Author: Sarah Goslee
Date: 2017-07-12

# Dissimilarity Cheat Sheet

#### Sarah Goslee

#### 2017-07-12

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)