-## ace.R (2007-12-14)
+## ace.R (2008-03-10)
## Ancestral Character Estimation
-## Copyright 2005-2007 Emmanuel Paradis and Ben Bolker
+## Copyright 2005-2008 Emmanuel Paradis and Ben Bolker
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
V <- corMatrix(Initialize(corStruct, data.frame(x)),
corr = FALSE)
invV <- solve(V)
- obj$ace <- varAY %*% invV %*% x
+ o <- gls(x ~ 1, correlation = Initialize(corStruct, data.frame(x)))
+ GM <- o$coefficients
+ obj$ace <- drop(varAY %*% invV %*% (x - GM) + GM)
+ names(obj$ace) <- (nb.tip + 1):(nb.tip + nb.node)
if (CI) {
CI95 <- matrix(NA, nb.node, 2)
se <- sqrt((varA - varAY %*% invV %*% t(varAY))[cbind(1:nb.node, 1:nb.node)])