DivPart {entropart} | R Documentation |

## Diversity Partition of a metacommunity

### Description

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

### Usage

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

### Arguments

`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. |

### Details

`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.

### Value

A `DivPart`

object. It is a list:

`MetaCommunity` |
The name of the |

`Order` |
The value of |

`Biased` |
Logical. If |

`Correction` |
The estimation bias correction used to calculate diversity. |

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

`Tree` |
The phylogenetic or functional tree used to calculate phylodiversity. |

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

`Z` |
The matrix used to calculate similarity-based entropy. |

`TotalAlphaDiversity` |
The alpha diversity of communities. |

`TotalBetaDiversity` |
The beta diversity of communities. |

`GammaDiversity` |
The gamma diversity of the metacommunity. |

`CommunityAlphaDiversities` |
A vector containing the alpha diversity of each community. |

`TotalAlphaEntropy` |
The alpha entropy of communities. |

`TotalBetaEntropy` |
The beta entropy of communities. |

`GammaEntropy` |
The gamma entropy of the metacommunity. |

`CommunityAlphaEntropies` |
A vector containing the alpha entropy of each community. |

`DivPart`

objects can be summarized and plotted.

### Author(s)

Eric Marcon <Eric.Marcon@agroparistech.fr>, Bruno Herault <Bruno.Herault@cirad.fr>

### References

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).

### See Also

### Examples

```
# 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)
plot(dp)
```

*entropart*version 1.6-13 Index]