% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/distance.R
\name{taxo_ordinate}
\alias{taxo_ordinate}
\title{Ordinate taxa in taxonomic distance space}
\usage{
taxo_ordinate(taxa, k = 2, ...)
}
\arguments{
\item{taxa}{A character vector of taxon names, or a \code{dist} object from
\code{\link[=distance_matrix]{distance_matrix()}}.}

\item{k}{Number of dimensions. Default \code{2}.}

\item{...}{Additional arguments passed to \code{\link[=distance_matrix]{distance_matrix()}}.}
}
\value{
An object of class \code{"taxodist_ord"} — a list with:
\describe{
\item{\code{points}}{A matrix of coordinates (taxa x k dimensions).}
\item{\code{dist}}{The underlying distance matrix.}
\item{\code{GOF}}{Goodness-of-fit from\code{\link[stats:cmdscale]{stats::cmdscale()}}.}
\item{\code{eig}}{The eigenvalues computed during PCoA.}
}
}
\description{
Computes pairwise taxonomic distances and applies classical multidimensional
scaling (PCoA) to project taxa into a low-dimensional space.
}
\examples{
\donttest{
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))
}
}
}
\seealso{
\code{\link[=taxo_cluster]{taxo_cluster()}}, \code{\link[=distance_matrix]{distance_matrix()}}
}
