Negative frequency-dependent selection in post-vaccine pneumococcal population

This repository contains resources to replicate the parameter inference experiments reported by Corander et al. [1]. The inference procedure is implemented with ELFI [2] in the attached notebook.

The notebook is tested with Python 3.5 and ELFI v. 0.7.4.

Files and folders

• code/simulator/ This folder contains the multilocus NFDS simulator.
• code/utils.py Contais operations which are used in parameter inference with ELFI and in visualisation.
• data/ This folder contains the observed data.
• inference.ipynb Jupyter notebook defining the ELFI model and running the inference.

References

• [1] Corander et al. (2017). Frequency-dependent selection in vaccine-associated pneumococcal population dynamics. Nature Ecology and Evolution. 1(12):1950–1960. doi:10.1038/s41559-017-0337-x
• [2] Lintusaari et al. (2018). ELFI: Engine for Likelihood Free Inference. Journal of Machine Learning Research. 19(16):1-7. Code https://github.com/elfi-dev/elfi.