View source: R/Diversity_Area_Relationships.R
div_rect  R Documentation 
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)
x0 
xcoordinate of lower left corner 
y0 
ycoordinate of lower left corner 
xsize 
Size of the subplot in xdirection 
ysize 
Size of the subplot in ydirection 
comm 

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
n_species: Number of species
n_endemics: Number of endemics
shannon: Shannon index index defined as H =  \sum p_i * log(p_i)
,
where p_i
is the relative abundance of species i:
ens_shannon: Effective number of species (ENS) based on the Shannon index exp(H)
simpson: Simpson index index (= probability of interspecific encounter PIE)
defined as D = 1  \sum p_i^2
ens_simpson: Effective number of species (ENS) based on the Simpson index 1/D
Jost 2006. Entropy and diversity. Oikos, 113, 363375.
Chao et al. 2014. Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies. Ecological Monographs, 84, 4567.
Hsieh et al. 2016. iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers). Methods Ecol Evol, 7, 14511456.
sim1 < sim_poisson_community(100,1000)
div_rect(0, 0, 0.3, 0.3, sim1)
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