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Population-scale genomics
After #2938 goes in, we need to do something so that the user knows whether the algorithm terminated because of running out of things to do or because it ran...
## Description A draft of randomized principal component analysis (PCA) using the `TreeSequence.genetic_relatedness_vector`. The implementation contains `spicy.sparse` which should eventually be removed. This part of the code is only used...
CI time
CI execution time has creeped back up to over half an hour - I'm seeing some that are 50min. This isn't ideal, would be good to get it back under...
This (hacky as heck) code generates a report on the doc status of functions and classes. You can see the result at https://lime-onida-78.tiiny.site/
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...
As usual we're waiting on `numba` here. The extension builds fine and passes all the tests that don't need `numba`.
For instance, creating a matrix of all pairwise comparisons - this is a common thing to want to do; this will also serve as a good way of demonstrating exactly...
## Description This PR adds a method to the `Tree` class in the Python API : `is_recip_monophylectic()`. It tests the current tree for reciprocal monophyly, a population genomics phenomenon as...
In our docs for Fst we provide the formula for how it's computed, but don't explain which version of Fst this corresponds to. Is this one of the estimators (Hudson/Weir...
AFAICT, like for `divergence_matrix` there is not an efficient algorithm of the same sort to calculate the site-mode value; rather, the natural corresponding thing is mutation-mode (https://github.com/tskit-dev/tskit/issues/2982). And, this should...