tutorials
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tskit-dev
A set of tutorials for msprime and tskit.
There's a lot of idioms and complicated code when implementing incremental algorithms, for example, that use the `edge_diffs()` iterator. For example it's a common idiom to iterate jointly over trees...
I was copying and pasting some of the tutorial code into a new repo, and realised that we should say somewhere the licence that applies to any code examples? My...
To encourage people to think of tree sequences as graph objects, I think it would be helpful to add the graph representation to the "What is a Tree Sequence" tutorial,...
We can simulate some ARGs in msprime, explain how we can losslessly represent ARGs and get all the information you could want.
The last one of the [subaudience tutorials](#191) to tick off is the one for statistical geneticists. This issue can collect some ideas. I have been chatting to Arni Gunnarson, and...
There is a lot of good material about parameter scaling in https://github.com/tskit-dev/tutorials/blob/main/old-content/docs/wfforward.md#starting-with-a-prior-history. The obvious place for this is in the tutorial about recapitation, at https://github.com/tskit-dev/tutorials/blob/main/completing_forward_sims.md. See https://github.com/tskit-dev/tutorials/issues/14#issuecomment-1657281145
There's two notebooks (wfforward.ipynb and wfcython.ipynb) in the old-content/notebooks directory that need to be converted to jupyterbook format. Hopefully this can be reasonably automatic using [jupytext](https://github.com/mwouts/jupytext). The only concern is...
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...
Not yet finished, but will close #52 when it is. Just making this PR now so that people can look and comment.
As discussed in #164 it might be more helpful to put the red "tree branch" colouring example into the list of examples at the end of the viz tutorial, rather...