More carefully define two-locus haplotypes in docs#3447
More carefully define two-locus haplotypes in docs#3447apragsdale wants to merge 3 commits intotskit-dev:mainfrom
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| {math}`n(a_i,\sim b_j)` is the number that carry the allele {math}`a_i` | ||
| and do not carry the allele {math}`b_j`, and | ||
| {math}`n(\sim a_i, b_j)` is the number that carry the allele {math}`b_j` | ||
| and do not carry the allele {math}`a_i`. We refer to these haplotypes |
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Perhaps say something more concrete here? "We refer to these haplotypes" is not very precise (what haplotypes? "ai ~bj" is not a haplotype). You've set up this notation, now use it?
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And a concrete example would help?
| derived alleles, as we do not compute the summary function for the ancestral | ||
| alleles. For unpolarised statistics, we compute the summary function over all |
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You don't mean "for the ancestral alleles" here, since no-where have you defined what it means to compute it "for" an allele. Don't you mean something like "the ancestral allele is not used as the focal allele", where "focal allele" is something that probably should have been defined earlier?
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Thanks for this. Good start, needs more preciseness. |
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Gotta run to some things today, but tried to add some preciseness here. Thanks Peter. |
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As pointed out in #3445, there is room for improvement in defining the haplotype counts that are passed to the summary functions in the two-locus statistics methods. This more carefully defines those, following advice from @petrelharp, and clarifies the number of times summary functions are called for a given number of alleles at the left and right loci.