R: Matrix P

matrix.p {SYNCSA} | R Documentation

## Matrix P

### Description

Function to obtain a matrix containing phylogeny-weighted species composition. For more details, see `syncsa`.

### Usage

    matrix.p(comm, phylodist, notification = TRUE)

### Arguments

`comm` | Community data, with species as columns and sampling units as rows. This matrix can contain either presence/absence or abundance data.
`phylodist` | Matrix containing phylogenetic distance between species. Must be a complete matrix (not a diagonal resemblance matrix).
`notification` | Logical argument (TRUE or FALSE) to specify if notifications for missing observations are to be shown (Default notification = TRUE).

### Value

`matrix.w` | Standardized community matrix, where rows are communities and columns species. Row totals (communities) = 1.
`matrix.q` | Standardized matrix containing the degree of belonging of species in relation to each other. Row totals (species) = 1.
`matrix.P` | Phylogeny-weighted species composition matrix. Row totals (communities) = 1.

### Note

IMPORTANT: Species sequence in the community data matrix MUST be the same as the one in the phylogenetic distance matrix. See `organize.syncsa`.

### Author(s)

Vanderlei Julio Debastiani <vanderleidebastiani@yahoo.com.br>

### References

Pillar, V.D.; Duarte, L.d.S. (2010). A framework for metacommunity analysis of phylogenetic structure. Ecology Letters, 13, 587-596.

### See Also

`syncsa`, `organize.syncsa`, `belonging`, `matrix.t`, `matrix.x`

### Examples

    data(ADRS)
    matrix.p(ADRS$community, ADRS$phylo)

[Package SYNCSA version 1.3.4 Index]