Rao's diversity coefficient also called quadratic entropy

Calculates Rao's diversity coefficient within samples.

Usage

divc(df, dis, scale)

Arguments

df

a data frame with elements as rows, samples as columns, and abundance, presence-absence or frequencies as entries

dis

an object of class dist containing distances or dissimilarities among elements. If dis is NULL, Gini-Simpson index is performed.

scale

a logical value indicating whether or not the diversity coefficient should be scaled by its maximal value over all frequency distributions.

Value

Returns a data frame with samples as rows and the diversity coefficient within samples as columns

References

Rao, C.R. (1982) Diversity and dissimilarity coefficients: a unified approach. Theoretical Population Biology, 21, 24–43.

Gini, C. (1912) Variabilità e mutabilità. Universite di Cagliari III, Parte II.

Simpson, E.H. (1949) Measurement of diversity. Nature, 163, 688.

Champely, S. and Chessel, D. (2002) Measuring biological diversity using Euclidean metrics. Environmental and Ecological Statistics, 9, 167–177.

Author

Sandrine Pavoine pavoine@mnhn.fr

Examples

data(ecomor)
dtaxo <- dist.taxo(ecomor$taxo)
divc(ecomor$habitat, dtaxo)
#>     diversity
#> Bu1  2.754458
#> Bu2  2.967895
#> Bu3  3.107200
#> Bu4  3.137755
#> Ca1  2.500000
#> Ca2  3.230769
#> Ca3  3.272727
#> Ca4  3.283203
#> Ch1  2.333333
#> Ch2  2.595041
#> Ch3  3.246528
#> Ch4  3.135734
#> Pr1  2.840000
#> Pr2  2.816327
#> Pr3  3.055556
#> Pr4  3.028355

data(humDNAm)
divc(humDNAm$samples, sqrt(humDNAm$distances))
#>           diversity
#> oriental 0.43100189
#> tharu    0.48255042
#> wolof    0.65884298
#> peul     0.55952920
#> pima     0.06198035
#> maya     0.17092768
#> finnish  0.33280992
#> sicilian 0.61913580
#> israelij 0.67061144
#> israelia 0.64036818