Unobserved factor levels no longer appear to work to indicate no censoring

[erikvona]

When no patients have been censored, this Stack Overflow answer indicates that as long as the first level of the factor is censoring, cuminc will work properly, even if that level has not been observed.

However, this no longer appears to be the case. Example from the linked question:

library(tidycmprsk)

data <- 
  trial %>%
  dplyr::mutate(
    death_cr_new = 
      dplyr::case_when(
        death_cr=="censor" ~ 2,
        death_cr=="death from cancer" ~ 2,
        death_cr=="death other causes" ~ 3
      ) %>%
      factor(levels = 1:3)
  )

data$death_cr_new %>% table()
#> .
#>   1   2   3 
#>   0 145  55

cuminc(Surv(ttdeath, death_cr_new) ~ trt, data)
#> 
#> ── cuminc() ────────────────────────────────────────────────────────────────────
#> • Failure type "3"
#> 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       0.021      0.015       0.004, 0.066    
#> Drug A   15.0   83       0.083      0.028       0.039, 0.150    
#> Drug A   20.0   61       0.219      0.044       0.140, 0.310    
#> Drug B   5.00   102      0.000      0.000       NA, NA          
#> Drug B   10.0   95       0.030      0.017       0.008, 0.079    
#> Drug B   15.0   75       0.108      0.033       0.055, 0.181    
#> Drug B   20.0   55       0.248      0.048       0.161, 0.346
#> • Tests
#> outcome   statistic   df     p.value    
#> 3         0.032       1.00   0.86

^{Created on 2023-02-07 with reprex v2.0.2}

Session info

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[ddsjoberg]

thanks for the report. we'll check it out soon (-ish?)

[erikvona]

Thanks! No hurry, I already have a silly workaround: if you add a row with the state set to censored and the time set to NA, it makes sure the censored level doesn't get dropped, while the row gets excluded from the analysis.

I fear I may be partly responsible as well 😅, the bug got introduced here #80, this line is the problem