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"mutation" mode for statistics

1

In #2948 @tforest is working on adding time windows to statistics. How this should work for `mode="branch"` is clear; however, it is not clear for `mode="site"`. (It doesn't make sense...

petrelharp

clarify that genetic_relatedness includes self comparisons

1

As discussed in #2888, usually "genetic relatedness" includes the self comparisons. (This makes sense if (a) you're computing the covariance matrix of additive traits, (b) if you want to know...

petrelharp

Support missing data in alignments

8

#1825 added support for alignments, which passed through arguments for supporting missing data to the haplotypes method. However, the initial implementation was wrong. Consider the following example: ```python # 2.00┊...

jeromekelleher

AFS folding (polarised=False)

6

Dear all, I was checking variable implementations of the (joint) allele frequency spectrum folding and went through the [polarisation subsection](https://tskit.dev/tskit/docs/stable/stats.html#polarisation) in `msprime`. I am not sure I clearly understood the...

sunyatin

add individual statistics (eg heterozygosity)

25

Something like ``` def individual_heterozygosity(ts, ind): ts.pairwise_diversity(ind.nodes) ``` should do it - very simple, but we want to make it easy and natural for people to deal with individuals.

petrelharp

Fix CI

1

Seems clang-format broke

benjeffery

Initial numba module

11

Part of #3135

benjeffery

Fix genetic_relatedness to allow single sample set with self-comparisons

1

## Description This PR fixes issue #3055 where `genetic_relatedness` would fail when computing self-comparisons with a single sample set. As @petrelharp pointed out there is no reason this shouldn't be...

andrewkern

`genetic_relatedness` thinks it needs 2 samples sets but is valid with only one

1

Self-comparisons are valid for this statistic, and so this should work: ``` >> ts.genetic_relatedness([[0]], indexes=[(0,0)]) Traceback (most recent call last): File "", line 1, in File "/home/peter/projects/tskit-dev/tsvenv/lib/python3.12/site-packages/tskit/trees.py", line 8403, in...

petrelharp

Warning on running setup.py

4

``` WARNING pyproject.toml does not contain a tool.setuptools_scm section ``` we probably need modernise the pyproject.toml a bit?

jeromekelleher