8  Case Study: Colon Cancer Survival

This chapter runs the whole pipeline on the colon trial that ships with the survival package, so it needs no download. The trial randomised patients with stage III colon cancer to adjuvant therapy, and the data record survival and recurrence. The exposure of interest here is node4, an indicator of more than four positive lymph nodes, and the endpoint is death.

8.1 Setup and cohort

library(forkflow)
library(survival)
library(broom)
library(furrr)
plan(multisession)

d <- colon |> dplyr::filter(etype == 2) |> tidyr::drop_na()

Filtering to etype == 2 keeps the death endpoint, and dropping incomplete rows ensures every specification sees the same cohort.

8.2 The multiverse

specs <- adjuster_sets(
  c("age", "sex", "obstruct", "perfor", "adhere", "differ", "surg")
)

results <- fit_multiverse(specs, function(spec) {
  f <- reformulate(c("node4", spec$adjusters[[1]]), "Surv(time, status)")
  coxph(f, data = d) |> tidy(conf.int = TRUE) |>
    dplyr::filter(term == "node4")
}, .parallel = TRUE, .seed = 2026)

The seven candidate adjusters give one hundred twenty-eight Cox models, each estimating the hazard ratio for node4 under a different adjustment set.

8.3 Reading the results

voe(results)
spec_curve(results)
voe_volcano(results, colour = n_adjusters)

The specification curve shows where the log hazard ratios concentrate and how much of the distribution crosses the null. The volcano shows how the hazard ratio for node4 vibrates as covariates enter and leave, with colour revealing whether more heavily adjusted models pull the estimate in one direction. The voe() summary reduces the spread to a relative hazard ratio and a Janus fraction, which together report how stable the association is.

8.4 A note on defensibility

Every adjuster in the pool is a plausible prognostic factor in colon cancer, so the grid reads as a reasonable sensitivity analysis rather than a fishing expedition. In a confirmatory study the pool would be fixed in advance from a causal diagram, a point the next chapter develops.