`DivPart.Rd`

Partitions the diversity of a metacommunity into alpha and beta components.

DivPart(q = 1, MC, Biased = TRUE, Correction = "Best", Tree = NULL, Normalize = TRUE, Z = NULL, CheckArguments = TRUE) is.DivPart(x) # S3 method for DivPart plot(x, ...) # S3 method for DivPart autoplot(object, col = ggplot2::GeomRect$default_aes$fill, border = ggplot2::GeomRect$default_aes$colour, ...) # S3 method for DivPart summary(object, ...)

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

MC | A |

Biased | Logical; if |

Correction | A string containing one of the possible corrections. The correction must be accepted by |

Tree | An object of class |

Normalize | If |

Z | A relatedness matrix, |

CheckArguments | Logical; if |

x | An object to be tested or plotted. |

object | A |

col | The color used to fill the bars. See "Color Specification" in |

border | The color of the borders around the bars. See |

... | Additional arguments to be passed to the generic methods. |

`DivPart`

partitions the diversity of the metacommunity into alpha and beta components. It supports estimation-bias correction.

If `Tree`

is provided, the phylogenetic diversity is calculated else if `Z`

is not `NULL`

, then similarity-based entropy is calculated.

Beta diversity/entropy is calculated from Gamma and Alpha when bias correction is required, so community values are not available.

A `DivPart`

object. It is a list:

The name of the `MetaCommunity`

object containing inventory data.

The value of `q`

.

Logical. If `FALSE`

, bias corrected values of diversity have been computed.

The estimation bias correction used to calculate diversity.

The method used to calculate entropy ("HCDT", "Similarity-based").

The phylogenetic or functional tree used to calculate phylodiversity.

Logical. Indicates whether phylodiversity is normalized or proportional to the height of the tree.

The matrix used to calculate similarity-based entropy.

The alpha diversity of communities.

The beta diversity of communities.

The gamma diversity of the metacommunity.

A vector containing the alpha diversity of each community.

The alpha entropy of communities.

The beta entropy of communities.

The gamma entropy of the metacommunity.

A vector containing the alpha entropy of each community.

Marcon, E., Herault, B., Baraloto, C. and Lang, G. (2012). The Decomposition of Shannon's Entropy and a Confidence Interval for Beta Diversity. *Oikos* 121(4): 516-522.

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).

Eric Marcon <Eric.Marcon@ecofog.gf> and Bruno Herault <Bruno.Herault@ecofog.gf>

# Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest) data(Paracou618) # Estimate Shannon diversity. summary(DivPart(q = 1, Paracou618.MC, Biased = FALSE) -> dp)#> HCDT diversity partitioning of order 1 of metaCommunity Paracou618.MC #> with correction: UnveilJ #> Alpha diversity of communities: #> P006 P018 #> 83.7268 118.2713 #> Total alpha diversity of the communities: #> [1] 97.06467 #> Beta diversity of the communities: #> UnveilJ #> 1.422843 #> Gamma diversity of the metacommunity: #> UnveilJ #> 138.1078