mace {phylolm} | R Documentation |
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)
[Package phylolm version 2.6.5 Index]