phangorn: designTree – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

designTree

Compute a design matrix or non-negative LS

Description

nnls.tree estimates the branch length using non-negative least squares given a tree and a distance matrix. designTree and designSplits compute design matrices for the estimation of edge length of (phylogenetic) trees using linear models. For larger trees a sparse design matrix can save a lot of memory. computes a contrast matrix if the method is "rooted".

Usage

designTree(tree, method = "unrooted", sparse = FALSE, ...)

nnls.tree(dm, tree, rooted = FALSE, trace = 1, weight = NULL, balanced = FALSE)

nnls.phylo(x, dm, rooted = FALSE, trace = 0, ...)

nnls.splits(x, dm, trace = 0)

nnls.networx(x, dm)

designSplits(x, splits = "all", ...)

Arguments

`tree`	an object of class `phylo`
`method`	design matrix for an "unrooted" or "rooted" ultrametric tree.
`sparse`	return a sparse design matrix.
`...`	further arguments, passed to other methods.
`dm`	a distance matrix.
`rooted`	compute a "rooted" or "unrooted" tree.
`trace`	defines how much information is printed during optimisation.
`weight`	vector of weights to be used in the fitting process. Weighted least squares is used with weights w, i.e., sum(w * e^2) is minimized.
`balanced`	use weights as in balanced fastME
`x`	number of taxa.
`splits`	one of "all", "star".

Value

nnls.tree return a tree, i.e. an object of class phylo. designTree and designSplits a matrix, possibly sparse.

Author(s)

Klaus Schliep klaus.schliep@gmail.com

Examples

example(NJ)
dm <-  as.matrix(dm)
y <- dm[lower.tri(dm)]
X <- designTree(tree)
lm(y~X-1)
# avoids negative edge weights
tree2 <- nnls.tree(dm, tree)

phangorn

Phylogenetic Reconstruction and Analysis

v2.7.0

GPL (>= 2)

Authors

Klaus Schliep [aut, cre] (<https://orcid.org/0000-0003-2941-0161>), Emmanuel Paradis [aut] (<https://orcid.org/0000-0003-3092-2199>), Leonardo de Oliveira Martins [aut] (<https://orcid.org/0000-0001-5247-1320>), Alastair Potts [aut], Tim W. White [aut], Cyrill Stachniss [ctb], Michelle Kendall [ctb], Keren Halabi [ctb], Richel Bilderbeek [ctb], Kristin Winchell [ctb], Liam Revell [ctb], Mike Gilchrist [ctb], Jeremy Beaulieu [ctb], Brian O'Meara [ctb], Long Qu [ctb]

Initial release