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hillR

hillR: taxonomic, functional, and phylogenetic diversity and similarity through Hill Numbers - Published in JOSS (2018)

https://github.com/daijiang/hillr

Science Score: 95.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
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    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 14 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org
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    2 of 8 committers (25.0%) from academic institutions
  • ○
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    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

biodiversity hill-numbers r
Last synced: 6 months ago · JSON representation

Repository

An R pakage to calculate diversity through Hill Numbers

Basic Info
  • Host: GitHub
  • Owner: daijiang
  • License: other
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 182 KB
Statistics
  • Stars: 34
  • Watchers: 4
  • Forks: 14
  • Open Issues: 3
  • Releases: 4
Topics
biodiversity hill-numbers r
Created almost 11 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---



```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "##",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

[![DOI](http://joss.theoj.org/papers/10.21105/joss.01041/status.svg)](https://doi.org/10.21105/joss.01041) [![Build Status](https://travis-ci.org/daijiang/hillR.svg?branch=master)](https://app.travis-ci.com/github/daijiang/hillR) [![Coverage status](https://codecov.io/gh/daijiang/hillR/branch/master/graph/badge.svg)](https://app.codecov.io/github/daijiang/hillR?branch=master)
[![CRAN status](https://www.r-pkg.org/badges/version/hillR)](https://cran.r-project.org/package=hillR)
[![CRAN RStudio mirror downloads](http://cranlogs.r-pkg.org/badges/hillR)](https://www.r-pkg.org/pkg/hillR)
[![CRAN RStudio mirror downloads](http://cranlogs.r-pkg.org/badges/grand-total/hillR?color=green)](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.

Owner

  • Name: Daijiang Li
  • Login: daijiang
  • Kind: user
  • Location: Baton Rouge, LA

JOSS Publication

hillR: taxonomic, functional, and phylogenetic diversity and similarity through Hill Numbers
Published
November 13, 2018
DOI
Volume 3, Issue 31, Page 1041
Authors
Daijiang Li ORCID
Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611
Editor
Karthik Ram ORCID
Tags
Hill numbers biodiversity phylogenetic diversity functional diversity
View PDF Review Thread Software Archive

GitHub Events

Total
  • Issues event: 2
  • Watch event: 3
  • Issue comment event: 1
Last Year
  • Issues event: 2
  • Watch event: 3
  • Issue comment event: 1

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 119
  • Total Committers: 8
  • Avg Commits per committer: 14.875
  • Development Distribution Score (DDS): 0.42
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Daijiang Li d****1@u****u 69
daijiang d****e@g****m 41
Alison Paulson a****n@u****u 3
Hugo Gruson h****n@p****m 2
ajrominger a****r@g****m 1
Pedro Neves n****r@g****m 1
Matthias Grenié m****e@e****r 1
Katrin Leinweber k****i@p****e 1
Committer Domains (Top 20 + Academic)
posteo.de: 1 ens-lyon.fr: 1 ucdavis.edu: 1 ufl.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 18
  • Total pull requests: 7
  • Average time to close issues: 6 months
  • Average time to close pull requests: about 14 hours
  • Total issue authors: 14
  • Total pull request authors: 6
  • Average comments per issue: 2.28
  • Average comments per pull request: 1.14
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: 6 days
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 4.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • daijiang (3)
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  • BErfanian (1)
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Pull Request Authors
  • p-neves (2)
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  • akpaulson (1)
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  • Bisaloo (1)
  • Rekyt (1)
Top Labels
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Packages

  • Total packages: 2
  • Total downloads:
    • cran 502 last-month
  • Total dependent packages: 1
    (may contain duplicates)
  • Total dependent repositories: 3
    (may contain duplicates)
  • Total versions: 5
  • Total maintainers: 1
cran.r-project.org: hillR

Diversity Through Hill Numbers

  • Versions: 4
  • Dependent Packages: 1
  • Dependent Repositories: 3
  • Downloads: 502 Last month
Rankings
Forks count: 5.8%
Stargazers count: 9.8%
Average: 13.0%
Downloads: 14.9%
Dependent repos count: 16.8%
Dependent packages count: 17.6%
Maintainers (1)
daijianglee@gmail.com
Last synced: 6 months ago
conda-forge.org: r-hillr
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 34.0%
Average: 42.9%
Stargazers count: 43.0%
Forks count: 43.4%
Dependent packages count: 51.2%
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.1 depends
  • FD * imports
  • ade4 * imports
  • ape * imports
  • geiger * imports
  • plyr * imports
  • tibble * imports
  • betapart * suggests
  • covr * suggests
  • testthat * suggests