-## birthdeath.R (2010-11-04)
+## birthdeath.R (2012-04-20)
## Estimation of Speciation and Extinction Rates
## with Birth-Death Models
## birthdeath: standard model
## bd.ext: extended version
-## Copyright 2002-2010 Emmanuel Paradis
+## Copyright 2002-2012 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
N <- length(phy$tip.label)
x <- c(NA, branching.times(phy))
dev <- function(a, r) {
- if (r <= 0) return(1e50)
+ if (r < 0 || a > 1) return(1e100)
-2 * (lfactorial(N - 1)
+ (N - 2) * log(r)
+ r * sum(x[3:N])
if (out$estimate[1] < 0) {
out <- nlm(function(p) dev(0, p), 0.2, hessian = TRUE)
para <- c(0, out$estimate)
- se <- c(0, sqrt(diag(solve(out$hessian))))
+ inv.hessian <- try(solve(out$hessian))
+ se <-
+ if (class(inv.hessian) == "try-error") NA
+ else sqrt(diag(inv.hessian))
+ se <- c(0, se)
}
else {
para <- out$estimate
- se <- sqrt(diag(solve(out$hessian)))
+ inv.hessian <- try(solve(out$hessian))
+ se <-
+ if (class(inv.hessian) == "try-error") c(NA, NA)
+ else sqrt(diag(inv.hessian))
}
Dev <- out$minimum
- ## compute the 95 % profile likelihood CIs
- ## (not very clean... but seems to work -- EP 2003-03-29)
- CI <- matrix(NA, 2, 2)
- foo <- function(p) dev(p, para[2]) - 3.84 - Dev
- inc <- 1e-2
- lo <- para[1] - inc
- up <- para[1] + inc
- while (foo(lo) < 0) lo <- lo - inc
- while (foo(up) < 0) up <- up + inc
- CI[1, 1] <- uniroot(foo, lower = lo, upper = para[1])$root
- if (CI[1, 1] < 0) CI[1, 1] <- 0
- CI[1, 2] <- uniroot(foo, lower = para[1], upper = up)$root
- foo <- function(p) dev(para[1], p) - 3.84 - Dev
- lo <- para[2] - inc
- up <- para[2] + inc
- while (foo(lo) < 0) lo <- lo - inc
- while (foo(up) < 0) up <- up + inc
- CI[2, 1] <- uniroot(foo, lower = lo, upper = para[2])$root
- CI[2, 2] <- uniroot(foo, lower = para[2], upper = up)$root
+
+ ## 95% profile likelihood CIs
+
+ ## which: index of the parameter (1 or 2)
+ ## s: sign of the increment (-1 or +1)
+ foo <- function(which, s) {
+ i <- 0.1
+
+ if (which == 1) {
+ p <- para[1] + s * i
+ bar <- function() dev(p, para[2])
+ } else { # which == 2
+ p <- para[2] + s * i
+ bar <- function() dev(para[1], p)
+ }
+
+ while (i > 1e-9) {
+ while (bar() < Dev + 3.84) p <- p + s * i
+ p <- p - s * i
+ i <- i / 10
+ }
+ p
+ }
+
+ CI <- mapply(foo, c(1, 2, 1, 2), c(-1, -1, 1, 1))
+ dim(CI) <- c(2, 2)
+
names(para) <- names(se) <- rownames(CI) <- c("d/b", "b-d")
colnames(CI) <- c("lo", "up")
obj <- list(tree = deparse(substitute(phy)), N = N,