Merge 5b62356 into e6fd6ff

R/brier_score.R

@@ -105,7 +105,7 @@ reverse_km_cen_first <- function(t, times, events) {
         survival::Surv(times, cen_events) ~ 1,
         data = dat
     )
-    preds <- summary(mod, times = t, extend = TRUE)$surv
+    preds <- summary(mod, times = t[order(t)], extend = TRUE)$surv
 
     assert_that(
         length(preds) == length(t)

tests/testthat/test-survival_plot.R

@@ -1,4 +1,10 @@
 
+## Code to re-run this from commandline
+# JMPOST_GRAPH_SNAPSHOT=TRUE \
+# NOT_CRAN=TRUE \
+# Rscript -e "devtools::load_all(); testthat::test_file('tests/testthat/test-survival_plot.R')"
+
+snap_dir <- file.path(testthat::test_path(), "_snaps", "survival_plot")
 
 test_that("survival_plot works as expected", {
 
@@ -55,54 +61,62 @@ test_that("survival_plot works as expected", {
         get_data(3, "C")
     )
 
-    p1 <- survival_plot(
-        res,
-        add_ci = TRUE,
-        add_wrap = TRUE,
-        kmdf = NULL,
-        y_label = expression(frac(1, 2) + S(t^2)),
-        x_label = expression(thd[3])
-    )
+    testthat::expect_no_error({
+        p1 <- survival_plot(
+            res,
+            add_ci = TRUE,
+            add_wrap = TRUE,
+            kmdf = NULL,
+            y_label = expression(frac(1, 2) + S(t^2)),
+            x_label = expression(thd[3])
+        )
+    })
 
+
+    announce_snapshot_file(file.path(snap_dir, "wrap-ci.svg"))
     if (is_graph_snapshot_enabled()) {
         vdiffr::expect_doppelganger(
-            "survival_plot with wrap and ci",
+            "wrap-ci",
             p1
         )
     }
 
+    testthat::expect_no_error({
+        p2 <- survival_plot(
+            res,
+            add_ci = FALSE,
+            add_wrap = FALSE,
+            kmdf = NULL,
+            y_label = expression(frac(1, 2) + S(t^2)),
+            x_label = expression(thd[3])
+        )
+    })
 
-    p2 <- survival_plot(
-        res,
-        add_ci = FALSE,
-        add_wrap = FALSE,
-        kmdf = NULL,
-        y_label = expression(frac(1, 2) + S(t^2)),
-        x_label = expression(thd[3])
-    )
-
+    announce_snapshot_file(file.path(snap_dir, "nowrap-noci.svg"))
     if (is_graph_snapshot_enabled()) {
         vdiffr::expect_doppelganger(
-            "survival_plot with no wrap and no ci",
+            "nowrap-noci",
             p2
         )
     }
 
-
-    p3 <- survival_plot(
-        res,
-        add_ci = FALSE,
-        add_wrap = FALSE,
-        kmdf = dat,
-        y_label = expression(frac(1, 2) + S(t^2)),
-        x_label = expression(thd[3])
-    ) +
-        theme(legend.position = "bottom") +
-        scale_y_continuous(trans = "sqrt")
-
+    testthat::expect_no_error({
+        p3 <- survival_plot(
+            res,
+            add_ci = FALSE,
+            add_wrap = FALSE,
+            kmdf = dat,
+            y_label = expression(frac(1, 2) + S(t^2)),
+            x_label = expression(thd[3])
+        ) +
+            theme(legend.position = "bottom") +
+            scale_y_continuous(trans = "sqrt")
+    })
+
+    announce_snapshot_file(file.path(snap_dir, "nowrap-noci-km-ggplot2.svg"))
     if (is_graph_snapshot_enabled()) {
         vdiffr::expect_doppelganger(
-            "survival_plot-no wrap + no ci + km + ggplot2 ",
+            "nowrap-noci-km-ggplot2",
             p3
         )
     }