Jerome Kelleher
Jerome Kelleher
The installation docs currently tell users to install to the conda root, which is a Bad Idea. Update the docs to use an environment, and put in an explicit warning...
As discussed in #2083 Since there is a use-case for this now though, we could probably actually implement the functionality within msprime and do it automatically like we do for...
Per discussion here https://github.com/tskit-dev/msprime/pull/2080#discussion_r912322118 Since there's some subtlety around ascertainment or not, we should document this point.
We need some reproducible statistical validation of the microsat mutation models in verification.py. Do we have analytical results we can compare to or to other simulators? Any thoughts @petrelharp @andrewkern?
The sectioning for the mutations page isn't working very well I think, and needs a bit of work. In particular, there's an awful lot of stuff under the "model" section,...
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...
And give an example of adding some
A significant usability limitation in the 1.0 API is that we can't easily include mutations in a simulation with replicates. I think we could improve this by allowing sim_mutations accept...
#1599 introduced the idea of an "unknown" rate within a RateMap using NaNs. This solves a lot of problems, but it doesn't tell us how we should run the actual...