Description Usage Arguments Details Value References See Also Examples

`calcDiversity`

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

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

`p` |
numeric vector of clone (species) counts or proportions. |

`q` |
numeric vector of diversity orders. |

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*.

A vector of diversity scores *D* for each *q*.

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

Used by rarefyDiversity and testDiversity.

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)
``` |

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