add set_seed

.gitignore

@@ -11,3 +11,4 @@ src/survivalmodels.so
 *.o
 
 *.so
+CRAN-RELEASE

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: survivalmodels
 Title: Models for Survival Analysis
-Version: 0.1.5
+Version: 0.1.6
 Authors@R: 
     person(given = "Raphael",
            family = "Sonabend",

NEWS.md

@@ -1,3 +1,7 @@
+# survivalmodels 0.1.6
+
+* Add `set_seed` for easier setting of seeds within R and Python environments
+
 # survivalmodels 0.1.5
 
 * Fixed bug in `risk` return type when `distr6 = FALSE`

R/helpers.R

@@ -10,3 +10,24 @@ setcollapse <- function(x) {
 requireNamespaces <- function(x) {
   all(vapply(x, requireNamespace, logical(1), quietly = TRUE))
 }
+
+#' @title Set seed in R numpy and torch
+#' @description To ensure consistent results, a seed has to be set in R
+#' using [set.seed] as usual but also in {numpy} and {torch} via {reticulate}.
+#' Therefore this function simplifies the process into one funciton.
+#' @param seed_R (`integer(1)`) `seed` passed to [set.seed].
+#' @param seed_np (`integer(1)`) `seed` passed to `numpy$random$seed`. Default is same as `seed_R`.
+#' @param seed_torch (`integer(1)`) `seed` passed to `numpy$random$seed`.
+#' Default is same as `seed_R`.
+set_seed <- function(seed_R, seed_np = seed_R, seed_torch = seed_R) {
+  set.seed(seed_R)
+  if (reticulate::py_module_available("numpy")) {
+    np <- reticulate::import("numpy")
+    np$random$seed(as.integer(seed_np))
+  }
+  if (reticulate::py_module_available("torch")) {
+    torch <- reticulate::import("torch")
+    torch$manual_seed(as.integer(seed_torch))
+  }
+  invisible(NULL)
+}

tests/testthat/test_helpers.R

@@ -21,3 +21,14 @@ test_that("clean_test_data", {
   expect_equal(clean_test_data(fit), fit$x)
   expect_error(clean_test_data(fit, rats[, 1:2]), "Names in")
 })
+
+test_that("set_seed", {
+  skip_if_no_pycox()
+  set_seed(1)
+  first <- deepsurv(Surv(time, status) ~ ., data = rats[1:50, ], verbose = FALSE,
+                          frac = 0.3)
+  set_seed(1)
+  second <- deepsurv(Surv(time, status) ~ ., data = rats[1:50, ], verbose = FALSE,
+                    frac = 0.3)
+  expect_equal(first, second)
+})