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Computation of Distance Matrices of Percentage Data

dist.prop.Rd

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

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.

Author

Daniel Chessel
Stéphane Dray stephane.dray@univ-lyon1.fr

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))
}
#> Error in s.label(dfxy = dudi.pco(lingoes(dist.prop(w, 1)), scann = FALSE)$li,     xax = 1, yax = 2, plot = FALSE, storeData = TRUE, pos = -3): non convenient selection for dfxy (can not be converted to dataframe)