hillR: taxonomic, functional, and phylogenetic diversity and similarity through Hill Numbers

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Authors Daijiang Li
Journal/Conference Name J. Open Source Software
Paper Category
Paper Abstract A unified framework to calculate biodiversity of ecological communities through Hill numbers (Hill, 1973; Jost, 2006) was recently proposed by Chao, Chiu, & Jost (2014). This framework can be applied to three facets of biodiversity: taxonomic, functional, and phylogenetic diversity. These three facets of biodiversity can be expressed as Hill numbers with the same units (effective number of species), facilitating direct comparisons between them (Chao et al., 2014). In addition, this framework can account for species abundance by changing the parameter q, which can be any non-negative number (e.g., 0, 0.99, 2). As q increases, the diversity values become more sensitive to common species. When q = 0, species abundance is ignored; q = 1, all species are weighted by their abundance equally (i.e., Shannon’s diversity for taxonomic diversity); q = 2, common species get more weight than rare species (i.e., inverse of Simpson diversity for taxonomic diversity). Furthermore, both alpha and beta diversity can be calculated with this framework. Given the above advantages, this framework has been adopted by an increasing number of researchers.
Date of publication 2018
Code Programming Language R
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