# GammaEntropy: Reduced-bias gamma entropy of a metacommunity In entropart: Entropy Partitioning to Measure Diversity

## Description

Calculates the reduced-bias Tsallis entropy of order q of a metacommunity.

## Usage

 ```1 2``` ```GammaEntropy(MC, q = 1, Correction = "Best", Tree = NULL, Normalize = TRUE, Z = NULL, PhyloDetails = FALSE, CheckArguments = TRUE) ```

## Arguments

 `MC` A `MetaCommunity` object. `q` A number: the order of entropy. Default is 1. `Correction` A string containing one of the possible corrections accepted by the bias-corrected entropy function (see details) or `"None"` or `"Best"`, the default value. `Tree` An object of class `hclust`, `phylo`, `phylog` or `PPtree`. The tree must be ultrametric. `Normalize` If `TRUE` (default), the entropy returned by the function is normalized by the height of the tree (it is the weighted average value of the entropy in each slice). If `FALSE`, it is the unnormalized weighted sum of the results. `Z` A relatedness matrix, i.e. a square matrix whose terms are all positive, strictly positive on the diagonal. Generally, the matrix is a similarity matrix, i.e. the diagonal terms equal 1 and other terms are between 0 and 1. `PhyloDetails` If `FALSE` (default), the function always returns a number. If `TRUE` and `Tree` is not Tree is not `NULL` then a `PhyloValue` object is returned with all details. That is used internally by `DivPart` to obtain the corrections used to estimate gamma entropy along the tree and apply them to the estimation of alpha diversity. `CheckArguments` Logical; if `TRUE`, the function arguments are verified. Should be set to `FALSE` to save time when the arguments have been checked elsewhere.

## Details

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`.

## Value

A number equal to the calculated entropy.

## Author(s)

Eric Marcon <[email protected]cofog.gf>

## References

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

`bcTsallis`, `bcPhyloEntropy`

## Examples

 ```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) # Calculate Simpson gamma entropy GammaEntropy(Paracou618.MC, 2) # Compare without correction GammaEntropy(Paracou618.MC, 2, Correction = "None") # Estimate phylogenetic Simpson gamma entropy GammaEntropy(Paracou618.MC, 2, Tree = Paracou618.Taxonomy) ```

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