Merge pull request #334 from Merck/333-simtrial-cran-release-043

LittleBeannie · web-flow · commit 7e656e3f0c5d · 2025-06-11T10:35:49.000-04:00
Cran release v1.0.0
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,11 +1,11 @@
 Package: simtrial
 Type: Package
 Title: Clinical Trial Simulation
-Version: 0.4.3
+Version: 1.0.0
 Authors@R: c(
     person("Keaven", "Anderson", email = "keaven_anderson@merck.com", role = c("aut")),
-    person("Yujie", "Zhao", email = "yujie.zhao@merck.com", role =  c("ctb","cre")),
-    person("John", "Blischak", role = c("ctb")),
+    person("Yujie", "Zhao", email = "yujie.zhao@merck.com", role =  c("aut","cre")),
+    person("John", "Blischak", role = c("aut")),
     person("Nan", "Xiao", role = c("ctb")),
     person("Yilong", "Zhang", role =  c("aut")),
     person("Jianxiao", "Yang", role = c("ctb")),
@@ -18,8 +18,8 @@ Authors@R: c(
     person("Heng", "Zhou", role = c("ctb")),
     person("Amin", "Shirazi", role = c("ctb")),
     person("Cole", "Manschot", role = c("ctb")),
-    person("Merck & Co., Inc., Rahway, NJ, USA and its affiliates", role = "cph",
-           comment = c(ROR = "02891sr49"))
+    person("Larry", "Leon", role = c("ctb")),
+    person("Merck & Co., Inc., Rahway, NJ, USA and its affiliates", role = "cph")
     )
 Description: Provides some basic routines for simulating a
     clinical trial. The primary intent is to provide some tools to
@@ -54,7 +54,7 @@ Suggests:
     dplyr,
     ggplot2,
     gsDesign,
-    gsDesign2 (>= 1.1.3.4),
+    gsDesign2 (>= 1.1.4),
     gt,
     knitr,
     rmarkdown,
@@ -63,8 +63,6 @@ Suggests:
     testthat (>= 3.0.0),
     tibble,
     tidyr
-Remotes:
-    Merck/gsDesign2
 LinkingTo:
     Rcpp
 Roxygen: list(markdown = TRUE)
diff --git a/LICENSE b/LICENSE
@@ -632,7 +632,7 @@ state the exclusion of warranty; and each file should have at least
 the "copyright" line and a pointer to where the full notice is found.
 
     simtrial: Clinical Trial Simulation
-    Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved.
+    Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved.
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
@@ -652,7 +652,7 @@ Also add information on how to contact you by electronic and paper mail.
   If the program does terminal interaction, make it output a short
 notice like this when it starts in an interactive mode:
 
-    simtrial  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved.
+    simtrial  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved.
     This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
     This is free software, and you are welcome to redistribute it
     under certain conditions; type `show c' for details.
diff --git a/NEWS.md b/NEWS.md
@@ -1,10 +1,28 @@
-# simtrial 0.4.2.9000
+# simtrial 1.0.0
+
+## Statistical improvements
+
+- Provide the updated boundary for objects generated by `sim_gs_n()` (#255, thanks to @LittleBeannie).
+- Users can now pass a formula to call the `wlr()` function (#280, thanks to @jdblischak).
+- `wlr()` is now a S3 class method for both `tte_data` class and `counting_process` class 
+(@276, #280, @281, thanks to @jdblischak)
+- The randomization ratio is output as attributes of `sim_pw_surv()` 
+(#279, #311 thanks to @LittleBeannie and @jdblischak).
+
+## Documentation
+
+- Add 3 vignettes introducing simulation of fixed or group sequential design 
+via a single function call of `sim_fixed_n()` and `sim_gs_n()` or from the ground up 
+(#302, #316, thanks to @LittleBeannie).
+- Add a vignette discussing the potential discrepancies between `simtrial` and `survdiff`
+(#308, thanks to @larry-leon).
+- Update parallel vignette to address `data.table` multithreading (#319, thanks to @jdblischak).
 
 ## Speed improvements
 
 - Optimize parallel simulation speed in `sim_fixed_n()` and `sim_gs_n()` by
   replacing `foreach(.combine = "rbind")` with manual data frame combination
-  (@nanxstats, #318).
+  (#318, thanks to @nanxstats).
 
 # simtrial 0.4.2
 
diff --git a/R/as_gt.R b/R/as_gt.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/check_args.R b/R/check_args.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/counting_process.R b/R/counting_process.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/cut_data_by_date.R b/R/cut_data_by_date.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/cut_data_by_event.R b/R/cut_data_by_event.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/early_zero_weight.R b/R/early_zero_weight.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/ex1_delayed_effect.R b/R/ex1_delayed_effect.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/ex2_delayed_effect.R b/R/ex2_delayed_effect.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/ex3_cure_with_ph.R b/R/ex3_cure_with_ph.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/ex4_belly.R b/R/ex4_belly.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/ex5_widening.R b/R/ex5_widening.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/ex6_crossing.R b/R/ex6_crossing.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/fh_weight.R b/R/fh_weight.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/fit_pwexp.R b/R/fit_pwexp.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/get_analysis_date.R b/R/get_analysis_date.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/get_cut_date_by_event.R b/R/get_cut_date_by_event.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/global.R b/R/global.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/input_checking.R b/R/input_checking.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/maxcombo.R b/R/maxcombo.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/mb_delayed_effect.R b/R/mb_delayed_effect.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/mb_weight.R b/R/mb_weight.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/milestone.R b/R/milestone.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/pvalue_maxcombo.R b/R/pvalue_maxcombo.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/randomize_by_fixed_block.R b/R/randomize_by_fixed_block.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/rmst.R b/R/rmst.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/rpwexp.R b/R/rpwexp.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/rpwexp_enroll.R b/R/rpwexp_enroll.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/rpwexp_naive.R b/R/rpwexp_naive.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/sim_fixed_n.R b/R/sim_fixed_n.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/sim_gs_n.R b/R/sim_gs_n.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/sim_pw_surv.R b/R/sim_pw_surv.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/simtrial-package.R b/R/simtrial-package.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the pkglite program.
diff --git a/R/summary.R b/R/summary.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/to_sim_pw_surv.R b/R/to_sim_pw_surv.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/wlr.R b/R/wlr.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/wlr_weight.R b/R/wlr_weight.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -21,7 +21,7 @@ footer:
     left: [developed_by, built_with, legal]
     right: [blank]
   components:
-    legal: "<br>Copyright &copy; 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved."
+    legal: "<br>Copyright &copy; 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved."
     blank: "<span></span>"
 
 reference:
diff --git a/man/simtrial-package.Rd b/man/simtrial-package.Rd
diff --git a/vignettes/sim_fixed_design_simple.Rmd b/vignettes/sim_fixed_design_simple.Rmd
@@ -88,7 +88,7 @@ The `timing_type` specifies one or more of the following cutoffs for setting the
 
 The `rho_gamma` argument is a data frame containing the variables `rho` and `gamma`, both of which should be greater than or equal to zero, to specify one Fleming-Harrington weighted log-rank test per row. 
 For instance, setting `rho = 0` and `gamma = 0` yields the standard unweighted log-rank test, while `rho = 0 and gamma = 0.5` provides the weighted Fleming-Harrington (0, 0.5) log-rank test. 
-If you are interested in tests other than the Fleming-Harrington weighted log-rank test, please refer to the vignette [Custom Fixed Design Simulations: A Tutorial on Writing Code from the Ground Up](https://merck.github.io/simtrial/articles/sim_fixed_design_custom.html).
+If you are interested in tests other than the Fleming-Harrington weighted log-rank test, please refer to the vignette at ["Articles"/"Simulate fixed/group sequential designs"/"Custom Fixed Design Simulations: A Tutorial on Writing Code from the Ground Up"](https://merck.github.io/simtrial/articles/sim_fixed_design_custom.html).
 
 ```{r, message=FALSE}
 sim_res <- sim_fixed_n(
diff --git a/vignettes/sim_gs_design_simple.Rmd b/vignettes/sim_gs_design_simple.Rmd
@@ -26,8 +26,6 @@ The `sim_gs_n()` function simulates group sequential designs with fixed sample s
 
 The process for simulating via `sim_gs_n()` is outlined in Steps 1 to 3 below.
 
-For those interested in more complicated simulations should refer to the vignette [Custom Group Sequential Design Simulations: Crafting from Scratch](https://merck.github.io/simtrial/articles/sim_gs_design_custom.html).
-
 # Step 1: Define design paramaters
 
 To run simulations for a group sequential design, several design characteristics are required. 

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-# Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.`
	`1`	`+# Copyright (c) 2025 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.`
`2`	`2`	`# All rights reserved.`
`3`	`3`	`#`
`4`	`4`	`# This file is part of the simtrial program.`