div_rect: Get local diversity indices

In mobsim: Spatial Simulation and Scale-Dependent Analysis of Biodiversity Changes

Get local diversity indices

Description

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

Usage

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

Arguments

x0	x-coordinate of lower left corner
y0	y-coordinate of lower left corner
xsize	Size of the subplot in x-direction
ysize	Size of the subplot in y-direction
comm	community object

Details

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.

Value

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

References

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.

Examples

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

mobsim documentation built on May 29, 2024, 8:15 a.m.