node_optimal_values: Computation of the optimal values at nodes and tips.

In pbastide/PhylogeneticEM: Automatic Shift Detection using a Phylogenetic EM

Computation of the optimal values at nodes and tips.

Description

compute_betas_from_shifts computes the optimal values at the nodes and tips of the tree, given the value at the root and the list of shifts occurring in the tree. It assumes an OU model.

Usage

node_optimal_values(param, phylo)

Arguments

param	an object of class params_process.
phylo	a phylogenetic tree, class phylo.

Value

Matrix of size ntraits x (ntaxa + Nnode) of the optimal values at the node and tips of the tree. Column names correspond to the number of the node in the phylo object.

Examples

set.seed(1792)
ntaxa = 10
tree <- rphylo(ntaxa, 1, 0.1)
# parameters of the process
par <- params_process("BM",                             ## Process
                      p = 2,                            ## Dimension
                      variance = diag(0.5, 2, 2) + 0.5, ## Rate matrix
                      edges = c(4, 10, 15),             ## Positions of the shifts
                      values = cbind(c(5, 4),           ## Values of the shifts
                                     c(-4, -5),
                                     c(5, -3)))
plot(par, phylo = tree, traits = 1, value_in_box = TRUE,
     shifts_bg = "white", root_bg = "white", ancestral_as_shift = TRUE, root_adj = 5)
nodelabels()
node_optimal_values(par, tree)

pbastide/PhylogeneticEM documentation built on Feb. 12, 2024, 1:27 a.m.