-## compar.ou.R (2009-05-10)
+## compar.ou.R (2010-11-04)
## Ornstein--Uhlenbeck Model for Continuous Characters
-## Copyright 2005-2009 Emmanuel Paradis
+## Copyright 2005-2010 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
compar.ou <- function(x, phy, node = NULL, alpha = NULL)
{
if (!inherits(phy, "phylo"))
- stop('object "phy" is not of class "phylo".')
+ stop('object "phy" is not of class "phylo".')
if (!is.numeric(x)) stop("'x' must be numeric.")
if (!is.null(names(x))) {
if (all(names(x) %in% phy$tip.label)) x <- x[phy$tip.label]
else warning('the names of argument "x" and the tip labels of the tree did not match: the former were ignored in the analysis.')
}
- nb.tip <- length(phy$tip.label)
- root <- nb.tip + 1
+ n <- length(phy$tip.label)
+ root <- n + 1L
if (is.null(node)) node <- numeric(0)
- if (root %in% node) node <- node[node != root]
+ if (is.character(node)) {
+ if (is.null(phy$node.label))
+ stop("argument 'node' is character but 'phy' has no node labels")
+ node <- match(node, phy$node.label) + n
+ phy$node.label <- NULL
+ }
+ if (root %in% node) node <- node[-1]
bt <- branching.times(phy)
Tmax <- bt[1]
- Wend <- matrix(0, nb.tip, length(node) + 1)
- colnames(Wend) <- c(names(sort(bt[node])), as.character(root))
+ Wend <- matrix(0, n, length(node) + 1)
+ colnames(Wend) <- c(names(sort(bt[node - n])), as.character(root))
Wstart <- Wend
Wstart[, ncol(Wstart)] <- Tmax
- root2tip <- .Call("seq_root2tip", phy$edge, nb.tip,
+ root2tip <- .Call("seq_root2tip", phy$edge, n,
phy$Nnode, PACKAGE = "ape")
- for (i in 1:nb.tip) {
+ for (i in 1:n) {
last.change <- names(Tmax)
- for (j in root2tip[[i]]) {#[-1]) {# don't need to look at the root
+ for (j in root2tip[[i]]) {
if (j %in% node) {
jb <- as.character(j)
Wend[i, last.change] <- Wstart[i, jb] <- bt[jb]
}
W <- cophenetic.phylo(phy)
dev <- function(p) {
- M <- rowSums(exp(-p[1] * Wstart) - exp(-p[1] * Wend) * p[-(1:2)])
- V <- exp(-p[1]*W) * (1 - exp(-2*p[1]*(Tmax - W/2)))
- nb.tip*log(2*pi*p[2]) + log(det(V)) +
- (t(x - M) %*% chol2inv(V) %*% (x - M)) / p[2]
+ alpha <- p[1]
+ sigma2 <- p[2]
+ if (sigma2 <= 0) return(1e100)
+ theta <- p[-(1:2)]
+ ## fixed a bug below: must be '%*% theta' instead of '* theta' (2010-03-15)
+ M <- rowSums((exp(-alpha * Wend) - exp(-alpha * Wstart)) %*% theta)
+ V <- exp(-alpha * W) * (1 - exp(-2 * alpha * (Tmax - W/2)))
+ R <- chol(V) # correction by Cecile Ane (2010-11-04)
+ n * log(2 * pi * sigma2) + 2 * sum(log(diag(R))) +
+ (t(x - M) %*% chol2inv(R) %*% (x - M)) / sigma2
}
- if (is.null(alpha))
- out <- nlm(function(p) dev(p),
- p = c(0.1, 1, rep(mean(x), ncol(Wstart))),
- hessian = TRUE)
- else
- out <- nlm(function(p) dev(c(alpha, p)),
- p = c(1, rep(mean(x), ncol(Wstart))),
- hessian = TRUE)
- para <- cbind(out$estimate, sqrt(diag(solve(out$hessian))))
+
+ out <- if (is.null(alpha))
+ nlm(function(p) dev(p),
+ p = c(0.1, 1, rep(mean(x), ncol(Wstart))), hessian = TRUE)
+ else nlm(function(p) dev(c(alpha, p)),
+ p = c(1, rep(mean(x), ncol(Wstart))), hessian = TRUE)
+
+ ## if alpha is estimated it may be that the Hessian matrix has the
+ ## corresponding column and row filled with 0, making solve() fail
+ se <- if (is.null(alpha) && all(out$hessian[1, ] == 0))
+ c(NA, sqrt(diag(solve(out$hessian[-1, -1]))))
+ else sqrt(diag(solve(out$hessian)))
+
+ para <- cbind(out$estimate, se)
nms <- c("sigma2", paste("theta", 1:ncol(Wstart), sep = ""))
if (is.null(alpha)) nms <- c("alpha", nms)
dimnames(para) <- list(nms, c("estimate", "stderr"))