matrix.p | R Documentation |
Function to obtain a matrix containing phylogeny-weighted species
composition. For more details, see syncsa
.
matrix.p(
comm,
phylodist,
transformation = "standardized",
spp.weights = NULL,
notification = TRUE
)
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 distance between species. Must be a complete matrix (not a diagonal resemblance matrix). |
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 for missing observations are to be shown (Default notification = TRUE). |
matrix.w |
Standardized community matrix, where rows are communities and columns species. If default transformation, row totals (communities) = 1. |
matrix.q |
Standardized matrix containing the degree of belonging of species in relation to each other. Row totals (species) = 1. |
matrix.P |
Phylogeny-weighted species composition matrix. If default transformation, row totals (communities) = 1. |
IMPORTANT: Species sequence in the community data
matrix MUST be the same as the one in the phylogenetic distance matrix or in the spp.weights vector. See
organize.syncsa
.
Vanderlei Julio Debastiani <vanderleidebastiani@yahoo.com.br>
Pillar, V.D.; Duarte, L.d.S. (2010). A framework for metacommunity analysis of phylogenetic structure. Ecology Letters, 13, 587-596.
syncsa
, organize.syncsa
, belonging
,
matrix.t
, matrix.x
data(ADRS)
matrix.p(ADRS$community, ADRS$phylo)
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