Merge pull request #201 from jdblischak/function-factory

Use function factory pattern to pass cutting functions to `sim_gs_n()`
Merck · Feb 23, 2024 · caadb3e · caadb3e
2 parents f9d7581 + b302c3e
commit caadb3e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: simtrial
 Type: Package
 Title: Clinical Trial Simulation
-Version: 0.3.2.4
+Version: 0.3.2.7
 Authors@R: c(
     person("Keaven", "Anderson", email = "[email protected]", role = c("aut")),
     person("Yilong", "Zhang", email = "[email protected]", role =  c("aut")),
@@ -44,7 +44,6 @@ Imports:
     future,
     methods,
     mvtnorm,
-    rlang,
     stats,
     survival,
     utils

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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved.
+    Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved.
+    simtrial  Copyright (c) 2024 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/NAMESPACE b/NAMESPACE
@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(counting_process)
+export(create_cutting)
 export(cut_data_by_date)
 export(cut_data_by_event)
 export(early_zero)

diff --git a/R/counting_process.R b/R/counting_process.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
@@ -18,38 +18,37 @@
 
 #' Maxcombo test
 #'
+#' WARNING: This experimental function is a work-in-progress. The function
+#' arguments will change as we add additional features.
+#'
 #' @param data a tte dataset
-#' @param test1 maxcombo test1
-#' @param test2 maxcombo test2
-#' @param ... additional tests
+#' @param rho Numeric vector passed to \code{\link{fh_weight}}. Must be greater
+#'   than or equal to zero. Must be the same length as \code{gamma}.
+#' @param gamma Numeric vector passed to \code{\link{fh_weight}}. Must be
+#'   greater than or equal to zero. Must be the same length as \code{rho}.
 #'
 #' @return pvalues
 #' @export
 #'
+#' @seealso \code{\link{fh_weight}}
+#'
 #' @examples
 #' sim_pw_surv(n = 200) |>
 #'   cut_data_by_event(150) |>
-#'   maxcombo(test1 = wlr(data, rho = 0, gamma = 0) |> quote(),
-#'            test2 = wlr(data, rho = 0, gamma = 0.5) |> quote())
-maxcombo <- function(data, test1, test2, ...){
-  all_args <- match.call(expand.dots = FALSE)
-  args <- all_args[-1]  # Exclude the first element (function name)
-
-  n_test <- length(args) - 1
-  rho_vector <- NULL
-  gamma_vector <- NULL
-
-  for (i in 1:n_test) {
-    test_i <- get(paste0("test", i))
-    rho_vector <- c(rho_vector, test_i$rho)
-    gamma_vector <- c(gamma_vector, test_i$gamma)
-  }
+#'   maxcombo(rho = c(0, 0), gamma = c(0, 0.5))
+maxcombo <- function(data, rho, gamma){
+  stopifnot(
+    is.numeric(rho), is.numeric(gamma),
+    rho >= 0, gamma >= 0,
+    length(rho) == length(gamma)
+  )
 
   ans <- data |>
     counting_process(arm = "experimental") |>
     fh_weight(
-      rho_gamma = data.frame(rho = rho_vector, gamma = gamma_vector),
-      return_corr = TRUE)
+      rho_gamma = data.frame(rho = rho, gamma = gamma),
+      return_corr = TRUE
+    )
 
   ans <-  data.frame(p_value = pvalue_maxcombo(ans))
 

diff --git a/R/mb_delayed_effect.R b/R/mb_delayed_effect.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 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) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.