calibrator: Build a calibration object.

In PiotrTymoszuk/coxExtensions: Extended Inference and Goodness of Fit for Cox Models

Build a calibration object.

Description

Generates a calibration object, used internally by the get_cox_calibration function. Contains all data used in calculation of Cox model calibration with the D'Agostino-Nam method (DOI: 10.1016/S0169-7161(03)23001-7) and visualization of the results.

Usage

calibrator(
  lp_scores,
  surv_fit,
  cox_fit,
  km_estimates,
  cox_estimates,
  strata_calibration,
  global_calibration,
  squares = NULL
)

Arguments

lp_scores	a data frame containing linear predictor scores.
surv_fit	a 'surv_fit' class instance storing the Kaplan-Meier survival estimates for the linear predictor score strata (see: surv_fit).
cox_fit	a Cox proportional hazard model of the survival as a function of the linear predictor score strata.
km_estimates	a data frame with Kaplan-Meier survival estimates.
cox_estimates	a data frame with cox survival estimates.
strata_calibration	a data frame with the calibration statistics for each linear predictor score strata.
global_calibration	a data frame with the global calibration statistics.
squares	an optional data frame with the time points, predicted and observed survival and the squared distance between the predicted and observed survival.

Value

an instance of 'calibrator' class.

References

• D’Agostino, R. B. & Nam, B. H. Evaluation of the Performance of Survival Analysis Models: Discrimination and Calibration Measures. Handb. Stat. 23, 1–25 (2003).

• Royston, P. Tools for checking calibration of a Cox model in external validation: Approach based on individual event probabilities. Stata J. 14, 738–755 (2014).

• Crowson, C. S. et al. Assessing calibration of prognostic risk scores. Stat. Methods Med. Res. 25, 1692–1706 (2016).

PiotrTymoszuk/coxExtensions documentation built on Feb. 6, 2024, 10:58 p.m.