Journal Article

Jaccard/Tanimoto similarity test and estimation methods for biological presence-absence data

Startek, Michał, Miasojedow, BłaŻej, Gambin, Anna, Chung, Neo Christopher

2019

Overview

Background A survey of presences and absences of specific species across multiple biogeographic units (or bioregions) are used in a broad area of biological studies from ecology to microbiology. Using binary presence-absence data, we evaluate species co-occurrences that help elucidate relationships among organisms and environments. To summarize similarity between occurrences of species, we routinely use the Jaccard/Tanimoto coefficient, which is the ratio of their intersection to their union. It is natural, then, to identify statistically significant Jaccard/Tanimoto coefficients, which suggest non-random co-occurrences of species. However, statistical hypothesis testing using this similarity coefficient has been seldom used or studied. Results We introduce a hypothesis test for similarity for biological presence-absence data, using the Jaccard/Tanimoto coefficient. Several key improvements are presented including unbiased estimation of expectation and centered Jaccard/Tanimoto coefficients, that account for occurrence probabilities. The exact and asymptotic solutions are derived. To overcome a computational burden due to high-dimensionality, we propose the bootstrap and measurement concentration algorithms to efficiently estimate statistical significance of binary similarity. Comprehensive simulation studies demonstrate that our proposed methods produce accurate p -values and false discovery rates. The proposed estimation methods are orders of magnitude faster than the exact solution, particularly with an increasing dimensionality. We showcase their applications in evaluating co-occurrences of bird species in 28 islands of Vanuatu and fish species in 3347 freshwater habitats in France. The proposed methods are implemented in an open source R package called jaccard ( https://cran.r-project.org/package=jaccard ). Conclusion We introduce a suite of statistical methods for the Jaccard/Tanimoto similarity coefficient for binary data, that enable straightforward incorporation of probabilistic measures in analysis for species co-occurrences. Due to their generality, the proposed methods and implementations are applicable to a wide range of binary data arising from genomics, biochemistry, and other areas of science.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Algorithms / Animals / Aquatic habitats / Associations / Asymptotic methods / Binary data / Binary similarity / Biogeography / Bioinformatics / Biomedical and Life Sciences / Biometry / Birds / Co-occurrences / Coefficients / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Computer applications / Computer simulation / Ecological monitoring / Estimates / Evaluation / Exact solutions / Expected values / Fishes / Freshwater Biology - methods / Freshwater environments / Freshwater fish / Genomics / Hypotheses / Jaccard / Life Sciences / Microarrays / Microbiology / P-value / Presence-absence / Probability / Production methods / Species / Statistical analysis / Statistical methods / Statistical significance / Statistics / Tanimoto / Test procedures