calcDiversity {alakazam} | R Documentation |

## Calculate the diversity index

### Description

`calcDiversity`

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

### Usage

```
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 `+\infty`

). At `q = 0`

different clones weight equally,
regardless of their size. As the parameter `q`

increase from `0`

to `+\infty`

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

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

### See Also

Used by alphaDiversity.

### Examples

```
# 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*version 1.3.0 Index]