nmds.Rd 1.63 KB
 Eric Coissac committed Jul 06, 2018 1 2 3 4 5 6 % Generated by roxygen2: do not edit by hand % Please edit documentation in R/multivariate.R \name{nmds} \alias{nmds} \title{Project a distance matrix in a euclidean space (NMDS).} \usage{  Eric Coissac committed Jun 09, 2019 7 nmds(distances, maxit = 100, trace = FALSE, tol = 0.001, p = 2)  Eric Coissac committed Jul 06, 2018 8 }  Eric Coissac committed Apr 30, 2019 9 10 11 12 13 14 15 16 17 18 19 20 21 \arguments{ \item{distances}{a \code{\link[stats]{dist}} object or a \code{\link[base]{matrix}} object representing a distance matrix.} \item{maxit}{The maximum number of iterations.} \item{trace}{Logical for tracing optimization. Default \code{TRUE}.} \item{tol}{convergence tolerance.} \item{p}{Power for Minkowski distance in the configuration space.} }  Eric Coissac committed Sep 12, 2019 22 23 24 25 26 \value{ a numeric matrix with at most \code{n-1} dimensions, with \code{n} the number pf observations. This matrix defines the coordinates of each point in the orthogonal space. }  Eric Coissac committed Jul 06, 2018 27 28 29 30 31 \description{ Project a set of points defined by a distance matrix in an eucleadean space using the Kruskal's Non-metric Multidimensional Scaling. This function is mainly a simplified interface on the \code{\link[MASS]{isoMDS}} function using as  Eric Coissac committed Sep 12, 2019 32 much as possible dimensions to limit the stress. The aims of this  Eric Coissac committed Jul 06, 2018 33 34 35 NDMS being only to project point in an orthogonal space therefore without any correlation between axis. Because a non-metric method is used no condition is required on the used distance.  Eric Coissac committed Oct 23, 2019 36 37 38 39 40 41 42 43 44 45 46 47 } \examples{ data(bacteria) bacteria_rel_freq <- sweep(bacteria, 1, rowSums(bacteria), "/") bacteria_hellinger <- sqrt(bacteria_rel_freq) bacteria_dist <- dist(bacteria_hellinger) project <- nmds(bacteria_dist)  Eric Coissac committed Jul 06, 2018 48 49 50 51 52 53 } \author{ Eric Coissac Christelle Gonindard-Melodelima }