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Competing Events Cumulative Incidence

Source: R/estimate_cuminc.R
estimate_cuminc.Rd

Function creates a cumulative incidence object using the tidycmprsk::cuminc() function.

Usage

estimate_cuminc(
  data = NULL,
  strata = NULL,
  CNSR = "CNSR",
  AVAL = "AVAL",
  conf.int = 0.95,
  ...
)

Arguments

data

A data frame. The dataset is expected to have one record per subject per analysis parameter. Rows with missing observations included in the analysis are removed.

AVAL, CNSR, strata

These arguments are used to construct a formula to be passed to tidycmprsk::cuminc(formula=).

  • AVAL Analysis value for Time-to-Event analysis. Default is "AVAL", as per CDISC ADaM guiding principles.

  • CNSR Column name indicating the outcome and censoring statuses. Column must be a factor and the first level indicates censoring, the next level is the outcome of interest, and the remaining levels are the competing events. Default is "CNSR"

  • strata Character vector, representing the strata for Time-to-Event analysis. When NULL, an overall analysis is performed. Default is NULL.

conf.int

Confidence internal level. Default is 0.95. Parameter is passed to tidycmprsk::cuminc(conf.level=)

...

Additional argument passed to tidycmprsk::cuminc()

Value

A cumulative incidence object as explained at https://mskcc-epi-bio.github.io/tidycmprsk/reference/cuminc.html

Examples

cuminc <-
  visR::estimate_cuminc(
    data = tidycmprsk::trial,
    strata = "trt",
    CNSR = "death_cr",
    AVAL = "ttdeath"
  )
cuminc
#> 
#> ── cuminc() ────────────────────────────────────────────────────────────────────
#> 
#> • Failure type "death from cancer"
#> strata   time   n.risk   estimate   std.error   95% CI          
#> Drug A   5.00   97       0.000      0.000       NA, NA          
#> Drug A   10.0   94       0.020      0.014       0.004, 0.065    
#> Drug A   15.0   83       0.071      0.026       0.031, 0.134    
#> Drug A   20.0   61       0.173      0.039       0.106, 0.255    
#> Drug B   5.00   102      0.000      0.000       NA, NA          
#> Drug B   10.0   95       0.039      0.019       0.013, 0.090    
#> Drug B   15.0   75       0.167      0.037       0.102, 0.246    
#> Drug B   20.0   55       0.255      0.043       0.175, 0.343    
#> 
#> • Failure type "death other causes"
#> strata   time   n.risk   estimate   std.error   95% CI          
#> Drug A   5.00   97       0.010      0.010       0.001, 0.050    
#> Drug A   10.0   94       0.020      0.014       0.004, 0.065    
#> Drug A   15.0   83       0.082      0.028       0.038, 0.147    
#> Drug A   20.0   61       0.204      0.041       0.131, 0.289    
#> Drug B   5.00   102      0.000      0.000       NA, NA          
#> Drug B   10.0   95       0.029      0.017       0.008, 0.077    
#> Drug B   15.0   75       0.098      0.030       0.050, 0.165    
#> Drug B   20.0   55       0.206      0.040       0.133, 0.289    
#> 
#> • Tests
#> outcome              statistic   df     p.value    
#> death from cancer    1.99        1.00   0.16       
#> death other causes   0.089       1.00   0.77       

cuminc %>%
  visR::visr() %>%
  visR::add_CI() %>%
  visR::add_risktable(statlist = c("n.risk", "cum.event"))
#> Warning: `visr.tidycuminc()` was deprecated in visR 0.4.0.
#> ℹ Please use `ggsurvfit::ggcuminc()` instead.