matrix.w.transformation: Community data transformation

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

Description

Function to transformation community data and replace missing data. See details.

Usage

matrix.w.transformation(
  comm,
  transformation = "standardized",
  spp.weights = NULL,
  reference = NULL,
  type = 0,
  include = TRUE,
  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.
transformation	Method to community data transformation, "none", "standardized", "weights" or "beals" (Default transformation = "standardized").
spp.weights	Vector with 0 or 1 to specify individual species weights (Default spp.weights = NULL).
reference	Data to compute joint occurrences in beals function. If NULL, comm is used as reference to compute the joint occurrences (Default reference = NULL).
type	Method to specifies how abundance values are used in beals function, type = 0 presence/absence, type = 1 abundances are used to compute conditioned probabilities, type = 2 abundances are used to compute weighted averages of conditioned probabilities or type = 3 abundances are used to compute both conditioned probabilities and weighted averages (Default type = 0).
include	Logical argument (TRUE or FALSE) to specify if target species are included when computing the mean of the conditioned probabilities in beals (Default include = TRUE).
notification	Logical argument (TRUE or FALSE) to specify if notifications for missing observations are to be shown (Default notification = TRUE).

Details

The function applies standardization/transformation for community data. The options are: "none" no transformation is applied; "standardized" the community data is standardized to row totals will be 1; "weights" community data is first "standardized" and when, individual species weights are multiplied to each species entries; and "beals" option applies Beals smoothing using the function beals. The arguments "reference", "type" and "include" are the same used in beals function. Missing data are replaced by 0 after the standardization/transformation.

Value

Transformed community matrix, where rows are communities and columns species.

Note

IMPORTANT: Species sequence in the community data matrix MUST be the same as the one in the reference matrix or in 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. De Cáceres, M.; Legendre, P. 2008. Beals smoothing revisited. Oecologia 156: 657–669.

See Also

syncsa, organize.syncsa, matrix.p, matrix.t, matrix.x

Examples

data(ADRS)
matrix.w.transformation(ADRS$community)

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