R Under development (unstable) (2024-09-18 r87177 ucrt) -- "Unsuffered Consequences"
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> 
> library("mlt")
Loading required package: basefun
Loading required package: variables
> library("survival")
> library("flexsurv")
> 
> chk <- function(x, y, ...) {
+ 
+     ret <- all.equal(x, y, ...)
+     if (isTRUE(ret)) return(ret)
+     print(ret)
+     return(TRUE)
+ }
> tol <- .001
> 
> ### right-censored veteran data
> ### exponential model
> fit1 <- coxph(Surv(time, status) ~ karno + age + trt, veteran)
> fit2 <- survreg(Surv(time, status) ~ karno + age + trt, veteran, dist = "exponential")
> fit3 <- flexsurvreg(Surv(time, status) ~ karno + age + trt, data= veteran, dist = "exponential")
> 
> veteran$ytime <- with(veteran, Surv(time, status))
> dy <- numeric_var("ytime", support = c(0.1, 1000))
> by <- log_basis(dy, ui = "increasing")
> m <- mlt(ctm(by, shift = ~ karno + age + trt, data = veteran, todistr = "MinExtr"),
+          data = veteran, fixed = c("log(ytime)" = 1))
> 
> stopifnot(chk(fit3$logliki, m$logliki(coef(m)[-2], weights(m)), 
+                     tol = tol, check.attributes = FALSE))
> 
> stopifnot(chk(logLik(fit2), logLik(m), tol = tol))
> stopifnot(chk(logLik(fit3), logLik(m), tol = tol, 
+               check.attributes = FALSE))
> 
> ### Weibull model
> fit2 <- survreg(Surv(time, status) ~ karno + age + trt, veteran, dist = "weibull")
> fit3 <- flexsurvreg(Surv(time, status) ~ karno + age + trt, data= veteran, dist = "weibull")
> 
> veteran$ytime <- with(veteran, Surv(time, status))
> dy <- numeric_var("ytime", support = c(0.1, 1000))
> # by <- Bernstein_basis(dy, order = 10, ui = "increasing")
> by <- log_basis(dy, ui = "increasing")
> m <- mlt(ctm(by, shift = ~ karno + age + trt, data = veteran, todistr = "MinExtr"),
+          data = veteran)
> 
> stopifnot(chk(fit3$logliki, m$logliki(coef(m), weights(m)), 
+               tol = tol, check.attributes = FALSE))
> 
> stopifnot(chk(logLik(fit2), logLik(m), tol = tol))
> stopifnot(chk(logLik(fit3), logLik(m), tol = tol,
+               check.attributes = FALSE))
> 
> ### now with time-dependent covariates
> vet2 <- survSplit(Surv(time, status) ~., veteran,
+                   cut=c(60, 120), episode ="timegroup")
> vet2$timegroup <- factor(vet2$timegroup)
> vet2$ytime <- with(vet2, Surv(tstart, time, status))
> 
> ## exponential model
> suppressWarnings(fit3 <- flexsurvreg(Surv(tstart, time, status) ~ 
+     karno + karno:timegroup + age + trt, data= vet2, dist = "exponential"))
> m <- mlt(ctm(by, shift = ~ karno + karno:timegroup + age + trt, data = vet2, todistr = "MinExtr"),
+          data = vet2, fixed = c("log(ytime)" = 1))
> 
> stopifnot(chk(fit3$logliki, m$logliki(coef(m)[-2], weights(m)), 
+               tol = tol, check.attributes = FALSE))
> stopifnot(chk(logLik(fit3), logLik(m), tol = tol, check.attributes = FALSE))
> 
> ### Weibull model
> fit3 <- flexsurvreg(Surv(tstart, time, status) ~ karno + karno:timegroup +
+                      age + trt, data= vet2, dist = "weibull")
> m <- mlt(ctm(by, shift = ~ karno + karno:timegroup + age + trt, data = vet2, todistr = "MinExtr"),
+          data = vet2, scale = TRUE)
> 
> stopifnot(chk(fit3$logliki, m$logliki(coef(m), weights(m)), 
+               tol = tol, check.attributes = FALSE))
> stopifnot(chk(logLik(fit3), logLik(m), tol = tol, check.attributes = FALSE))
> 
> ## Cox model, see ?survival::survSplit
> fit1 <- coxph(Surv(tstart, time, status) ~ karno + karno:strata(timegroup) +
+               age + trt, data= vet2)
> 
> ### refit this model using mlt
> btg <- as.basis(vet2$timegroup)
> by <- Bernstein_basis(dy, order = 3, ui = "increasing")
> m <- mlt(ctm(by, interacting = btg, 
+          shift = ~ karno + karno:timegroup + age + trt, data = vet2, todistr = "MinExtr"),
+          data = vet2, scale = TRUE)
> 
> ### noLD issues, unclear where they come from
> #max(abs(coef(fit1) - coef(m)[-(1:12)])) < 1e-1
> #max(abs(diag(vcov(m))[-(1:12)] - diag(vcov(fit1)))) < 1e-2
> 
> proc.time()
   user  system elapsed 
    7.0     0.7     7.7