Dissimilarity Cheat Sheet

Things to do with dissimilarity matrices

(ecodist functions are marked in bold)

(untested ideas marked with ?)

Description | Notation | Name | R function ------------|----------|------|----------- Relationship between two matrices | D1 ~ D2 | Mantel test | mantel(D1 ~ D2) Relationship between two matrices given more | D1 ~ D2 | D3 ... Dn | Partial Mantel test | mantel(D1 ~ D2 + D3 + ...) ||| Spatial structure in one matrix relative to all distance classes | D1 x S | Mantel correlogram | mgram(D1, S) Spatial structure in one matrix given more relative to all distance classes | D1 | D2 ... Dn x S | Partial Mantel correlogram | ?mgram(residuals(lm(D1 ~ D2 + ...)), space) Spatial structuce in one matrix by distance class | D1 x S | Piecewise multivariate correlogram | pmgram(D1, S) Spatial structure in one matrix by distance class given more | D1 | D2 ... Dn x S | Piecewise partial multivariate correlogram | pmgram(D1, S, D2) ||| Spatial structure in the relationship between two matrices | D1 ~ D2 x S | Piecewise Mantel cross-correlogram | pmgram(cbind(lower(D1), lower(D2)), S) Spatial structure in the relationship between two matrices given more | D1 ~ D2 | D3 ... Dn x S | Piecewise partial Mantel cross-correlogram | pmgram(cbind(lower(D1), lower(D2)), S, D3) ||| Ordination of one matrix | | (N)MDS | nmds(y) or pco(y) Ordination of one matrix given more | | (Partial (N)MDS | ?nmds(residuals(lm(y ~ z1 + ...))) ||| Grouping of items based on one matrix | | Cluster analysis | eg hclust(y) Grouping of items based on one matrix given more | | Partial cluster analysis | ?hclust(residuals(lm(y ~ z1 + ...))) Grouping of items given space | | Spatially-constrained cluster analysis | NA ||| Multiple regression | D1 ~ D2 | D3 ... Dn | Multiple regression on distance matrices | MRM(D1 ~ D2 + D3 + ...)

Ways to calculate dissimilarity matrices

Description | Result | R function ------------|--------|----------- From a site by sample matrix | Symmetric matrix with zero diagonals | dist(x) or bcdist(x) or distance(x)


Things to do with cross-dissimilarity matrices

Description | Notation | Name | R function ------------|----------|------|----------- Relationship between two cross-dissimilarity matrices | D12 ~ D34 | Cross-Mantel test | xmantel(D12 ~ D34) Relationship between two cross-dissimilarity matrices given more | D12 ~ D34 | D56 ... Dn | Partial cross-Mantel test | xmantel(D12 ~ D34 + D56 + ...) ||| Spatial structure in one cross-dissimilarity matrix | D12 x S | Cross-Mantel correlogram | xmgram(D12, spaceX) Spatial structure in one cross-dissimilarity matrix given more | D12 | D34 ... Dn x S | Partial cross-Mantel correlogram | ?xmgram(residuals(lm(D12 ~ D34 + ...)), spaceX)

Ways to calculate cross-dissimilarity matrices

Source | Result | R function -------|--------|----------- From 2 site by sample matrixes for the same sites and samples (e.g. different years) | nonsymmetric matrix with nonzero diagonals | xdistance(x, y)



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ecodist documentation built on Nov. 2, 2023, 6:01 p.m.