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

View source: R/AlphaDiversity.R

Calculates the eeduced-bias total alpha diversity of order *q* of 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 `AlphaEntropy`

and transformed into diversity.

An `MCdiversity`

object containing diversity values of each community and of the metacommunity.

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.

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

entropart documentation built on Feb. 6, 2018, 1:04 a.m.

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.