This R/Bioconductor 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, and is based on the
(Tree)SummarizedExperiment data container.
The package website provides further tutorials and references for the implemented models, which include Hubbell's neutral model, the generalized Lotka-Volterra model, and the self-organised instability model.
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("miaSim")
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("miaSim")
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 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, and Emma Gheysen and Karoline Faust for developing the microsimR package that the miaSim package converts to the TreeSummarizedExperiment universe. This project is part of miaverse.
Kindly cite this work. For citation details, see R command
citation("miaSim").
Please note that the project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.