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Work on the stats/analysis tutorial

Open gregorgorjanc opened this issue 1 year ago • 1 comments

@hyanwong I had a bash at the stats/analysis tutorial following your previous style. Let me know what you think.

There are two outstanding TODO's in there:

  • tree sequence has no time units so I wonder if we should say anything there about that - any suggestions?
  • I don't fully understand what node-stat refers to so struggle to write that up - any suggestions?

Other edits are from https://github.com/tskit-dev/tutorials/pull/280 (I struggled with squashing commits so openning this PR from a branch).

gregorgorjanc avatar Oct 05 '24 19:10 gregorgorjanc

Thinking a bit more, we currently have in this tutorial:

  1. an intro to stats by showcasing diversity and divergence in combination with windows/sample_sets/indexes/span_normalise/mode arguments and

  2. an intro to AFS.

There is a lot of other analysis functionality available https://tskit.dev/tskit/docs/stable/python-api.html#statistics and users might be keen on different functionality, but we don’t want to cover each function in the tutorial. Are there some that should/must be mentioned or is above enough?

gregorgorjanc avatar Oct 06 '24 06:10 gregorgorjanc