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Fix mutation rate in time units example #344

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Jun 10, 2024
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Fix mutation rate in time units example #344

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4 changes: 2 additions & 2 deletions docs/time_units.md
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Expand Up @@ -231,13 +231,13 @@ multiplied by the expected number of mutations per unit time.
(We get the mean branch length using the {meth}`ts.diversity <tskit.TreeSequence.diversity>` method with ``mode="branch"``;
see the [tskit documentation](tskit:sec_stats) for details.)
This involves the generation time because "mutations per unit time" is equal to
"mutations per generation" (here, the mutation rate per bp, {math}`10^{-8}`)
"mutations per generation" (here, the mutation rate per bp, {math}`2 \times 10^{-8}`)
divided by "time per generation" (i.e., mean generation time).


```{code-cell}
slim_diversity = gts.diversity(mode = 'site')
ts_diversity = gts.diversity(mode='branch') * 1e-8 / np.mean(gentimes)
ts_diversity = gts.diversity(mode='branch') * 2e-8 / np.mean(gentimes)

print(f"slim diversity: {slim_diversity}\n"
f"scaled tree sequence diversity: {ts_diversity}\n"
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