matrix.p.null {PCPS}

Auxiliar function to generate sets of null P matrix or null PCPS

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