chronopl(phy, lambda, node.age = 1, node = "root", CV = FALSE)
"phylo"
.node.age
; "root"
is a short-cut the number of the
node."phylo"
with branch lengths as estimated by
the function. There are two or three further attributes:CV = TRUE
). lambda
must be given. The known ages are given in
node.age
, and the correponding node numbers in node
.
These two arguments must obviously be of the same length. By default,
an age of 1 is assumed for the root, and the ages of the other nodes
are estimated.
The cross-validation used here is different from the one proposed by Sanderson (2002). Here, each tip is dropped successively and the analysis is repeated with the reduced tree: the estimated dates for the remaining nodes are compared with the estimates from the full data. For the $i$th tip the following is calculated:
$$\sum_{j=1}^{n-2}{\frac{(t_j - t_j^{-i})^2}{t_j}}$$,
where $t_j$ is the estimated date for the $j$th node with the full phylogeny, $t_j^{-i}$ is the estimated date for the $j$th node after removing tip $i$ from the tree, and $n$ is the number of tips.
chronogram
, ratogram
,
NPRS.criterion
, chronoMPL