Bipartite phylogenetic interaction marker

phylo_interaction() marks a pair-level phylogenetic interaction between two partner clades. It is the friendly route for bipartite ecological-network effects where rows are plant-pollinator, host-symbiont, predator-prey, or other two-partner interactions. The first fitted slice is a single q=1 location random intercept whose latent precision is the sparse Kronecker product of the two phylogenetic augmented precisions. Use relmat(1 | pair, Q = Q_pair) as the lower-level user-supplied precision escape hatch.

Usage

phylo_interaction(term, tree1, tree2)

Arguments

term

Structured pair random-effect term, currently 1 | partner1:partner2.

tree1

Ultrametric phylogeny for the first partner clade.

tree2

Ultrametric phylogeny for the second partner clade.

Value

A formula marker; never evaluated by users.

Details

The fitted first slice supports ordinary Gaussian, ordinary Poisson, and ordinary NB2 location models wherever the existing q=1 structured mu machinery is active. Binary/Bernoulli incidence models and additive models that combine partner main phylogenies and the pair-level interaction are planned after the corresponding likelihood and multi-layer structured recovery tests are in place.

Examples

bf(
  count ~ x + phylo_interaction(
    1 | plant:pollinator,
    tree1 = plant_tree,
    tree2 = pollinator_tree
  )
)
#> <drm_formula>
#> count ~ x + phylo_interaction(1 | plant:pollinator, tree1 = plant_tree, tree2 =
#> pollinator_tree)