Diversity index: Difference between revisions

Revision as of 23:10, 4 January 2012

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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){
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) (type: truth; paradigms: science: attack)

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)}
out <- diversity(data, individual = individual)
print(xtable(out), type = 'html')

Rationale

Diversity indices are thoroughly described in Wikipedia.

References

Related files