test_dfs_JointFPM {JointFPM}

Tests DFs for JointFPMs.

Description

Test of different degrees of freedoms (DFs) for joint flexible parametric survival models.

Usage

test_dfs_JointFPM(
  surv,
  re_model,
  ce_model,
  re_indicator,
  ce_indicator,
  dfs_ce,
  dfs_re,
  tvc_re_terms = NULL,
  tvc_ce_terms = NULL,
  cluster,
  data
)

Arguments

surv

A formula of the following form Surv(...) ~ 1. The Surv objects needs to be of type == 'counting' with the following arguments:

time:

Start of follow-up time for each event episode, i.e., usually 0 for the competing event and the first occurrence of the recurrent event. For every subsequent event the follow-up can either be 0 if gap time is the underlying time scale or the time of the previous event if total time is the underlying time scale.

time2:

End of follow-up, i.e., either occurrence of a terminal or recurrent event, or time of censoring.

status:

Event indicator for both terminal and recurrent event.

type:

Has to be counting.

re_model

A formula object specifying the model for the recurrent event with an empty right hand side of the formula, e.g. ~ sex.

ce_model

A formula object specifying the model for the competing event with an empty right hand side of the formula, e.g. ~ sex.

re_indicator

Indicator that defined which rows in the dataset belong to the recurrent event process. These are usually more than one row per observations. The variable name needs to be passed as a character vector.

ce_indicator

Indicator that defined which row in the dataset belong to the competing event process. The variable name needs to be passed as a character vector.

dfs_ce

Defines the number of knots used to model the baseline hazard function for the competing event process.

dfs_re

Defines the number of knots used to model the baseline hazard function for the recurrent event process.

tvc_re_terms

A named list defining the numbers of knots used to model potential time-varying effects of variables included in the recurrent event model. This list should be of form ⁠list(<var_name> = <no. of knots>)⁠.

tvc_ce_terms

A named list defining the numbers of knots used to model potential time-varying effects of variables included in the competing event model. This list should be of form ⁠list(<var_name> = <no. of knots>)⁠.

cluster

A chara vector specifying the name of the variable that defines unique observation in the dataset passed to the function.

data

A stacked dataset that including both data on the recurrent and competing event process. The dataset should have one row for each observation including the follow-up time and event indicator for the competing event and possibly multiple rows for each observation including the follow-up times and event indicator for the recurrent event, e.g.:

id st_start  st_end re status
 1      0      6.88  0      1
 1      0      6.88  1      0
 2      0      8.70  0      1
 2      0      8.70  1      0
 3      0     10     0      0
 3      0      1.78  1      1
 3      1.78   6.08  1      1
 3      6.08  10     1      0
 4      0      6.07  0      1
 4      0      6.07  1      0

Value

A data.frame with one row per combination of baseline hazards DFs, and the DFs of the time varying covariates, and the corresponding AIC and BIC.

Examples

# Test different dfs
test_dfs_JointFPM(Surv(time  = start,
                       time2 = stop,
                       event = event,
                       type  = 'counting') ~ 1,
                  re_model = ~ pyridoxine + thiotepa,
                  ce_model = ~ pyridoxine + thiotepa,
                  re_indicator = "re",
                  ce_indicator = "ce",
                  dfs_ce = 1:3,
                  dfs_re = 2,
                  tvc_ce_terms = list(thiotepa   = 1:2),
                  tvc_re_terms = list(pyridoxine = 2),
                  cluster  = "id",
                  data     = bladder1_stacked)