divc {ade4}R Documentation

Rao's diversity coefficient also called quadratic entropy

Description

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

Author(s)

Sandrine Pavoine pavoine@biomserv.univ-lyon1.fr

References

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

Gini, C. (1912) Variabilit\'a e mutabilit\'a. 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.

Examples

data(ecomor)
dtaxo <- dist.taxo(ecomor$taxo)
divc(ecomor$habitat, dtaxo)

data(humDNAm)
divc(humDNAm$samples, sqrt(humDNAm$distances))

Worked out examples


> library(ade4)
> ### Name: divc
> ### Title: Rao's diversity coefficient also called quadratic entropy
> ### Aliases: divc
> ### Keywords: multivariate
> 
> ### ** 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
> 
> 
> 
> 

[Package ade4 Index]