This project is setup to perform large scale population genetic simulations and perform time-series analysis of the data. A detailed description of the motivation and use of these simulations can be found in Zhou et al. 2017.
clonal is a pybind11 extension module for fwdpy11
In the main repo directory, you can run python3 setup.py install --user
In 'project/' you will see scripts names evolve_.py. These are set up to run simulations in parallel and dump results to 'project/data/'
The recroder class in project/RecordStats.py is a critical piece to this project. It collect's time series data during the simulations. I am currently collecting the following data
- Generation time
- Population size
- Relative load = one minus the mean fitness divided the maximum fitness in the population
- Segregating load = one minus the mean fitness divided the maximum theoretical fitness
- Fixed load = load due to fixations, not considered in other loads
- Number of fixed mutations - neutral and deleterious separately
- Mean number of deleterious mutatiosn per individual
- Sum of derived allele frequencies - neutral and deleterious separately
- Tajima's D at neutral sites
- Tajima's D at all sites
- Heterozygosity (pi) at neutral sites
- Heterozygosity (pi) at all sites
- Fay and Wu's Hprime at neutral sites
- Fay and Wu's Hprime at all sites
Please see 'project/Example' for shorter example jupyter notebooks or just take a look at any of the notebooks in the main project directory.