Description Usage Arguments Details Value Author(s) References See Also Examples

Calculates the HCDT (generalized) diversity of order *q* of a probability vector.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ```
Diversity(NorP, q = 1, ...)
bcDiversity(Ns, q = 1, Correction = "Best", CheckArguments = TRUE)
## S3 method for class 'ProbaVector'
Diversity(NorP, q = 1, ...,
CheckArguments = TRUE, Ps = NULL)
## S3 method for class 'AbdVector'
Diversity(NorP, q = 1, Correction = "Best", ...,
CheckArguments = TRUE, Ns = NULL)
## S3 method for class 'integer'
Diversity(NorP, q = 1, Correction = "Best", ...,
CheckArguments = TRUE, Ns = NULL)
## S3 method for class 'numeric'
Diversity(NorP, q = 1, Correction = "Best", ...,
CheckArguments = TRUE, Ps = NULL, Ns = NULL)
``` |

`Ps` |
A probability vector, summing to 1. |

`Ns` |
A numeric vector containing species abundances. |

`NorP` |
A numeric vector, an integer vector, an abundance vector ( |

`q` |
A number: the order of diversity. Default is 1. |

`Correction` |
A string containing one of the possible corrections: |

`...` |
Additional arguments. Unused. |

`CheckArguments` |
Logical; if |

`Diversity`

calls `Tsallis`

to calculate entropy and transforms it into diversity by calculating its deformed exponential.

Bias correction requires the number of individuals to estimate sample `Coverage`

. Use `bcDiversity`

and choose the `Correction`

.

The functions are designed to be used as simply as possible. `Diversity`

is a generic method. If its first argument is an abundance vector, an integer vector or a numeric vector which does not sum to 1, the bias corrected function `bcDiversity`

is called. Explicit calls to `bcDiversity`

(with bias correction) or to `Diversity.ProbaVector`

(without correction) are possible to avoid ambiguity. The `.integer`

and `.numeric`

methods accept `Ps`

or `Ns`

arguments instead of `NorP`

for backward compatibility.

A named number equal to the calculated diversity. The name is that of the bias correction used.

Eric Marcon <[email protected]>

Marcon, E., Scotti, I., Herault, B., Rossi, V. and Lang, G. (2014). Generalization of the partitioning of Shannon diversity. *PLOS One* 9(3): e90289.

`Tsallis`

, `expq`

, `AbdVector`

, `ProbaVector`

1 2 3 4 5 6 7 8 9 10 11 12 | ```
# Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest)
data(Paracou618)
# Ns is the total number of trees per species
Ns <- as.AbdVector(Paracou618.MC$Ns)
# Species probabilities
Ps <- as.ProbaVector(Paracou618.MC$Ns)
# Whittaker plot
plot(Ns)
# Calculate diversity of order 1, i.e. Shannon's diversity
Diversity(Ps, 1)
# Calculate it with estimation bias correction
Diversity(Ns, 1)
``` |

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