tskit
tskit copied to clipboard
Add examples to Statistics page
It would be good to add an example of using at least some of the statistics on the Statistics page. It's a bit of a wall of text at the moment, and it's hard to get an intuitive feel for what, e.g., `allele_frequency_spectrum`` returns.
To avoid duplication we could point, for example, to https://tskit.dev/tutorials/analysing_tree_sequences.html#allele-frequency-spectra in that particular case. I'm not sure on the exact balance between examples in tutorials and in the docs. ISWYM about having a few examples there though.
It's tricky, I agree. We could try to draw the line between "explanatory" (tutorials) and "illustrative examples" (docs)?
It's tricky, I agree. We could try to draw the line between "explanatory" (tutorials) and "illustrative examples" (docs)?
Yes, a good distinction.I even wonder if we have an "examples" section up top (just after the "Available Statistic" section - and I want to move the "notes" to the end: I have a branch somewhere to PR with this) :
## Examples
:::{code-cell}
:"tags": ["hide-input"]
import msprime
ts = msprime.sim_ancestry(4, sequence_length=1000, recombination_rate=0.001, random_seed=1234)
ts = msprime.sim_mutations(ts, rate=0.001, random_seed=2)
print(
"Example tree sequence has sequence length",
int(ts.sequence_length),
"with",
ts.num_samples,
"samples:",
ts.num_trees,
"trees &",
ts.num_sites,
"variable sites",
)
:::
:::{code-cell}
afs = ts.allele_frequency_spectrum(polarised=True, span_normalise=False)
print(afs) # afs[1] gives number of singletons, afs[2] doubletons, etc:::