-## chronopl.R (2008-03-26)
+## chronopl.R (2009-07-06)
## Molecular Dating With Penalized Likelihood
-## Copyright 2005-2008 Emmanuel Paradis
+## Copyright 2005-2009 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
-chronopl <- function(phy, lambda, age.min = 1, age.max = NULL,
- node = "root", S = 1, tol = 1e-8,
- CV = FALSE, eval.max = 500, iter.max = 500, ...)
+chronopl <-
+ function(phy, lambda, age.min = 1, age.max = NULL,
+ node = "root", S = 1, tol = 1e-8,
+ CV = FALSE, eval.max = 500, iter.max = 500, ...)
{
n <- length(phy$tip.label)
ROOT <- n + 1
real.edge.length <- ini.time[e[, 1]] - ini.time[e[, 2]]
while (any(real.edge.length <= 0)) {
for (i in EDGES) {
- if (real.edge.length[i] <= 0) {
- if (e[i, 1] %in% node) {
- ini.time[e[i, 2]] <-
- ini.time[e[, 2]] - 2*real.edge.length[i]
- next
- }
- if (e[i, 2] %in% node) {
- ini.time[e[i, 1]] <-
- ini.time[e[, 1]] + 2*real.edge.length[i]
- next
- }
- ini.time[e[i, 2]] <-
- ini.time[e[, 2]] - real.edge.length[i]
- ini.time[e[i, 1]] <-
- ini.time[e[, 1]] + real.edge.length[i]
+ if (real.edge.length[i] > 0) next
+ if (e[i, 1] %in% node) {
+ ini.time[e[i, 2]] <- ini.time[e[1, 2]] - 2 * real.edge.length[i]
+ next
}
+ if (e[i, 2] %in% node) {
+ ini.time[e[i, 1]] <- ini.time[e[1, 1]] + 2 * real.edge.length[i]
+ next
+ }
+ browser()
+ ini.time[e[i, 2]] <- ini.time[e[1, 2]] - real.edge.length[i]
+ ini.time[e[i, 1]] <- ini.time[e[1, 1]] + real.edge.length[i]
}
real.edge.length <- ini.time[e[, 1]] - ini.time[e[, 2]]
+ print(min(real.edge.length))
}
}
-
## `unknown.ages' will contain the index of the nodes of unknown age:
unknown.ages <- n + 1:m
if (length(node)) {
chr <- chronopl(tr, lambda, age.min, age.max, node,
S, tol, FALSE, eval.max, iter.max, ...)
+ tmp <-
+ if (Nnode(chr) == Nnode(ophy)) BT else BT[-(ophy$edge[j, 1] - n)]
D2[i] <- sum((tmp - branching.times(chr))^2 / tmp)
} else D2[i] <- 0
}