Reorganise "Statistics and Analysis"

[hyanwong]

There's going to be an awful lot of detail in the "Analysing trees" tutorial about fundamental operations like tree traversal. I wonder if we should hive that off into its own tutorial and reorganise that part of the tutorial book as follows:

• Analysis and Statistics
  • ~~Basic~~ Fundamental operations (sectioned into "~~basic~~ fundamental operations on trees" (e.g. traversals, branch lengths, common ancestors) and "~~basic~~ fundamental operations on tree sequences" (e.g. edge diffs, incremental algorithms, coiteration). This is mainly for people writing their own algorithms. We should aim to make this a bit of a summary, and spin off more detailed examples into other tutorials, e.g. #233 )
  • Analysing trees (stuff about built-in tree analysis algorithms, e.g. map_mutations, balance metrics)
  • Analysing tree sequences (stuff about built-in tree-sequence analysis algorithms, e.g. the stats framework, GNN, pair_coalescence, genetic_relatedness & PCA. Again, this should probably be a summary, with details spun into their own tutorials)
  • Counting topologies (https://github.com/tskit-dev/tutorials/issues/93)
  • High performance (https://github.com/tskit-dev/tutorials/issues/151)

Many phylogenetic and popgen people will be want to apply stats or parsimony etc to their tree (sequences) without having to read all about the different traversal methods.

[jeromekelleher]

SGTM. Maybe change "Basic" to "Fundamental"?

[hyanwong]

Good call. I agree with this.

[hyanwong]

It would also be useful to have an "advanced analysis topics" section, like we have an "advanced msprime topics" section. We could put the topology counting tutorial in there, and also a tutorial on plotting cross coalescence rates, based on https://github.com/tskit-dev/tutorials/issues/277

[hyanwong]

This is potentially a good thing for @agladstein to have a go at