Rentropy {adiv} | R Documentation |

## Pavoine et al. (2017) functional or phylogenetic entropy

### Description

Function `Rentropy`

calculates Pavoine et al. (2017) functional or phylogenetic R entropy within communities; this index is closely related to Rao's quadratic entropy

### Usage

```
Rentropy(comm, dis = NULL, scale = FALSE)
```

### Arguments

`comm` |
a data frame or a matrix with communities as rows and species as columns. Entries are abundances of species within sites. |

`dis` |
either |

`scale` |
a logical value indicating whether or not the diversity coefficient should be scaled by its maximal value over all species abundance distributions. |

### Details

The definition of the R entropy is:

`R(\mathbf{p}_i,\mathbf{D})=\sum_{k=1}^S\sum_{l=1}^S \sqrt{p_{k|i}}\sqrt{p_{k|j}}d_{kl}`

where `\mathbf{p}_i=(p_{1|i}, ..., p_{k|i}, ..., p_{S|i})`

is the vector of relative species abundance within community *i*; *S* is the number of species; `\mathbf{D}=(d_{kl})`

is the matrix of (phylogenetic or functional) dissimilarities among species, and `d_{kl}`

is the (phylogenetic or functional) dissimilarity between species
*k* and *l*.

### Value

Function `Rentropy`

returns a data frame with communities as rows and the R entropy within communities as columns.

### Author(s)

Sandrine Pavoine sandrine.pavoine@mnhn.fr

### References

Pavoine, S., Bonsall, M.B., Dupaix, A., Jacob, U., Ricotta, C. (2017) From phylogenetic to functional originality: guide through indices and new developments. *Ecological Indicators*, **82**, 196–205.

### Examples

```
## Not run:
if(require(ade4)){
data(ecomor, package="ade4")
dtaxo <- dist.taxo(ecomor$taxo)
bird.R <- Rentropy(t(ecomor$habitat), dtaxo^2/2)
dotchart(bird.R$diversity, labels = rownames(bird.R))
}
## End(Not run)
## Not run:
if(require(ape)){
data(batcomm)
phy <- read.tree(text=batcomm$tre)
dphy <- as.dist(cophenetic(phy))/2
ab <- batcomm$ab[, phy$tip.label]
bat.R <- Rentropy(ab, dphy)
dotchart(bat.R$diversity, labels = rownames(bat.R), xlab = "Entropy")
}
## End(Not run)
```

*adiv*version 2.2.1 Index]