# Microbiome data simulation with miaSim <!-- badges: start --> [](https://codecov.io/gh/microbiome/miaSim?branch=master) [](https://gitter.im/microbiome/miaverse) [![Watch on GitHub][github-watch-badge]][github-watch] [![Star on GitHub][github-star-badge]][github-star] [](https://github.com/microbiome/miaSim/actions) <!-- badges: end --> ## miaSim This miaSim R/Bioconductor package can be used to simulate (longitudinal) data for the benchmarking and analysis of quantitative models of microbial communities. For installation and use, see the [Getting started](https://microbiome.github.io/miaSim/articles/miaSim.html) page. The package [homepage](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. The package is based on the `(Tree)SummarizedExperiment` data container. ### miaSimShiny The accompanying [miaSimShiny](https://github.com/gaoyu19920914/miaSimShiny) package allows users to explore the parameter space of their models in real-time in an intuitive graphical interface. You can experiment with miaSimShiny [online](https://gaoyu.shinyapps.io/shiny_rep/). ### 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 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/) We are grateful to all [contributors](https://github.com/microbiome/miaSim/graphs/contributors). ### Citing the package **Kindly cite this work** as follows: Gao _et al._ (2023). Methods in Ecology and Evolution. DOI: [10.1111/2041-210X.14129](https://doi.org/10.1111/2041-210X.14129) For citation details, see R command `citation("miaSim")`. # Code of conduct Please note that the project is released with a [Bioconductor Code of Conduct](https://bioconductor.github.io/bioc_coc_multilingual/). By contributing to this project, you agree to abide by its terms. [github-watch-badge]: https://img.shields.io/github/watchers/microbiome/miaSim.svg?style=social [github-watch]: https://github.com/microbiome/miaSim/watchers [github-star-badge]: https://img.shields.io/github/stars/microbiome/miaSim.svg?style=social [github-star]: https://github.com/microbiome/miaSim/stargazers