specieseve {adiv} | R Documentation |

The function `specieseve`

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

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

`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 - |

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.

Function `specieseve`

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

Sandrine Pavoine sandrine.pavoine@mnhn.fr

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.

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

[Package *adiv* version 2.1.1 Index]