dist.prop {ade4}R Documentation

Computation of Distance Matrices of Percentage Data

Description

computes for percentage data some distance matrices.

Usage

dist.prop(df, method = NULL, diag = FALSE, upper = FALSE)

Arguments

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'

Details

1 = Manly
d1 = sum|p(i) - q(i)|/2
2 = Overlap index Manly
d2 = 1 - Sum(p(i)q(i))/sqrt(Sum(p(i)^2)/sqrt(Sum(q(i)^2)
3 = Rogers 1972 (one locus)
d3 = sqrt(0.5*Sum(p(i)-q(i)^2))
4 = Nei 1972 (one locus)
d4 = -ln(Sum(p(i)q(i)/sqrt(Sum(p(i)^2)/sqrt(Sum(q(i)^2))
5 = Edwards 1971 (one locus)
d5= sqrt (1 - (Sum(sqrt(p(i)q(i))))

Value

returns a distance matrix, object of class 'dist'

References

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.

Examples

data(microsatt)
w <- microsatt$tab[1:microsatt$loci.eff[1]]
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))

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