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At PopGroup57, I chatted for a while to Moritz Otto from Univ of Cologne (Köln), who recently published this paper: https://doi.org/10.1016/j.tpb.2023.08.001
This describes a method for using mspri…
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It would be useful to have a method to change who is a `sample`, as for instance at https://github.com/tskit-dev/pyslim/issues/23 .
Here is a prototype:
```
def mark_samples(ts, samples, keep=Tru…
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We claim that tsinfer, not being particularly model-based, should be robust to selection. We can test this by carrying out a selective sweep and inferring + dating the result.
The plots below show …
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The docs for identity segments use the string summary for showing examples.
We should probably adapt the ``html_table`` functionality in msprime to make it easy to make these HTML summaries for var…
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Hi,
I'm having issues converting my Demes graphs to msprime `Demography` objects; both population sizes and migration rates are missing unexpectedly. My Demes graphs match what I think I'm trying t…
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Originally discussed in PR #1953:
> I think the solution to this (for the next msprime?) is to include a `generation_time` argument that scales all the times, and would make this warning go away. T…
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After we run SLiM, we simplify down to the requested samples, here:
https://github.com/popsim-consortium/stdpopsim/blob/main/stdpopsim/slim_engine.py#L1764
We do *not* pass in the `keep_input_roo…
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A simplification made in #1846 was to disallow samples that are internal nodes in the pedigree (i.e., samples cannot have children). It would not be difficult to implement, it just needs some thinking…
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We should create an automated docker image, linked to the official releases. This was brought up in the first workshop.
If someone else doesn't volunteer to set this up, I can work on it (eventuall…
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It's always bothered me that the `record_full_arg` output has 2 nodes that are only identifiable as grouped together because they are at the same time (unique in the nonWF case, but not necessarily in…