summary.sl.time: Summaries of a Super Learner

In RISCA: Causal Inference and Prediction in Cohort-Based Analyses

Summaries of a Super Learner

Description

Return goodness-of-fit indicators of a Super Learner obtained by the function sl.time.

Usage

## S3 method for class 'sl.time'
summary(object, ..., method, pro.time, newdata, times, failures)

Arguments

object	An object returned by the function sl.time.
...	Additional arguments affecting the plot.
method	A character string with the name of the algorithm included in the SL for wich the calibration plot is performed. The defaut is "sl" for the Super Learner.
pro.time	The prognostic time up to which the time-dependent indicators are estimated.
newdata	An optional data frame containing the new sample for validation with covariate values, folow-up times, and event status. The default value isNULL, the calibration plot is performed from the same subjects of the training sample.
times	The name of the variable related the numeric vector with the follow-up times in newdata. If NULL, the default is the name used in the learning sample.
failures	The name of the variable related the numeric vector with the event indicators (0=right censored, 1=event) in newdata. If NULL, the default is the name used in the learning sample.

Details

The following metrics are returned: "brier" for the Brier score at the prognostic time pro.time, "ibs" for the Integrated Brier score up to the last observed time of event, "ibll" for the Integrated Binomial Log-likelihood up to the last observed time of event, "bll" for the binomial Log-likelihood, "ribs" for the restricted Integrated Brier score up to the prognostic time pro.time, "ribll" for the restricted Integrated Binomial Log-likelihood Log-likelihood up to the last observed time of event, "bll" for the binomial Log-likelihood, "auc" for the area under the time-dependent ROC curve up to the prognostic time pro.time.

Author(s)

Yohann Foucher <[e-mail]>

Camille Sabathe <[e-mail]>

Examples

data(dataDIVAT2)

dataDIVAT2$train <- 1*rbinom(n=dim(dataDIVAT2)[1], size = 1, prob=1/2)

# The training of the super learner with 2 algorithms from the
   # first 100 patients of the training sample
sl<-sl.time(method=c("aft.gamma", "ph.gompertz"),  metric="ibs",
  data=dataDIVAT2[dataDIVAT2$train==1,][1:100,],  times="times", failures="failures", pro.time = 12,
  cov.quanti=c("age"),  cov.quali=c("hla", "retransplant", "ecd"),  cv=3)

# The prognostic capacities from the same training sample
summary(sl)

RISCA documentation built on March 31, 2023, 11:06 p.m.