Difference between revisions of "Diversity index"

Revision as of 23:20, 4 January 2012

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

true <- function(pi, q){
qD <- (sum(pi^q))^(1 / (1 - q))
return(qD)
}
diversity <- function(data, individual = TRUE){
if(individual == FALSE) {pi <- data} else {
     pi <- tapply(data, data, length)
     pi <- pi/sum(pi)
}

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

⇤# : With the example data, H' shows 0 which is not plausible. What's wrong? --Jouni 01:10, 5 January 2012 (EET)

Example to use function

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)}
out <- diversity(data, individual = individual)
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.

See also

References

Related files

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