sim_history: Simulate history of discrete-character changes over a...

In jsigao/prioritree: A utility for improving phylodynamic analyses in BEAST

Simulate history of discrete-character changes over a bifurcation tree conditional or unconditional on the tip states

Description

Simulate history of discrete-character changes over a bifurcation tree conditional or unconditional on the tip states

Usage

sim_history(
  tree,
  Q,
  Q_ages = NULL,
  root_freq = NULL,
  nsim = 1L,
  conditional = F,
  trait = NULL
)

Arguments

tree	A bifurcation tree of class "phylo"
Q	An instantaneous-rate matrix (or a list of matrices for a piecewise constant geographic model) characterizes the CTMC
Q_ages	Boundaries of time intervals for a piecewise constant geographic model (NULL means a constant model)
root_freq	The vector state frequencies at the root of the tree (that we will draw the root state from); if NULL then it's uniform
nsim	Number of simulations to perform
conditional	Whether condition on the observed states at the tip (i.e., stochastic mapping) or not (i.e., forward simulation)
trait	Name of the discrete trait used in the tree file (e.g., "states")

Value

A phylo and simmap object (or a multiPhylo and multiSimmap object when nsim > 1) that contains the simulated full history

Examples

tree <- ape::rtree(7)
Q <- matrix(c(-1, 1, 1, -1), ncol = 2, byrow = TRUE)
root_freq <- setNames(rep(0.5, 2), c("A", "B"))
one_history <- sim_history(tree, Q, root_freq = root_freq, conditional = FALSE)

jsigao/prioritree documentation built on Jan. 9, 2023, 5:35 a.m.