-## chronopl.R (2009-07-06)
+## chronopl.R (2011-07-04)
## Molecular Dating With Penalized Likelihood
-## Copyright 2005-2009 Emmanuel Paradis
+## Copyright 2005-2011 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
ratio <- age.min[1]/ini.time[node[1]]
ini.time <- ini.time*ratio
+ ## because if (!is.null(age.max)), 'node' is modified, so we copy it in case CV = TRUE:
+ node.bak <- node
+
if (length(node) > 1) {
ini.time[node] <- age.min
real.edge.length <- ini.time[e[, 1]] - ini.time[e[, 2]]
ini.time[e[i, 1]] <- ini.time[e[1, 1]] + 2 * real.edge.length[i]
next
}
- browser()
+ ##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))
+ ##print(min(real.edge.length))
}
}
## `unknown.ages' will contain the index of the nodes of unknown age:
if (CV) ophy <- phy
phy$edge.length <- age[e[, 1]] - age[e[, 2]]
if (CV) attr(phy, "D2") <-
- chronopl.cv(ophy, lambda, age.min, age.max, node,
+ chronopl.cv(ophy, lambda, age.min, age.max, node.bak,
n, S, tol, eval.max, iter.max, ...)
phy
}
BT <- branching.times(ophy)
D2 <- numeric(n)
- cat(" dropping tip")
for (i in 1:n) {
- cat(" ", i, sep = "")
+ cat("\r dropping tip ", i, " / ", n, sep = "")
tr <- drop.tip(ophy, i)
j <- which(ophy$edge[, 2] == i)
if (ophy$edge[j, 1] %in% nodes) {