At the end of the day, Foreman-Mackey, Bovy, and I discussed how we might model the Lyman-alpha absorption in quasar spectra, such that the continuum (which is unobservable) becomes a fit parameter usefully constrained by the data. The long-term goal is to do Lyman-alpha clustering. The key thing is that this would be hierarchical: The parameters we care about would be parameters of the state and clustering of the IGM.
In some sense, you can use the pixel flux distribution to do this, instead of zeroth order estimates like D_A which would have the continuum as a fit parameter.
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