Diversity index: Difference between revisions

Revision as of 23:20, 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

+ Show code - Hide code


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

+ Show code - Hide code

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.

References

Related files

@@ Line 37: / Line 37: @@
 <rcode include="page:Diversity_index|name:answer" variables="
-name:data|description:Give your data in R format c(4,2,4,6,1,2,3,8,9) or leave empty for example data|
+name:data|description:Give your data in R format or leave empty for example data|
 name:individual|description:Is your data individual data or group abundancies?|type:selection|options:TRUE;Individual;FALSE;Group|default:TRUE
 ">
@@ Line 45: / Line 45: @@
 print(xtable(out), type = 'html')
 </rcode>
+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==