PhylogeneticEM (version 1.8.0)

equivalent_shifts: Find all equivalent shifts allocations and values.

Description

equivalent_shifts computes the equivalent shifts positions and their corresponding values, assuming an ultrametric tree.

Usage

equivalent_shifts(
  phylo,
  params,
  T_tree = incidence.matrix(phylo),
  part.list = enumerate_tips_under_edges(phylo),
  times_shared = NULL
)

Value

object of class equivalent_shifts, with entries:

eq_shifts_edges

matrix of equivalent shifts

shifts_and_betas

matrix of corresponding shifts values

phylo

the entry phylogenetic tree

p

the dimension

Arguments

phylo

a phylogenetic tree, of class phylo.

params

an object of class params_process, result inference by function PhyloEM, or constructed through function params_process

T_tree

(optional) matrix of incidence of the tree, result of function incidence.matrix

part.list

(optional) list of partition of the tree, result of function enumerate_tips_under_edges.

times_shared

(optional) a matrix, result of function compute_times_ca.

Details

This function is only valid for ultrametric trees, and for models: BM, OU with fixed root or stationary root. It assumes that there are no homoplasies.

See Also

plot.equivalent_shifts, extract.equivalent_shifts, params_BM, params_OU, enumerate_parsimony

Examples

if (requireNamespace("TreeSim", quietly = TRUE)) {
  ## Simualte a tree
  set.seed(17920902)
  ntaxa = 20
  phylo <- TreeSim::sim.bd.taxa.age(n = ntaxa, numbsim = 1, lambda = 0.1,
                                   mu = 0, age = 1, mrca = TRUE)[[1]]
  
  ## Define parameters (BM, fixed root)
  params <- params_BM(p = 4, edges = c(6, 17, 31),
                     values = cbind(1:4, -(1:4), rep(1, 4)))
  ## Find equivalent solutions and plot them
  eq_shifts <- equivalent_shifts(phylo, params)
  eq_shifts
  plot(eq_shifts)
  ## Extract the values
  # Shifts values for trait 2, for the three shifts (rows), and three solutions (columns)
  extract(eq_shifts, trait = 2, what = "shifts_values")
  # Root values for trait 4, for the tree solutions (columns)
  extract(eq_shifts, trait = 4, what = "root_values")
  ## Define parameters (OU, stationary root
  params <- params_OU(p = 4, edges = c(6, 17, 31),
                     selection.strength = 0.1,
                     values = cbind(1:4, -(1:4), rep(1, 4)),
                     random = TRUE)
  ## Find equivalent solutions and plot them
  eq_shifts <- equivalent_shifts(phylo, params)
  eq_shifts
  plot(eq_shifts)
  ## Extract the values
  # Shifts values for trait 2, for the three shifts (rows), and three solutions (columns)
  extract(eq_shifts, trait = 2, what = "shifts_values")
  # Root values for trait 4, for the three solutions (columns)
  extract(eq_shifts, trait = 4, what = "root_values")
}