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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r setup, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "##",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
[](https://doi.org/10.21105/joss.01041) [](https://app.travis-ci.com/github/daijiang/hillR) [](https://app.codecov.io/github/daijiang/hillR?branch=master)
[](https://cran.r-project.org/package=hillR)
[](https://www.r-pkg.org/pkg/hillR)
[](https://www.r-pkg.org/pkg/hillR)
# hillR
This package contains R functions to calculate taxonomic, functional, and phylogenetic diversity and site similarity through Hill Numbers. The underlying methods are based on Chao, Chiu and Jost 2014 and Chiu & Chao 2014.
# Installation
To install this package, run the following code:
```{r, eval=FALSE}
install.packages("hillR")
# or install from Github
install.packages("hillR", repos = c('https://daijiang.r-universe.dev', 'https://cloud.r-project.org'))
```
# Examples
```{r data}
dummy = FD::dummy
comm = dummy$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
```{r}
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
```{r}
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
```{r}
# 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](LICENSE). ([More information here](https://en.wikipedia.org/wiki/MIT_License).)
# 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
```bibtex
@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},
}
```
# Reference
- [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.](https://doi.org/10.1146/annurev-ecolsys-120213-091540)
- [Chiu, Chun-Huo, and Anne Chao. “Distance-Based Functional Diversity Measures and Their Decomposition: A Framework Based on Hill Numbers.” PLoS ONE 9, no. 7 (July 7, 2014): e100014. doi:10.1371/journal.pone.0100014.](https://doi.org/10.1371/journal.pone.0100014)
# Contributing
Contributions are welcome. You can provide comments and feedback or ask questions by filing an issue on Github [here](https://github.com/daijiang/hillR/issues) or making pull requests.