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Fixed some parameter subscripts in docs/inference.rst.
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davipatti committed Nov 24, 2021
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Expand Up @@ -27,35 +27,36 @@ Standardizing

Log dilution is standardized to have mean of zero and standard deviation of one for inference.

Response is left unstandardized to help set priors for `c` and `d`.
Response is left unstandardized in order to set informative priors for `c` and `d`.
For instance, it is often known *a priori* that at theoretical minimum or maximum concentrations the response will have some known value.

Priors
------

Weakly informative priors are used throughout.

Weakly informative priors are used by default throughout.
When parameters `a`, `b`, and `c` are fully pooled, they given a prior of :math:`\text{dnorm}(0, 1)`.
When `a`, `b`, and `c` are partially pooled they are given priors of:
When `a`, `b`, and `c` are partially pooled across samples, `s`, they are given priors of:

.. math::
\mu_p \sim \text{dnorm}(0, 1)
\sigma_p \sim \text{dexp}(1)
p_i \sim \text{dnorm}(\mu_p, \sigma_p)
p_s \sim \text{dnorm}(\mu_p, \sigma_p)
To prevent redundancy between the values of `c` and `d`, `d` is constrained to be positive.
When it is fully pooled: :math:`d \sim \text{dexp}(1)`. When it is partially pooled:
When it is fully pooled: :math:`d \sim \text{dexp}(1)`.
When it is partially pooled:

.. math::
\sigma_d \sim \text{dexp}(1)
d_i \sim \text{dnorm}(\sigma_d)
d_s \sim \text{dexp}(\sigma_d)
These priors will be applicable for most users.

Partial pooling for `a`, full pooling for `b` and `d`, and setting `c=0` gives the following prior predictive distribution:

.. image:: prior-predictive.png
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