# Microbiome time series manipulation with miaTime <img src="man/figures/mia_logo.png" align="right" width="120" />
<!-- badges: start -->
[](https://bioconductor.org/packages/release/bioc/html/miaTime.html)
[](https://github.com/microbiome/miaTime/actions)
[](http://bioconductor.org/packages/release/bioc/html/miaTime.html)
[](https://bioconductor.org/packages/release/bioc/html/miaTime.html)
[](https://codecov.io/gh/microbiome/miaTime?branch=devel)
[](https://bioconductor.org/packages/release/bioc/html/miaTime.html)
<!-- badges: end -->
## Using the package
This R package can be used to analyse time series data for microbial
communities. The package is part of [miaverse](https://microbiome.github.io/),
and is based on the `TreeSummarizedExperiment` data container.
See the [package homepage](https://microbiome.github.io/miaTime) for
example workflows.
## Installation
### Bioc-release
```
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("miaTime")
```
### Bioc-devel
```
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("miaTime")
```
### GitHub
```
remotes::install_github("microbiome/miaTime")
```
## Contributions and acknowledgments
You can find us online from [Gitter](https://gitter.im/microbiome/miaverse).
Contributions are very welcome through issues and pull requests at the
[development site](https://github.com/microbiome/miaTime). We follow a git
flow kind of approach. Development version should be done against the
`main` branch and then merged to `release` for release.
(https://guides.github.com/introduction/flow/)
**Kindly cite this work**. For citation details, see R command
```r
citation("miaTime")
```
## Code of conduct
The project is released with a
[Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).
By contributing to this project, you agree to abide by its terms.
