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Streamlined format for estimating abundance parameters

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@bdwilliamson bdwilliamson released this 02 Jul 19:53

The core idea in paramedic is to combine absolute and relative abundance measurements and model efficiency to estimate parameters of the true distribution of absolute abundance. This may be done in a variety of ways by placing different priors on hyperparameters and likelihood functions on the data. In this release, we have streamlined this approach in paramedic by:

  1. Removing the function run_paramedic_centered; this can now be achieved by passing centered=TRUE to run_paramedic
  2. Removing the function no_efficiency; if efficiency is truly not desired (we emphasize that this is probably not the case), pass alpha_sigma=0 and kappa_sigma=0 to run_paramedic
  3. Streamlining the underlying stan models so that it is simpler to add/change distributions.

We have also added a new vignette that discusses the various hierarchical modeling options in paramedic.