From 19a6683c688702b5ecb24c2880b361031985cfd8 Mon Sep 17 00:00:00 2001 From: John Blischak Date: Tue, 7 May 2024 10:12:06 -0400 Subject: [PATCH] sim_gs_n: move "method" and "parameter" to 2nd and 3rd columns --- R/sim_gs_n.R | 17 +++++---- tests/testthat/test-unvalidated-sim_gs_n.R | 40 +++++++++++----------- 2 files changed, 30 insertions(+), 27 deletions(-) diff --git a/R/sim_gs_n.R b/R/sim_gs_n.R index fc0efed1..c385836d 100644 --- a/R/sim_gs_n.R +++ b/R/sim_gs_n.R @@ -286,13 +286,16 @@ sim_gs_n <- function( # Test ans_1sim_new <- test[[i_analysis]](simu_data_cut, ...) - ans_1sim_new <- c( - sim_id = sim_id, - analysis = i_analysis, - cut_date = cut_date[i_analysis], - n = nrow(simu_data_cut), - event = sum(simu_data_cut$event), - ans_1sim_new + ans_1sim_new <- c(sim_id = sim_id, ans_1sim_new) + ans_1sim_new <- append( + x = ans_1sim_new, + values = c( + analysis = i_analysis, + cut_date = cut_date[i_analysis], + n = nrow(simu_data_cut), + event = sum(simu_data_cut$event) + ), + after = 3 ) ans_1sim_new <- convert_list_to_df_w_list_cols(ans_1sim_new) diff --git a/tests/testthat/test-unvalidated-sim_gs_n.R b/tests/testthat/test-unvalidated-sim_gs_n.R index fdf5522c..fc9abe8f 100644 --- a/tests/testthat/test-unvalidated-sim_gs_n.R +++ b/tests/testthat/test-unvalidated-sim_gs_n.R @@ -16,12 +16,12 @@ test_that("regular logrank test", { ) expected <- data.frame( sim_id = rep(1:3, each = 3L), + method = rep("WLR", 9L), + parameter = rep("FH(rho=0, gamma=0)", 9L), analysis = rep(1:3, 3), cut_date = c(24, 32, 45, 24, 32, 46.219327415802894, 24, 32, 50.86585486314699), n = rep(400L, 9L), event = c(229, 295, 355, 241, 290, 350, 226, 282, 350), - method = rep("WLR", 9L), - parameter = rep("FH(rho=0, gamma=0)", 9L), estimate = c( -28.194825408790173, -38.32580538077858, -39.49229553865729, -26.84871111584948, -32.548237296118835, -30.06631062297029, @@ -54,12 +54,12 @@ test_that("weighted logrank test by FH(0, 0.5)", { ) expected <- data.frame( sim_id = rep(1:3, each = 3L), + method = rep("WLR", 9L), + parameter = rep("FH(rho=0, gamma=0.5)", 9L), analysis = rep(1:3, 3), cut_date = c(24, 32, 45, 24, 32, 46.219327415802894, 24, 32, 50.86585486314699), n = rep(400L, 9L), event = c(229, 295, 355, 241, 290, 350, 226, 282, 350), - method = rep("WLR", 9L), - parameter = rep("FH(rho=0, gamma=0.5)", 9L), estimate = c( -16.934217242190208, -24.448179085866208, -25.51076208491462, -15.500239367897708, -19.967690764549445, -17.5390556887186, @@ -92,12 +92,12 @@ test_that("weighted logrank test by MB(3)", { ) expected <- data.frame( sim_id = rep(1:3, each = 3L), + method = rep("WLR", 9L), + parameter = rep("MB(delay = 3, max_weight = Inf)", 9L), analysis = rep(1:3, 3), cut_date = c(24, 32, 45, 24, 32, 46.219327415802894, 24, 32, 50.86585486314699), n = rep(400L, 9L), event = c(229, 295, 355, 241, 290, 350, 226, 282, 350), - method = rep("WLR", 9L), - parameter = rep("MB(delay = 3, max_weight = Inf)", 9L), estimate = c( -34.1924345680359, -46.745479781695614, -48.190848712798775, -32.192766832733724, -39.186116293163025, -36.14077883676622, @@ -130,12 +130,12 @@ test_that("weighted logrank test by early zero (6)", { ) expected <- data.frame( sim_id = rep(1:3, each = 3L), + method = rep("WLR", 9L), + parameter = rep("Xu 2017 with first 6 months of 0 weights", 9L), analysis = rep(1:3, 3), cut_date = c(24, 32, 45, 24, 32, 46.219327415802894, 24, 32, 50.86585486314699), n = rep(400L, 9L), event = c(229, 295, 355, 241, 290, 350, 226, 282, 350), - method = rep("WLR", 9L), - parameter = rep("Xu 2017 with first 6 months of 0 weights", 9L), estimate = c( -21.998993527998245, -32.129973499986654, -33.29646365786535, -17.199406900467533, -22.89893308073689, -20.417006407588342, @@ -168,12 +168,12 @@ test_that("RMST", { ) expected <- data.frame( sim_id = rep(1:3, each = 3L), + method = rep("RMST", 9L), + parameter = rep(20, 9L), analysis = rep(1:3, 3), cut_date = c(24, 32, 45, 24, 32, 46.219327415802894, 24, 32, 50.86585486314699), n = rep(400L, 9L), event = c(229, 295, 355, 241, 290, 350, 226, 282, 350), - method = rep("RMST", 9L), - parameter = rep(20, 9L), estimate = c( 2.8811516510432966, 2.8531309198097876, 2.834507997939104, 2.567389750892662, 2.3996923551365086, 2.36833514283823, 2.287497785439662, 2.4481174776559786, @@ -207,12 +207,12 @@ test_that("Milestone", { ) expected <- data.frame( sim_id = rep(1:3, each = 3L), + method = rep("milestone", 9L), + parameter = rep(10, 9L), analysis = rep(1:3, 3), cut_date = c(24, 32, 45, 24, 32, 46.219327415802894, 24, 32, 50.86585486314699), n = rep(400L, 9L), event = c(229, 295, 355, 241, 290, 350, 226, 282, 350), - method = rep("milestone", 9L), - parameter = rep(10, 9L), estimate = c( 0.16097092361893622, 0.1752731092436976, 0.1752731092436976, 0.12045851966961263, 0.11738941400903585, 0.11738941400903585, @@ -248,12 +248,12 @@ test_that("WLR with fh(0, 0.5) test at IA1, WLR with mb(6, Inf) at IA2, and mile ) expected <- data.frame( sim_id = rep(1:3, each = 3L), + method = rep(c("WLR", "WLR", "milestone"), 3), + parameter = rep(c("FH(rho=0, gamma=0.5)", "MB(delay = 6, max_weight = Inf)", "10"), 3), analysis = rep(1:3, 3), cut_date = c(24, 32, 45, 24, 32, 46.219327415802894, 24, 32, 50.86585486314699), n = rep(400L, 9L), event = c(229, 295, 355, 241, 290, 350, 226, 282, 350), - method = rep(c("WLR", "WLR", "milestone"), 3), - parameter = rep(c("FH(rho=0, gamma=0.5)", "MB(delay = 6, max_weight = Inf)", "10"), 3), estimate = c( -16.934217242190208, -55.13395025199291, 0.1752731092436976, -15.500239367897708, -44.437051762182506, 0.11738941400903585, @@ -287,12 +287,12 @@ test_that("MaxCombo (WLR-FH(0,0) + WLR-FH(0, 0.5))", { ) expected <- data.frame( sim_id = rep(1:3, each = 3L), + method = rep("MaxCombo", 9L), + parameter = rep("FH(0, 0) + FH(0, 0.5)", 9L), analysis = rep(1:3, 3), cut_date = c(24, 32, 45, 24, 32, 46.219327415802894, 24, 32, 50.86585486314699), n = rep(400L, 9L), event = c(229, 295, 355, 241, 290, 350, 226, 282, 350), - method = rep("MaxCombo", 9L), - parameter = rep("FH(0, 0) + FH(0, 0.5)", 9L), z = I(list( c(-3.7486049782713247, -4.149161171743935), c(-4.53034007934394, -4.778107819550277), @@ -329,12 +329,12 @@ test_that("sim_gs_n() accepts different tests per cutting", { ) expected <- data.frame( sim_id = rep(1:3, each = 3L), + method = rep("WLR", 9L), + parameter = rep(c("FH(rho=0, gamma=0)", "FH(rho=0, gamma=0.5)", "FH(rho=0.5, gamma=0)"), 3), analysis = rep(1:3, 3), cut_date = c(24, 32, 45, 24, 32, 46.219327415802894, 24, 32, 50.86585486314699), n = rep(400L, 9L), event = c(229, 295, 355, 241, 290, 350, 226, 282, 350), - method = rep("WLR", 9L), - parameter = rep(c("FH(rho=0, gamma=0)", "FH(rho=0, gamma=0.5)", "FH(rho=0.5, gamma=0)"), 3), estimate = c( -28.194825408790173, -24.448179085866208, -28.98456223760244, -26.84871111584948, -19.967690764549445, -23.830324019953483, @@ -390,12 +390,12 @@ test_that("sim_gs_n() can combine wlr(), rmst(), and milestone() tests", { ) expected <- data.frame( sim_id = rep(1:3, each = 3L), + method = rep(c("WLR", "RMST", "milestone"), 3), + parameter = rep(c("FH(rho=0, gamma=0)", "20", "10"), 3), analysis = rep(1:3, 3), cut_date = c(24, 32, 45, 24, 32, 46.219327415802894, 24, 32, 50.86585486314699), n = rep(400L, 9L), event = c(229, 295, 355, 241, 290, 350, 226, 282, 350), - method = rep(c("WLR", "RMST", "milestone"), 3), - parameter = rep(c("FH(rho=0, gamma=0)", "20", "10"), 3), estimate = c( -28.194825408790173, 2.8531309198097876, 0.1752731092436976, -26.84871111584948, 2.3996923551365086, 0.11738941400903585,