Dissimilarity analysis based on diffusion maps

Compositional measurements from species assemblages define a high dimensional dataspace in which the data can form complex structures, termed manifolds. Comparing assemblages in this dataspace is difficult because the data is often sparse relative to its dimensionality and the complex structure of t...

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Bibliographic Details
Published inOikos Vol. 2023; no. 12
Main Authors Gault, Jordan A., Freund, Jan A., Hillebrand, Helmut, Gross, Thilo
Format Journal Article
LanguageEnglish
Published Oxford, UK Blackwell Publishing Ltd 01.12.2023
Subjects
biodiversity change
compositional dissimilarity
Data points
Diffusion
diffusion maps
dimensionality reduction
Distance
Distance measurement
Error analysis
Euclidean geometry
Manifolds
Manifolds (mathematics)
Species diffusion
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Summary:Compositional measurements from species assemblages define a high dimensional dataspace in which the data can form complex structures, termed manifolds. Comparing assemblages in this dataspace is difficult because the data is often sparse relative to its dimensionality and the complex structure of the manifold introduces bias and error in measurements of distance. Here, we apply diffusion maps, a manifold learning method, to find and characterize manifolds in high‐dimensional compositional data. We show that diffusion maps embed the data in reduced dimensions in which the Euclidean distance between data points approximates the distance between them along the manifold. This is especially useful when species turnover is high, as it provides a way to measure meaningful distances between assemblages even when they harbor disjoint sets of species. We anticipate diffusion maps will therefore be particularly useful for characterizing community change over large spatial and temporal scales.
ISSN:0030-1299
1600-0706
DOI:10.1111/oik.10249