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. Tutorial on edge_diffs / incremental algorithms #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 (Tutorial: combinatorics #93)
  • High performance (High performance tute(s) #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 #277

[hyanwong]

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