phylolm (version 2.6.5)

three.point.compute: Computations with a (generalized) three-point structured tree

Description

Computes \(P'V^{-1}Q\) and the \(\log(\det V)\) of a (generalized) three-point structured matrix.

Usage

three.point.compute(phy, P, Q = NULL, diagWeight = NULL, 
            check.pruningwise = TRUE, check.names = TRUE, check.precision = TRUE)

Value

vec11

\(1'V^{-1}1\).

P1

\(P'V^{-1}1\).

PP

\(P'V^{-1}P\).

Q1

\(Q'V^{-1}1\).

QQ

\(Q'V^{-1}Q\).

PQ

\(P'V^{-1}Q\).

logd

\(\log(\det V)\).

Arguments

phy

a rooted phylogenetic tree of type phylo with branch lengths, to represent the 3-point structured matrix \(V_0\). Note that the matrix of interest is \(V = D V_0 D\).

P,Q

two matrices.

diagWeight

a vector containing the diagonal elements of the diagonal matrix \(D\) if \(V\) has a generalized 3-point structure: \(V = D V_0 D\)

check.pruningwise

If FALSE, the tree is assumed to be in pruningwise order.

check.names

if FALSE, the row names of P, Q, and the names of diagWeight are assumed to be the same as the labels of the tips in the tree.

check.precision

if FALSE, diagWeight will be allowed to be below Machine epsilon. Recommended to remain TRUE.

Author

Lam Si Tung Ho, Robert Lachlan

References

Ho, L. S. T. and An?, C. (2014). "A linear-time algorithm for Gaussian and non-Gaussian trait evolution models". Systematic Biology 63(3):397-408.

See Also

transf.branch.lengths.

Examples

tre1 = rtree(500)
tre2 = transf.branch.lengths(phy=tre1, model="OUrandomRoot",
                             parameters = list(alpha = 0.5))
Q = rTrait(n=2,tre1)
y = rTrait(n=1,tre1)
P = cbind(1,y)
three.point.compute(tre2$tree,P,Q,tre2$diagWeight)