associate$compare

Formal comparison analyses for PolyGeniusData

Description

associate$compare() runs formal comparison workflows on observation-side data resolved from a PolyGeniusData object.

Supported comparison families currently include:

nested model comparisons
heterogeneity tests through pooled interaction models
omnibus group comparisons
pairwise group contrasts

Summary mode returns a PolyGeniusAssociations object using associate.schema.comparison. Curve-style comparisons reuse the same artifact names as association regression where possible so downstream visualization can stay object-loyal.

Usage

associate.compare(
  data,
  outcome = NULL,
  outcomes = NULL,
  predictors = NULL,
  groups.by = NULL,
  covariates = NULL,
  model = c("auto", "lm", "glm", "cox", "crr", "km"),
  time = NULL,
  event = NULL,
  competing = NULL,
  weights = NULL,
  comparison.type = c("nested", "heterogeneity", "group", "pairwise"),
  comparison.test = "auto",
  reference = NULL,
  conf.level = 0.95,
  p.adjust.method = "BH",
  output = c("summary", "models"),
  ...
)

Arguments

`data`	A `PolyGeniusData` object.
`outcome`	Optional unquoted expression specifying a single outcome.
`outcomes`	Optional unquoted expression specifying one or more outcomes.
`predictors`	Optional unquoted expression specifying tested predictors.
`groups.by`	Optional unquoted expression specifying the grouping or modifier variable used by the comparison.
`covariates`	Optional unquoted expression specifying adjustment variables.
`model`	Comparison family to use. `“auto”` infers the family from the outcome and supplied survival inputs.
`time`	Optional unquoted expression defining follow-up time for survival-style analyses.
`event`	Optional unquoted expression defining the event indicator for survival-style analyses. When omitted, `outcome` or `outcomes` supplies the event indicator.
`competing`	Optional unquoted expression defining a competing-event indicator for Fine-Gray comparisons.
`weights`	Optional unquoted expression or numeric vector of regression weights.
`comparison.type`	Comparison family to run.
`comparison.test`	Comparison test override. `“auto”` chooses the family-appropriate default.
`reference`	Optional reference level used by pairwise contrasts.
`conf.level`	Confidence level for interval estimates.
`p.adjust.method`	P-value adjustment method passed to `stats::p.adjust()`.
`output`	One of `“summary”` or `“models”`.
`…`	Additional arguments are currently not supported.

Value

“summary” returns a PolyGeniusAssociations object using the comparison schema.
“models” returns a data.frame with one row per attempted comparison and list-columns for fitted objects and diagnostics.

See Also

associate, PolyGeniusData, PolyGeniusAssociations, associate.schema.comparison