lkirk
lkirk
Implement a python interface to the 2-locus statistics so that we may begin more rigorous testing.
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...
As mentioned [here](https://github.com/tskit-dev/tskit/pull/2805#issuecomment-1646665089) by @petrelharp during the review of #2805, we'd like a better treatment of missing data. As implemented, we compute $w_{AB}$, $w_{Ab}$, $w_{aB}$, but use the total number...
We'd like to implement two-population versions of the statistics we've implemented thus far: $D$, $D^{\prime}$, $D^{2}$, $D_{z}$, $\pi_{2}$, $r$, $r^{2}$ This means that we'll strictly require two sample sets, comparing...
Introduces the ability to subset the branch LD matrix with genomic positions. This is a little trickier than subsetting the LD matrix with sites because positions can map to duplicate...
For the purposes of assessing how the two-locus framework performs relative to the LD Calculator, I've performed a series of benchmarks. In our initial benchmarks, the two-locus framework was rather...