Calculates the reduced-bias total alpha entropy of order *q* of communities.

1 2 |

`MC` |
A |

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

`Correction` |
A string containing one of the possible corrections accepted by the bias-corrected entropy function (see details) or |

`Tree` |
An object of class |

`Normalize` |
If |

`Z` |
A relatedness matrix, |

`CheckArguments` |
Logical; if |

If `Tree`

is not `NULL`

, then phylogenetic entropy is calculated by `bcPhyloEntropy`

; else, if `Z`

is not `NULL`

, then similarity-based entropy is calculated by `bcHqz`

; else, neutral entropy is calculated by `bcTsallis`

.

The alpha entropy of each community is calculated and summed according to community weights.

The possible corrections are detailed in `Tsallis`

.

An `MCentropy`

object containing entropy values of each community and 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 1).

1 2 3 4 5 6 7 8 9 | ```
# Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest)
data(Paracou618)
# Calculate Simpson alpha entropy
summary(AlphaEntropy(Paracou618.MC, 2))
# Compare without correction
summary(AlphaEntropy(Paracou618.MC, 2, Correction = "None"))
# Estimate phylogenetic Simpson alpha entropy
summary(AlphaEntropy(Paracou618.MC, 2, Tree = Paracou618.Taxonomy) -> e)
plot(e)
``` |

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

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