dist.quant: Computation of Distance Matrices on Quantitative Variables

In ade4: Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences

Description

computes on quantitative variables, some distance matrices as canonical, Joreskog and Mahalanobis.

Usage

dist.quant(df, method = NULL, diag = FALSE, upper = FALSE, 
    tol = 1e-07)

Arguments

df	a data frame containing only quantitative variables
method	an integer between 1 and 3. If NULL the choice is made with a console message. See details
diag	a logical value indicating whether the diagonal of the distance matrix should be printed by ‘print.dist’
upper	a logical value indicating whether the upper triangle of the distance matrix should be printed by ‘print.dist’
tol	used in case 3 of method as a tolerance threshold for null eigenvalues

Details

All the distances are of type d = ||x-y||_A = sqrt((x-y)^t A (x-y))

1 = Canonical

A = Identity

2 = Joreskog

A = 1 / diag(cov)

3 = Mahalanobis

A = inv(cov)

Value

an object of class dist

Author(s)

Daniel Chessel
Stéphane Dray [e-mail]

Examples

data(ecomor)

if(adegraphicsLoaded()) {
  g1 <- scatter(dudi.pco(dist.quant(ecomor$morpho, 3), scan = FALSE), plot = FALSE)
  g2 <- scatter(dudi.pco(dist.quant(ecomor$morpho, 2), scan = FALSE), plot = FALSE)
  g3 <- scatter(dudi.pco(dist(scalewt(ecomor$morpho)), scan = FALSE), plot = FALSE)
  g4 <- scatter(dudi.pco(dist.quant(ecomor$morpho, 1), scan = FALSE), plot = FALSE)
  G <- ADEgS(list(g1, g2, g3, g4), layout = c(2, 2))
  
} else {
  par(mfrow = c(2, 2))
  scatter(dudi.pco(dist.quant(ecomor$morpho, 3), scan = FALSE))
  scatter(dudi.pco(dist.quant(ecomor$morpho, 2), scan = FALSE))
  scatter(dudi.pco(dist(scalewt(ecomor$morpho)), scan = FALSE))
  scatter(dudi.pco(dist.quant(ecomor$morpho, 1), scan = FALSE))
  par(mfrow = c(1, 1))
}

ade4 documentation built on May 2, 2019, 5:50 p.m.