R/create_generative_trees.R

In richelbilderbeek/pirouette: Create a Bayesian Posterior from a Phylogeny

#' Create a Yule tree.
#'
#' A Yule model is also known as a pure-birth model;
#' a birth-death model without extinction.
#' @inheritParams default_params_doc
#' @return a phylogenetic tree of type \link[ape]{phylo}
#' @author Giovanni Laudanno, Richèl J.C. Bilderbeek
#' @examples
#' n_taxa <- 31
#' crown_age <- 41
#'
#' create_yule_tree(
#'   n_taxa = 31,
#'   crown_age = 41
#' )
#' @export
create_yule_tree <- function(
  n_taxa = 6,
  crown_age = 10,
  n_0 = 2
) {
  diff <- (log(n_taxa) - log(n_0)) / crown_age
  mu <- 0
  lambda <- diff + mu
  sim_tree <- TESS::tess.sim.taxa.age(
    n = 1,
    lambda = lambda,
    mu     = mu,
    nTaxa = n_taxa,
    age = crown_age,
    MRCA = TRUE
  )[[1]]
  sim_tree
}

#' Create a (constant-rate) birth-death (BD) tree
#' @inheritParams default_params_doc
#' @return a phylogenetic tree of type \link[ape]{phylo}
#' @author Giovanni Laudanno, Richèl J.C. Bilderbeek
#' @examples
#' n_taxa <- 31
#' crown_age <- 41
#' phylogeny <- create_bd_tree(
#'   n_taxa = n_taxa,
#'   crown_age = crown_age
#' )
#' @export
create_bd_tree <- function(
  n_taxa = 6,
  crown_age = 10,
  n_0 = 2,
  mu = 0.1
) {
  diff <- (log(n_taxa) - log(n_0)) / crown_age
  lambda <- diff + mu
  sim_tree <- TESS::tess.sim.taxa.age(
    n = 1,
    lambda = lambda,
    mu     = mu,
    nTaxa = n_taxa,
    age = crown_age,
    MRCA = TRUE
  )[[1]]
  sim_tree
}