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Describe one outer-grid hyperparameter axis

Source: R/hyper_axis_spec.R
hyper_axis_spec.Rd

Builds a single axis spec for tulpa_hyper_grid(). Carries the candidate values, the optional log-prior, and the metadata (log-scale, bounds, refinable flag) that the generic refinement / consistency passes need.

Usage

hyper_axis_spec(
  name,
  grid,
  log_prior = NULL,
  log_scale = FALSE,
  bounds = NULL,
  refinable = FALSE,
  atom_mass = NULL,
  slab_bounds = NULL,
  log_prior_coord = c("integration", "natural"),
  extend = TRUE
)

Arguments

name

Character. Axis label, used as the column name of the grid matrix and in posterior summaries.

grid

Numeric vector of length >= 1. The per-axis candidate values (the outer integration nodes on this axis). The full outer grid is the Cartesian product across axes.

log_prior

Optional function(x) returning the scalar log prior density at axis value x. NULL (default) is a flat / improper prior (zero log-prior contribution). log_prior_coord says which coordinate the function is a density on.

log_scale

Logical. Does the axis live naturally on a log scale (sigma, tau, lengthscale, ...)? Drives geometric vs arithmetic spacing in refinement and log-axis quantile fits. Default FALSE.

bounds

Numeric vector of length 2 giving the natural support (lower, upper) of the axis, e.g. c(0, Inf) for sigma, c(0, 1) for a BYM2 mixing coefficient. NULL (default) is unbounded. A finite endpoint is treated as OPEN: it is the value the parameterisation degenerates at, so refinement clamps new points to the interior and the axis's quadrature cells and reported support are closed strictly inside it rather than half a node step past the outermost node.

refinable

Logical. When TRUE, the axis participates in the adaptive-grid and var-of-means consistency passes (when those are enabled at the driver level). Spatial prior amplitudes (sigma) are typically left at the user-specified grid (refinable = FALSE); the copy coefficient alpha and per-arm dispersion phi typically opt in. Default FALSE.

atom_mass

Numeric in [0, 1), or NULL (default). Prior probability of the zero level on a log-scale axis. A 0 is a point mass, not a point of the log continuum, so its prior share has to be declared rather than inherited from the node count; the continuum nodes then share 1 - atom_mass by quadrature weight. Required when grid contains a 0 on a log_scale axis. A log_prior on such an axis is a density on the continuum: it is not evaluated at the zero level and it shapes the continuum's share without moving the declared split, so atom_mass is the prior probability the fit integrates whatever the density is (gcol33/tulpa#624, gcol33/tulpa#626).

slab_bounds

Numeric c(lower, upper), or NULL (default). Fixed support of the continuum part of the prior. A flat measure on a log axis is improper, so the truncation bounds are what make it a proper density and they are therefore a prior choice: the weights normalise over slab_bounds and refinement is not allowed to move outside it. NULL leaves the node span acting as the support, which makes the prior depend on where refinement put the outermost node.

log_prior_coord

One of "integration" (default) or "natural", naming the coordinate log_prior is a density on. The contribution is added to the cell's log_marginal, which the integrator weights by cell widths measured on the axis's INTEGRATION coordinate (log x on a log_scale axis), so "integration" is carried through as written and is what the flat default's zero contribution is flat on. "natural" declares a density on x itself – a PC prior, dexp, dgamma – and the engine adds the change of variables log(x) on a log_scale axis. Every path that meets a declared density carries it across in one place (.hyper_prior_carry()). Inert on a linear axis, where the two coordinates coincide (gcol33/tulpa#623).

extend

Logical. On a refinable axis, may the passes place a node beyond the outermost value in grid? TRUE (default) lets refinement follow the posterior out past the declared span, which is what an axis the engine placed wants. FALSE confines every new node to the interior of the declared span: the axis is integrated more finely over exactly the range given, and a mode outside it shows up as mass at the edge instead of moving the range. Inert when refinable = FALSE.

Value

An object of class tulpa_hyper_axis_spec (a validated list with the fields listed above).

See also

tulpa_hyper_grid().