Survival Task Generator for Package 'simsurv'

A mlr3::TaskGenerator calling simsurv::simsurv() from package simsurv.

This generator currently only exposes a small subset of the flexibility of simsurv, and just creates a small dataset with the following numerical covariates:

• treatment: Bernoulli distributed with hazard ratio 0.5.

• height: Normally distributed with hazard ratio 1.

• weight: normally distributed with hazard ratio 1.

See simsurv::simsurv() for an explanation of the hyperparameters. Initial values for hyperparameters are lambdas = 0.1, gammas = 1.5 and maxt = 5. The last one, by default generates samples which are administratively censored at \(\tau = 5\), so increase this value if you want to change this.

Dictionary

This TaskGenerator can be instantiated via the dictionary mlr_task_generators or with the associated sugar function tgen():

mlr_task_generators$get("simsurv")
tgen("simsurv")

Parameters

Id	Type	Default	Levels	Range
dist	character	weibull	weibull, exponential, gompertz	-
lambdas	numeric	-		\([0, \infty)\)
gammas	numeric	-		\([0, \infty)\)
maxt	numeric	-		\([0, \infty)\)

References

Brilleman, L. S, Wolfe, Rory, Moreno-Betancur, Margarita, Crowther, J. M (2021). “Simulating Survival Data Using the simsurv R Package.” Journal of Statistical Software, 97(3), 1–27. doi:10.18637/JSS.V097.I03 .

See also

• Dictionary of TaskGenerators: mlr3::mlr_task_generators

• as.data.table(mlr_task_generators) for a table of available TaskGenerators in the running session

Other TaskGenerator: mlr_task_generators_coxed, mlr_task_generators_simdens

Super class

mlr3::TaskGenerator -> TaskGeneratorSimsurv

Methods

Public methods

• TaskGeneratorSimsurv$new()

• TaskGeneratorSimsurv$help()

• TaskGeneratorSimsurv$clone()

Inherited methods

• mlr3::TaskGenerator$format()
• mlr3::TaskGenerator$generate()
• mlr3::TaskGenerator$print()

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Method new()

Creates a new instance of this R6 class.

Usage

TaskGeneratorSimsurv$new()

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Method help()

Opens the corresponding help page referenced by field $man.

Usage

TaskGeneratorSimsurv$help()

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Method clone()

The objects of this class are cloneable with this method.

Usage

TaskGeneratorSimsurv$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

  # generate 20 samples with Weibull survival distribution
  gen = tgen("simsurv")
  task = gen$generate(20)
  head(task)
#>    eventtime status   height treatment   weight
#>        <num>  <int>    <num>     <int>    <num>
#> 1: 5.0000000      0 195.0268         0 80.45247
#> 2: 0.6306407      1 174.0041         1 96.48540
#> 3: 5.0000000      0 180.7211         1 72.44317
#> 4: 2.5334734      1 170.5500         1 77.11821
#> 5: 0.7165469      1 169.3864         1 72.69849
#> 6: 4.3512901      1 159.2356         1 85.24149

  # generate 100 samples with exponential survival distribution and tau = 40
  gen = tgen("simsurv", dist = "exponential", gammas = NULL, maxt = 40)
  task = gen$generate(100)
  head(task)
#>     eventtime status   height treatment    weight
#>         <num>  <int>    <num>     <int>     <num>
#> 1: 14.0902730      1 163.7044         1  69.81636
#> 2:  9.5564871      1 173.8492         1  84.80034
#> 3:  1.6580893      1 175.4791         0 104.04713
#> 4:  1.0691358      1 176.7335         0  86.03244
#> 5:  6.7565146      1 171.8410         0 100.06418
#> 6:  0.4434743      1 175.9910         0  67.76009