Diversity index: Difference between revisions

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Question

How to calculate diversity indices?

Answer

Upload your data to Opasnet Base. Use the function diversity to calculate the most common indices.

Actual function diversity

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true <- function(pi, q){
if(q != 1){qD <- (sum(pi^q))^(1 / (1 - q))} else
{qD <- exp(-sum(pi * log(pi)))}
return(qD)
}
diversity <- function(species = 1:length(amount), amount = rep(1,length(species))){
print(species)
print(amount)
     pi <- tapply(amount, species, sum)
     pi <- pi/sum(pi)

out <- data.frame(Name = c("True diversity with q=0", "True diversity with q=1", "True diversity with q=2", "True diversity with q=∞", "Richness", "Shannon index", "Simpson index", "Inverse Simpson index", "Gini-Simpson index", "Berger-Parker index"), 
     Symbol = c("0D", "1D", "2D", "∞D", "S", "H' or log(1D)", "λ or 1/(2D)", "1/λ or 2D", "1-λ or 1-1/(2D)", "1/(∞D)"),
     Value = c(true(pi,0), true(pi,1), true(pi,2), 1/max(pi), length(pi), log(true(pi,1)), 1/true(pi,2), true(pi,2), 1-1/true(pi,2), max(pi)))
return(out)
}

Example to use function

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library(xtable)
if(is.null(data)) {data <- c(1,4,6,9,3,4,5,6,5,4,3,3,5,5,7,5,5,4,3,4,5,6,8,9,5,4,5,4,3,3,4,9,6,6,4,5,3,2,1,1,2,3,4,3,2,3,4,5,6,7,7)}
data
species <- NA
amount <- NA
if(individual==TRUE) species <- data else amount <- data
out <- diversity(species, amount)
print(xtable(out), type = 'html')

The data should be given in R format as a list of values in parenthesis, beginning with c:

c(3,5,3,5,2,1,3,3,4,2) or equivalently c(0.1,0.2,0.4,0.1,0.2)

where the values are either

identifiers of the species 1,2,3... in which the individuals belong (one entry per individual), or
abundancies of species, i.e. proportions of individuals belonging to each species among the whole population (one entry per species).

Rationale

Diversity indices are thoroughly described in Wikipedia.

References

Related files