Classify cross-omic braid patterns using inferential evidence

Braid labels are deliberately conservative. Opposite statistically supported layer directions confirm inversion. Buffering and emergence require practical equivalence in the appropriate downstream/upstream layers. Concordance, attenuation, and amplification require all observed layers to support one direction and use a covariance-aware GLS trajectory test. If the joint-null omnibus test is not rejected and practical equivalence is not established, the result is labelled `no_detectable_effect` rather than incorrectly claiming equivalence.

Usage

classify_braids(
  equivalence,
  omic_order,
  covariance = NULL,
  integrated = NULL,
  trend = NULL,
  trajectory_margin = 0.15,
  alpha = 0.05,
  min_slope = NULL
)

Arguments

equivalence: Output of `test_equivalence()`.
omic_order: Ordered character vector describing the biological/display order of omics.
covariance: Optional covariance object used when a trend table must be computed internally.
integrated: Optional output of `integrate_effects()`. Supplying it allows `no_detectable_effect` to be distinguished from generic uncertainty.
trend: Optional output of `test_braid_trend()`. If absent it is computed.
trajectory_margin: Smallest meaningful effect change per one-layer transition for attenuation/amplification.
alpha: Local inferential significance level.
min_slope: Deprecated alias for `trajectory_margin` retained for early OmicsBraid prototypes.

Value

One row per entity containing confirmatory and suggestive labels plus trajectory diagnostics.

Details

A separate `suggestive_pattern` is derived from effect geometry only. It can be useful when the inferential pattern is unresolved because the data are too imprecise, but it is not a confirmatory conclusion.