matrix.p: Matrix P

In vanderleidebastiani/SYNCSA: Analysis of Functional and Phylogenetic Patterns in Metacommunities

Description

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

Usage

matrix.p(
  comm,
  phylodist,
  transformation = "standardized",
  spp.weights = NULL,
  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).
transformation	Method to community data transformation, "none", "standardized" or "weights" (Default transformation = "standardized").
spp.weights	Vector with 0 or 1 to specify individual species weights (Default spp.weights = NULL).
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. If default transformation, 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. If default transformation, 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 or in the spp.weights vector. See organize.syncsa.

Author(s)

Vanderlei Julio Debastiani <[e-mail]>

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)

vanderleidebastiani/SYNCSA documentation built on Sept. 4, 2020, 10:57 p.m.