krisrs1128/mbtransfer

`mbtransfer` is an R package for modeling microbiome dynamics. It provides functions for fitting transfer function models, simulating counterfactual trajectories, and selecting significantly perturbed taxa using mirror statistics.

Microbiome Intervention Analysis using mbtransfer

mbtransfer is an R package for modeling and inference of microbial communities under dynamic environmental interventions. It supports simulation of hypothetical community trajectories under user-specified perturbations and can be used to select for taxa that are significantly impacted by this change in a statistically rigorous sense. It accomplishes this by learning a separate transfer function model for each taxon, relating its changes in abundance to its immediate community and environmental context. The fitted models can be used to measure the significance of the intervention on individual taxa,

(larger mirror statistics correspond to stronger effects) and to simulate trajectory differences between counterfactual treatments,

You can read more about the methodology in our preprint and can browse complete examples in the package documentation.

Installation

You can install mbtransfer from this repository using:

#install.packages("devtools")
devtools::install_github("krisrs1128/mbtransfer")

Help

We welcome questions and comments about the package! You can reach us either through github or email.