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jeromekelleher merged 2 commits into from
Oct 17, 2026
Merged

Doc corrections to LD stats and simulation #3491

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724b70d
Point out some simulators can store non-coal nodes
hyanwong Oct 16, 2026
5fe7119
Replace references to the outdated LDCalculator
hyanwong Oct 17, 2026
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9 changes: 6 additions & 3 deletions docs/ibd.md
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Expand Up @@ -337,10 +337,13 @@ of what's stored in the tree sequence.
As discussed in
[Fritze et al](https://doi.org/10.1093/genetics/iyaf198),
most tree sequence simulators (at time of writing)
will produce this tree sequence even if node ``2``
will produce this tree sequence by default, even if node ``2``
does in fact inherit from ``3`` over the entire sequence.
Using {meth}`.TreeSequence.extend_haplotypes` will
"put the unary nodes back":
For the [msprime](https://tskit.dev/msprime/) simulator, intermediate
nodes can be retained using
{ref}`coalescing_segments_only=False<msprime:sec_additional_nodes_cso>`.
More generally, {meth}`.TreeSequence.extend_haplotypes` will
attempt to "put the unary nodes back":
```{code-cell}
ets = ts.extend_haplotypes()
SVG(ets.draw_svg())
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14 changes: 9 additions & 5 deletions docs/stats.md
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Expand Up @@ -53,15 +53,19 @@ Here are the statistics that can be computed using `tskit`,
grouped by basic classification and type. Single-site statistics are ones that are
averages across sites in windows of the genome, returning numpy arrays whose
dimensions are determined by the parameters (see {ref}`sec_stats_output_dimensions`).
Multi-site statistics summarize relationships between different sites along the genome,
such as linkage disequilibium (LD).

{ref}`sec_stats_sample_sets_one_way` are defined over a single sample set,
whereas {ref}`sec_stats_sample_sets_multi_way` compare 2 or more sets of samples.
Both single and multi-site approaches require specifying the sample genomes on which
a statistic is based. {ref}`sec_stats_sample_sets_one_way` are defined over a single
sample set, whereas {ref}`sec_stats_sample_sets_multi_way` compare 2 or more sets
of samples.

Some of the methods below benefit from a little extra discussion, provided in the
{ref}`sec_stats_notes` section at the end of this chapter: if so, a link to the note
appears beside the listed method.

* Single site
* {ref}`Single site<sec_stats_single_site>`
* One-way
* {meth}`~TreeSequence.allele_frequency_spectrum` (see {ref}`notes<sec_stats_notes_afs>`)
* {meth}`~TreeSequence.diversity`
Expand All @@ -86,8 +90,8 @@ appears beside the listed method.
(see {ref}`sec_stats_notes_y`)
* {meth}`~TreeSequence.genealogical_nearest_neighbours` (see {ref}`sec_stats_notes_gnn`)
* {meth}`~TreeSequence.Fst` (see {ref}`sec_stats_notes_derived`)
* Multi site
* {meth}`~LdCalculator` (note this is soon to be deprecated)
* {ref}`Multi site<sec_stats_multi_site>`
* {meth}`~TreeSequence.ld_matrix` (see {ref}`sec_stats_two_locus`)

:::{note}
There is a general framework provided for calculating additional single site
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