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tskit-dev / msprime

Simulate genealogical trees and genomic sequence data using population genetic models
GNU General Public License v3.0
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Interaction between "population size" and "recombination rate" missing? #2025

Open molpopgen opened 2 years ago

molpopgen commented 2 years ago

(This is related to #2024)

The docs for recombination_rate under sim_ancestry state:

See the [Recombination](https://tskit.dev/msprime/docs/stable/ancestry.html#sec-ancestry-recombination) section for usage examples for this parameter and how it interacts with other parameters.

However, the Recombination section does not discuss the interaction with other parameters. Specifically, population_size, which makes a big difference in run times, etc., due to its effect on the scaled rates:

>>> import msprime
>>> for N in [1, 100, 1000]:
...     x = msprime.sim_ancestry(40, sequence_length=50000000, recombination_rate=1e-8, population_size=N)
...     print(x.num_trees)
... 
9
847
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benjeffery commented 2 years ago

I thought this might have been lost in the big doc re-org that happened for 1.0, but I can't see such a mention in the old 0.7 docs either. Would you mind drafting something @molpopgen?

molpopgen commented 2 years ago

Sure. I'll try to get to it this week.

molpopgen commented 2 years ago

There are some unresolved comments over in #2026, so I'll be punting on this for a bit.