summary.calibrator: Statistic summary of the D'Agostino-Nam calibration and...

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

Statistic summary of the D'Agostino-Nam calibration and square errors.

Description

The function returns two types of data:

• a data frame storing the numbers of events and survivors, survival probabilities, relative survival probability (Kaplan - Meier to Cox ratio), relative risk (rr: Kaplan-Meier to Cox ratio) and the D'Agostino-Nam chi-squared statistic (x2_dn) for each strata (type = 'strata') or for the entire model (type = 'global').

• a data frame with mean, SEM, median, and 95% percentile range for square errors averaged over either unique time points or observations or unique values of the Cox model's linear predictor score.

Usage

## S3 method for class 'calibrator'
summary(
  object,
  type = c("global", "strata", "squares"),
  by = c("time", "observation", "lp"),
  ...
)

Arguments

object	a calibrator object.
type	type of the calibration statistic: 'global' (default) and 'strata' return the output of the D'Agostino - Nam algorithm, while 'squares' returns a data frame with summary statistics of square errors.
by	type of averaging of the square errors by unique time points ('time', default), observations or unique values of the Cox model linear predictor score ('lp').
...	additional arguments, currently none.

Value

a data frame with the calibration statistics.

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).

• Graf, E., Schmoor, C., Sauerbrei, W. & Schumacher, M. Assessment and comparison of prognostic classification schemes for survival data. Stat. Med. 18, 2529–2545 (1999).

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