liks[cbind(TIPS, x)] <- 1
phy <- reorder(phy, "pruningwise")
- E <- if (use.expm) expm::expm else ape::matexpo
+ ## E <- if (use.expm) expm::expm else ape::matexpo
+ E <- if (use.expm) {
+ library(expm)
+ get("expm", "package:expm")
+ } else ape::matexpo
Q <- matrix(0, nl, nl)
dev <- function(p, output.liks = FALSE) {