Phylogenetic Network
splitsNetwork estimates weights for a splits graph from a distance
matrix.
splitsNetwork(dm, splits = NULL, gamma = 0.1, lambda = 1e-06, weight = NULL)
dm |
A distance matrix. |
splits |
a splits object, containing all splits to consider, otherwise all possible splits are used |
gamma |
penalty value for the L1 constraint. |
lambda |
penalty value for the L2 constraint. |
weight |
a vector of weights. |
splitsNetwork fits non-negative least-squares phylogenetic networks
using L1 (LASSO), L2(ridge regression) constraints. The function minimizes
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 L1 or L2 constraints.
splitsNetwork returns a splits object with a matrix added.
The first column contains the indices of the splits, the second column an
unconstrained fit without penalty terms and the third column the constrained
fit.
Klaus Schliep klaus.schliep@gmail.com
Efron, Hastie, Johnstone and Tibshirani (2004) Least Angle Regression (with discussion) Annals of Statistics 32(2), 407–499
K. P. Schliep (2009). Some Applications of statistical phylogenetics (PhD Thesis)
data(yeast) dm <- dist.ml(yeast) fit <- splitsNetwork(dm) net <- as.networx(fit) plot(net, "2D") write.nexus.splits(fit)
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