R Under development (unstable) (2024-12-13 r87441 ucrt) -- "Unsuffered Consequences"
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> # 
> # Check that my updates to a. remove survival:: out of formulas and
> #  b: ensure that Surv(), cluster(), strata(), pspline(), and tt() use
> #   these functions from the survival namespace, when called in a coxph,
> #   survfit, survreg, etc formula
> library(survival)
> aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y))
> 
> c1 <- coxph(Surv(time, status) ~ age + strata(inst), lung)
> 
> # a local Surv that gives the wrong answer but won't error out (makes it
> #  simpler to write the tests)
> Surv <- function(x, ...) survival::Surv(x, rep(1, length(x)))
> c2 <-  coxph(Surv(time, status) ~ age + strata(inst), lung)
> 
> c3 <- coxph(survival::Surv(time, status) ~ age + survival::strata(inst), lung)
> # in prior releases the above fits a different model, stata is not recognized
> #  as a special and becomes a factor
> 
> all.equal(coef(c1), coef(c2))
[1] TRUE
> all.equal(coef(c1), coef(c3))
[1] TRUE
> 
> !(c2$call$formula == c3$call$formula)  # the call doesn't get changed
[1] TRUE
> c2$formula == c3$formula               # but the formula is changed
[1] TRUE
> 
> nocall <- function(x, omit="call") {
+     z <- unclass(x)  # needed for any object with a [ method
+     z[-match(omit, names(z))]  # all but $call
+ }
> y2 <- with(lung, survival::Surv(time, status)) # outside a formula
> 
> fit1a <- coxph(Surv(time, status) ~ age + strata(sex) + cluster(inst), lung)
> fit1b <- coxph(Surv(time, status) ~ age + survival::strata(sex) +
+                    survival::cluster(inst), lung)
> fit1c <- coxph(y2 ~ age + strata(sex) + survival::cluster(inst), lung)
> all.equal(nocall(fit1a), nocall(fit1b))
[1] TRUE
> aeq(coef(fit1a), coef(fit1c))
[1] TRUE
> 
> fit2a <- survdiff(Surv(time, status) ~ sex + strata(inst), lung)
> fit2b <- survdiff(survival::Surv(time, status) ~ sex + survival::strata(inst),
+                   data= lung)
> all.equal(nocall(fit2a), nocall(fit2b))
[1] TRUE
> aeq(rowSums(fit2a$obs), c(111, 53))  # make sure it use the correct Surv
[1] TRUE
> 
> fit3a <- survreg(Surv(time, status) ~ ph.ecog + strata(sex), lung)
> fit3b <- survreg(survival::Surv(time, status) ~ ph.ecog + survival::strata(sex),
+                  data= survival::lung)
> all.equal(nocall(fit3a), nocall(fit3b))
[1] TRUE
> 
> fit4a <- concordance(Surv(time, status) ~ ph.ecog + strata(sex), lung)
> fit4b <- concordance(Surv(time, status) ~ ph.ecog + survival::strata(sex), lung)
> all.equal(nocall(fit4a), nocall(fit4b))
[1] TRUE
> 
> fit5a <- survfit(Surv(time, status) ~ sex, lung)
> fit5b <- survfit(Surv(time, status) ~ strata(sex), lung)
> fit5c <- survfit(survival::Surv(time, status) ~  survival::strata(sex), lung)
> fit5d <- survfit(y2 ~  survival::strata(sex), lung)
> all.equal(nocall(fit5a, c("call", "strata")), nocall(fit5b, c("call", "strata")))
[1] TRUE
> all.equal(nocall(fit5b), nocall(fit5c))
[1] TRUE
> aeq(fit5a$surv, fit5d$surv)
[1] TRUE
> 
> proc.time()
   user  system elapsed 
   0.82    0.14    0.93