| hillR {hillR} | R Documentation |
hillR: Diversity Through Hill Numbers
Description
The R package 'hillR' implements the framework proposed by Chao, et al. 2014 and makes it easy to calculate taxonomic, functional, and phylogenetic diversity of ecological communities as Hill numbers. For each facet of diversity, 'hillR' has three functions. The first set of functions (hill_taxa, hill_func, and hill_phylo) calculates alpha diversity of each site. The second set of functions (hill_taxa_parti, hill_func_parti, and hill_phylo_parti) calculates diversity across all sites. The third set of functions (hill_taxa_parti_pairwise, hill_func_parti_pairwise, and hill_phylo_parti_pairwise) calculates all possible pairwise diversity across all sites. Users can set the argument _q_ to control the weight of species abundance.
Details
Users may be interested in other similar packages such as vegetarian and iNEXT.
Taxonomic Hill Numbers
hill_taxa, hill_taxa_parti, hill_taxa_parti_pairwise
Functional Hill Numbers
hill_func, hill_func_parti, hill_func_parti_pairwise
Phylogenetic Hill Numbers
hill_phylo, hill_phylo_parti, hill_phylo_parti_pairwise
References
Chao, Anne, Chun-Huo Chiu, and Lou Jost. Unifying Species Diversity, Phylogenetic Diversity, Functional Diversity, and Related Similarity and Differentiation Measures Through Hill Numbers. Annual Review of Ecology, Evolution, and Systematics 45, no. 1 (2014): 297–324. <doi:10.1146/annurev-ecolsys-120213-091540>.