Nate Pope
Nate Pope
WIP related to #1315. Edited 14 Feb 22 into something resembling a usable API. @petrelharp @gregorgorjanc This mock-up consists of a class in `test_stats.py` that: (a) walks over nodes in...
I'm thinking that the `CoalescenceTimeDistribution` class would be best moved to a separate package (where it can be numba-fied), and that instead we'll want to put an efficient algorithm for...
Low level extension of #2915
with: [afs_error.trees.gz](https://github.com/tskit-dev/tskit/files/14940747/afs_error.trees.gz) ```python import tskit print(tskit.__version__) # '0.5.7.dev0' ts = tskit.load("afs_error.trees") ts.allele_frequency_spectrum() # works ts.allele_frequency_spectrum(sample_sets=[[x for x in range(64)]]) # segfaults # Bug detected in lib/tskit/trees.c at line 2721. If...
It'll frequently be the case that singletons are not phased. Singleton variants aren't used by tsinfer, but are crucial for correct dating. Here's how we'll handle unphased singletons: 1. Split...
We've been looking at site vs branch diversity to assess at a glance whether an inferred + dated tree sequence has a reasonable timescale. However, this may not be the...
I'm running tsdate on a large tree sequence (74mil edges) and noticing that the pre-algorithm steps are quite costly. In particular, there's a call to `ts.simplify()` in `util.reduce_to_contemporaneous()` that really...
It'd be good to be able to "adjust" the span of edges so as to remove missing sites, that are ubiquitous in real data. It's typical for these exclusion masks...
The "variational_gamma" algorithm produces gamma approximations for posterior distributions of node ages. It'd also be nice to have a way to get gamma approximations for posterior distributions of *mutation* ages....
For tree sequences inferred from simulations, we can't directly compare inferred dates to true dates because node sets differ between the inference and the simulation. Instead, we've been looking at...