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Unifying stat method desc and linking to math summary

Open gregorgorjanc opened this issue 1 year ago • 3 comments

I was working through the stats tutorial at https://tskit.dev/tutorials/analysing_tree_sequences.html (incoming PR) and thought that linking stats/math summaries (https://tskit.dev/tskit/docs/stable/stats.html#summary-functions) to method docs would be very useful.

I also followed a style from the diversity method doc (what is the stat, then links to sample_sets, windows, ...).

@petrelharp can you have a look at this PR?

gregorgorjanc avatar Sep 28 '24 09:09 gregorgorjanc

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 89.82%. Comparing base (bc5a73c) to head (6371edc). Report is 9 commits behind head on main.

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+ Coverage   89.81%   89.82%   +0.01%     
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  Files          29       29              
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lwt-tests 80.78% <ø> (ø)
python-c-tests 89.05% <ø> (ø)
python-tests 99.04% <100.00%> (+0.02%) :arrow_up:

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Files with missing lines Coverage Δ
python/tskit/trees.py 98.80% <100.00%> (ø)

... and 1 file with indirect coverage changes

codecov[bot] avatar Sep 28 '24 09:09 codecov[bot]

In general I like the rearrangments, but I don't think we should add "please see summary functions for a precise definition". Instead, we should make what's said there in the documentation precise enough, if it isn't already? I am pretty sure that what's there for diversity, for instance, is precise - did you find it ambiguous? The 'summary function' definition is nice and concrete once you understand it, but most readers won't be on board with this. Some other way of referring to the summary functions could be helpful but more like "if you want the computational details, see XXX"?

petrelharp avatar Oct 01 '24 18:10 petrelharp

@petrelharp I followed your suggestions in the last commit.

I thought adding the link to computational/mathematical definition would be useful to provide concrete/mathematical detail of what is calculated. This makes things concrete, but since it's only a link, it does not overwhelm a user (I agree that simple descriptive text should be preferred). Also, you have written these math details for some stats, so adding these links exposes/leverages that part of the doc (most users will only look at function docs and won't go over the whole stats doc to find math detail).

Happy to iterate.

gregorgorjanc avatar Oct 05 '24 10:10 gregorgorjanc