Address comments from Jerome

Author: apragsdale

docs/stats.md

@@ -700,12 +700,11 @@ statistics methods in that it provides a unified API with an argument to
 specify different two-locus summaries of the data. It otherwise behaves
 similarly to most other functions with respect to `sample_sets` and `indexes`.
 
-Two-locus statistics can be computed using two modes, either `sites` or
+Two-locus statistics can be computed using two modes, either `site` or
 `branch`, and these should be interpreted in the same way as these modes in the
-single-site statistics. Site statistics allow for multi-allelic data, while
-branch statistics assume an infinite sites model. Within this framework, we
-also implement polarisation, but do not expose it to the user, opting to
-provide statistics that are polarised where appropriate.
+single-site statistics. Within this framework, we also implement polarisation,
+but do not expose it to the user, opting to provide statistics that are
+polarised where appropriate.
 
 (sec_stats_two_locus_site)=
 
@@ -762,7 +761,7 @@ 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 (which mutation rate 1), conditioned on the pair of trees.
+sites model (with mutation rate 1), conditioned on the pair of trees.
 
 The time complexity of this method is quadratic, due to the pairwise
 comparisons of branches from a pair of trees. By default, this method computes
@@ -931,13 +930,6 @@ Where {math}`D` is defined above.
 And `D2_unbiased`, which can be found in [Ragsdale and Gravel
 (2020)](https://doi.org/10.1093/molbev/msz265).
 
-:::{todo}
-Document statistics that use information about correlation between sites, such as
-LdCalculator (and perhaps reference {ref}`sec_identity`). Note that if we have a general
-framework which has the same calling conventions as the single site stats,
-we can rework the sections above.
-:::
-
 
 (sec_stats_notes)=
 

python/tskit/trees.py

@@ -10956,7 +10956,7 @@ def ld_matrix(
 
         Similarly, in the branch mode, the ``positions`` argument specifies
         loci for which the expectation for the two-locus statistic is computed
-        over pairs of trees at those positions. LD statis are computed between
+        over pairs of trees at those positions. LD stats are computed between
         trees whose ``[start, end)`` contains the given position (such that
         repeats of trees are possible). Similar to the site mode, a nested list
         of row and column positions can be specified separately (resulting in a