div_rect: Get local diversity indices

View source: R/Diversity_Area_Relationships.R

div_rectR Documentation

Get local diversity indices


Get diversity indices including species richness, no. of endemics, Shannon and Simpson diversity for one rectangle subplot in the community.


div_rect(x0, y0, xsize, ysize, comm)



x-coordinate of lower left corner


y-coordinate of lower left corner


Size of the subplot in x-direction


Size of the subplot in y-direction


community object


The effective number of species is defined as the number of equally abundant species that produce the same value of a certain diversity index as an observed community (Jost 2006). According to Chao et al. 2014 and Chiu et al. 20 ENS_shannon can be interpreted as the number of common species and ENS_simpson as the number of dominant species in a community.


Named vector with six diversity indices

  1. n_species: Number of species

  2. n_endemics: Number of endemics

  3. shannon: Shannon index index defined as H = - \sum p_i * log(p_i), where p_i is the relative abundance of species i:

  4. ens_shannon: Effective number of species (ENS) based on the Shannon index exp(H)

  5. simpson: Simpson index index (= probability of interspecific encounter PIE) defined as D = 1 - \sum p_i^2

  6. ens_simpson: Effective number of species (ENS) based on the Simpson index 1/D


Jost 2006. Entropy and diversity. Oikos, 113, 363-375.

Chao et al. 2014. Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies. Ecological Monographs, 84, 45-67.

Hsieh et al. 2016. iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers). Methods Ecol Evol, 7, 1451-1456.


sim1 <- sim_poisson_community(100,1000)
div_rect(0, 0, 0.3, 0.3, sim1)

MoBiodiv/MoBspatial documentation built on May 22, 2024, 7:44 p.m.