Difference between revisions of "Diversity index"
From Testiwiki
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true <- function(pi, q){ | true <- function(pi, q){ | ||
| − | qD <- (sum(pi^q))^(1 / (1 - q)) | + | if(q != 1){qD <- (sum(pi^q))^(1 / (1 - q))} else |
| + | {qD <- exp(-sum(pi * log(pi)))} | ||
return(qD) | return(qD) | ||
} | } | ||
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} | } | ||
| − | out <- data.frame(Name = c("Richness", "Shannon index", "Simpson index", "Inverse Simpson index", | + | out <- data.frame(Name = c("Richness", "True diversity with q=1", "True diversity with q=2", "True diversity with q=∞", "Shannon index", "Simpson index", "Inverse Simpson index", |
"Gini-Simpson index", "Berger-Parker 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"), | + | Symbol = c("S or 0D", "1D", "2D", "∞D", "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), log(true(pi,1)), 1/true(pi,2), true(pi,2), 1-1/true(pi,2), max(pi))) | + | Value = c(true(pi,0), true(pi,1), true(pi,2), 1/max(pi), log(true(pi,1)), 1/true(pi,2), true(pi,2), 1-1/true(pi,2), max(pi))) |
return(out) | return(out) | ||
} | } | ||
Revision as of 21:16, 5 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
⇤# : 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
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
<mfanonymousfilelist></mfanonymousfilelist>
