evaluate$risk.strata

Risk-strata evaluation for PRS models

Description

evaluate$risk.strata() summarizes outcome behavior across PRS-defined quantile strata.

Usage

evaluate$risk.strata(models = NULL, on, outcome, type = c("auto", "binary", "continuous", "survival"), time = NULL, event = NULL, obs = NULL, scores.layer = X, score.mode = c("compute.if.missing", "require", "recompute"), score.args = list(), metrics = NULL, quantiles = c(0.2, 0.8), reference = "lowest", conf.level = 0.95)

Arguments

models	Optional model specification.
on	Evaluation context (PolyGeniusData or genotype input). When genotype input is supplied, PolyGenius internally materializes a temporary PolyGeniusData object to resolve and evaluate scores.
outcome	Outcome definition. When on is PolyGeniusData: unquoted expression resolved on observations. When on is genotype input: vector of length n_obs, list of vectors (each length n_obs), or table with one or more columns and nrow == n_obs.
type	Outcome type (“auto”, “binary”, “continuous”, “survival”).
time	Unquoted time-to-event expression (required for survival).
event	Unquoted event-indicator expression (required for survival).
obs	Optional unquoted observation subset expression.
scores.layer	Score layer to read/use (symbol or single string).
score.mode	Score resolution mode. If on is a PolyGeniusData object, computed scores are written into that object. If on is genotype input, computed scores exist only in the temporary internal evaluation data object and are not returned.
score.args	Named list passed to compute$scores(…) when needed.
metrics	Optional metric subset; defaults by outcome type when NULL.
quantiles	Numeric cut points in ⁠(0,1)⁠ used to define risk groups.
reference	Reference group for relative-effect metrics. “lowest” uses the lowest stratum.
conf.level	Confidence level for interval estimates.
logger	Optional logger to pass and use within the function. Defaults NULL - creates a new logger

Value

A PolyGeniusEvaluation object only. Any temporary PolyGeniusData constructed from genotype input is not returned. Risk-strata artifacts are available via slotArtifacts(), including strata.profile: one row per evaluated observation after assigning each score to a quantile-defined stratum, with evaluation.outcome, model, model.idx, stratum, score, and outcome; survival outcomes add time. This artifact is the observation-level substrate used for lift and stratum-profile visualizations. Risk-strata diagnostics are available via slotDiagnostics(), including metric.flags for muffled model-fit warnings in relative-effect metrics.

See Also

Other evaluate: evaluate.benchmark(), evaluate.calibration(), evaluate.compare(), evaluate.discrimination(), evaluate.incremental(), evaluate.similarity()