448: fix full test

R/simulate.R

@@ -453,7 +453,7 @@ SimJointDataResults <- function(
 
     return(
         .SimJointData(
-            survival = os_dat |> dplyr::rename(all_of(original_names)),
+            survival = os_dat |> dplyr::rename(dplyr::all_of(original_names)),
             longitudinal = lm_dat2[, c(
                 "subject",
                 "arm",
@@ -462,7 +462,7 @@ SimJointDataResults <- function(
                 "sld",
                 "observed"
             )] |>
-                dplyr::rename(all_of(original_names))
+                dplyr::rename(dplyr::all_of(original_names))
         )
     )
 }

tests/testthat/helper-setup.R

@@ -9,6 +9,14 @@ is_full_test <- function() {
     toupper(Sys.getenv("JMPOST_FULL_TEST")) == "TRUE"
 }
 
+activate_full_test <- function() {
+    Sys.setenv(JMPOST_FULL_TEST = "TRUE")
+}
+
+disable_full_test <- function() {
+    Sys.setenv(JMPOST_FULL_TEST = "FALSE")
+}
+
 is_graph_snapshot_enabled <- function() {
     toupper(Sys.getenv("JMPOST_GRAPH_SNAPSHOT")) == "TRUE"
 }

tests/testthat/test-LongitudinalGSF.R

@@ -487,7 +487,8 @@ test_that("Can recover known distributional parameters from unscaled variance GS
                 iter_sampling = 800,
                 chains = 2,
                 refresh = 200,
-                parallel_chains = 2
+                parallel_chains = 2,
+                seed = 123
             )
         })
     })

tests/testthat/test-SurvivalExponential.R

@@ -31,7 +31,10 @@ test_that("SurvivalExponential can recover true parameter (including covariates)
             beta_cat = c("A" = 0, "B" = true_beta[1], "C" = true_beta[2]),
             beta_cont = true_beta[3],
         ),
-        longitudinal = SimLongitudinalRandomSlope(slope_mu = 0)
+        longitudinal = SimLongitudinalRandomSlope(
+            slope_mu = 0,
+            slope_sigma = 0.5
+        )
     )
 
     dat_os <- jdat@survival
@@ -59,7 +62,8 @@ test_that("SurvivalExponential can recover true parameter (including covariates)
             iter_warmup = 500,
             chains = 1,
             refresh = 0,
-            parallel_chains = 1
+            parallel_chains = 1,
+            seed = 123
         )
     })
 

tests/testthat/test-SurvivalGamma.R

@@ -59,7 +59,10 @@ test_that("SurvivalGamma can recover known values", {
             beta_cat = c("A" = 0, "B" = true_beta[1], "C" = true_beta[2]),
             beta_cont = true_beta[3],
         ),
-        longitudinal = SimLongitudinalRandomSlope(slope_mu = 0),
+        longitudinal = SimLongitudinalRandomSlope(
+            slope_mu = 0,
+            slope_sigma = 0.5
+        ),
         .silent = TRUE
     )
 
@@ -94,7 +97,8 @@ test_that("SurvivalGamma can recover known values", {
                 iter_sampling = 400,
                 chains = 2,
                 refresh = 100,
-                parallel_chains = 2
+                parallel_chains = 2,
+                seed = 123
             )
         })
     })

tests/testthat/test-SurvivalLoglogistic.R

@@ -43,7 +43,10 @@ test_that("SurvivalLogLogistic can recover known values", {
             beta_cat = c("A" = 0, "B" = true_beta[1], "C" = true_beta[2]),
             beta_cont = true_beta[3],
         ),
-        longitudinal = SimLongitudinalRandomSlope(slope_mu = 0),
+        longitudinal = SimLongitudinalRandomSlope(
+            slope_mu = 0,
+            slope_sigma = 0.5
+        ),
         .silent = TRUE
     )
 
@@ -77,7 +80,8 @@ test_that("SurvivalLogLogistic can recover known values", {
             iter_sampling = 450,
             chains = 1,
             refresh = 0,
-            parallel_chains = 1
+            parallel_chains = 1,
+            seed = 123
         )
     })
 

tests/testthat/test-SurvivalWeibullPH.R

@@ -50,7 +50,10 @@ test_that("SurvivalWeibullPH can recover known values", {
             beta_cat = c("A" = 0, "B" = true_beta[1], "C" = true_beta[2]),
             beta_cont = true_beta[3],
         ),
-        longitudinal = SimLongitudinalRandomSlope(slope_mu = 0),
+        longitudinal = SimLongitudinalRandomSlope(
+            slope_mu = 0,
+            slope_sigma = 0.5
+        ),
         .silent = TRUE
     )
 
@@ -84,7 +87,8 @@ test_that("SurvivalWeibullPH can recover known values", {
             iter_sampling = 400,
             chains = 1,
             refresh = 0,
-            parallel_chains = 1
+            parallel_chains = 1,
+            seed = 123
         )
     })
 

tests/testthat/test-simulate.R

@@ -160,9 +160,9 @@ test_that("simulate works with lambda_censor", {
     )
 
     joined <- dplyr::left_join(
-        results@survival[, c("subject", "time", "event")],
-        results@longitudinal[, c("subject", "time", "observed")],
-        by = "subject"
+        results@survival[, c("id", "time", "event")],
+        results@longitudinal[, c("id", "time", "observed")],
+        by = "id"
     )
 
     expect_true(all(!joined$observed[joined$time.y > joined$time.x]))