A simulator package in R containing a collection of basic community models that outputs count data of microbial communities, integrating various statistical and computational methodologies for minimal runtime.
Most recent development version can be pulled from this repository and installed directly from R command line.
First load the devtools package.
library(devtools)
Then install from Github with following command.
devtools::install_github("gheysenemma/microsimR")
library(microsim)
The most recent version of this package contains the following simulation models:
- The Generalised Lotka-Voltera Model:
microsim::glv() - The Hubbell Neutral Model:
microsim::hubbell() - The Self Organised Instability Model:
microsim::soi()
Other functions included in the package:
- RMSE-based sampling function given a time series:
microsim::rmse_sample() phyloseqwrapper function (samples / full time series):microsim::asPhyloseq()- Power-law interaction matrix decomposition
microsim::powerlawA() - Random interaction matrix by uniform distribution
microsim::randomA()
This package is constructed as part of a master's thesis at KU Leuven 2020-2021.
- Author: Emma Gheysen
Under supervision of:
- Promotor: Prof. Karoline Faust (KU Leuven)
- Co-promotor: Prof. Leo Lahti (Turku University)
- Mentor: Daniel Rios Garza (KU Leuven)