Ecodive provides the fastest implementations of alpha and beta diversity metrics for R, including UniFrac, Faith’s PD, Bray-Curtis, Shannon, and many others. It works with any matrix-like object, including phyloseq, rbiom, and BioConductor data structures. With zero dependencies, it’s quick to install and ideal for end users and package developers alike.
Installation
The latest stable version can be installed from CRAN.
install.packages('ecodive')The development version is available on GitHub. Please note that this method requires a compiler - see http://www.rstudio.com/ide/docs/packages/prerequisites if the installation does not succeed on the first try.
install.packages('pak')
pak::pak('cmmr/ecodive')Usage
## Example Data ----------------------
counts <- rarefy(ex_counts)
counts
#> Saliva Gums Nose Stool
#> Streptococcus 162 309 6 1
#> Bacteroides 2 2 0 341
#> Corynebacterium 0 0 171 1
#> Haemophilus 180 34 0 1
#> Propionibacterium 1 0 82 0
#> Staphylococcus 0 0 86 1
## Alpha Diversity -------------------
shannon(counts)
#> Saliva Gums Nose Stool
#> 0.74119910 0.35692121 1.10615349 0.07927797
faith(counts, tree = ex_tree)
#> Saliva Gums Nose Stool
#> 180 155 101 202
## Beta Diversity --------------------
bray_curtis(counts)
#> Saliva Gums Nose
#> Gums 0.4260870
#> Nose 0.9797101 0.9826087
#> Stool 0.9884058 0.9884058 0.9913043
weighted_unifrac(counts, tree = ex_tree)
#> Saliva Gums Nose
#> Gums 36.97681
#> Nose 67.23768 55.97101
#> Stool 109.77971 109.44058 110.00870Documentation
The online manual for ecodive is available at https://cmmr.github.io/ecodive/. It includes a getting started guide, articles on alpha/beta diversity, and reference pages for each function.
Automated tests
The following commands will check if ecodive passes the bundled testing suite.
install.packages('testthat')
testthat::test_check('ecodive')Community guidelines
Support
Bug reports, feature requests, and general questions can be submitted at https://github.com/cmmr/ecodive/issues.
Contributing
Pull requests are welcome. Please ensure contributed code is covered by tests and documentation (add additional tests and documentation as needed) and passes all automated tests.
New functions should leverage C and pthreads to minimize memory and CPU time.
Please note that the ecodive project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.