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)
"print"(x, ...)
"plot"(x, col = "blue", lty = 1, lwd = 1, alpha = 0.5, arrows = 0, arrow.type = "classical", ...)
"as.phylo"(x, ...)
"as.networx"(x, weight = NA, ...)
"as.network"(x, directed = TRUE, ...)
"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 phangorn, network, and
igraph, respectively.
as.networx in package phangorn
tr <- rcoal(5)
(x <- evonet(tr, 6:7, 8:9))
plot(x)
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