In daijiang/hillR: Diversity Through Hill Numbers

knitr::opts_chunk$set(
  collapse = TRUE,
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hillR

This package contains R functions to calculate taxonomic, functional, and phylogenetic diversity and site similarity through Hill Numbers. The underlying methods are based on Chao, Chiu and Jost 2014 and Chiu & Chao 2014.

Installation

To install this package, run the following code:

install.packages("hillR")
# or install from Github
install.packages("hillR", repos = c('https://daijiang.r-universe.dev', 'https://cloud.r-project.org'))

Examples

dummy = FD::dummy
comm = dummy$abun
traits = dummy$trait
set.seed(123)
tree = ape::rtree(n = ncol(comm), tip.label = paste0("sp", 1:ncol(comm)))
library(hillR)

Calculate taxonomic, functional, and phylogenetic diversity of each site

hill_taxa(comm, q = 0) # taxonomic alpha diversity

hill_func(comm, traits, q = 0) # functional alpha diversity

hill_phylo(comm, tree, q = 0) # phylogenetic alpha diversity

Calculate taxonomic, functional, and phylogenetic diversity across multiple sites

hill_taxa_parti(comm, q = 0) # taxonomic diversity across all sites

hill_func_parti(comm, traits, q = 0) # functional diversity across all sites

hill_phylo_parti(comm, tree, q = 0) # phylogenetic diversity across all sites

Calculate pairwise taxonomic, functional, and phylogenetic diversity

# pairwise taxonomic diversity
hill_taxa_parti_pairwise(comm, q = 0, show_warning = FALSE, .progress = FALSE) 
# pairwise functional diversity
hill_func_parti_pairwise(comm, traits, q = 0, show_warning = FALSE, .progress = FALSE) 
# pairwise phylogenetic diversity
hill_phylo_parti_pairwise(comm, tree, q = 0, show_warning = FALSE, .progress = FALSE)

Licenses

Licensed under the MIT license. (More information here.)

Citation

Please cite this package if you use it. The citation information can be obtained by running citation('hillR') in R.

Li, (2018). hillR: taxonomic, functional, and phylogenetic diversity and similarity through Hill Numbers. Journal of Open Source Software, 3(31), 1041. https://doi.org/10.21105/joss.01041

@Article{,
    title = {hillR: taxonomic, functional, and phylogenetic diversity and similarity through Hill Numbers},
    author = {Daijiang Li},
    journal = {Journal of Open Source Software},
    year = {2018},
    volume = {3},
    number = {31},
    pages = {1041},
    url = {https://doi.org/10.21105/joss.01041},
 }