msprime
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Simulate genealogical trees and genomic sequence data using population genetic models
Docs for the following `Demography` methods: [`add_population_split()`](https://tskit.dev/msprime/docs/latest/api.html#msprime.Demography.add_population_split), `add_admixture()`, `add_mass_migration()`, `add_migration_rate_change()`, `add_simple_bottleneck()`, `add_instantaneous_bottleneck()`; all have problematic formatting of types in the parameters section. In addition, they all accept either an integer...
The docs for `msprime.sim_ancestry` say that ploidy defaults to 2, yet the function defaults to `None`. It would be preferable if the function default were acutally 2, especially for people...
Msprime is much slower than MaCS when simulating long genomes/lots of recombination, as we've seen with the BosTau model in stdpopsim. There may be some low-hanging fruit in making this...
This would make a nice tutorial, as discussed in #1687, by simulating over a range of smallish values and extrapolating.
It would be useful to have a method that would combine two or more RateMaps and return an iterator over the distinct intervals at the rates. So, in usage, it...
I have all permission to share our scripts to simulate genome with variation (piecewise) of selfing and dormancy. @jeromekelleher, let me know how to proceed. Since it's all rescaling we...
Here's a small three population example without recombination. ```sh # ms.sh $MS 2 1 \ -t 1.0 \ -I 3 1 0 1 \ -em 0.0 3 2 1.0 \...
that was added in #1524
There's some typos in the commands, and ``asv run HEAD^!`` works better for me than the first command given.
We should provide simple methods for reading/writing RateMaps in binary and text formats. These should use numpy methods only, we don't need anything like zarr here. This is separate to...