ade4 (version 1.2-2)

dist.prop: 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'

Value

• returns a distance matrix, object of class dist

Details

1 = Manly{$d_1=\frac{1}{2} \sum_{i=1}^{K}{|{p_i-q_i}|}$} 2 = Overlap index Manly{$d_2=1-\frac{\sum_{i=1}^{K}{p_i}}{\sqrt{\sum_{i=1}^{K}{p_i^2}}{\sqrt{\sum_{i=1}^{K}{q_i^2}}}}$} 3 = Rogers 1972 (one locus){$d_3=\frac{1}{n} \sqrt{\frac{1}{2} \sum_{i=1}^{K}{({p_i-q_i})^2}}$} 4 = Nei 1972 (one locus){$d_4=\frac{1}{n} \ln{\frac{\sum_{i=1}^{K}{p_i q_i}}{\sqrt{\sum_{i=1}^{K}{p_i^2}}{\sqrt{\sum_{i=1}^{K}{q_i^2}}}}}$} 5 = Edwards 1971 (one locus){$d_5=\sqrt{1-\sum_{i=1}^{K}{\sqrt{p_1 q_i}}}$}

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))
par(mfrow = c(1,1))