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.
matrix.p.null(
comm,
phylodist,
runs = NULL,
calcpcps = FALSE,
method = "bray",
squareroot = TRUE,
adjpcps = FALSE,
choices = NULL
)Community data, with species as columns and sampling units as rows. This matrix can contain either presence/absence or abundance data.
Matrix containing phylogenetic distances between species.
Number of matrix will be generated (Default runs = NULL).
Logical argument (TRUE or FALSE) to specify if generate the PCPS (Default calcpcps = FALSE).
Dissimilarity index, as accepted by vegdist (Default dist = "bray").
Logical argument (TRUE or FALSE) to specify if use square root of dissimilarity index (Default squareroot = TRUE).
Logical argument (TRUE or FALSE) to specify if return fitted PCPS (Default adjpcps = FALSE).
Numeric vector to choose the PCPS to adjust (Default pcps.choices = NULL).
The arguments used.
Observed phylogeny-weighted species composition matrix.
Observed principal coordinates of phylogenetic structure (PCPS).
A matrix with sequence of permutation for site shuffle null model, each permutation in one row.
A matrix with sequence of permutation for taxa shuffle null model, each permutation in one row.
A list with each permuted P matrix according with site shuffle null model.
A list with each permuted P matrix according with taxa shuffle null model.
A list with each permuted PCPS according with site shuffle null model.
A list with each permuted PCPS according with taxa shuffle null model.
A list with each permuted PCPS (adjusted) according with taxa shuffle null model.