to = NULL
) giving the node
or tip numbers involved in the reticulations.from
.fancyarrows
."networx"
(recycled or shortened if needed).TRUE
by default."igraph"
.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.
evonet
is a constructor function that checks the arguments. The classes "networx"
, "network"
, and "igraph"
are defined in the packages
as.networx
in package tr <- rcoal(5)
(x <- evonet(tr, 6:7, 8:9))
plot(x)
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