-
Notifications
You must be signed in to change notification settings - Fork 18
/
README.Rmd
63 lines (40 loc) · 3.56 KB
/
README.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
# breakaway <img src="docs/breakaway-logo.png" align="right" width="165px"/>
[](https://github.com/adw96/breakaway/actions)
[](https://codecov.io/github/adw96/breakaway?branch=main)
Understanding the drivers of microbial diversity is an important frontier of microbial ecology, and investigating the diversity of samples from microbial ecosystems is a common step in any microbiome analysis.
`breakaway` is the premier package for statistical analysis of microbial diversity. `breakaway` implements the latest and greatest estimates of richness, as well as the most commonly used estimates.
[`DivNet`](https://github.com/adw96/DivNet) is a package by the `breakaway` authors for estimating Shannon diversity, and other diversity indices. `breakaway` focuses on richness while `DivNet` focuses on Shannon, Simpson, and other alpha diversities as well as some beta diversity indices. Check it out!
### Citing breakaway
The `R` package `breakaway` implements a number of different richness estimates. Please cite the following if you use them:
- `breakaway()` and `kemp()`: Willis, A. & Bunge, J. (2015). Estimating diversity via frequency ratios. Biometrics.
- `betta()`: Willis, A., Bunge, J., & Whitman, T. (2017). Improved detection of changes in species richness in high diversity microbial communities. JRSS-C.
- `breakaway_nof1()`: Willis, A. (2016+). Species richness estimation with high diversity but spurious singletons. arXiv.
- `objective_bayes_*()`: Barger, K. & Bunge, J. (2010). Objective Bayesian estimation for the number of species. Bayesian Analysis.
## Installation
You can install `breakaway` from github by running:
```R
install.packages("devtools")
devtools::install_github("adw96/breakaway")
```
`breakaway` is actively maintained and continually expanding and developing its scope! Is there a method you would like to have implemented in breakaway? Submit a pull request or contact the [maintainer](http://statisticaldiversitylab.com/team/amy-willis)!
### Documentation
- The best place to start is the [vignettes](https://adw96.github.io/breakaway/articles/).
- Documentation for functions can be found [here](https://adw96.github.io/breakaway/reference/index.html)
- A pdf of all documentation can be found in the [breakaway-manual.pdf](https://github.com/adw96/breakaway/tree/master/breakaway-manual.pdf)
- We try to answer frequently asked questions on the [wiki](https://github.com/adw96/breakaway/wiki)
## Humans
Maintainer: [Amy Willis](http://statisticaldiversitylab.com)
Authors: [Amy Willis](http://statisticaldiversitylab.com), John Bunge, [Bryan Martin](https://bryandmartin.github.io/), [Pauline Trinh](https://twitter.com/paulinetrinh), Kathryn Barger, [David Clausen](https://www.biostat.washington.edu/people/david-clausen) and [Sarah Teichman](https://svteichman.github.io/).
Do you have a request for us? Let us know! We want folks to use `breakaway` and are committed to making it as easy to use as possible.
Do you have a question? Check out the above documentation list, then shoot us an email or open a [Discussion](https://github.com/adw96/breakaway/discussions). We receive a lot of emails from users, so we try to answer questions on the Wiki rather than responding to everyone individually.