Survival Task

Source: R/TaskSurv.R

This task specializes mlr3::Task and mlr3::TaskSupervised for possibly-censored survival problems. The target is comprised of survival times and an event indicator. Predefined tasks are stored in mlr3::mlr_tasks.

The task_type is set to "surv".

See also

Other Task: TaskDens

Super classes

mlr3::Task -> mlr3::TaskSupervised -> TaskSurv

Active bindings

censtype

character(1)
Returns the type of censoring, one of "right", "left", "counting", "interval", "interval2" or "mstate".

Methods

Public methods

Inherited methods

Method new()

Creates a new instance of this R6 class.

Usage

TaskSurv$new(
  id,
  backend,
  time,
  event,
  time2,
  type = c("right", "left", "counting", "interval", "interval2", "mstate")
)

Arguments

id

(character(1))
Identifier for the new instance.

backend

(DataBackend)
Either a DataBackend, or any object which is convertible to a DataBackend with as_data_backend(). E.g., a data.frame() will be converted to a DataBackendDataTable.

time

(character(1))
Name of the column for event time if data is right censored, otherwise starting time if interval censored.

event

(character(1))
Name of the column giving the event indicator. If data is right censored then "0"/FALSE means alive (no event), "1"/TRUE means dead (event). If type is "interval" then "0" means right censored, "1" means dead (event), "2" means left censored, and "3" means interval censored. If type is "interval2" then event is ignored.

time2

(character(1))
Name of the column for ending time for interval censored data, otherwise ignored.

type

(character(1))
Name of the column giving the type of censoring. Default is 'right' censoring.

Method truth()

True response for specified row_ids. Format depends on the task type. Defaults to all rows with role "use".

Usage

TaskSurv$truth(rows = NULL)

Arguments

rows

integer()
Row indices.

Returns

numeric().

Method formula()

Creates a formula for survival models with survival::Surv on the LHS.

Usage

TaskSurv$formula(rhs = NULL)

Arguments

rhs

If NULL RHS is ., otherwise gives RHS of formula.

Returns

numeric().

Method clone()

The objects of this class are cloneable with this method.

Usage

TaskSurv$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

library(mlr3)
lung = mlr3misc::load_dataset("lung", package = "survival")
lung$status = (lung$status == 2L)
b = as_data_backend(lung)
task = TaskSurv$new("lung", backend = b, time = "time",
   event = "status")

task$target_names
#> [1] "time"   "status"
task$feature_names
#> [1] "age"       "inst"      "meal.cal"  "pat.karno" "ph.ecog"   "ph.karno" 
#> [7] "sex"       "wt.loss"  
task$formula()
#> Surv(time, status, type = "right") ~ .
#> <environment: namespace:survival>
task$truth()
#>   [1]  306   455  1010+  210   883  1022+  310   361   218   166   170   654 
#>  [13]  728    71   567   144   613   707    61    88   301    81   624   371 
#>  [25]  394   520   574   118   390    12   473    26   533   107    53   122 
#>  [37]  814   965+   93   731   460   153   433   145   583    95   303   519 
#>  [49]  643   765   735   189    53   246   689    65     5   132   687   345 
#>  [61]  444   223   175    60   163    65   208   821+  428   230   840+  305 
#>  [73]   11   132   226   426   705   363    11   176   791    95   196+  167 
#>  [85]  806+  284   641   147   740+  163   655   239    88   245   588+   30 
#>  [97]  179   310   477   166   559+  450   364   107   177   156   529+   11 
#> [109]  429   351    15   181   283   201   524    13   212   524   288   363 
#> [121]  442   199   550    54   558   207    92    60   551+  543+  293   202 
#> [133]  353   511+  267   511+  371   387   457   337   201   404+  222    62 
#> [145]  458+  356+  353   163    31   340   229   444+  315+  182   156   329 
#> [157]  364+  291   179   376+  384+  268   292+  142   413+  266+  194   320 
#> [169]  181   285   301+  348   197   382+  303+  296+  180   186   145   269+
#> [181]  300+  284+  350   272+  292+  332+  285   259+  110   286   270    81 
#> [193]  131   225+  269   225+  243+  279+  276+  135    79    59   240+  202+
#> [205]  235+  105   224+  239   237+  173+  252+  221+  185+   92+   13   222+
#> [217]  192+  183   211+  175+  197+  203+  116   188+  191+  105+  174+  177+