CoxRegression

Cox-regression family for associate$regression()

Description

CoxRegression implements right-censored Cox proportional-hazards models. It supports covariates, split.by through the engine fit grid, and predictor-by-modifier interactions in the Cox formula.

In the user-facing associate$regression() call, outcomes is the biological or clinical endpoint being modeled and is supplied as the event indicator. time is the observed age or follow-up time at endpoint or censoring.

Summary rows follow the cox association schema on the log-hazard scale. Returned artifacts are:

  • observed.curves, the overall observed survival curve for the fit cell

  • predicted.curves, adjusted survival curves for predictor profiles

  • prediction.grid, the profile values used for adjusted curves

  • risk.table, the plotting-ready risk table

  • group.summary, survival summary values for the analysis curve

Super class

PolyGenius::RegressionFamily -> CoxRegression

Methods

Public methods

Inherited methods

Method new()

Register the canonical family key used by the engine.

Usage 
CoxRegression$new()
Returns

The initialized family object with family.name = “cox”.

Method validate.frame()

Ensure one survival time column is available.

Usage 
CoxRegression$validate.frame(frame, cell, fit.specs, conf.level)
Arguments
frame

Cell-specific PolyGeniusFrame.

cell

Named fit-grid cell.

fit.specs

Additional family-specific fitting arguments.

conf.level

Confidence level for intervals.

Returns

Invisibly TRUE when validation succeeds.

Method prepare.frame()

Build the complete-case Cox fit payload.

Usage 
CoxRegression$prepare.frame(frame, cell, fit.specs, conf.level)
Arguments
frame

Cell-specific PolyGeniusFrame.

cell

Named fit-grid cell.

fit.specs

Additional family-specific fitting arguments.

conf.level

Confidence level for intervals.

Returns

A model-ready survival fit payload.

Method build.formula()

Build the Cox formula for one fit payload.

Usage 
CoxRegression$build.formula(frame)
Arguments
frame

Fit payload returned by prepare.frame().

Returns

A model formula object.

Method fit.model()

Fit the Cox proportional-hazards model for one cell.

Usage 
CoxRegression$fit.model(formula, frame, ...)
Arguments
formula

Model formula returned by build.formula().

frame

Fit payload returned by prepare.frame().

…

Additional arguments passed to survival::coxph().

Returns

A fitted survival::coxph object.

Method build.summary.rows()

Convert fitted Cox coefficients to regression-schema rows.

Usage 
CoxRegression$build.summary.rows(
  fit,
  fit.data,
  cell,
  fit.specs,
  conf.level,
  formula
)
Arguments
fit

Fitted survival::coxph object.

fit.data

Fit payload returned by prepare.frame().

cell

Named fit-grid cell.

fit.specs

Additional family-specific fitting arguments.

conf.level

Confidence level for intervals.

formula

Display formula string.

Returns

A data.table following the concrete association schema.

Method build.artifacts()

Return observed and adjusted survival-curve artifacts.

Usage 
CoxRegression$build.artifacts(
  fit,
  fit.data,
  cell,
  fit.specs,
  conf.level,
  formula
)
Arguments
fit

Fitted survival::coxph object.

fit.data

Fit payload returned by prepare.frame().

cell

Named fit-grid cell.

fit.specs

Additional family-specific fitting arguments.

conf.level

Confidence level for intervals.

formula

Display formula string.

Returns

A named list with observed curves, predicted curves, prediction profiles, risk table, and group summary.

Method clone()

The objects of this class are cloneable with this method.

Usage 
CoxRegression$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.