try to clarify branch mode

Author: apragsdale

docs/stats.md

@@ -776,18 +776,18 @@ Out of all of the available summary functions, only {math}`r^2` uses
 
 #### Branch
 
-The `branch` mode computes two-locus statistics between pairs of trees. The
-resulting statistic is a summary depending on marginal tree topologies and the
-branch lengths of the trees at a pair of positions. To perform this
-computation, we consider the counts of all possible two-locus haplotypes that
-could be generated by mutations on each pair of branches between the two
-trees, which is summarized using an LD statistic. We then sum each pairwise
-comparison weighted by the product of the two branch lengths above the nodes on
-each tree.
-
-Similar to the single-site statistics computed in `branch` mode, this results
-in a statistic that is proportional to the expected statistic under an infinite
-sites model (with mutation rate 1), conditioned on the pair of trees.
+The `branch` mode computes expected two-locus statistics between pairs of
+trees, conditioned on the marginal topologies and branch lengths of those
+trees. The trees for which we compute statistics are specified by positions,
+and for a pair of positions we consider all possible haplotypes that could be
+generated by a single mutation occurring at the two trees.
+
+For two trees, one with {math}`n` branches and the other with {math}`m`
+branches, there are {math}`nm` possible pairs of branches that may carry the
+pair of mutations. For each pair, we compute the two-locus statistic, and then
+sum these values weighted by the product of the two branch lengths. Given the
+two mutations occur, this accounts for the relative probability that the two
+mutations fall on any pair of branches.
 
 The time complexity of this method is quadratic in the number of samples,
 due to the pairwise comparisons of branches from each pair of trees.
@@ -892,7 +892,7 @@ input. Each of our summary functions has the signature
 : {math}`f(w_{Ab}, w_{aB}, w_{AB}, n) = p_{ab} - p_{a}p_{b}`
 
   This statistic is polarised, as the unpolarised result, which averages over
-  allele labelings, is zero. Uses the `total` normalisation method.
+  allele labelings, is zero. Uses the `total` weighting method.
 
 `D_prime`
 : {math}`f(w_{Ab}, w_{aB}, w_{AB}, n) = \frac{D}{D_{\max}}`,