# Microbiome data simulation with miaSim
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This R package can be used to simulate (longitudinal) data for the
benchmarking and analysis of quantitative models of microbial
communities. The package is part of
[miaverse](microbiome.github.io), and is based on the
`(Tree)SummarizedExperiment` data container.
The package [website](https://microbiome.github.io/miaSim/) provides
further tutorials and references for the [implemented
models](https://microbiome.github.io/miaSim/reference/index.html),
which include Hubbell's neutral model, the generalized Lotka-Volterra
model, and the self-organised instability model.
## Installation
### Bioc-release
```{r, eval=FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("miaSim")
```
### Bioc-devel
```{r, eval=FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("miaSim")
```
### 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/miaSim). We 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/)
We are grateful to all
[contributors](https://github.com/microbiome/miaSim/graphs/contributors),
and Emma Gheysen and Karoline Faust for developing the
[microsimR](https://github.com/gheysenemma/microsimR) package that the
miaSim package converts to the SummarizedExperiment universe. This
project is part of [miaverse](microbiome.github.io).
**Kindly cite this work**. For citation details, see R command
`citation("miaSim")`.
# Code of conduct
Please note that 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.
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