| evonet {ape} | R Documentation |
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, ...)
phy, x |
an object of class |
from |
a vector (or a matrix if |
to |
a vector of the same length than |
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 |
arrow.type |
idem. |
weight |
a numeric vector giving the weights for the
reticulations when converting to the class |
directed |
a logical: should the network be considered as
directed? |
use.labels |
a logical specifying whether to use the tip and node
labels when building the network of class |
... |
arguments passed to other methods. |
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.
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.
Emmanuel Paradis
as.networx in package phangorn
tr <- rcoal(5) (x <- evonet(tr, 6:7, 8:9)) plot(x)