mobsim (version 0.1.0)

div_rect: 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

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 \(1/D\)

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.

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

# NOT RUN {
sim1 <- sim_poisson_community(100,1000)
div_rect(0, 0, 0.3, 0.3, sim1)

# }