Georgia Tsambos

Add adjust_for_silent option to sim_mutations

6

@petrelharp and I had an extended convo in Slack this week about silent mutations and the complications they introduce for users. I have some strong opinions about changes we could...

Comments on page /demography.html

3

Not an 'issue', just a log of some comments I'm making while reading this page. > In continuous-time models, when {math}`M_{j,k}` is close to zero, this rate is approximately equivalent...

Provide option to squash IBD output?

20

One of the most important comments I got in my thesis examination was regarding our definition of IBD. Our current implementation of `ibd_segments` treats segments as distinct if they have...

Mock-up of ibd-segments trash collection method.

5

## Description This is a Python mockup of some functions that might help to keep the internal memory requirements of `ibd_segments` in check. Would work similarly for `link_ancestors` (and perhaps...

Garbage collection in ibd_segments, link_ancestors and simplify

1

All three of these methods rely on an object called `ancestor_map` (C codebase) or `A` (Python mockups) to store segments that descend from each ancestral node in the tree sequence....

Added methods to sort and squash segments in the IbdFinder output.

7

Fixes #2459 -- see the issue for discussion about why this is needed. Draft only at the moment. ### PR Checklist: - [ ] Tests that fully cover new/changed functionality....

population-specific recombination rates?

10

Milan and Marion have inquired (in a private communication) about implementing population-specific recombination rates in msprime. I now have a few more technical thoughts about it, and I'll stick them...

First draft of a simplification tute.

2

Not yet finished, but will close #52 when it is. Just making this PR now so that people can look and comment.

Update population diagrams in demography tutorial

3

The labels of all diagrams need to be updated, and some new ones need to be made for admixture + divergence.