splitsNetwork {phangorn}R Documentation

Phylogenetic Network

Description

splitsNetwork estimates a splits graph from a distance matrix.

Usage

splitsNetwork(dm, gamma=.1, lambda=1e-6, weight=NULL)

Arguments

dm A distance matrix.
gamma penalty value for the L1 constraint.
lambda penalty value for the L2 constraint.
weight a vector of weights.

Details

splitsNetwork fits phylogenetic networks using L1, L2 and non-negativity constraints. The function minimises the penalized least squares

beta = sum(dm - X*beta)^2 + lambda |beta|^2_2

with respect to

|beta|_1 = gamma, beta >= 0

where X is a design matrix constructed with designSplits. External edges are fitted without constraints.

Value

splitsNetwork returns a matrix. The first column contains the indices of the splits, the second column an unconstraint fit without penalty terms and the third column the constraint fit.

Author(s)

Klaus Schliep klaus.schliep@gmail.com

References

K. P. Schliep (2009). Some Applications of statistical phylogenetics (PhD Thesis)

See Also

distanceHadamard, designTree

Examples

data(yeast)
dm = dist.ml(yeast)
fit = splitsNetwork(dm)
write.nexus.splits(fit)

[Package phangorn version 0.99-6 Index]