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README.Rmd
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# Microbiome data simulation with miaSim <img src="man/figures/mia_logo.png" align="right" width="120" />
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## miaSim
This R/Bioconductor package provides tools to simulate (longitudinal)
time series data from popular models in microbial ecology. The
[homepage](https://microbiome.github.io/miaSim/) provides tutorials
and references for the [implemented
models](https://microbiome.github.io/miaSim/reference/index.html):
* Self-organised instability (SOI)
* Hubbell's neutral model
* generalized Lotka-Volterra (gLV)
* Ricker model (discrete gLV)
* Stochastic logistic model
* Consumer-resource model
These methods can be used for _in silico_ studies of microbial
community dynamics or multi-omic or host-microbiome interactions. The
miaSim package supports the Bioconductor [multi-assay data science
framework](https://microbiome.github.io/OMA) for multi-omic data
integration and time series analysis, and utilizes the
`(Tree)SummarizedExperiment` data container.
[Getting started](https://microbiome.github.io/miaSim/articles/miaSim.html).
### 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).
This research has received funding from
* the Horizon 2020 Programme of the European Union within the [FindingPheno project](https://www.findingpheno.eu/) under grant agreement No 952914.
* Research Council of Finland (grant 330887)
<img src="man/figures/FindingPheno2.jpg" alt="FindingPheno logo" style="height: 50px"/>
### 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