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 page.
The package is based on the (Tree)SummarizedExperiment data
container that supports microbiome data analysis. The package
homepage provides further
tutorials and references for the implemented
models:
- Self-organised instability (SOI)
- Hubbell's neutral model
- generalized Lotka-Volterra (gLV)
- Ricker model (discrete gLV)
- Stochastic logistic model
- Consumer-resource model
The accompanying 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.
You can find us online from Gitter.
Contributions are very welcome through issues and pull requests at the
development site. 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.
Kindly cite this work as follows:
Gao et al. (2023). Methods in Ecology and Evolution. DOI: 10.1111/2041-210X.14129
For citation details, see R command citation("miaSim").
Please note that the project is released with a Bioconductor Code of Conduct. By contributing to this project, you agree to abide by its terms.