-## ace.R (2010-05-12)
+## ace.R (2010-12-08)
## Ancestral Character Estimation
liks[anc, ] <- v/comp[anc]
}
if (output.liks) return(liks[-TIPS, ])
- -2 * sum(log(comp[-TIPS]))
+ dev <- -2 * sum(log(comp[-TIPS]))
+ if (is.na(dev)) Inf else dev
}
out <- nlminb(rep(ip, length.out = np), function(p) dev(p),
lower = rep(0, np), upper = rep(1e50, np))
cat("Parameter estimates:\n")
names(estim) <- c("rate index", "estimate", "std-err")
print(estim, row.names = FALSE)
- cat("\nScaled likelihoods at the root (type 'x$lik.anc' to get them for all nodes):\n")
+ cat("\nScaled likelihoods at the root (type '...$lik.anc' to get them for all nodes):\n")
print(x$lik.anc[1, ])
}
}