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
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 q_i}}{\sqrt{\sum_{i=1}^{K}{p_i^2}}{\sqrt{\sum_{i=1}^{K}{q_i^2}}}}
- 3 = Rogers 1972 (one locus)
d_3=\sqrt{\frac{1}{2} \sum_{i=1}^{K}{(p_i-q_i)^2}}
- 4 = Nei 1972 (one locus)
d_4=\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}}}
Value
returns a distance matrix, object of class dist
Author(s)
Daniel Chessel
Stéphane Dray stephane.dray@univ-lyon1.fr
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]]
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))
}