# splitsNetwork

0th

Percentile

##### Phylogenetic Network

splitsNetwork estimates weights for a splits graph from a distance matrix.

Keywords
cluster
##### Usage
splitsNetwork(dm, splits = NULL, gamma = 0.1, lambda = 1e-06,
weight = NULL)
##### Arguments
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.

##### Details

splitsNetwork fits non-negative least-squares phylogenetic networks using L1 (LASSO), L2(ridge regression) constraints. The function minimizes the penalized least squares $$\beta = min \sum(dm - X\beta)^2 + \lambda \|\beta \|^2_2$$ 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.

##### Value

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.

##### References

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)

distanceHadamard, designTree consensusNet, plot.networx

##### Aliases
• splitsNetwork
##### Examples
# NOT RUN {
data(yeast)
dm <- dist.ml(yeast)
fit <- splitsNetwork(dm)
net <- as.networx(fit)
plot(net, "2D")
write.nexus.splits(fit)

# }

Documentation reproduced from package phangorn, version 2.5.5, License: GPL (>= 2)

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