tskit-dev / what-is-an-arg-paper

Manuscript and code for the "What is an ARG?" paper
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Converting eARG to gARG - reprise #380

Closed hyanwong closed 11 months ago

hyanwong commented 11 months ago

This is stacked on top of #378 and is my attempt to

a) tie together the "retrospective vs prospective" and "converting and eARG to a gARG" sections, which both talk about simplification / Hudson. I have tried to use the mention of "ancestral material" to act as a lead-in from the first to the second.

b) clarify that converting an eARG to a gARG does not have to involve sample-resolving (and in fact, we would normally simulate the sample-resolved form directly). I.e. eARG -> gARG is just one step. Sample resolving is a further (lossy) "option", which helps with efficiency. My previous worry was:

The conversion process from eARG to gARG is only the first of the two steps in the figure. The second step is a lossy one from a gARG to another sort of gARG (a sample resolved one) ...

As with #378, this is supposed to be food for general discussion rather than necessarily a polished suggestion.