Function obtains the correlation between two matrices, similar to the function mantel. The significance of the statistics is evaluated differently from mantel. For more details, see syncsa.
● Data Source:
CranContrib
● Keywords: SYNCSA
● Alias: cor.matrix
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Calculates Rao's quadratic entropy, functional and phylogenetic redundancy.
● Data Source:
CranContrib
● Keywords: SYNCSA
● Alias: rao.diversity
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This function integrates several steps for the analysis of phylogenetic assembly patterns and their links to traits and ecological processes in a metacommunity (Pillar et al. 2009, Pillar & Duarte 2010). It requires data organized into the following matrices: (1) the presences or abundances of species in a set of communities (W); (2) the phylogenetic pairwise dissimilarities of these species (DF, in the range 0 to 1); (3) a set of functional traits describing the species (B), which may be a mixture of binary and quantitative traits (ordinal, interval, ratio scales), but not nominal ones (these should be expanded into binary traits); and (4) the ecological gradient of interest, which may be one or more factors to which the communities respond or ecosystem effects of the communities (E). The function computes several matrix correlations that express trait-convergence assembly patterns (TCAP), trait-divergence assembly patterns (TDAP), and phylogenetic signal in functional traits at the species pool level and at the metacomunity level. This function also generates P-values by permutation testing based on null models (Pillar et al. 2009, Pillar & Duarte 2010).
● Data Source:
CranContrib
● Keywords: SYNCSA
● Alias: syncsa
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Analysis of metacommunities based on functional traits and phylogeny of the community components. The functions, that are offered here, implement methods that have been available in the SYNCSA application written in C++ (by Valério Pillar, available at http://ecoqua.ecologia.ufrgs.br/ecoqua/SYNCSA.html) for the R environment.
● Data Source:
CranContrib
● Keywords: package
● Alias: SYNCSA, SYNCSA-package
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Internal function to permutate rows in a matrix.
● Data Source:
CranContrib
● Keywords: SYNCSA
● Alias: permut.row.matrix
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Function to obtain a matrix containing trait averages at community level. For more details, see syncsa.
● Data Source:
CranContrib
● Keywords: SYNCSA
● Alias: matrix.t
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Internal function for centralization and standardization in a matrix.
● Data Source:
CranContrib
● Keywords: SYNCSA
● Alias: cent.norm
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organize.syncsa
(Package: SYNCSA) :
Function for organize data for Package SYNCSA
Package SYNCSA requires that the species and community sequence in the data matrix must be the same for all matrices.
● Data Source:
CranContrib
● Keywords: SYNCSA
● Alias: organize.syncsa
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belonging
(Package: SYNCSA) :
Degree of belonging of species
Function to obtain a matrix containing the degree of belonging of each species based on its ecological or phylogenetic resemblance to other species. For more details, see matrix.p, matrix.x and syncsa.
● Data Source:
CranContrib
● Keywords: SYNCSA
● Alias: belonging
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Function to obtain a matrix containing phylogeny-weighted species composition. For more details, see syncsa.
● Data Source:
CranContrib
● Keywords: SYNCSA
● Alias: matrix.p
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providing 
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