sim_history_conditional: 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 conditioning on the tip states (currently on all node states) we can relax this to allow only conditioning on the tip states, which would require an implementation of pruning algorithm (including transition-probablity matrix computation)

Description

Simulate history of discrete-character changes over a bifurcation tree conditioning on the tip states (currently on all node states) we can relax this to allow only conditioning on the tip states, which would require an implementation of pruning algorithm (including transition-probablity matrix computation)

Usage

sim_history_conditional(
  tree,
  Q,
  Q_ages = NULL,
  states,
  nsim = 1L,
  trait = NULL
)

Arguments

tree	A bifurcation tree of class "phylo" (here we assume it either has a node.states, node.data, or maps component so that we can fetch the state of each node, both internal and tip, in the tree to condition on)
Q	An instantaneous-rate matrix (or a list of matrices for a piecewise constant geographic model) characterizes the CTMC
Q_ages	A vector containing boundaries of time intervals for a piecewise constant geographic model (NULL means a constant model); the length of this vector should be one shorter than the Q-matrix list, sorted from oldest to youngest.
states	States of the discrete character
nsim	Number of simulations to perform
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

## Not run: 
tree <- ape::rtree(7)
Q <- list(matrix(c(-1, 1, 1, -1), ncol = 2, byrow = TRUE))
states <- c("A", "B")
one_history <- sim_history_conditional(tree, Q, states = states)
# todo: add a tree to data file

## End(Not run)

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