matrix.x: Matrix X

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

Description

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

Usage

matrix.x(
  comm,
  traits,
  scale = TRUE,
  ranks = TRUE,
  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.
traits	Matrix or data frame of species described by traits, with traits as columns and species as rows.
scale	Logical argument (TRUE or FALSE) to specify if the traits are measured on different scales (Default scale = TRUE). When scale = TRUE traits are measured on different scales the matrix of traits is subjected to standardization within each trait, and Gower Index is used to calculate the degree of belonging to the species. When scale = FALSE traits are measured on the same scale the matrix of traits is not subjected to standardization, and Euclidean distance is calculated to determine the degree of belonging to the species.
ranks	Logical argument (TRUE or FALSE) to specify if ordinal variables are convert to ranks (Default ranks = TRUE).
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 of missing observations are shown (Default notification = TRUE).
...	Parameters for gowdis function.

Value

matriz.w	Standardized community matrix, where rows are communities and columns species. If default transformation, row totals (communities) = 1.
matriz.u	Standardized matrix containing the degree of belonging of each species in relation to each other species. Row totals (species) = 1.
matriz.X	Trait-weighted species composition matrix. If default transformation, row totals (communities) = 1.

Note

IMPORTANT: The sequence species show up in community data matrix MUST be the same as they show up in traits 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.

Pillar, V.D., Duarte, L.d.S., Sosinski, E.E. & Joner, F. (2009). Discriminating trait-convergence and trait-divergence assembly patterns in ecological community gradients. Journal of Vegetation Science, 20, 334:348.

See Also

syncsa, organize.syncsa, belonging, matrix.t, matrix.p, gowdis

Examples

data(ADRS)
matrix.x(ADRS$community, ADRS$traits)

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