Computation of Distance Matrices of Percentage Data
computes for percentage data some distance matrices.
dist.prop(df, method = NULL, diag = FALSE, upper = FALSE)
df |
a data frame containing only positive or null values, used as row percentages |
method |
an integer between 1 and 5. 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’ |
d1 = sum|p(i) - q(i)|/2
d2 = 1 - Sum(p(i)q(i))/sqrt(Sum(p(i)^2))/sqrt(Sum(q(i)^2))
d3 = sqrt(0.5*Sum(p(i)-q(i)^2))
d4 = -ln(Sum(p(i)q(i))/sqrt(Sum(p(i)^2))/sqrt(Sum(q(i)^2)))
d5= sqrt (1 - (Sum(sqrt(p(i)q(i)))))
returns a distance matrix, object of class dist
Daniel Chessel
Stéphane Dray stephane.dray@univ-lyon1.fr
Edwards, A. W. F. (1971) Distance between populations on the basis of gene frequencies. Biometrics, 27, 873–881.
Manly, B. F. (1994) Multivariate Statistical Methods. A primer., Second edition. Chapman & Hall, London.
Nei, M. (1972) Genetic distances between populations. The American Naturalist, 106, 283–292.
data(microsatt)
w <- microsatt$tab[1:microsatt$loci.eff[1]]
if(adegraphicsLoaded()) {
g1 <- scatter(dudi.pco(lingoes(dist.prop(w, 1)), scann = FALSE), plot = FALSE)
g2 <- scatter(dudi.pco(lingoes(dist.prop(w, 2)), scann = FALSE), plot = FALSE)
g3 <- scatter(dudi.pco(dist.prop(w, 3), scann = FALSE), plot = FALSE)
g4 <- scatter(dudi.pco(lingoes(dist.prop(w, 4)), scann = FALSE), plot = FALSE)
G <- ADEgS(list(g1, g2, g3, g4), layout = c(2, 2))
} else {
par(mfrow = c(2, 2))
scatter(dudi.pco(lingoes(dist.prop(w, 1)), scann = FALSE))
scatter(dudi.pco(lingoes(dist.prop(w, 2)), scann = FALSE))
scatter(dudi.pco(dist.prop(w, 3), scann = FALSE))
scatter(dudi.pco(lingoes(dist.prop(w, 4)), scann = FALSE))
par(mfrow = c(1, 1))
}Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.