taxo_ordinate: Ordinate taxa in taxonomic distance space

In taxodist: Taxonomic Distance and Phylogenetic Lineage Computation

Ordinate taxa in taxonomic distance space

Description

Computes pairwise taxonomic distances and applies classical multidimensional scaling (PCoA) to project taxa into a low-dimensional space.

Usage

taxo_ordinate(taxa, k = 2, ...)

Arguments

taxa	A character vector of taxon names, or a dist object from distance_matrix().
k	Number of dimensions. Default 2.
...	Additional arguments passed to distance_matrix().

Value

An object of class "taxodist_ord" — a list with:

points

A matrix of coordinates (taxa x k dimensions).

dist

The underlying distance matrix.

GOF

Goodness-of-fit fromstats::cmdscale().

eig

The eigenvalues computed during PCoA.

See Also

taxo_cluster(), distance_matrix()

Examples

taxa <- c("Tyrannosaurus", "Velociraptor", "Triceratops", "Brachiosaurus")
ord <- taxo_ordinate(taxa)
if (!is.null(ord$points)) {
  plot(ord$points, type = "n")
  text(ord$points, labels = rownames(ord$points))
}

taxodist documentation built on May 6, 2026, 1:06 a.m.