I've been looking at the algorithm.c and algorithm.py files in msprime and noticed some differences. The algorithm.c file seems to use diploid as a default setting, which affects how the simulations are run and the results we get. On the other hand, the algorithm.py file doesn't seem to have a setting for ploidy, which might lead to different results.
One clear difference I saw is in the single sweep model simulations. The Python version gives different diversity plots compared to the C version. I'm also not sure how forward simulations are run in the algorithm.py file, which might be part of the reason for the differences.
Thank you for looking into this!
I've been looking at the
algorithm.candalgorithm.pyfiles inmsprimeand noticed some differences. Thealgorithm.cfile seems to use diploid as a default setting, which affects how the simulations are run and the results we get. On the other hand, thealgorithm.pyfile doesn't seem to have a setting for ploidy, which might lead to different results.One clear difference I saw is in the single sweep model simulations. The Python version gives different diversity plots compared to the C version. I'm also not sure how forward simulations are run in the
algorithm.pyfile, which might be part of the reason for the differences.Thank you for looking into this!