Function mantel.correlog computes a multivariate Mantel correlogram. Proposed by Sokal (1986) and Oden and Sokal (1986), the method is also described in Legendre and Legendre (2012, pp. 819–821).
Function model.frame.cca reconstructs a data.frame with the variables used in the constrained ordination method (cca, rda or capscale. Function model.matrix.cca creates a list of design matrices used in constrained ordination. The items of the list are called Conditions and Constraints. If either partial (Conditions) or constrained component was missing, a single matrix is returned.
treedive
(Package: vegan) :
Functional Diversity and Community Distances from Species Trees
Functional diversity is defined as the total branch length in a trait dendrogram connecting all species, but excluding the unnecessary root segments of the tree (Petchey and Gaston 2006). Tree distance is the increase in total branch length when combining two sites.
Automatic stepwise model building for constrained ordination methods (cca, rda, capscale). The function ordistep is modelled after step and can do forward, backward and stepwise model selection using permutation tests. Function ordiR2step performs forward model choice solely on adjusted R2 and P-value, for ordination objects created by rda or capscale.
mantel
(Package: vegan) :
Mantel and Partial Mantel Tests for Dissimilarity Matrices
Function mantel finds the Mantel statistic as a matrix correlation between two dissimilarity matrices, and function mantel.partial finds the partial Mantel statistic as the partial matrix correlation between three dissimilarity matrices. The significance of the statistic is evaluated by permuting rows and columns of the first dissimilarity matrix.
Function rotates a multidimensional scaling result so that its first dimension is parallel to an external (environmental variable). The function can handle the results from metaMDS or monoMDS functions.
prc
(Package: vegan) :
Principal Response Curves for Treatments with Repeated Observations
Principal Response Curves (PRC) are a special case of Redundancy Analysis (rda) for multivariate responses in repeated observation design. They were originally suggested for ecological communities. They should be easier to interpret than traditional constrained ordination. They can also be used to study how the effects of a factor A depend on the levels of a factor B, that is A + A:B, in a multivariate response experiment.
vegemite
(Package: vegan) :
Display Compact Ordered Community Tables
Functions vegemite and tabasco display compact community tables. Function vegemite prints text tables where species are rows, and each site takes only one column without spaces. Function tabasco provides interface for heatmap for a colour image of the data. The community table can be ordered by explicit indexing, by environmental variables or results from an ordination or cluster analysis.
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