evodiss {adiv} | R Documentation |

## Pair-wise Phylogenetic Dissimilarities between Communities

### Description

The function calculates PD-dissimilarity indices described and/or discussed in Pavoine (2016). Part of them are parametric indices.

### Usage

```
evodiss(phyl, comm, method = NULL, q = NULL,
w = c("evoab", "even", "speciesab"), diag = FALSE,
upper = FALSE, tol = 1e-08)
```

### Arguments

`phyl` |
an object inheriting the class |

`comm` |
a data frame typically with communities as rows, species as columns and an index of abundance as entries. Species should be labeled as in the phylogenetic tree where they are the tips. |

`method` |
one of the following string codes: |

`q` |
a vector with nonnegative value(s) for parameter |

`w` |
either a numeric vector giving weights for communities (same order as in |

`diag` |
logical argument passed to function as.dist (R base). |

`upper` |
logical argument passed to function as.dist (R base). |

`tol` |
numeric tolerance threshold: values between - |

### Details

The indices available are (formulas can be found in Supplementary material Appendix 1 of Pavoine 2016):

`"Minkowski"`

:`^qevoD_{Minkowski}`

`"Euclidean"`

: `evoD_{Euclidean}`

`"Manhattan"`

: `evoD_{Manhattan}`

`Chord`

: `evoD_{Chord}`

`ScaledCanberra`

: `evoD_{ScaledCanberra}`

`Divergence`

: `evoD_{Divergence}`

`BC`

: `evoD_{Bray-Curtis}`

`MH`

: `evoD_{Morisita-Horn}`

`LG`

: `evoD_{Profile}`

`Hellinger`

: `evoD_{Hellinger}`

`chi2`

: `evoD_{Chi2}`

`Hill`

: `1-\bar{V}_{q2}`

`Renyi`

: `^qevoD_{Renyi}`

`C`

: `1-\bar{C}_{q2}`

`U`

: `1-\bar{U}_{q2}`

`S`

: `1-\bar{S}_{q2}`

The weights of the communities (argument `w`

) can be `"even"`

(even weights, i.e. relative abundances are considered for evolutionary units), `"evoab"`

(proportional to the summed abundances of all evolutionary units, i.e. absolute abundances are considered for evolutionary units), or `"speciesab"`

(proportional to the summed abundances of all species). Note that if the phylogenetic tree is ultrametric (the distance from any species to the root is constant), then
options `"evoab"`

and `"speciesab"`

are equivalent.

### Value

An object of class `dist`

containing the PD-dissimilarities (phylogenetic dissimilarities) between communities.

### Author(s)

Sandrine Pavoine sandrine.pavoine@mnhn.fr

### References

The methodologies are presented in

Pavoine, S. (2016) A guide through a family of phylogenetic dissimilarity measures among sites. *Oikos*, **125**, 1719–1732.

They gather, in a common framework, indices introduced in

Chiu, C.-H., Jost, L., Chao, A. (2014) Phylogenetic beta diversity, similarity and differentiation measures based on Hill numbers. *Ecological Monographs*, **84**, 21–44.

and earlier work extended here in a phylogenetic context and reviewed in

Legendre, P. and De Caceres, M. (2013) Beta diversity as the variance of community data: dissimilarity coefficients and partitioning. *Ecology Letters*, **16**, 951–963.

### See Also

### Examples

```
## Not run:
if(require(ape)){
data(batcomm)
phy <- read.tree(text=batcomm$tre)
ab <- batcomm$ab[,phy$tip.label]
evodiss(phy, ab, "LG")
evodiss(phy, ab, "Hellinger")
evodiss(phy, ab, "Chord")
evodiss(phy, ab, "Hill", q=2)
evodiss(phy, ab, "Hill", q=2, w="even")
}
## End(Not run)
```

*adiv*version 2.2.1 Index]