matrix.p.null: Auxiliar function to generate sets of null P matrix or null...

In PCPS: Principal Coordinates of Phylogenetic Structure

Description

Auxiliar function to generate sets of null P matrix or null PCPS used in matrix.p.sig or pcps.sig. The result are long lists with permuted matrices.

Usage

matrix.p.null(
  comm,
  phylodist,
  runs = NULL,
  calcpcps = FALSE,
  method = "bray",
  squareroot = TRUE,
  adjpcps = FALSE,
  choices = NULL
)

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 distances between species.
runs	Number of matrix will be generated (Default runs = NULL).
calcpcps	Logical argument (TRUE or FALSE) to specify if generate the PCPS (Default calcpcps = FALSE).
method	Dissimilarity index, as accepted by vegdist (Default dist = "bray").
squareroot	Logical argument (TRUE or FALSE) to specify if use square root of dissimilarity index (Default squareroot = TRUE).
adjpcps	Logical argument (TRUE or FALSE) to specify if return fitted PCPS (Default adjpcps = FALSE).
choices	Numeric vector to choose the PCPS to adjust (Default pcps.choices = NULL).

Value

call	The arguments used.
P.obs	Observed phylogeny-weighted species composition matrix.
pcps.obs	Observed principal coordinates of phylogenetic structure (PCPS).
permutation.site	A matrix with sequence of permutation for site shuffle null model, each permutation in one row.
permutation.taxa	A matrix with sequence of permutation for taxa shuffle null model, each permutation in one row.
P.null.site	A list with each permuted P matrix according with site shuffle null model.
P.null.taxa	A list with each permuted P matrix according with taxa shuffle null model.
pcps.null.site	A list with each permuted PCPS according with site shuffle null model.
pcps.null.taxa	A list with each permuted PCPS according with taxa shuffle null model.
pcps.null.taxa.adj	A list with each permuted PCPS (adjusted) according with taxa shuffle null model.

Author(s)

Vanderlei Julio Debastiani <[e-mail]>

See Also

matrix.p, pcps, matrix.p.sig, pcps.sig

PCPS documentation built on Jan. 16, 2020, 1:03 a.m.