edgeLength methods
These functions give information about and allow replacement of edge lengths.
hasEdgeLength(x)
## S4 method for signature 'phylo4'
hasEdgeLength(x)
edgeLength(x, ...)
## S4 method for signature 'phylo4'
edgeLength(x, node)
edgeLength(x, use.names = TRUE, ...) <- value
## S4 replacement method for signature 'phylo4'
edgeLength(x, use.names = TRUE, ...) <- value
depthTips(x)
## S4 method for signature 'phylo4'
depthTips(x)
nodeDepth(x, node)
## S4 method for signature 'phylo4'
nodeDepth(x, node)
nodeHeight(x, node, from)
## S4 method for signature 'phylo4'
nodeHeight(x, node, from = c("root", "all_tip", "min_tip", "max_tip"))
sumEdgeLength(x, node)
## S4 method for signature 'phylo4'
sumEdgeLength(x, node)
isUltrametric(x, tol = .Machine$double.eps^0.5)
## S4 method for signature 'phylo4'
isUltrametric(x, tol = .Machine$double.eps^0.5)x |
a |
... |
optional arguments (none used at present). |
node |
optional numeric or character vector indicating the nodes for which edge |
use.names |
should the the name attributes of |
value |
a numeric vector indicating the new values for the edge lengths |
from |
The point of reference for calculating the height of
the node. |
tol |
the tolerance to decide whether all the tips have the
same depth to test if the tree is ultrametric. Default is
|
The edgeLength function returns the edge length in the same
order as the edges in the matrix.
whether or not the object has edge lengths (logical)
a named vector of the edge length for the object
whether or not the tree is ultrametric (all the tips are have the same depth (distance from the root) (logical)
the sum of the edge lengths for a set of
nodes (intended to be used with ancestors or descendants)
the distance between a node and the root or the tips. The format of the result will depend on the options and the number of nodes provided, either a vector or a list.
Deprecated, now replaced by nodeHeight. A
named vector indicating the “depth” (the distance between
the root and a given node).
Deprecated, now replaced by nodeHeight.
ancestors, descendants, .Machine for
more information about tolerance.
data(geospiza)
hasEdgeLength(geospiza) # TRUE
topoGeo <- geospiza
edgeLength(topoGeo) <- NULL
hasEdgeLength(topoGeo) # FALSE
edgeLength(geospiza)[2] # use the position in vector
edgeLength(geospiza)["16-17"] # or the name of the edge
edgeLength(geospiza, 17) # or the descendant node of the edge
## The same methods can be used to update an edge length
edgeLength(geospiza)[2] <- 0.33
edgeLength(geospiza)["16-17"] <- 0.34
edgeLength(geospiza, 17) <- 0.35
## Test if tree is ultrametric
isUltrametric(geospiza) # TRUE
## indeed all tips are at the same distance from the root
nodeHeight(geospiza, nodeId(geospiza, "tip"), from="root")
## compare distances from tips of two MRCA
nodeHeight(geospiza, MRCA(geospiza, c("pallida", "psittacula")), from="min_tip")
nodeHeight(geospiza, MRCA(geospiza, c("fortis", "difficilis")), from="min_tip")
## or the same but from the root
nodeHeight(geospiza, MRCA(geospiza, c("pallida", "psittacula")), from="root")
nodeHeight(geospiza, MRCA(geospiza, c("fortis", "difficilis")), from="root")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.