phylolm (version 2.0)

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, diagMatrix = NULL, 
            check.pruningwise = TRUE, check.names = TRUE)

Arguments

phy

a rooted phylogenetic tree of type phylo with branch lengths, to represent the 3-point structured matrix $V_0$.

P,Q

two matrices.

diagMatrix

a vector containing the diagonal elements of the diagonal matrix D if V has a generalized 3-point structure.

check.pruningwise

the tree is assumed to be in pruningwise order if check.pruningwise = FALSE.

check.names

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

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).

encoding

latin1

References

Ho, L. S. T. and An�, C. "A linear-time algorithm for Gaussian and non-Gaussian trait evolution models". Systematic Biology in review.

See Also

transf.branch.lengths.

Examples

tre1 = rtree(500)
tre2 = transf.branch.lengths(phy=tre1, model="OUrandomRoot",
                             parameters = list(alpha = 0.5))
x1 = rTrait(tre1)
x2 = rTrait(tre1)
y = rTrait(tre1)
one = rep(1,50)
P = cbind(one,y)
Q = cbind(x1,x2)
three.point.compute(tre2$tree,P,Q,tre2$diagMatrix)