R/Phybase_sim.coaltree.R

In emanuelmfonseca/P2C2M.GMYC: Model violations under the Generalized Mixed Yule Coalescent (GMYC)

sim.coaltree <- function (nspecies, theta)
{
  treestr <- paste(1:nspecies)
  height <- 0
  brlens <- rep(0, nspecies)
  for (i in nspecies:2) {
    b <- sample(1:i, 2)
    height <- height + rexp(1, rate = i * (i - 1)/theta)
    newname <- paste("(", treestr[b[1]], sep = "")
    newname <- paste(newname, ":", sep = "")
    newname <- paste(newname, round(height - brlens[b[1]],
                                    5), sep = "")
    newname <- paste(newname, ",", sep = "")
    newname <- paste(newname, treestr[b[2]], sep = "")
    newname <- paste(newname, ":", sep = "")
    newname <- paste(newname, round(height - brlens[b[2]],
                                    5), sep = "")
    newname <- paste(newname, ")", sep = "")
    treestr[b[1]] <- newname
    brlens[b[1]] <- height
    index <- 1:i
    index[b[2]] <- 0
    index <- index[index > 0]
    treestr <- treestr[index]
    brlens <- brlens[index]
  }
  treestr
}