Reconstruct ancestral embeddings under Ornstein-Uhlenbeck (pure-R reference)

Computes the fixed-root OU covariance among all nodes and then evaluates the conditional expectation of the internal nodes given the tip observations. If `z_anc` is `NULL` it is estimated by GLS using the provided (or default) OU parameters.

Usage

reconstruct_ancestral_ou_r(
  tree,
  z_obs,
  sigma2 = NULL,
  alpha = NULL,
  z_anc = NULL,
  obs_sigma = 0
)

Arguments

tree

A `phylo` object.

z_obs

Numeric matrix (`S x D`) of observed tip embeddings.

sigma2

Diffusion variance per dimension. Defaults to 1.

alpha

Selection strength per dimension. Defaults to 1.

z_anc

Optional root state per dimension.

obs_sigma

Observation noise sd.

Value

List with `z_anc`, `sigma2`, `alpha`, and `node_estimates`.