survival 3.7-0 breaks censored

[hfrick]

The new version of survival allows for infinite evaluation time points in the summary method for survfit objects instead of omitting them. It also now preserves the order of the time points.

censored captured those time points (and their order) and returned survival probabilities 1 and 0 for eval times of -Inf and Inf, respectively. We can depend on the new version of survival and remove our own handling of these cases.

With survival 3.7-0

library(survival)
library(glmnet)
#> Loading required package: Matrix
#> Loaded glmnet 4.1-8

pred_time <- c(1022, -Inf, 0, Inf, 1022, -Inf)

# for coxph
lung_pred <- tidyr::drop_na(lung)
mod <- coxph(Surv(time, status) ~ ., data = lung)
surv_fit <- survfit(mod, newdata = lung_pred[1:2, ])
summary(surv_fit, times = pred_time, extend = TRUE)
#> Call: survfit(formula = mod, newdata = lung_pred[1:2, ])
#> 
#>  time n.risk n.event survival1 survival2
#>  1022      1       0     0.117   0.00158
#>  -Inf    167       0     1.000   1.00000
#>     0    167       0     1.000   1.00000
#>   Inf      0       0     0.117   0.00158
#>  1022      1       0     0.117   0.00158
#>  -Inf    167       0     1.000   1.00000

# for general survfit
lung2 <- lung[-14, ]
lung_x <- as.matrix(lung2[, c("age", "ph.ecog")])
lung_y <- Surv(lung2$time, lung2$status)
lung_pred <- lung_x[1:2, ]

mod <- suppressWarnings(
  glmnet::glmnet(x = lung_x, y = lung_y, family = "cox")
)
surv_fit <- survfit(mod, newx = lung_pred, s = 0.1, x = lung_x, y = lung_y)
summary(surv_fit, times = pred_time, extend = TRUE)
#> Call: survfit.coxnet(formula = mod, s = 0.1, newx = lung_pred, x = lung_x, 
#>     y = lung_y)
#> 
#>  time n.risk n.event survival1 survival2
#>  1022      1       0    0.0476    0.0969
#>  -Inf    227       0    1.0000    1.0000
#>     0    227       0    1.0000    1.0000
#>   Inf      0       0    0.0476    0.0969
#>  1022      1       0    0.0476    0.0969
#>  -Inf    227       0    1.0000    1.0000

^{Created on 2024-06-09 with reprex v2.1.0}

With survival 3.6-4

library(survival)
library(glmnet)
#> Loading required package: Matrix
#> Loaded glmnet 4.1-8

pred_time <- c(1022, -Inf, 0, Inf, 1022, -Inf)

# for coxph
lung_pred <- tidyr::drop_na(lung)
mod <- coxph(Surv(time, status) ~ ., data = lung)
surv_fit <- survfit(mod, newdata = lung_pred[1:2, ])
summary(surv_fit, times = pred_time, extend = TRUE)
#> Call: survfit(formula = mod, newdata = lung_pred[1:2, ])
#> 
#>  time n.risk n.event survival1 survival2
#>     0    167       0     1.000   1.00000
#>  1022      1     120     0.117   0.00158
#>  1022      1       0     0.117   0.00158

# for general survfit
lung2 <- lung[-14, ]
lung_x <- as.matrix(lung2[, c("age", "ph.ecog")])
lung_y <- Surv(lung2$time, lung2$status)
lung_pred <- lung_x[1:2, ]

mod <- suppressWarnings(
  glmnet::glmnet(x = lung_x, y = lung_y, family = "cox")
)
surv_fit <- survfit(mod, newx = lung_pred, s = 0.1, x = lung_x, y = lung_y)
summary(surv_fit, times = pred_time, extend = TRUE)
#> Call: survfit.coxnet(formula = mod, s = 0.1, newx = lung_pred, x = lung_x, 
#>     y = lung_y)
#> 
#>  time n.risk n.event survival1 survival2
#>     0    227       0    1.0000    1.0000
#>  1022      1     164    0.0476    0.0969
#>  1022      1       0    0.0476    0.0969

^{Created on 2024-06-09 with reprex v2.1.0}

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