R: Song and Zhou's TPR Survival Measure

mlr_measures_surv.song_tpr {mlr3proba} | R Documentation

## Song and Zhou's TPR Survival Measure

### Description

Calls `survAUC::sens.sh()`.

Assumes Cox PH model specification.

`times` and `lp_thresh` are arbitrarily set to `0` to prevent crashing, these should be further specified.

### Details

All measures implemented from survAUC should be used with care, we are aware of problems in implementation that sometimes cause fatal errors in R. In future updates these measures will all be re-written and implemented directly in `mlr3proba`.

### Dictionary

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

    MeasureSurvSongTPR$new()
    mlr_measures$get("surv.song_tpr")
    msr("surv.song_tpr")

### Meta Information

- Type: `"surv"`

- Range: [0, 1]

- Minimize: `FALSE`

- Required prediction: `lp`

### Super classes

`mlr3::Measure` -> `mlr3proba::MeasureSurv` -> `mlr3proba::MeasureSurvIntegrated` -> `mlr3proba::MeasureSurvAUC` -> `MeasureSurvSongTPR`

### Active bindings

`lp_thresh`

  `numeric(1)`
  Threshold for linear predictor when calculating TPR/TNR.

`type`

  (`character(1)`)
  Type of measure, one of: `'cumulative'`, `'incident'`.

### Methods

#### Public methods

- `MeasureSurvSongTPR$new()`

- `MeasureSurvSongTPR$clone()`

Inherited methods

- `mlr3::Measure$aggregate()`

- `mlr3::Measure$format()`

- `mlr3::Measure$help()`

- `mlr3::Measure$score()`

- `mlr3proba::MeasureSurv$print()`

#### Method `new()`

Creates a new instance of this R6 class.

##### Usage

    MeasureSurvSongTPR$new(
      times = 0,
      lp_thresh = 0,
      type = c("incident", "cumulative")
    )

##### Arguments

`times`

  (`numeric()`)
  If `integrate == TRUE` then a vector of time-points over which to integrate the score. If `integrate == FALSE` then a single time point at which to return the score.

`lp_thresh`

  `numeric(1)`
  Determines where to threshold the linear predictor for calculating the TPR/TNR.

`type`

  (`character(1)`)
  Determines the type of score, one of: `'cumulative'`, `'incident'`.

#### Method `clone()`

The objects of this class are cloneable with this method.

##### Usage

    MeasureSurvSongTPR$clone(deep = FALSE)

##### Arguments

`deep`

  Whether to make a deep clone.

### References

Song, Xiao, Zhou, Xiao-Hua (2008). “A semiparametric approach for the covariate specific ROC curve with survival outcome.” Statistica Sinica, 18(3), 947–65. https://www.jstor.org/stable/24308524.

### See Also

Other survival measures: `mlr_measures_surv.calib_alpha`, `mlr_measures_surv.calib_beta`, `mlr_measures_surv.chambless_auc`, `mlr_measures_surv.cindex`, `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.rmse`, `mlr_measures_surv.schmid`, `mlr_measures_surv.song_auc`, `mlr_measures_surv.song_tnr`, `mlr_measures_surv.uno_auc`, `mlr_measures_surv.uno_tnr`, `mlr_measures_surv.uno_tpr`, `mlr_measures_surv.xu_r2`

Other AUC survival measures: `mlr_measures_surv.chambless_auc`, `mlr_measures_surv.hung_auc`, `mlr_measures_surv.song_auc`, `mlr_measures_surv.song_tnr`, `mlr_measures_surv.uno_auc`, `mlr_measures_surv.uno_tnr`, `mlr_measures_surv.uno_tpr`

Other lp survival measures: `mlr_measures_surv.calib_beta`, `mlr_measures_surv.chambless_auc`, `mlr_measures_surv.hung_auc`, `mlr_measures_surv.nagelk_r2`, `mlr_measures_surv.oquigley_r2`, `mlr_measures_surv.song_auc`, `mlr_measures_surv.song_tnr`, `mlr_measures_surv.uno_auc`, `mlr_measures_surv.uno_tnr`, `mlr_measures_surv.uno_tpr`, `mlr_measures_surv.xu_r2`

[Package mlr3proba version 0.4.2 Index]