-## birthdeath.R (2010-10-17)
+## birthdeath.R (2010-11-04)
## Estimation of Speciation and Extinction Rates
## with Birth-Death Models
cat(" b - d: [", x$CI[2, 1], ", ", x$CI[2, 2], "]", "\n\n", sep = "")
}
-bd.ext <- function(phy, S)
+bd.ext <- function(phy, S, conditional = TRUE)
{
- if (!inherits(phy, "phylo")) stop('object "phy" is not of class "phylo"')
+ if (!inherits(phy, "phylo"))
+ stop('object "phy" is not of class "phylo"')
if (!is.null(names(S))) {
if (all(names(S) %in% phy$tip.label)) S <- S[phy$tip.label]
else warning('the names of argument "S" and the tip labels
x <- branching.times(phy)
x <- c(x[1], x)
trm.br <- phy$edge.length[phy$edge[, 2] <= N]
- dev <- function(a, r)
- {
- -2 * (lfactorial(N - 1)
- + (N - 2) * log(r)
- + (3 * N) * log(1 - a)
- + 2 * r * sum(x[2:N])
- - 2 * sum(log(exp(r * x[2:N]) - a))
- + r * sum(trm.br)
- + sum((S - 1) * log(exp(r * trm.br) - 1))
- - sum((S + 1) * log(exp(r * trm.br) - a)))
- }
- out <- nlm(function(p) dev(p[1], p[2]), c(0, 0.2), hessian = TRUE)
- 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$hessian))))
- }
- else {
- para <- out$estimate
- se <- sqrt(diag(solve(out$hessian)))
+ if (conditional) {
+ dev <- function(a, r) {
+ if (a >= 1 || a < 0 || r <= 0) return(1e50)
+ ert <- exp(r * trm.br)
+ zeta <- (ert - 1)/(ert - a)
+ -2 * (lfactorial(N - 1)
+ + (N - 2) * log(r)
+ + N * log(1 - a)
+ + 2 * r * sum(x[2:N])
+ - 2 * sum(log(exp(r * x[2:N]) - a))
+ + sum(log(1 - zeta) + (S - 1)*log(zeta)))
+ }
+ } else {
+ dev <- function(a, r) {
+ if (a >= 1 || a < 0 || r <= 0) return(1e50)
+ -2 * (lfactorial(N - 1)
+ + (N - 2) * log(r)
+ + (3 * N) * log(1 - a)
+ + 2 * r * sum(x[2:N])
+ - 2 * sum(log(exp(r * x[2:N]) - a))
+ + r * sum(trm.br)
+ + sum((S - 1) * log(exp(r * trm.br) - 1))
+ - sum((S + 1) * log(exp(r * trm.br) - a)))
+ }
}
+ out <- nlm(function(p) dev(p[1], p[2]), c(0.1, 0.2), hessian = TRUE)
+ para <- out$estimate
+ se <- sqrt(diag(solve(out$hessian)))
Dev <- out$minimum
cat("\nExtended Version of the Birth-Death Models to\n")
cat(" Estimate Speciation and Extinction Rates\n\n")