pcoa {ProcMod}

Project a distance matrix in a euclidean space (PCOA).

Description

Project a set of points defined by a distance matrix in an eucleadean space using the Principal Coordinates Analysis method. This function is mainly a simplified interface on the cmdscale function using as much as possible dimensions for the projection. The aims of this PCoA being only to project point in an orthogonal space therefore without any correlation between axis. Because a metric method is used the used distance must be euclidean (cf is_euclid).

Usage

pcoa(distances)

Arguments

distances

a dist object or a matrix object representing a distance matrix.

Value

a numeric matrix with at most n-1 dimensions, with n the number pf observations. This matrix defines the coordinates of each point in the orthogonal space.

Author(s)

Eric Coissac

Christelle Gonindard-Melodelima

Examples

data(bacteria)
bacteria_rel_freq <- sweep(bacteria,
                           1,
                           rowSums(bacteria),
                           "/")
bacteria_hellinger <- sqrt(bacteria_rel_freq)
bacteria_dist <- dist(bacteria_hellinger)

project <- pcoa(bacteria_dist)