Last updated on 2024-05-25 04:57:03 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1-8 | 13.86 | 302.47 | 316.33 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.1-8 | 8.95 | 239.86 | 248.81 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1-8 | 405.46 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1-8 | 391.14 | OK | |||
| r-devel-windows-x86_64 | 1.1-8 | 11.00 | 268.00 | 279.00 | OK | |
| r-patched-linux-x86_64 | 1.1-8 | 8.02 | 298.61 | 306.63 | OK | |
| r-release-linux-x86_64 | 1.1-8 | 7.67 | 291.41 | 299.08 | OK | |
| r-release-macos-arm64 | 1.1-8 | 151.00 | OK | |||
| r-release-macos-x86_64 | 1.1-8 | 336.00 | OK | |||
| r-release-windows-x86_64 | 1.1-8 | 11.00 | 266.00 | 277.00 | OK | |
| r-oldrel-macos-arm64 | 1.1-8 | 156.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.1-8 | 346.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.1-8 | 15.00 | 338.00 | 353.00 | OK |
Version: 1.1-8
Check: tests
Result: ERROR
Running ‘AFT-Ex.R’ [5s/8s]
Comparing ‘AFT-Ex.Rout’ to ‘AFT-Ex.Rout.save’ ... OK
Running ‘GBSG2.R’ [3s/5s]
Running ‘KM-Ex.R’ [3s/5s]
Comparing ‘KM-Ex.Rout’ to ‘KM-Ex.Rout.save’ ... OK
Running ‘faithful.R’ [7s/8s]
Comparing ‘faithful.Rout’ to ‘faithful.Rout.save’ ... OK
Running ‘orm-Ex.R’ [16s/23s]
Comparing ‘orm-Ex.Rout’ to ‘orm-Ex.Rout.save’ ... OK
Running ‘timedep_covar.R’ [11s/16s]
Running ‘truncreg-Ex.R’ [4s/5s]
Comparing ‘truncreg-Ex.Rout’ to ‘truncreg-Ex.Rout.save’ ... OK
Running the tests in ‘tests/timedep_covar.R’ failed.
Complete output:
>
> 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)
Error in optim(par = par, fn = fun, gr = gradient, control = control.optim, :
non-finite value supplied by optim
Error in ret$convergence : $ operator is invalid for atomic vectors
Error in ret$par : $ operator is invalid for atomic vectors
Calls: mlt -> do.call -> .mlt_fit -> <Anonymous>
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang