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

View source: R/BetaDiversity.R

Calculates the reduced-bias beta diversity of order *q* between communities.

1 2 |

`MC` |
A |

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

`Correction` |
A string containing one of the possible corrections accepted by |

`Tree` |
An object of class |

`Normalize` |
If |

`Z` |
A relatedness matrix, |

`CheckArguments` |
Logical; if |

Entropy is calculated by `BetaEntropy`

and transformed into diversity.

Diversity values of communities are not defined: community entropies are averaged to obtain the metacommunity entropy wich is transformed into diversity (Marcon et al., 2014).

An `MCdiversity`

object containing diversity value of the metacommunity.

Eric Marcon <Eric.Marcon@ecofog.gf>

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

Marcon, E., Herault, B. (2015). Decomposing Phylodiversity. *Methods in Ecology and Evolution* 6(3): 333-339.

Marcon, E., Zhang, Z. and Herault, B. (2014). The decomposition of similarity-based diversity and its bias correction. *HAL* hal-00989454(version 3).

1 2 3 4 5 6 7 8 | ```
# Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest)
data(Paracou618)
# Estimate Shannon beta diversity
summary(BetaDiversity(Paracou618.MC, 1))
# Compare without correction
summary(BetaDiversity(Paracou618.MC, 1, Correction = "None"))
# Estimate phylogenetic Shannon beta diversity
summary(BetaDiversity(Paracou618.MC, 1, Tree = Paracou618.Taxonomy) -> e)
``` |

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