Watch this space…
SIMPLEGEN is currently in development and is not yet ready for real analysis sorry! We hope to have a working release version start of 2024.
SIMPLEGEN is an R package for efficiently simulating Plasmodium genetic data. It does this by breaking the simulation process down into a series of steps:
There are several types of models along this pipeline, including epidemiological models, genetic models, and observation models. SIMPLEGEN contains in-built versions of these models that are calibrated against publicly available data. Alternatively you can use your own model, just as long as you follow the same input/output conventions.
If you’d like to know more about the logic behind the SIMPLEGEN pipeline then please see here, or if you’d like to jump straight into using the package then please start here.