examples/simulations/NELSI_RCodeOnly/simulate.clock.R

In josephwb/chronosCI: Molecular Dating by Penalised Likelihood and Maximum Likelihood

simulate.clock <-
function(tree, params = list(rate = 0.006, noise = 0.00001)){
    rate <- params$rate
    noise <- params$noise
    data.matrix <- get.tree.data.matrix(tree)
    branch.rates <- rep(rate, times = length(tree$edge.length))
    branch.rates <- abs(branch.rates + rnorm(length(tree$edge.length), mean = 0, sd = noise))
    data.matrix[, 5] <- branch.rates
    data.matrix[, 6] <- data.matrix[, 5] * data.matrix[, 7]
    tree$edge.length <- data.matrix[, 6]
    res <- list(tree, data.matrix)
    names(res) <- c("phylogram", "tree.data.matrix")
    class(res) <- "ratesim"
    return(res)
}