miaSim

Microbiome data simulation with miaSim

R/Bioconductor package for simulating microbial community dynamics
Common ecological models
miaSimShiny: Graphical user interface

Implemented models

Self-organised instability (SOI)
Hubbell’s neutral model
Generalized Lotka–Volterra (gLV)
Ricker model (discrete gLV)
Stochastic logistic model
Consumer–resource model

Stochastic logistic model

\[ \frac{dN}{dt} = r N \left(1 - \frac{N}{K}\right) + \sigma N \, \eta(t) \]

\(N\): population size
\(r\): intrinsic growth rate
\(K\): carrying capacity
\(\sigma\): noise strength
\(\eta(t)\): random fluctuation (white noise)

Logistic growth (deterministic)

\[ \frac{dN}{dt} = rN\!\left(1 - \frac{N}{K}\right) \]

\(N\): population size
\(r\): intrinsic growth rate
\(K\): carrying capacity

Add randomness → Stochastic logistic model

\[ \frac{dN}{dt} = rN\!\left(1 - \frac{N}{K}\right) + \sigma N\,\eta(t) \]

\(\sigma\): noise strength
\(\eta(t)\): random fluctuation (white noise)

Stochastic logistic model

Single-species microbial dynamics under resource limits
Effects of random perturbations (e.g., host variability)
Benchmark for statistical methods before multi-species models

Learn more

miaSim package vignette (tutorials, examples, and model descriptions)

(Gao et al. 2023) (publication)

References

Gao, Yu, Yağmur Şimşek, Emma Gheysen, Tuomas Borman, Yi Li, Leo Lahti, Karoline Faust, and Daniel Rios Garza. 2023. “miaSim: An R/Bioconductor Package to Easily Simulate Microbial Community Dynamics.” Methods in Ecology and Evolution 14 (8): 1967–80. https://doi.org/10.1111/2041-210x.14129.