specificity: an R package for generalized specificity analysis, with example analyses of Hawaiian foliar endophytic Fungi, human gut microbiome bacteria, and Antarctic glacier bacteria

Understanding the factors that influence microbes9 environmental distributions is important for determining drivers of microbial community composition. Species distributions are governed by parameters that influence their dispersal or survival. These include environmental variables like temperature and pH, and higher-dimensional variables like geographic distance and host species phylogenies. In microbial ecology, "specificity" is often described in the context of symbiotic or host parasitic interactions, but specificity can be more broadly used to describe the extent to which a species occupies a narrower range of an environmental variable than expected by chance. Using a standardization we describe here, Rao9s (1982, 2010) Quadratic Entropy can be conveniently applied to calculate specificity of a focal species to many different environmental variables, including 1-dimensional variables (vectors), dissimilarity matrices, phylogenies, and ontologies. We present our R package "specificity" for performing the above analyses, and apply it to four real-life microbial datasets to demonstrate its application: fungi living within the leaves of native Hawaiian plants, bacteria from the human gut microbiome, bacteria living within Antarctic glacier ice, and the Earth Microbiome Project data set. Finally, we present an interactive visualization and data exploration tool for these analyses, available as a companion R-package called "specificity.shiny".