Name Mode Size
.github 040000
R 040000
inst 040000
man 040000
tests 040000
vignettes 040000
.Rbuildignore 100644 0 kb
.gitignore 100644 0 kb
DESCRIPTION 100644 2 kb
LICENSE 100644 9 kb
NAMESPACE 100644 1 kb
NEWS 100644 0 kb
README.Rmd 100644 3 kb 100644 3 kb
codecov.yml 100644 0 kb
# Microbiome data simulation with miaSim <!-- badges: start --> [![R-CMD-check](]( [![R-CMD-check-bioc](]( [![R-CMD-check-bioc-devel](]( [![Codecov test coverage](]( [![Gitter](]( [![Watch on GitHub][github-watch-badge]][github-watch] [![Star on GitHub][github-star-badge]][github-star] <!-- badges: end --> 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](, 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. ## 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]( 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. ( We are grateful to all [contributors](, and Emma Gheysen and Karoline Faust for developing the [microsimR]( package that the miaSim package converts to the SummarizedExperiment universe. This project is part of [miaverse]( **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]( By contributing to this project, you agree to abide by its terms. [github-watch-badge]: [github-watch]: [github-star-badge]: [github-star]: