tskit

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## Description This function calculates the total distance between two nodes in the tree. This is expressed as the sum of the "branch lengths" from both nodes to their most...

Billyzhang1229

Update docs for improved seek-from-null performance

1

Following up on #2661, need to improve look at the documentation for methods where we seek, and explain the performance differences in the different contexts. Also need to review the...

jeromekelleher

Error if boolean passed as row index or slice?

3

I was recently helping a new user who has R experience who tried `tables.nodes['individual'==0]` which gave the first node as it is equal to `tables.nodes[False]` which gets interpreted as `tables.nodes[0]`....

benjeffery

Document RateMap etc

5

At the moment the documentation is in msprime under its own section within Utilities: [Rate Maps](https://tskit.dev/msprime/docs/stable/rate_maps.html). Since it is purely a python thing, I wonder if in `tskit` it should...

hyanwong

Add unweighted_rf_distance (symmetric_distance) function and tests

10

Add Unweighted Robinson–Foulds Distance (symmetric difference of two trees) function with tests See also: - #995 - #996

Billyzhang1229

Make tqdm(ts.variants()) work better

6

It would be nice if this would pull out the overall length of the iter. Should be easy enough?

jeromekelleher

I was trying to run `_tskit.lshmm` using recombination rates obtained by calling `msprime.RateMap.get_rates()`. `_tskit.lshmm` doesn't really handle NaN. I recall encountering this before. Setting the NaN values to zero bypassed...

szhan

Add test_imputation.py file

27

We want to test some specific examples against the new backward matrix code in #2799. To be certain that we're interpreting the model correctly, we can output the forward and...

jeromekelleher

Multichrom example

28

~Stacked on #2663 (and #2619)~ @petrelharp @bhaller @molpopgen You might be interested in this: the new file `c/examples/multichrom_wright_fisher.c` gives a simple example of multi chromosome simulations with parallel simplify (most...

jeromekelleher

Windows/Site masking for two-site statistics

10

Implement a method of masking sites for two-site statistics. Since we're interested in slicing a subset of the correlation matrix, we won't need windows for sites. Or, rather, we'll want...

lkirk