survalis 1.3.0 introduced a seven-verb interface. It keeps every prior function working – nothing you have written breaks. The granular helpers are now marked internal in the manual and print a one-time note per session; they are scheduled to become unexported in a future release. This vignette shows the recommended replacements.
| Granular (still works) | Verb interface (recommended) |
|---|---|
fit_ranger(f, data, num.trees = 500) |
fit(f, data, "ranger", spec = list(num.trees = 500)) |
predict_ranger(m, nd, times) |
predict(m, nd, times) |
predict_*() then survmat_to_rmst() |
predict(m, nd, times, type = "rmst", tau = ...) |
predict_*() then
survmat_to_quantile() |
predict(m, nd, times, type = "median") /
type = "quantile" |
cv_survlearner(f, data, fit_ranger, predict_ranger, times, folds = 5) |
evaluate(f, data, "ranger", times = ..., resampling = cv(5)) |
score_survmodel(m, times, metrics) |
evaluate(m, times = ..., resampling = cv()) |
tune_ranger(f, data, times, param_grid, refit_best = TRUE) |
tune(f, data, "ranger", grid = param_grid, times = ...) |
benchmark(f, data, learners, times) |
compare(f, data, models = learners, times = ...) |
best_survlearner(bench, metric) |
print() a survalis_compare (best is
flagged) |
compute_pdp(m, data, "karno", times) |
interpret(m, "pdp", feature = "karno", times = ...) |
compute_shap(m, nd, data, times) |
interpret(m, "shap", newdata = nd, times = ...) |
compute_varimp(m, times) |
interpret(m, "varimp", times = ...) |
plot_pdp(res, "karno") |
plot() a survalis_interpret |
estimate_rmst(m, data, tau, times, trt_col = "trt") |
estimate(f, data, "<model>", treatment = "trt", tau = ...) |
library(survalis)
f <- Surv(time, status) ~ age + karno + celltype
# 1.x
m1 <- fit_ranger(f, veteran, num.trees = 200)
p1 <- predict_ranger(m1, veteran[1:3, ], times = c(90, 180))
# 2.0
m2 <- fit(f, veteran, "ranger", spec = list(num.trees = 200), seed = 1)
p2 <- predict(m2, veteran[1:3, ], times = c(90, 180))
round(as.matrix(p2), 3)
#> t=90 t=180
#> [1,] 0.404 0.269
#> [2,] 0.857 0.484
#> [3,] 0.649 0.435predict() always returns a
survmat for the curve types: an
n x length(times) matrix with the grid in
attr(x, "times"). The "t=<time>" column
names are still there, so the *_survmat() metric helpers
keep accepting it.times is optional. When omitted,
default_times() builds a grid over the observed event times
and records it on the result (res$times), so a run is
reproducible.evaluate() / compare() take a
resampling object (cv(), holdout(),
group_cv(), bootstrap()) instead of a bare
folds integer, and compare() evaluates every
model on the same folds.fit() engine arguments go in
spec, not ....