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 | D1 x S | Mantel correlogram | mgram(D1, S) |
| Spatial structure in one matrix given more | D1 | D2 … Dn x S | Partial Mantel correlogram | ?mgram(residuals(lm(D1 ~ D2 + …)), space) |
| Spatial structuce in one matrix | D1 x S | Multivariate correlogram | pmgram(D1, S) |
| Spatial structure in one matrix given more | D1 | D2 … Dn x S | Partial multivariate correlogram | pmgram(D1, S, D2) |
| Spatial structure in the relationship between two matrices | D1 ~ D2 x S | 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 | 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 | 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) |