mlr_measures_surv.cindex: Concordance Statistics Survival Measure

In mlr-org/mlr3proba: Probabilistic Supervised Learning for 'mlr3'

Concordance Statistics Survival Measure

Description

Calculates weighted concordance statistics, which, depending on the chosen weighting method (weight_meth) and tied times parameter (tiex), are equivalent to several proposed methods. By default, no weighting is applied and this is equivalent to Harrell's C-index.

Details

For the Kaplan-Meier estimate of the training survival distribution (S), and the Kaplan-Meier estimate of the training censoring distribution (G), we have the following options for time-independent concordance statistics (C-indexes) given the weighted method:

weight_meth:

• "I" = No weighting. (Harrell)

• "GH" = Gonen and Heller's Concordance Index

• "G" = Weights concordance by 1/G.

• "G2" = Weights concordance by 1/G^2. (Uno et al.)

• "SG" = Weights concordance by S/G (Shemper et al.)

• "S" = Weights concordance by S (Peto and Peto)

The last three require training data. "GH" is only applicable to LearnerSurvCoxPH.

The implementation is slightly different from survival::concordance. Firstly this implementation is faster, and secondly the weights are computed on the training dataset whereas in survival::concordance the weights are computed on the same testing data.

Dictionary

This Measure can be instantiated via the dictionary mlr_measures or with the associated sugar function msr():

MeasureSurvCindex$new()
mlr_measures$get("surv.cindex")
msr("surv.cindex")

Parameters

Id	Type	Default	Levels	Range
t_max	numeric	-		[0, \infty)
p_max	numeric	-		[0, 1]
weight_meth	character	I	I, G, G2, SG, S, GH	-
tiex	numeric	0.5		[0, 1]
eps	numeric	0.001		[0, 1]

Meta Information

• Type: "surv"

• Range: [0, 1]

• Minimize: FALSE

• Required prediction: crank

Parameter details

• eps (numeric(1))
  Very small number to substitute zero values in order to prevent errors in e.g. log(0) and/or division-by-zero calculations. Default value is 0.001.

• t_max (numeric(1))
  Cutoff time (i.e. time horizon) to evaluate concordance up to.

• p_max (numeric(1))
  The proportion of censoring to evaluate concordance up to in the given dataset. When t_max is specified, this parameter is ignored.

• weight_meth (character(1))
  Method for weighting concordance. Default "I" is Harrell's C. See details.

• tiex (numeric(1))
  Weighting applied to tied rankings, default is to give them half (0.5) weighting.

Super classes

mlr3::Measure -> mlr3proba::MeasureSurv -> MeasureSurvCindex

Methods

Public methods

• MeasureSurvCindex$new()

• MeasureSurvCindex$clone()

Inherited methods

• mlr3::Measure$aggregate()
• mlr3::Measure$format()
• mlr3::Measure$help()
• mlr3::Measure$print()
• mlr3::Measure$score()

---

Method new()

This is an abstract class that should not be constructed directly.

Usage

MeasureSurvCindex$new()

---

Method clone()

The objects of this class are cloneable with this method.

Usage

MeasureSurvCindex$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

References

Peto, Richard, Peto, Julian (1972). “Asymptotically efficient rank invariant test procedures.” Journal of the Royal Statistical Society: Series A (General), 135(2), 185–198.

Harrell, E F, Califf, M R, Pryor, B D, Lee, L K, Rosati, A R (1982). “Evaluating the yield of medical tests.” Jama, 247(18), 2543–2546.

Goenen M, Heller G (2005). “Concordance probability and discriminatory power in proportional hazards regression.” Biometrika, 92(4), 965–970. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/biomet/92.4.965")}.

Schemper, Michael, Wakounig, Samo, Heinze, Georg (2009). “The estimation of average hazard ratios by weighted Cox regression.” Statistics in Medicine, 28(19), 2473–2489. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/sim.3623")}.

Uno H, Cai T, Pencina MJ, D'Agostino RB, Wei LJ (2011). “On the C-statistics for evaluating overall adequacy of risk prediction procedures with censored survival data.” Statistics in Medicine, n/a–n/a. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/sim.4154")}.

See Also

Other survival measures: mlr_measures_surv.calib_alpha, mlr_measures_surv.calib_beta, mlr_measures_surv.calib_index, mlr_measures_surv.chambless_auc, mlr_measures_surv.dcalib, mlr_measures_surv.graf, mlr_measures_surv.hung_auc, mlr_measures_surv.intlogloss, mlr_measures_surv.logloss, mlr_measures_surv.mae, mlr_measures_surv.mse, mlr_measures_surv.nagelk_r2, mlr_measures_surv.oquigley_r2, mlr_measures_surv.rcll, mlr_measures_surv.rmse, mlr_measures_surv.schmid, mlr_measures_surv.song_auc, mlr_measures_surv.song_tnr, mlr_measures_surv.song_tpr, mlr_measures_surv.uno_auc, mlr_measures_surv.uno_tnr, mlr_measures_surv.uno_tpr, mlr_measures_surv.xu_r2

Examples

library(mlr3)
task = tsk("rats")
learner = lrn("surv.coxph")
part = partition(task) # train/test split
learner$train(task, part$train)
p = learner$predict(task, part$test)

# Harrell's C-index
p$score(msr("surv.cindex")) # same as `p$score()`

# Uno's C-index
p$score(msr("surv.cindex", weight_meth = "G2"),
        task = task, train_set = part$train)

# Harrell's C-index evaluated up to a specific time horizon
p$score(msr("surv.cindex", t_max = 97))

# Harrell's C-index evaluated up to the time corresponding to 30% of censoring
p$score(msr("surv.cindex", p_max = 0.3))

mlr-org/mlr3proba documentation built on April 12, 2025, 4:38 p.m.