# calcDiversity: Calculate the diversity index In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

## Description

`calcDiversity` calculates the clonal diversity index for a vector of diversity orders.

## Usage

 `1` ```calcDiversity(p, q) ```

## Arguments

 `p` numeric vector of clone (species) counts or proportions. `q` numeric vector of diversity orders.

## Details

This method, proposed by Hill (Hill, 1973), quantifies diversity as a smooth function (D) of a single parameter q. Special cases of the generalized diversity index correspond to the most popular diversity measures in ecology: species richness (q = 0), the exponential of the Shannon-Weiner index (q approaches 1), the inverse of the Simpson index (q = 2), and the reciprocal abundance of the largest clone (q approaches +∞). At q = 0 different clones weight equally, regardless of their size. As the parameter q increase from 0 to +∞ the diversity index (D) depends less on rare clones and more on common (abundant) ones, thus encompassing a range of definitions that can be visualized as a single curve.

Values of q < 0 are valid, but are generally not meaningful. The value of D at q=1 is estimated by D at q=0.9999.

## Value

A vector of diversity scores D for each q.

## References

1. Hill M. Diversity and evenness: a unifying notation and its consequences. Ecology. 1973 54(2):427-32.

## See Also

Used by rarefyDiversity and testDiversity.

## Examples

 ```1 2 3 4 5 6 7 8``` ```# May define p as clonal member counts p <- c(1, 1, 3, 10) q <- c(0, 1, 2) calcDiversity(p, q) # Or proportional abundance p <- c(1/15, 1/15, 1/5, 2/3) calcDiversity(p, q) ```

alakazam documentation built on April 1, 2018, 11:58 a.m.