Genentech / jmpost

https://genentech.github.io/jmpost/
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Generating survival only quantities results in an error due to missing tumour times #305

Closed gowerc closed 7 months ago

gowerc commented 7 months ago
jdat <- DataJoint(
    subject = DataSubject(
        data = dat,
        subject = "pt",
        arm = "arm",
        study = "study"
    ),
    survival = DataSurvival(
        data = dat,
        formula = Surv(recyrs, censrec) ~ group
    )
)

sq_surv <- SurvivalQuantities(
    mp,
    grid = GridFixed(
        subjects = selected_patients,
        times = prediction_times
    ),
    type = "surv"
)
Error in seq.default(from = 0, to = max_time, length = 201) : 
  'to' must be a finite number
In addition: Warning message:
In max(data_list[["tumour_time"]]) :
  no non-missing arguments to max; returning -Inf
> traceback()
7: stop("'to' must be a finite number")
6: seq.default(from = 0, to = max_time, length = 201)
5: seq(from = 0, to = max_time, length = 201) at utilities.R#221
4: expand_time_grid(object@times, max(data_list[["tumour_time"]])) at GridFixed.R#31
3: as.QuantityGenerator.GridFixed(grid, object@data) at generics.R#403
2: as.QuantityGenerator(grid, object@data) at SurvivalQuantities.R#75
1: SurvivalQuantities(mp, grid = GridFixed(subjects = selected_patients, 
       times = prediction_times), type = "surv")