coanc_tree {bnpsd}

Calculate coancestry matrix corresponding to a tree

Description

This function calculates the coancestry matrix of the subpopulations which are tip nodes in the input tree. The edges of this tree are coancestry values relative to the parent node of each child node.

Usage

coanc_tree(tree)

Arguments

tree

The coancestry tree relating the k_subpops subpopulations. Must be a phylo object from the ape package (see ape::read.tree()). This tree may have a valid root edge (non-NULL tree$root.edge between 0 and 1), which is incorporated in the output calculations.

Details

The calculation takes into account that total coancestries are non-linear functions of the per-edge coancestries. Interestingly, the calculation can be simplified by a simple transformation performed by tree_additive(), see that for more information. The self-coancestry (diagonal values) are the total coancestries of the tip nodes. The coancestry between different subpopulations is the total coancestry of their last common ancestor node.

Value

The k_subpops-by-k_subpops coancestry matrix. The order of subpopulations along the rows and columns of this matrix matches tree$tip.label. The tip labels of the tree are copied to the row and column names of this matrix.

See Also

fit_tree() for the inverse function (when applied to coancestry matrices generated by a tree without noise).

tree_additive() for calculating the additive edges. This function is called internally by coanc_tree but the additive edges are not returned here, so call tree_additive() if you desired them.

Examples

# for simulating a tree with `rtree`
library(ape)

# a typical, non-trivial example
# number of tip subpopulations
k_subpops <- 3
# simulate a random tree
tree_subpops <- rtree( k_subpops )
# coancestry matrix of subpopulations
coancestry <- coanc_tree( tree_subpops )