specieseve {adiv}R Documentation

Indices of Species Evenvess

Description

The function specieseve calculates evenness indices that rely on relative or absolute species abundance.

Usage

specieseve(comm, method = "full", tol = 1e-8)

Arguments

comm

a data frame or a matrix typically with communities as rows, species as columns and abundance as entry.

method

a string or a vector of strings: one or several of "GiniSimpson", "Simpson", "Shannon", "Heip", "McIntosh", "SmithWilson", "full". See details.

tol

a tolerance threshold (a value between -tol and tol is considered equal to zero)

Details

Let S_i be the number of species in community i, n_ij be the absolute abundance of species j in community i, N_i the sum of all species abundance in community i (N_i=sum_j n_ij; the sum of row i in comm), p_ij the relative abundance of species j in community i (p_ij=n_ij/N_i). If method="GiniSimpson", the evenness index is that associated with Gini (1912) and Simpson (1949) diversity index: (1-∑_j p_ij^2)*S_i/(S_i-1). If method="Simpson", the evenness index is (Simpson 1949; Magurran 2004): (1/sum_j p_ij^2)/S_i. If method="Shannon", the evenness index is that associated with Shannon (1948) diversity index with neperian logarithm: (-sum_j p_ij ln(p_ij))/ln(S_i). If method="Heip", the evenness index is that of Heip (1974) (Magurran 2004): [exp(-sum_j p_ij log(p_ij)) - 1]/(S_i-1). If method="McIntosh", the evenness index is that of Pielou (1975) associated with McIntosh (1967) index of diversity: (N_i-sqrt(sum_j n_ij^2)/(N_i-N_i/sqrt(S_i)). If method="SmithWilson", the Smith and Wilson (1996) evenness index is calculated (Magurran 2004): 1-[2/pi*arctan(sum_j (log(n_ij) - sum_k log(n_ik)/S_i)^2/S_i)]. The function uses neperian logarithm for all indices. If one of the strings is "full", then all indices are calculated.

Value

Function specieseve returns a matrix with communities as rows and the evenness indices as columns.

Author(s)

Sandrine Pavoine sandrine.pavoine@mnhn.fr

References

Gini, C. (1912) Variabilita e mutabilita. Studi economicoaguridici delle facoltta di giurizprudenza dell, Universite di Cagliari III, Parte II.

Heip, C. (1974) A new index measuring evenness. Journal of the Marine Biological Association UK, 54, 555–557.

Magurran, A.E. (2004) Measuring biological diversity. Oxford, UK: Blackwell Publishing.

McIntosh, R.P. (1967) An index of diversity and the relation of certain conepts to diversity. Ecology, 48, 392–404.

Pielou, E.C. (1975) Ecological diversity. New York: Wiley InterScience.

Shannon, C.E. (1948) A mathematical theory of communication. Bell System technical journal, 27, 379–423, 623–656.

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

Smith, B. and Wilson, J.B. (1996) A consumer's guide to evenness measures. Oikos, 76, 70–82.

Examples

data(batcomm)
ab <- batcomm$ab
specieseve(ab)

[Package adiv version 2.1.1 Index]