mace: Multi-task learning for ancestral state estimation.

In lamho86/phylolm: Phylogenetic Linear Regression

Multi-task learning for ancestral state estimation.

Description

Estimate the ancestral states of multiple traits simultaneously using a regularized maximum likelihood objective.

Usage

mace(trait, phy, lambda = NULL)

Arguments

trait	a matrix of trait values. Each row is one species and each column is a trait.
phy	a phylogenetic tree of type phylo with branch lengths.
lambda	regularizer parameter.

Details

Traits are assumed to evolve according to the Brownian motion model.

Value

a numeric vector of estimated ancestral states.

Note

The default choice for lambda was proposed by Ho et al. (2019).

Author(s)

Lam Si Tung Ho

References

Ho, Lam Si Tung, Vu Dinh, and Cuong V. Nguyen. "Multi-task learning improves ancestral state reconstruction." Theoretical Population Biology 126 (2019): 33-39.

Examples

m = 3
anc = c(0, 8, 16)
sig2 = c(1, 1, 2)
tree = rtree(50)

trait = rTrait(n = 1, phy = tree, model = "BM",
               parameters=list(ancestral.state = anc[1], sigma2 = sig2[1]))
for (i in 2:m) {
  trait = cbind(trait,rTrait(n = 1, phy = tree, model = "BM",
                             parameters=list(ancestral.state = anc[i], sigma2 = sig2[i])))
}
res = mace(trait, tree)
print(res)

lamho86/phylolm documentation built on Nov. 11, 2023, 6:17 a.m.