RITHMS

Our framework, an R Implementation of a Transgenerational Hologenomic Model-based Simulator (RITHMS) an open-source package, builds upon the MoBPS package and incorporates the distinctive architecture of the microbiota, notably vertical and horizontal transfer as well as modulation due to the environment and host genetics. In addition, RITHMS can account for a variety of selection strategies, is adaptable to different genetic architectures.

Full documentation website on: https://SolenePety.github.io/RITHMS

Here is a little summary of how RITHMS work, but you can read the preprint for more details.

Schema

Installation

You can install the development version of RITHMS from GitHub with:

# install.packages("pak")
pak::pak("SolenePety/RITHMS")

Example

This is a basic example which shows you how to solve a common problem:

library(RITHMS)
## basic example code

You already have a toy dataset that show you the expected structure of input data :

# datafile <- system.file("BesePopTest.rds", package = "RITHMS")
# ToyData <- readRDS(datafile)

But we can do much more… you can check also this vignette to generate the beautiful figures coming from the article