fixes in mantel.test() and extract.clade()

[ape.git] / R / CDF.birth.death.R

diff --git a/R/CDF.birth.death.R b/R/CDF.birth.death.R
index 3608a35f1d08b3bb1a63232cf54b25de1ef464bc..847c37dcd20dd60ecc4649a725ff27ccfe27fd59 100644 (file)
--- a/R/CDF.birth.death.R
+++ b/R/CDF.birth.death.R
@@ -287,7 +287,7 @@ rlineage <-
     .makePhylo(edge[1:j, ], edge.length[1:j], i)
 }
 
-drop.fossil <- function(phy, tol = 0)
+drop.fossil <- function(phy, tol = 1e-8)
 {
     n <- Ntip(phy)
     x <- dist.nodes(phy)[n + 1, ][1:n]
@@ -468,7 +468,7 @@ bd.time <- function(phy, birth, death, BIRTH = NULL, DEATH = NULL,
         PAR <- matrix(NA, boot, np)
         i <- 1L
         while (i <= boot) {
-            cat("i =", i, "\n")
+            cat("\rDoing bootstrap no.", i, "\n")
             x <- sort(sample(x, replace = TRUE))
             o <- try(nlminb(ip, foo, control = list(trace = 0, eval.max = 500),
                             upper = upper, lower = lower))