mvr: Minimum Variance Reduction

In ape: Analyses of Phylogenetics and Evolution

Minimum Variance Reduction

Description

Phylogenetic tree construction based on the minimum variance reduction.

Usage

mvr(X, V)
mvrs(X, V, fs = 15)

Arguments

X	a distance matrix.
V	a variance matrix.
fs	agglomeration criterion parameter: it is coerced as an integer and must at least equal to one.

Details

The MVR method can be seen as a version of BIONJ which is not restricted to the Poison model of variance (Gascuel 2000).

Value

an object of class "phylo".

Author(s)

Andrei Popescu

References

Criscuolo, A. and Gascuel, O. (2008). Fast NJ-like algorithms to deal with incomplete distance matrices. BMC Bioinformatics, 9.

Gascuel, O. (2000). Data model and classification by trees: the minimum variance reduction (MVR) method. Journal of Classification, 17, 67–99.

See Also

bionj, fastme, njs, SDM

Examples

data(woodmouse)
rt <- dist.dna(woodmouse, variance = TRUE)
v <- attr(rt, "variance")
tr <- mvr(rt, v)
plot(tr, "u")

ape documentation built on May 29, 2024, 10:50 a.m.