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 evonet
print(x, ...)
# S3 method for evonet
plot(x, col = "blue", lty = 1, lwd = 1, alpha = 0.5,
arrows = 0, arrow.type = "classical", ...)
# S3 method for evonet
as.phylo(x, ...)
# S3 method for evonet
as.networx(x, weight = NA, ...)
# S3 method for evonet
as.network(x, directed = TRUE, ...)
# S3 method for evonet
as.igraph(x, directed = TRUE, use.labels = TRUE, ...)an object of class "phylo" or "evonet".
a vector (or a matrix if to = NULL) giving the node
or tip numbers involved in the reticulations.
a vector of the same length than from.
colors, line type and width of the reticulations (recycled if necessary).
a value between 0 and 1 specifying the transparency of the reticulations.
see fancyarrows.
idem.
a numeric vector giving the weights for the
reticulations when converting to the class "networx"
(recycled or shortened if needed).
a logical: should the network be considered as
directed? TRUE by default.
a logical specifying whether to use the tip and node
labels when building the network of class "igraph".
arguments passed to other methods.
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.
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
# NOT RUN {
tr <- rcoal(5)
(x <- evonet(tr, 6:7, 8:9))
plot(x)
# }
Run the code above in your browser using DataLab