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inst/doc/validation.R
In ph2rand: Randomized Phase II Oncology Trials with Bernoulli Outcomes
## ----setup, include = FALSE, cache = TRUE-------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
## ----ph2rand, echo = FALSE, cache = TRUE--------------------------------------
suppressPackageStartupMessages(library(ph2rand))
## ----default, cache = TRUE----------------------------------------------------
des_jung <- des_two_stage()
## ----opchar, cache = TRUE-----------------------------------------------------
des_jung$opchar
## ----sim, cache = TRUE--------------------------------------------------------
sim_jung <- sim(des_jung, replicates = 1e5)
sim_jung$sim
## ----table_I, eval = FALSE, cache = TRUE--------------------------------------
# fact <- rep(seq(0.1, 0.75, 0.05), each = 2)
# p0p1 <- rbind(c(0.05, 0.15),
# c(0.05, 0.20),
# c(0.05, 0.25),
# cbind(fact, fact + rep(c(0.15, 0.2), 14)),
# c(0.80, 0.95),
# c(0.85, 0.95))
# # Table I
# table_I <- cbind(p0p1, matrix(0, nrow(p0p1), 11))
# colnames(table_I) <- c("p0", "p1", "Single-stage design: (n,a)",
# "Single-stage design: alpha",
# "Single-stage design: 1-beta",
# "Minimax design: (n,n1,a1,a)", "Minimax design: alpha",
# "Minimax design: 1-beta", "Minimax design: EN",
# "Optimal design: (n,n1,a1,a)", "Optimal design: alpha",
# "Optimal design: 1-beta", "Optimal design: EN")
# table_I <- tibble::as_tibble(table_I)
# for (i in 1:nrow(p0p1)) {
# des_i <- des_one_stage(alpha = 0.15,
# beta = 0.2,
# delta = table_I$p1[i] - table_I$p0[i],
# Pi0 = table_I$p0[i],
# Pi1 = table_I$p0[i],
# nCmax = 100L)
# table_I$`Single-stage design: (n,a)`[i] <- paste0("(", des_i$nC, ",",
# des_i$boundaries$e1, ")")
# table_I$`Single-stage design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_I$`Single-stage design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# message("..Table I single-stage design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(50, 22, 16, 38, 24, 46, 32, 57, 33, 67, 39, 70, 41,
# 78, 42, 78, 45, 78, 46, 78, 45, 77, 43, 76, 40, 68,
# 38, 63, 33, 52, 29, 42, 76)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# delta = table_I$p1[i] - table_I$p0[i],
# Pi0 = table_I$p0[i],
# Pi1 = table_I$p0[i],
# equal = FALSE,
# w = c(1e-6, 0, 0, 0, 1),
# nCmax = nCmax[i])
# table_I$`Minimax design: (n,n1,a1,a)`[i] <-
# paste0("(", sum(des_i$nC), ",", des_i$nC[1], ",",
# des_i$boundaries$f1 + 1, ",", des_i$boundaries$e2, ")")
# table_I$`Minimax design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_I$`Minimax design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_I$`Minimax design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table I minimax design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(57, 27, 22, 56, 28, 51, 32, 66, 39, 78, 43, 77, 46,
# 95, 50, 90, 49, 90, 49, 90, 53, 90, 48, 89, 45, 75,
# 44, 73, 36, 60, 33, 46, 89)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# delta = table_I$p1[i] - table_I$p0[i],
# Pi0 = table_I$p0[i],
# Pi1 = table_I$p0[i],
# equal = FALSE,
# w = c(1, 0, 0, 0, 0),
# nCmax = nCmax[i])
# table_I$`Optimal design: (n,n1,a1,a)`[i] <-
# paste0("(", sum(des_i$nC), ",", des_i$nC[1], ",",
# des_i$boundaries$f1 + 1, ",", des_i$boundaries$e2, ")")
# table_I$`Optimal design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_I$`Optimal design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_I$`Optimal design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table I optimal design ", i, " completed..")
# }
## ----other_tables, eval = FALSE, cache = TRUE---------------------------------
# table_II <- cbind(p0p1, matrix(0, nrow(p0p1), 11))
# colnames(table_II) <- c("p0", "p1", "Single-stage design: (n,a)",
# "Single-stage design: alpha",
# "Single-stage design: 1-beta",
# "Minimax design: (n,n1,a1,a)", "Minimax design: alpha",
# "Minimax design: 1-beta", "Minimax design: EN",
# "Optimal design: (n,n1,a1,a)", "Optimal design: alpha",
# "Optimal design: 1-beta", "Optimal design: EN")
# table_II <- tibble::as_tibble(table_II)
# for (i in 1:nrow(p0p1)) {
# des_i <- des_one_stage(alpha = 0.15,
# beta = 0.15,
# delta = table_II$p1[i] - table_II$p0[i],
# Pi0 = table_II$p0[i],
# Pi1 = table_II$p0[i],
# nCmax = 100L)
# table_II$`Single-stage design: (n,a)`[i] <- paste0("(", des_i$nC, ",",
# des_i$boundaries$e1, ")")
# table_II$`Single-stage design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_II$`Single-stage design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# message("..Table II single-stage design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(58, 34, 19, 49, 28, 62, 36, 74, 43, 78, 46, 87, 50,
# 91, 54, 98, 54, 98, 54, 98, 54, 96, 53, 88, 51, 83,
# 44, 73, 41, 67, 32, 53, 95)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.15,
# beta = 0.15,
# delta = table_II$p1[i] - table_II$p0[i],
# Pi0 = table_II$p0[i],
# Pi1 = table_II$p0[i],
# equal = FALSE,
# w = c(1e-6, 0, 0, 0, 1),
# nCmax = nCmax[i])
# table_II$`Minimax design: (n,n1,a1,a)`[i] <-
# paste0("(", sum(des_i$nC), ",", des_i$nC[1], ",",
# des_i$boundaries$f1 + 1, ",", des_i$boundaries$e2, ")")
# table_II$`Minimax design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_II$`Minimax design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_II$`Minimax design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table II minimax design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(69, 34, 22, 59, 32, 73, 44, 89, 45, 87, 52, 98, 55,
# 103, 63, 112, 61, 109, 63, 100, 60, 107, 60, 99, 55,
# 94, 49, 82, 47, 69, 37, 60, 103)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.15,
# beta = 0.15,
# delta = table_II$p1[i] - table_II$p0[i],
# Pi0 = table_II$p0[i],
# Pi1 = table_II$p0[i],
# equal = FALSE,
# w = c(1, 0, 0, 0, 0),
# nCmax = nCmax[i])
# table_II$`Optimal design: (n,n1,a1,a)`[i] <-
# paste0("(", sum(des_i$nC), ",", des_i$nC[1], ",",
# des_i$boundaries$f1 + 1, ",", des_i$boundaries$e2, ")")
# table_II$`Optimal design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_II$`Optimal design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_II$`Optimal design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table II optimal design ", i, " completed..")
# }
# # Table III
# table_III <- cbind(p0p1, matrix(0, nrow(p0p1), 11))
# colnames(table_III) <- c("p0", "p1", "Single-stage design: (n,a)",
# "Single-stage design: alpha",
# "Single-stage design: 1-beta",
# "Minimax design: (n,n1,a1,a)", "Minimax design: alpha",
# "Minimax design: 1-beta", "Minimax design: EN",
# "Optimal design: (n,n1,a1,a)", "Optimal design: alpha",
# "Optimal design: 1-beta", "Optimal design: EN")
# table_III <- tibble::as_tibble(table_III)
# for (i in 1:nrow(p0p1)) {
# des_i <- des_one_stage(alpha = 0.2,
# beta = 0.2,
# delta = table_III$p1[i] - table_III$p0[i],
# Pi0 = table_III$p0[i],
# Pi1 = table_III$p0[i],
# nCmax = 100L)
# table_III$`Single-stage design: (n,a)`[i] <- paste0("(", des_i$nC, ",",
# des_i$boundaries$e1, ")")
# table_III$`Single-stage design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_III$`Single-stage design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# message("..Table III single-stage design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(41, 22, 16, 34, 17, 41, 25, 48, 27, 53, 32, 60, 35,
# 60, 35, 62, 35, 64, 35, 64, 35, 61, 34, 58, 33, 57,
# 32, 49, 26, 43, 23, 33, 63)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.2,
# beta = 0.2,
# delta = table_III$p1[i] -
# table_III$p0[i],
# Pi0 = table_III$p0[i],
# Pi1 = table_III$p0[i],
# equal = FALSE,
# w = c(1e-6, 0, 0, 0, 1),
# nCmax = nCmax[i])
# table_III$`Minimax design: (n,n1,a1,a)`[i] <-
# paste0("(", sum(des_i$nC), ",", des_i$nC[1], ",",
# des_i$boundaries$f1 + 1, ",", des_i$boundaries$e2, ")")
# table_III$`Minimax design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_III$`Minimax design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_III$`Minimax design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table III minimax design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(42, 27, 18, 35, 18, 42, 28, 53, 29, 56, 35, 68, 41,
# 67, 38, 69, 39, 69, 38, 67, 38, 66, 37, 63, 36, 69,
# 38, 51, 28, 47, 24, 34, 69)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.2,
# beta = 0.2,
# delta = table_III$p1[i] -
# table_III$p0[i],
# Pi0 = table_III$p0[i],
# Pi1 = table_III$p0[i],
# equal = FALSE,
# w = c(1, 0, 0, 0, 0),
# nCmax = nCmax[i])
# table_III$`Optimal design: (n,n1,a1,a)`[i] <-
# paste0("(", sum(des_i$nC), ",", des_i$nC[1], ",",
# des_i$boundaries$f1 + 1, ",", des_i$boundaries$e2, ")")
# table_III$`Optimal design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_III$`Optimal design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_III$`Optimal design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table III ptimal design ", i, " completed..")
# }
# # Table IV
# table_IV <- cbind(p0p1, matrix(0, nrow(p0p1), 11))
# colnames(table_IV) <- c("p0", "p1", "Single-stage design: (n,a)",
# "Single-stage design: alpha",
# "Single-stage design: 1-beta",
# "Minimax design: (n,n1,a1,a)", "Minimax design: alpha",
# "Minimax design: 1-beta", "Minimax design: EN",
# "Optimal design: (n,n1,a1,a)", "Optimal design: alpha",
# "Optimal design: 1-beta", "Optimal design: EN")
# table_IV <- tibble::as_tibble(table_IV)
# for (i in 1:nrow(p0p1)) {
# des_i <- des_one_stage(alpha = 0.2,
# beta = 0.15,
# delta = table_IV$p1[i] - table_IV$p0[i],
# Pi0 = table_IV$p0[i],
# Pi1 = table_IV$p0[i],
# nCmax = 100L)
# table_IV$`Single-stage design: (n,a)`[i] <- paste0("(", des_i$nC, ",",
# des_i$boundaries$e1, ")")
# table_IV$`Single-stage design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_IV$`Single-stage design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# message("..Table IV single-stage design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(58, 26, 19, 40, 27, 53, 30, 58, 36, 67, 39, 70, 40,
# 78, 43, 80, 47, 80, 47, 80, 47, 78, 44, 75, 39, 66,
# 36, 62, 34, 50, 26, 42, 73)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.2,
# beta = 0.15,
# delta = table_IV$p1[i] - table_IV$p0[i],
# Pi0 = table_IV$p0[i],
# Pi1 = table_IV$p0[i],
# equal = FALSE,
# w = c(1e-6, 0, 0, 0, 1),
# nCmax = nCmax[i])
# table_IV$`Minimax design: (n,n1,a1,a)`[i] <-
# paste0("(", sum(des_i$nC), ",", des_i$nC[1], ",",
# des_i$boundaries$f1 + 1, ",", des_i$boundaries$e2, ")")
# table_IV$`Minimax design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_IV$`Minimax design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_IV$`Minimax design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table IV minimax design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(70, 27, 22, 43, 27, 59, 32, 61, 40, 74, 43, 78, 45,
# 85, 45, 90, 49, 94, 53, 94, 50, 85, 45, 77, 41, 71,
# 39, 69, 42, 54, 27, 46, 79)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.2,
# beta = 0.15,
# delta = table_IV$p1[i] - table_IV$p0[i],
# Pi0 = table_IV$p0[i],
# Pi1 = table_IV$p0[i],
# equal = FALSE,
# w = c(1, 0, 0, 0, 0),
# nCmax = nCmax[i])
# table_IV$`Optimal design: (n,n1,a1,a)`[i] <-
# paste0("(", sum(des_i$nC), ",", des_i$nC[1], ",",
# des_i$boundaries$f1 + 1, ",", des_i$boundaries$e2, ")")
# table_IV$`Optimal design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_IV$`Optimal design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_IV$`Optimal design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table IV optimal design ", i, " completed..")
# }
## ----examples, eval = FALSE, cache = TRUE-------------------------------------
# # Example 1
# single_stage <- des_one_stage(alpha = 0.15,
# beta = 0.2,
# Pi0 = 0.7,
# Pi1 = 0.7,
# delta = 0.15)
# minimax <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# Pi0 = 0.7,
# Pi1 = 0.7,
# delta = 0.15,
# equal = FALSE,
# w = c(1e-6, 0, 0, 0, 1))
# optimal <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# Pi0 = 0.7,
# Pi1 = 0.7,
# delta = 0.15,
# equal = FALSE,
# w = c(1, 0, 0, 0, 0))
# calgb <- des_two_stage(alpha = 0.16,
# beta = 0.2,
# Pi0 = 0.7,
# Pi1 = 0.7,
# delta = 0.15,
# equal = FALSE,
# w = c(1, 0, 0, 0, 0))
# # Example 2
# minimax <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# Pi0 = 0.7,
# Pi1 = 0.7,
# delta = 0.15,
# equal = FALSE,
# ratio = 2,
# w = c(1e-6, 0, 0, 0, 1))
# optimal <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# Pi0 = 0.7,
# Pi1 = 0.7,
# delta = 0.15,
# equal = FALSE,
# ratio = 2,
# w = c(1, 0, 0, 0, 0))
# # Section 3.2
# minimax <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# Pi0 = c(0, 1),
# Pi1 = c(0, 0.85),
# delta = 0.15,
# equal = FALSE,
# w = c(1e-6, 0, 0, 0, 1))
# optimal <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# Pi0 = c(0, 1),
# Pi1 = c(0, 0.85),
# delta = 0.15,
# equal = FALSE,
# w = c(1, 0, 0, 0, 0))
## ----jung_sargent, eval = FALSE, cache = TRUE---------------------------------
# # Table 2
# table_2 <-
# cbind(p0p1, p0p1[, 2]*(1 - p0p1[, 1])/(p0p1[, 1]*(1 - p0p1[, 2])),
# matrix(0, nrow(p0p1), 11))
# colnames(table_2) <- c("py", "px", "theta", "Single-stage design: n",
# "Single-stage design: alpha",
# "Single-stage design: 1-beta",
# "Minimax design: (n,n1)", "Minimax design: alpha",
# "Minimax design: 1-beta", "Minimax design: EN",
# "Optimal design: (n,n1)", "Optimal design: alpha",
# "Optimal design: 1-beta", "Optimal design: EN")
# table_2 <- tibble::as_tibble(table_2)
# for (i in 1:nrow(p0p1)) {
# des_i <- des_one_stage(alpha = 0.15,
# beta = 0.2,
# type = "fisher",
# delta = table_2$px[i] - table_2$py[i],
# Pi0 = table_2$py[i],
# Pi1 = table_2$py[i],
# nCmax = 100L)
# table_2$`Single-stage design: n`[i] <- des_i$nC
# table_2$`Single-stage design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_2$`Single-stage design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# message("..Table 2 single-stage design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(78, 44, 29, 56, 36, 65, 41, 74, 46, 81, 47, 85, 49,
# 86, 54, 87, 54, 87, 54, 86, 49, 85, 47, 81, 46, 74,
# 41, 65, 36, 56, 29, 44, 78)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# type = "fisher",
# delta = table_2$px[i] - table_2$py[i],
# Pi0 = table_2$py[i],
# Pi1 = table_2$py[i],
# equal = FALSE,
# w = c(1e-6, 0, 0, 0, 1),
# nCmax = nCmax[i])
# table_2$`Minimax design: (n,n1)`[i] <- paste0("(", sum(des_i$nC), ",",
# des_i$nC[1], ")")
# table_2$`Minimax design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_2$`Minimax design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_2$`Minimax design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table 2 minimax design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(81, 44, 29, 58, 37, 69, 42, 79, 49, 84, 50, 95, 52,
# 95, 55, 94, 56, 94, 55, 95, 52, 96, 50, 84, 50, 81,
# 43, 69, 38, 59, 30, 46, 83)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# delta = table_2$px[i] - table_2$py[i],
# Pi0 = table_2$py[i],
# Pi1 = table_2$py[i],
# equal = FALSE,
# w = c(1, 0, 0, 0, 0),
# nCmax = nCmax[i])
# table_2$`Optimal design: (n,n1)`[i] <- paste0("(", sum(des_i$nC), ",",
# des_i$nC[1], ")")
# table_2$`Optimal design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_2$`Optimal design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_2$`Optimal design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table 2 optimal design ", i, " completed..")
# }
# # Table 3
# table_3 <-
# cbind(p0p1, p0p1[, 2]*(1 - p0p1[, 1])/(p0p1[, 1]*(1 - p0p1[, 2])),
# matrix(0, nrow(p0p1), 11))
# colnames(table_3) <- c("p0", "p1", "theta", "Single-stage design: n",
# "Single-stage design: alpha",
# "Single-stage design: 1-beta",
# "Minimax design: (n,n1)", "Minimax design: alpha",
# "Minimax design: 1-beta", "Minimax design: EN",
# "Optimal design: (n,n1)", "Optimal design: alpha",
# "Optimal design: 1-beta", "Optimal design: EN")
# table_3 <- tibble::as_tibble(table_3)
# for (i in 1:nrow(p0p1)) {
# des_i <- des_one_stage(alpha = 0.15,
# beta = 0.15,
# type = "fisher",
# delta = table_3$px[i] - table_2$py[i],
# Pi0 = table_3$py[i],
# Pi1 = table_3$py[i],
# nCmax = 100L)
# table_3$`Single-stage design: n`[i] <- des_i$nC
# table_3$`Single-stage design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_3$`Single-stage design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# message("..Table 3 single-stage design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(92, 51, 34, 65, 41, 78, 49, 88, 52, 94, 59, 100, 60,
# 106, 61, 107, 61, 107, 61, 106, 60, 100, 59, 94, 52,
# 88, 49, 78, 41, 65, 34, 51, 92)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.15,
# beta = 0.15,
# type = "fisher",
# delta = table_3$px[i] - table_3$py[i],
# Pi0 = table_3$py[i],
# Pi1 = table_3$py[i],
# equal = FALSE,
# w = c(1e-6, 0, 0, 0, 1),
# nCmax = nCmax[i])
# table_3$`Minimax design: (n,n1)`[i] <- paste0("(", sum(des_i$nC), ",",
# des_i$nC[1], ")")
# table_3$`Minimax design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_3$`Minimax design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_3$`Minimax design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table 3 minimax design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(94, 52, 34, 68, 42, 82, 51, 93, 56, 102, 62, 107, 65,
# 114, 65, 115, 66, 115, 65, 114, 65, 107, 62, 102, 56,
# 93, 52, 84, 43, 69, 35, 53, 98)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.15,
# beta = 0.15,
# delta = table_3$px[i] - table_3$py[i],
# Pi0 = table_3$py[i],
# Pi1 = table_3$py[i],
# equal = FALSE,
# w = c(1, 0, 0, 0, 0),
# nCmax = nCmax[i])
# table_3$`Optimal design: (n,n1)`[i] <- paste0("(", sum(des_i$nC), ",",
# des_i$nC[1], ")")
# table_3$`Optimal design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_3$`Optimal design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_3$`Optimal design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table 3 optimal design ", i, " completed..")
# }
# # Table 4
# table_4 <-
# cbind(p0p1, p0p1[, 2]*(1 - p0p1[, 1])/(p0p1[, 1]*(1 - p0p1[, 2])),
# matrix(0, nrow(p0p1), 11))
# colnames(table_4) <- c("p0", "p1", "theta", "Single-stage design: n",
# "Single-stage design: alpha",
# "Single-stage design: 1-beta",
# "Minimax design: (n,n1)", "Minimax design: alpha",
# "Minimax design: 1-beta", "Minimax design: EN",
# "Optimal design: (n,n1)", "Optimal design: alpha",
# "Optimal design: 1-beta", "Optimal design: EN")
# table_4 <- tibble::as_tibble(table_4)
# for (i in 1:nrow(p0p1)) {
# des_i <- des_one_stage(alpha = 0.2,
# beta = 0.2,
# type = "fisher",
# delta = table_4$px[i] - table_4$py[i],
# Pi0 = table_4$py[i],
# Pi1 = table_4$py[i],
# nCmax = 100L)
# table_4$`Single-stage design: n`[i] <- des_i$nC
# table_4$`Single-stage design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_4$`Single-stage design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# message("..Table 4 single-stage design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(65, 38, 25, 47, 30, 54, 34, 62, 39, 67, 40, 68, 41,
# 69, 42, 70, 42, 70, 42, 69, 41, 68, 41, 67, 39, 62,
# 34, 54, 30, 47, 25, 38, 65)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.2,
# beta = 0.2,
# type = "fisher",
# delta = table_4$px[i] - table_4$py[i],
# Pi0 = table_4$py[i],
# Pi1 = table_4$py[i],
# equal = FALSE,
# w = c(1e-6, 0, 0, 0, 1),
# nCmax = nCmax[i])
# table_4$`Minimax design: (n,n1)`[i] <- paste0("(", sum(des_i$nC), ",",
# des_i$nC[1], ")")
# table_4$`Minimax design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_4$`Minimax design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_4$`Minimax design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table 4 minimax design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(68, 38, 25, 47, 31, 60, 35, 65, 40, 73, 45, 75, 45,
# 76, 46, 77, 45, 77, 46, 76, 45, 77, 45, 73, 40, 65,
# 36, 60, 33, 48, 26, 40, 70)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.2,
# beta = 0.2,
# delta = table_4$px[i] - table_4$py[i],
# Pi0 = table_4$py[i],
# Pi1 = table_4$py[i],
# equal = FALSE,
# w = c(1, 0, 0, 0, 0),
# nCmax = nCmax[i])
# table_4$`Optimal design: (n,n1)`[i] <- paste0("(", sum(des_i$nC), ",",
# des_i$nC[1], ")")
# table_4$`Optimal design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_4$`Optimal design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_4$`Optimal design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table 4 optimal design ", i, " completed..")
# }
# # Table 5
# table_5 <-
# cbind(p0p1, p0p1[, 2]*(1 - p0p1[, 1])/(p0p1[, 1]*(1 - p0p1[, 2])),
# matrix(0, nrow(p0p1), 11))
# colnames(table_5) <- c("p0", "p1", "theta", "Single-stage design: n",
# "Single-stage design: alpha",
# "Single-stage design: 1-beta",
# "Minimax design: (n,n1)", "Minimax design: alpha",
# "Minimax design: 1-beta", "Minimax design: EN",
# "Optimal design: (n,n1)", "Optimal design: alpha",
# "Optimal design: 1-beta", "Optimal design: EN")
# table_5 <- tibble::as_tibble(table_5)
# for (i in 1:nrow(p0p1)) {
# des_i <- des_one_stage(alpha = 0.2,
# beta = 0.15,
# type = "fisher",
# delta = table_5$px[i] - table_4$py[i],
# Pi0 = table_5$py[i],
# Pi1 = table_5$py[i],
# nCmax = 100L)
# table_5$`Single-stage design: n`[i] <- des_i$nC
# table_5$`Single-stage design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_5$`Single-stage design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# message("..Table 5 single-stage design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(78, 44, 30, 56, 35, 65, 42, 74, 45, 78, 46, 87, 50,
# 89, 53, 89, 53, 89, 53, 89, 50, 87, 46, 78, 45, 74,
# 42, 65, 35, 56, 30, 44, 78)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.2,
# beta = 0.15,
# type = "fisher",
# delta = table_5$px[i] - table_4$py[i],
# Pi0 = table_5$py[i],
# Pi1 = table_5$py[i],
# equal = FALSE,
# w = c(1e-6, 0, 0, 0, 1),
# nCmax = nCmax[i])
# table_5$`Minimax design: (n,n1)`[i] <- paste0("(", sum(des_i$nC), ",",
# des_i$nC[1], ")")
# table_5$`Minimax design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_5$`Minimax design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_5$`Minimax design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table 5 minimax design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(81, 44, 30, 59, 37, 69, 43, 80, 48, 84, 50, 92, 52,
# 93, 55, 96, 57, 96, 55, 92, 52, 92, 50, 85, 48, 82,
# 44, 69, 37, 59, 31, 46, 83)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.2,
# beta = 0.15,
# delta = table_5$px[i] - table_4$py[i],
# Pi0 = table_5$py[i],
# Pi1 = table_5$py[i],
# equal = FALSE,
# w = c(1, 0, 0, 0, 0),
# nCmax = nCmax[i])
# table_5$`Optimal design: (n,n1)`[i] <- paste0("(", sum(des_i$nC), ",",
# des_i$nC[1], ")")
# table_5$`Optimal design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_5$`Optimal design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_5$`Optimal design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table 5 optimal design ", i, " completed..")
# }
## ----shan, eval = FALSE, cache = TRUE-----------------------------------------
# fact <- rep(seq(0.1, 0.5, 0.1), each = 4)
# p0p1 <- cbind(fact, fact + rep(c(0.15, 0.15, 0.2, 0.2), 5))
# # Table 2
# table_2 <- cbind(p0p1, matrix(0, nrow(p0p1), 4))
# colnames(table_2) <- c("p0", "p1", "Method", "Total sample size",
# "Type I error", "Power")
# table_2 <- tibble::as_tibble(table_2)
# table_2$Method <- rep(c("barnard", "fisher"), 10)
# nCmax <-
# as.integer(ceiling(1.1*c(90, 112, 58, 72, 128, 148, 78, 92, 154, 170, 86, 106,
# 156, 174, 96, 108, 156, 172, 86, 106)/2))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_one_stage(alpha = 0.15,
# beta = 0.2,
# type = table_2$Method[i],
# delta = table_2$p1[i] - table_2$p0[i],
# Pi0 = table_2$p0[i],
# Pi1 = table_2$p0[i],
# nCmax = nCmax[i])
# table_2$`Total sample size`[i] <- des_i$nC + des_i$nE
# table_2$`Type I error`[i] <- des_i$opchar$`P(pi)`[1]
# table_2$`Power`[i] <- des_i$opchar$`P(pi)`[2]
# message("..Table 2 single-stage design ", i, " completed..")
# }
# # Table 3
# table_3 <- cbind(p0p1, matrix(0, nrow(p0p1), 13))
# colnames(table_3) <- c("p0", "p1", "Method", "Minimax design: n1",
# "Minimax design: n2", "Minimax design: N",
# "Minimax design: ESS", "Optimal design: n1",
# "Optimal design: n2", "Optimal design: N",
# "Optimal design: ESS", "Constrained design: n1",
# "Constrained design: n2", "Constrained design: N",
# "Constrained design: ESS")
# table_3 <- tibble::as_tibble(table_3)
# table_3$Method <- rep(c("barnard", "fisher"), 10)
# nCmax <-
# as.integer(ceiling(1.2*c(72, 112, 42, 72, 94, 148, 60, 92, 112, 170, 72, 98,
# 120, 174, 76, 108, 122, 172, 76, 98)/2))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# type = table_3$Method[i],
# delta = table_3$p1[i] - table_3$p0[i],
# Pi0 = table_3$p0[i],
# Pi1 = table_3$p0[i],
# equal = FALSE,
# w = c(1e-6, 0, 0, 0, 1),
# nCmax = nCmax[i], summary = TRUE)
# table_3$`Minimax design: n1`[i] <- des_i$nC[1]
# table_3$`Minimax design: n2`[i] <- des_i$nC[2]
# table_3$`Minimax design: N`[i] <- sum(des_i$nC) + sum(des_i$nE)
# table_3$`Minimax design: ESS`[i] <- des_i$opchar$`ESS(pi)`[1]
# message("..Table 3 minimax design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(118, 116, 108, 74, 132, 158, 94, 98, 140, 190, 140,
# 104, 140, 188, 132, 112, 140, 190, 140, 104)/2))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# type = table_3$Method[i],
# delta = table_3$p1[i] - table_3$p0[i],
# Pi0 = table_3$p0[i],
# Pi1 = table_3$p0[i],
# equal = FALSE,
# w = c(1, 0, 0, 0, 0),
# nCmax = nCmax[i])
# table_3$`Optimal design: n1`[i] <- des_i$nC1
# table_3$`Optimal design: n2`[i] <- des_i$nC2
# table_3$`Optimal design: N`[i] <-
# des_i$nC1 + des_i$nC2 + des_i$nE1 + des_i$nE2
# table_3$`Optimal design: ESS`[i] <- des_i$opchar$`ESS(pi)`[1]
# message("..Table 3 optimal design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(84, 52, 126, 72, 140, 80, 140, 82, 140, 78)/2))
# for (i in seq(1, nrow(p0p1), 2)) {
# des_i <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# type = table_3$Method[i],
# delta = table_3$p1[i] - table_3$p0[i],
# Pi0 = table_3$p0[i],
# Pi1 = table_3$p0[i],
# equal = FALSE,
# w = c(1, 0, 0, 0, 0),
# nCmax = nCmax[i])
# n1_ge_n2_i <- dplyr::filter(des_i$feasible,
# n1C >= n2C)
# table_3$`Constrained design: n1`[i] <- n1_gs_n2_i$n1C[1]
# table_3$`Constrained design: n2`[i] <- n1_gs_n2_i$n2C[1]
# table_3$`Constrained design: N`[i] <- n1_gs_n2_i$`max N`
# table_3$`Constrained design: ESS`[i] <- n1_gs_n2_i$`ESS(piO,piO)`[1]
# message("..Table 3 constrained design ", i, " completed..")
# }
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## ----setup, include = FALSE, cache = TRUE-------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
## ----ph2rand, echo = FALSE, cache = TRUE--------------------------------------
suppressPackageStartupMessages(library(ph2rand))
## ----default, cache = TRUE----------------------------------------------------
des_jung <- des_two_stage()
## ----opchar, cache = TRUE-----------------------------------------------------
des_jung$opchar
## ----sim, cache = TRUE--------------------------------------------------------
sim_jung <- sim(des_jung, replicates = 1e5)
sim_jung$sim
## ----table_I, eval = FALSE, cache = TRUE--------------------------------------
# fact <- rep(seq(0.1, 0.75, 0.05), each = 2)
# p0p1 <- rbind(c(0.05, 0.15),
# c(0.05, 0.20),
# c(0.05, 0.25),
# cbind(fact, fact + rep(c(0.15, 0.2), 14)),
# c(0.80, 0.95),
# c(0.85, 0.95))
# # Table I
# table_I <- cbind(p0p1, matrix(0, nrow(p0p1), 11))
# colnames(table_I) <- c("p0", "p1", "Single-stage design: (n,a)",
# "Single-stage design: alpha",
# "Single-stage design: 1-beta",
# "Minimax design: (n,n1,a1,a)", "Minimax design: alpha",
# "Minimax design: 1-beta", "Minimax design: EN",
# "Optimal design: (n,n1,a1,a)", "Optimal design: alpha",
# "Optimal design: 1-beta", "Optimal design: EN")
# table_I <- tibble::as_tibble(table_I)
# for (i in 1:nrow(p0p1)) {
# des_i <- des_one_stage(alpha = 0.15,
# beta = 0.2,
# delta = table_I$p1[i] - table_I$p0[i],
# Pi0 = table_I$p0[i],
# Pi1 = table_I$p0[i],
# nCmax = 100L)
# table_I$`Single-stage design: (n,a)`[i] <- paste0("(", des_i$nC, ",",
# des_i$boundaries$e1, ")")
# table_I$`Single-stage design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_I$`Single-stage design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# message("..Table I single-stage design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(50, 22, 16, 38, 24, 46, 32, 57, 33, 67, 39, 70, 41,
# 78, 42, 78, 45, 78, 46, 78, 45, 77, 43, 76, 40, 68,
# 38, 63, 33, 52, 29, 42, 76)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# delta = table_I$p1[i] - table_I$p0[i],
# Pi0 = table_I$p0[i],
# Pi1 = table_I$p0[i],
# equal = FALSE,
# w = c(1e-6, 0, 0, 0, 1),
# nCmax = nCmax[i])
# table_I$`Minimax design: (n,n1,a1,a)`[i] <-
# paste0("(", sum(des_i$nC), ",", des_i$nC[1], ",",
# des_i$boundaries$f1 + 1, ",", des_i$boundaries$e2, ")")
# table_I$`Minimax design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_I$`Minimax design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_I$`Minimax design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table I minimax design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(57, 27, 22, 56, 28, 51, 32, 66, 39, 78, 43, 77, 46,
# 95, 50, 90, 49, 90, 49, 90, 53, 90, 48, 89, 45, 75,
# 44, 73, 36, 60, 33, 46, 89)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# delta = table_I$p1[i] - table_I$p0[i],
# Pi0 = table_I$p0[i],
# Pi1 = table_I$p0[i],
# equal = FALSE,
# w = c(1, 0, 0, 0, 0),
# nCmax = nCmax[i])
# table_I$`Optimal design: (n,n1,a1,a)`[i] <-
# paste0("(", sum(des_i$nC), ",", des_i$nC[1], ",",
# des_i$boundaries$f1 + 1, ",", des_i$boundaries$e2, ")")
# table_I$`Optimal design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_I$`Optimal design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_I$`Optimal design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table I optimal design ", i, " completed..")
# }
## ----other_tables, eval = FALSE, cache = TRUE---------------------------------
# table_II <- cbind(p0p1, matrix(0, nrow(p0p1), 11))
# colnames(table_II) <- c("p0", "p1", "Single-stage design: (n,a)",
# "Single-stage design: alpha",
# "Single-stage design: 1-beta",
# "Minimax design: (n,n1,a1,a)", "Minimax design: alpha",
# "Minimax design: 1-beta", "Minimax design: EN",
# "Optimal design: (n,n1,a1,a)", "Optimal design: alpha",
# "Optimal design: 1-beta", "Optimal design: EN")
# table_II <- tibble::as_tibble(table_II)
# for (i in 1:nrow(p0p1)) {
# des_i <- des_one_stage(alpha = 0.15,
# beta = 0.15,
# delta = table_II$p1[i] - table_II$p0[i],
# Pi0 = table_II$p0[i],
# Pi1 = table_II$p0[i],
# nCmax = 100L)
# table_II$`Single-stage design: (n,a)`[i] <- paste0("(", des_i$nC, ",",
# des_i$boundaries$e1, ")")
# table_II$`Single-stage design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_II$`Single-stage design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# message("..Table II single-stage design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(58, 34, 19, 49, 28, 62, 36, 74, 43, 78, 46, 87, 50,
# 91, 54, 98, 54, 98, 54, 98, 54, 96, 53, 88, 51, 83,
# 44, 73, 41, 67, 32, 53, 95)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.15,
# beta = 0.15,
# delta = table_II$p1[i] - table_II$p0[i],
# Pi0 = table_II$p0[i],
# Pi1 = table_II$p0[i],
# equal = FALSE,
# w = c(1e-6, 0, 0, 0, 1),
# nCmax = nCmax[i])
# table_II$`Minimax design: (n,n1,a1,a)`[i] <-
# paste0("(", sum(des_i$nC), ",", des_i$nC[1], ",",
# des_i$boundaries$f1 + 1, ",", des_i$boundaries$e2, ")")
# table_II$`Minimax design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_II$`Minimax design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_II$`Minimax design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table II minimax design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(69, 34, 22, 59, 32, 73, 44, 89, 45, 87, 52, 98, 55,
# 103, 63, 112, 61, 109, 63, 100, 60, 107, 60, 99, 55,
# 94, 49, 82, 47, 69, 37, 60, 103)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.15,
# beta = 0.15,
# delta = table_II$p1[i] - table_II$p0[i],
# Pi0 = table_II$p0[i],
# Pi1 = table_II$p0[i],
# equal = FALSE,
# w = c(1, 0, 0, 0, 0),
# nCmax = nCmax[i])
# table_II$`Optimal design: (n,n1,a1,a)`[i] <-
# paste0("(", sum(des_i$nC), ",", des_i$nC[1], ",",
# des_i$boundaries$f1 + 1, ",", des_i$boundaries$e2, ")")
# table_II$`Optimal design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_II$`Optimal design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_II$`Optimal design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table II optimal design ", i, " completed..")
# }
# # Table III
# table_III <- cbind(p0p1, matrix(0, nrow(p0p1), 11))
# colnames(table_III) <- c("p0", "p1", "Single-stage design: (n,a)",
# "Single-stage design: alpha",
# "Single-stage design: 1-beta",
# "Minimax design: (n,n1,a1,a)", "Minimax design: alpha",
# "Minimax design: 1-beta", "Minimax design: EN",
# "Optimal design: (n,n1,a1,a)", "Optimal design: alpha",
# "Optimal design: 1-beta", "Optimal design: EN")
# table_III <- tibble::as_tibble(table_III)
# for (i in 1:nrow(p0p1)) {
# des_i <- des_one_stage(alpha = 0.2,
# beta = 0.2,
# delta = table_III$p1[i] - table_III$p0[i],
# Pi0 = table_III$p0[i],
# Pi1 = table_III$p0[i],
# nCmax = 100L)
# table_III$`Single-stage design: (n,a)`[i] <- paste0("(", des_i$nC, ",",
# des_i$boundaries$e1, ")")
# table_III$`Single-stage design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_III$`Single-stage design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# message("..Table III single-stage design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(41, 22, 16, 34, 17, 41, 25, 48, 27, 53, 32, 60, 35,
# 60, 35, 62, 35, 64, 35, 64, 35, 61, 34, 58, 33, 57,
# 32, 49, 26, 43, 23, 33, 63)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.2,
# beta = 0.2,
# delta = table_III$p1[i] -
# table_III$p0[i],
# Pi0 = table_III$p0[i],
# Pi1 = table_III$p0[i],
# equal = FALSE,
# w = c(1e-6, 0, 0, 0, 1),
# nCmax = nCmax[i])
# table_III$`Minimax design: (n,n1,a1,a)`[i] <-
# paste0("(", sum(des_i$nC), ",", des_i$nC[1], ",",
# des_i$boundaries$f1 + 1, ",", des_i$boundaries$e2, ")")
# table_III$`Minimax design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_III$`Minimax design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_III$`Minimax design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table III minimax design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(42, 27, 18, 35, 18, 42, 28, 53, 29, 56, 35, 68, 41,
# 67, 38, 69, 39, 69, 38, 67, 38, 66, 37, 63, 36, 69,
# 38, 51, 28, 47, 24, 34, 69)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.2,
# beta = 0.2,
# delta = table_III$p1[i] -
# table_III$p0[i],
# Pi0 = table_III$p0[i],
# Pi1 = table_III$p0[i],
# equal = FALSE,
# w = c(1, 0, 0, 0, 0),
# nCmax = nCmax[i])
# table_III$`Optimal design: (n,n1,a1,a)`[i] <-
# paste0("(", sum(des_i$nC), ",", des_i$nC[1], ",",
# des_i$boundaries$f1 + 1, ",", des_i$boundaries$e2, ")")
# table_III$`Optimal design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_III$`Optimal design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_III$`Optimal design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table III ptimal design ", i, " completed..")
# }
# # Table IV
# table_IV <- cbind(p0p1, matrix(0, nrow(p0p1), 11))
# colnames(table_IV) <- c("p0", "p1", "Single-stage design: (n,a)",
# "Single-stage design: alpha",
# "Single-stage design: 1-beta",
# "Minimax design: (n,n1,a1,a)", "Minimax design: alpha",
# "Minimax design: 1-beta", "Minimax design: EN",
# "Optimal design: (n,n1,a1,a)", "Optimal design: alpha",
# "Optimal design: 1-beta", "Optimal design: EN")
# table_IV <- tibble::as_tibble(table_IV)
# for (i in 1:nrow(p0p1)) {
# des_i <- des_one_stage(alpha = 0.2,
# beta = 0.15,
# delta = table_IV$p1[i] - table_IV$p0[i],
# Pi0 = table_IV$p0[i],
# Pi1 = table_IV$p0[i],
# nCmax = 100L)
# table_IV$`Single-stage design: (n,a)`[i] <- paste0("(", des_i$nC, ",",
# des_i$boundaries$e1, ")")
# table_IV$`Single-stage design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_IV$`Single-stage design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# message("..Table IV single-stage design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(58, 26, 19, 40, 27, 53, 30, 58, 36, 67, 39, 70, 40,
# 78, 43, 80, 47, 80, 47, 80, 47, 78, 44, 75, 39, 66,
# 36, 62, 34, 50, 26, 42, 73)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.2,
# beta = 0.15,
# delta = table_IV$p1[i] - table_IV$p0[i],
# Pi0 = table_IV$p0[i],
# Pi1 = table_IV$p0[i],
# equal = FALSE,
# w = c(1e-6, 0, 0, 0, 1),
# nCmax = nCmax[i])
# table_IV$`Minimax design: (n,n1,a1,a)`[i] <-
# paste0("(", sum(des_i$nC), ",", des_i$nC[1], ",",
# des_i$boundaries$f1 + 1, ",", des_i$boundaries$e2, ")")
# table_IV$`Minimax design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_IV$`Minimax design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_IV$`Minimax design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table IV minimax design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(70, 27, 22, 43, 27, 59, 32, 61, 40, 74, 43, 78, 45,
# 85, 45, 90, 49, 94, 53, 94, 50, 85, 45, 77, 41, 71,
# 39, 69, 42, 54, 27, 46, 79)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.2,
# beta = 0.15,
# delta = table_IV$p1[i] - table_IV$p0[i],
# Pi0 = table_IV$p0[i],
# Pi1 = table_IV$p0[i],
# equal = FALSE,
# w = c(1, 0, 0, 0, 0),
# nCmax = nCmax[i])
# table_IV$`Optimal design: (n,n1,a1,a)`[i] <-
# paste0("(", sum(des_i$nC), ",", des_i$nC[1], ",",
# des_i$boundaries$f1 + 1, ",", des_i$boundaries$e2, ")")
# table_IV$`Optimal design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_IV$`Optimal design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_IV$`Optimal design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table IV optimal design ", i, " completed..")
# }
## ----examples, eval = FALSE, cache = TRUE-------------------------------------
# # Example 1
# single_stage <- des_one_stage(alpha = 0.15,
# beta = 0.2,
# Pi0 = 0.7,
# Pi1 = 0.7,
# delta = 0.15)
# minimax <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# Pi0 = 0.7,
# Pi1 = 0.7,
# delta = 0.15,
# equal = FALSE,
# w = c(1e-6, 0, 0, 0, 1))
# optimal <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# Pi0 = 0.7,
# Pi1 = 0.7,
# delta = 0.15,
# equal = FALSE,
# w = c(1, 0, 0, 0, 0))
# calgb <- des_two_stage(alpha = 0.16,
# beta = 0.2,
# Pi0 = 0.7,
# Pi1 = 0.7,
# delta = 0.15,
# equal = FALSE,
# w = c(1, 0, 0, 0, 0))
# # Example 2
# minimax <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# Pi0 = 0.7,
# Pi1 = 0.7,
# delta = 0.15,
# equal = FALSE,
# ratio = 2,
# w = c(1e-6, 0, 0, 0, 1))
# optimal <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# Pi0 = 0.7,
# Pi1 = 0.7,
# delta = 0.15,
# equal = FALSE,
# ratio = 2,
# w = c(1, 0, 0, 0, 0))
# # Section 3.2
# minimax <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# Pi0 = c(0, 1),
# Pi1 = c(0, 0.85),
# delta = 0.15,
# equal = FALSE,
# w = c(1e-6, 0, 0, 0, 1))
# optimal <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# Pi0 = c(0, 1),
# Pi1 = c(0, 0.85),
# delta = 0.15,
# equal = FALSE,
# w = c(1, 0, 0, 0, 0))
## ----jung_sargent, eval = FALSE, cache = TRUE---------------------------------
# # Table 2
# table_2 <-
# cbind(p0p1, p0p1[, 2]*(1 - p0p1[, 1])/(p0p1[, 1]*(1 - p0p1[, 2])),
# matrix(0, nrow(p0p1), 11))
# colnames(table_2) <- c("py", "px", "theta", "Single-stage design: n",
# "Single-stage design: alpha",
# "Single-stage design: 1-beta",
# "Minimax design: (n,n1)", "Minimax design: alpha",
# "Minimax design: 1-beta", "Minimax design: EN",
# "Optimal design: (n,n1)", "Optimal design: alpha",
# "Optimal design: 1-beta", "Optimal design: EN")
# table_2 <- tibble::as_tibble(table_2)
# for (i in 1:nrow(p0p1)) {
# des_i <- des_one_stage(alpha = 0.15,
# beta = 0.2,
# type = "fisher",
# delta = table_2$px[i] - table_2$py[i],
# Pi0 = table_2$py[i],
# Pi1 = table_2$py[i],
# nCmax = 100L)
# table_2$`Single-stage design: n`[i] <- des_i$nC
# table_2$`Single-stage design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_2$`Single-stage design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# message("..Table 2 single-stage design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(78, 44, 29, 56, 36, 65, 41, 74, 46, 81, 47, 85, 49,
# 86, 54, 87, 54, 87, 54, 86, 49, 85, 47, 81, 46, 74,
# 41, 65, 36, 56, 29, 44, 78)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# type = "fisher",
# delta = table_2$px[i] - table_2$py[i],
# Pi0 = table_2$py[i],
# Pi1 = table_2$py[i],
# equal = FALSE,
# w = c(1e-6, 0, 0, 0, 1),
# nCmax = nCmax[i])
# table_2$`Minimax design: (n,n1)`[i] <- paste0("(", sum(des_i$nC), ",",
# des_i$nC[1], ")")
# table_2$`Minimax design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_2$`Minimax design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_2$`Minimax design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table 2 minimax design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(81, 44, 29, 58, 37, 69, 42, 79, 49, 84, 50, 95, 52,
# 95, 55, 94, 56, 94, 55, 95, 52, 96, 50, 84, 50, 81,
# 43, 69, 38, 59, 30, 46, 83)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# delta = table_2$px[i] - table_2$py[i],
# Pi0 = table_2$py[i],
# Pi1 = table_2$py[i],
# equal = FALSE,
# w = c(1, 0, 0, 0, 0),
# nCmax = nCmax[i])
# table_2$`Optimal design: (n,n1)`[i] <- paste0("(", sum(des_i$nC), ",",
# des_i$nC[1], ")")
# table_2$`Optimal design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_2$`Optimal design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_2$`Optimal design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table 2 optimal design ", i, " completed..")
# }
# # Table 3
# table_3 <-
# cbind(p0p1, p0p1[, 2]*(1 - p0p1[, 1])/(p0p1[, 1]*(1 - p0p1[, 2])),
# matrix(0, nrow(p0p1), 11))
# colnames(table_3) <- c("p0", "p1", "theta", "Single-stage design: n",
# "Single-stage design: alpha",
# "Single-stage design: 1-beta",
# "Minimax design: (n,n1)", "Minimax design: alpha",
# "Minimax design: 1-beta", "Minimax design: EN",
# "Optimal design: (n,n1)", "Optimal design: alpha",
# "Optimal design: 1-beta", "Optimal design: EN")
# table_3 <- tibble::as_tibble(table_3)
# for (i in 1:nrow(p0p1)) {
# des_i <- des_one_stage(alpha = 0.15,
# beta = 0.15,
# type = "fisher",
# delta = table_3$px[i] - table_2$py[i],
# Pi0 = table_3$py[i],
# Pi1 = table_3$py[i],
# nCmax = 100L)
# table_3$`Single-stage design: n`[i] <- des_i$nC
# table_3$`Single-stage design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_3$`Single-stage design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# message("..Table 3 single-stage design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(92, 51, 34, 65, 41, 78, 49, 88, 52, 94, 59, 100, 60,
# 106, 61, 107, 61, 107, 61, 106, 60, 100, 59, 94, 52,
# 88, 49, 78, 41, 65, 34, 51, 92)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.15,
# beta = 0.15,
# type = "fisher",
# delta = table_3$px[i] - table_3$py[i],
# Pi0 = table_3$py[i],
# Pi1 = table_3$py[i],
# equal = FALSE,
# w = c(1e-6, 0, 0, 0, 1),
# nCmax = nCmax[i])
# table_3$`Minimax design: (n,n1)`[i] <- paste0("(", sum(des_i$nC), ",",
# des_i$nC[1], ")")
# table_3$`Minimax design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_3$`Minimax design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_3$`Minimax design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table 3 minimax design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(94, 52, 34, 68, 42, 82, 51, 93, 56, 102, 62, 107, 65,
# 114, 65, 115, 66, 115, 65, 114, 65, 107, 62, 102, 56,
# 93, 52, 84, 43, 69, 35, 53, 98)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.15,
# beta = 0.15,
# delta = table_3$px[i] - table_3$py[i],
# Pi0 = table_3$py[i],
# Pi1 = table_3$py[i],
# equal = FALSE,
# w = c(1, 0, 0, 0, 0),
# nCmax = nCmax[i])
# table_3$`Optimal design: (n,n1)`[i] <- paste0("(", sum(des_i$nC), ",",
# des_i$nC[1], ")")
# table_3$`Optimal design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_3$`Optimal design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_3$`Optimal design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table 3 optimal design ", i, " completed..")
# }
# # Table 4
# table_4 <-
# cbind(p0p1, p0p1[, 2]*(1 - p0p1[, 1])/(p0p1[, 1]*(1 - p0p1[, 2])),
# matrix(0, nrow(p0p1), 11))
# colnames(table_4) <- c("p0", "p1", "theta", "Single-stage design: n",
# "Single-stage design: alpha",
# "Single-stage design: 1-beta",
# "Minimax design: (n,n1)", "Minimax design: alpha",
# "Minimax design: 1-beta", "Minimax design: EN",
# "Optimal design: (n,n1)", "Optimal design: alpha",
# "Optimal design: 1-beta", "Optimal design: EN")
# table_4 <- tibble::as_tibble(table_4)
# for (i in 1:nrow(p0p1)) {
# des_i <- des_one_stage(alpha = 0.2,
# beta = 0.2,
# type = "fisher",
# delta = table_4$px[i] - table_4$py[i],
# Pi0 = table_4$py[i],
# Pi1 = table_4$py[i],
# nCmax = 100L)
# table_4$`Single-stage design: n`[i] <- des_i$nC
# table_4$`Single-stage design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_4$`Single-stage design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# message("..Table 4 single-stage design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(65, 38, 25, 47, 30, 54, 34, 62, 39, 67, 40, 68, 41,
# 69, 42, 70, 42, 70, 42, 69, 41, 68, 41, 67, 39, 62,
# 34, 54, 30, 47, 25, 38, 65)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.2,
# beta = 0.2,
# type = "fisher",
# delta = table_4$px[i] - table_4$py[i],
# Pi0 = table_4$py[i],
# Pi1 = table_4$py[i],
# equal = FALSE,
# w = c(1e-6, 0, 0, 0, 1),
# nCmax = nCmax[i])
# table_4$`Minimax design: (n,n1)`[i] <- paste0("(", sum(des_i$nC), ",",
# des_i$nC[1], ")")
# table_4$`Minimax design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_4$`Minimax design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_4$`Minimax design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table 4 minimax design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(68, 38, 25, 47, 31, 60, 35, 65, 40, 73, 45, 75, 45,
# 76, 46, 77, 45, 77, 46, 76, 45, 77, 45, 73, 40, 65,
# 36, 60, 33, 48, 26, 40, 70)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.2,
# beta = 0.2,
# delta = table_4$px[i] - table_4$py[i],
# Pi0 = table_4$py[i],
# Pi1 = table_4$py[i],
# equal = FALSE,
# w = c(1, 0, 0, 0, 0),
# nCmax = nCmax[i])
# table_4$`Optimal design: (n,n1)`[i] <- paste0("(", sum(des_i$nC), ",",
# des_i$nC[1], ")")
# table_4$`Optimal design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_4$`Optimal design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_4$`Optimal design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table 4 optimal design ", i, " completed..")
# }
# # Table 5
# table_5 <-
# cbind(p0p1, p0p1[, 2]*(1 - p0p1[, 1])/(p0p1[, 1]*(1 - p0p1[, 2])),
# matrix(0, nrow(p0p1), 11))
# colnames(table_5) <- c("p0", "p1", "theta", "Single-stage design: n",
# "Single-stage design: alpha",
# "Single-stage design: 1-beta",
# "Minimax design: (n,n1)", "Minimax design: alpha",
# "Minimax design: 1-beta", "Minimax design: EN",
# "Optimal design: (n,n1)", "Optimal design: alpha",
# "Optimal design: 1-beta", "Optimal design: EN")
# table_5 <- tibble::as_tibble(table_5)
# for (i in 1:nrow(p0p1)) {
# des_i <- des_one_stage(alpha = 0.2,
# beta = 0.15,
# type = "fisher",
# delta = table_5$px[i] - table_4$py[i],
# Pi0 = table_5$py[i],
# Pi1 = table_5$py[i],
# nCmax = 100L)
# table_5$`Single-stage design: n`[i] <- des_i$nC
# table_5$`Single-stage design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_5$`Single-stage design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# message("..Table 5 single-stage design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(78, 44, 30, 56, 35, 65, 42, 74, 45, 78, 46, 87, 50,
# 89, 53, 89, 53, 89, 53, 89, 50, 87, 46, 78, 45, 74,
# 42, 65, 35, 56, 30, 44, 78)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.2,
# beta = 0.15,
# type = "fisher",
# delta = table_5$px[i] - table_4$py[i],
# Pi0 = table_5$py[i],
# Pi1 = table_5$py[i],
# equal = FALSE,
# w = c(1e-6, 0, 0, 0, 1),
# nCmax = nCmax[i])
# table_5$`Minimax design: (n,n1)`[i] <- paste0("(", sum(des_i$nC), ",",
# des_i$nC[1], ")")
# table_5$`Minimax design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_5$`Minimax design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_5$`Minimax design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table 5 minimax design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(81, 44, 30, 59, 37, 69, 43, 80, 48, 84, 50, 92, 52,
# 93, 55, 96, 57, 96, 55, 92, 52, 92, 50, 85, 48, 82,
# 44, 69, 37, 59, 31, 46, 83)))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.2,
# beta = 0.15,
# delta = table_5$px[i] - table_4$py[i],
# Pi0 = table_5$py[i],
# Pi1 = table_5$py[i],
# equal = FALSE,
# w = c(1, 0, 0, 0, 0),
# nCmax = nCmax[i])
# table_5$`Optimal design: (n,n1)`[i] <- paste0("(", sum(des_i$nC), ",",
# des_i$nC[1], ")")
# table_5$`Optimal design: alpha`[i] <- des_i$opchar$`P(pi)`[1]
# table_5$`Optimal design: 1-beta`[i] <- des_i$opchar$`P(pi)`[2]
# table_5$`Optimal design: EN`[i] <- des_i$opchar$`ESS(pi)`[1]/2
# message("..Table 5 optimal design ", i, " completed..")
# }
## ----shan, eval = FALSE, cache = TRUE-----------------------------------------
# fact <- rep(seq(0.1, 0.5, 0.1), each = 4)
# p0p1 <- cbind(fact, fact + rep(c(0.15, 0.15, 0.2, 0.2), 5))
# # Table 2
# table_2 <- cbind(p0p1, matrix(0, nrow(p0p1), 4))
# colnames(table_2) <- c("p0", "p1", "Method", "Total sample size",
# "Type I error", "Power")
# table_2 <- tibble::as_tibble(table_2)
# table_2$Method <- rep(c("barnard", "fisher"), 10)
# nCmax <-
# as.integer(ceiling(1.1*c(90, 112, 58, 72, 128, 148, 78, 92, 154, 170, 86, 106,
# 156, 174, 96, 108, 156, 172, 86, 106)/2))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_one_stage(alpha = 0.15,
# beta = 0.2,
# type = table_2$Method[i],
# delta = table_2$p1[i] - table_2$p0[i],
# Pi0 = table_2$p0[i],
# Pi1 = table_2$p0[i],
# nCmax = nCmax[i])
# table_2$`Total sample size`[i] <- des_i$nC + des_i$nE
# table_2$`Type I error`[i] <- des_i$opchar$`P(pi)`[1]
# table_2$`Power`[i] <- des_i$opchar$`P(pi)`[2]
# message("..Table 2 single-stage design ", i, " completed..")
# }
# # Table 3
# table_3 <- cbind(p0p1, matrix(0, nrow(p0p1), 13))
# colnames(table_3) <- c("p0", "p1", "Method", "Minimax design: n1",
# "Minimax design: n2", "Minimax design: N",
# "Minimax design: ESS", "Optimal design: n1",
# "Optimal design: n2", "Optimal design: N",
# "Optimal design: ESS", "Constrained design: n1",
# "Constrained design: n2", "Constrained design: N",
# "Constrained design: ESS")
# table_3 <- tibble::as_tibble(table_3)
# table_3$Method <- rep(c("barnard", "fisher"), 10)
# nCmax <-
# as.integer(ceiling(1.2*c(72, 112, 42, 72, 94, 148, 60, 92, 112, 170, 72, 98,
# 120, 174, 76, 108, 122, 172, 76, 98)/2))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# type = table_3$Method[i],
# delta = table_3$p1[i] - table_3$p0[i],
# Pi0 = table_3$p0[i],
# Pi1 = table_3$p0[i],
# equal = FALSE,
# w = c(1e-6, 0, 0, 0, 1),
# nCmax = nCmax[i], summary = TRUE)
# table_3$`Minimax design: n1`[i] <- des_i$nC[1]
# table_3$`Minimax design: n2`[i] <- des_i$nC[2]
# table_3$`Minimax design: N`[i] <- sum(des_i$nC) + sum(des_i$nE)
# table_3$`Minimax design: ESS`[i] <- des_i$opchar$`ESS(pi)`[1]
# message("..Table 3 minimax design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(118, 116, 108, 74, 132, 158, 94, 98, 140, 190, 140,
# 104, 140, 188, 132, 112, 140, 190, 140, 104)/2))
# for (i in 1:nrow(p0p1)) {
# des_i <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# type = table_3$Method[i],
# delta = table_3$p1[i] - table_3$p0[i],
# Pi0 = table_3$p0[i],
# Pi1 = table_3$p0[i],
# equal = FALSE,
# w = c(1, 0, 0, 0, 0),
# nCmax = nCmax[i])
# table_3$`Optimal design: n1`[i] <- des_i$nC1
# table_3$`Optimal design: n2`[i] <- des_i$nC2
# table_3$`Optimal design: N`[i] <-
# des_i$nC1 + des_i$nC2 + des_i$nE1 + des_i$nE2
# table_3$`Optimal design: ESS`[i] <- des_i$opchar$`ESS(pi)`[1]
# message("..Table 3 optimal design ", i, " completed..")
# }
# nCmax <-
# as.integer(ceiling(1.1*c(84, 52, 126, 72, 140, 80, 140, 82, 140, 78)/2))
# for (i in seq(1, nrow(p0p1), 2)) {
# des_i <- des_two_stage(alpha = 0.15,
# beta = 0.2,
# type = table_3$Method[i],
# delta = table_3$p1[i] - table_3$p0[i],
# Pi0 = table_3$p0[i],
# Pi1 = table_3$p0[i],
# equal = FALSE,
# w = c(1, 0, 0, 0, 0),
# nCmax = nCmax[i])
# n1_ge_n2_i <- dplyr::filter(des_i$feasible,
# n1C >= n2C)
# table_3$`Constrained design: n1`[i] <- n1_gs_n2_i$n1C[1]
# table_3$`Constrained design: n2`[i] <- n1_gs_n2_i$n2C[1]
# table_3$`Constrained design: N`[i] <- n1_gs_n2_i$`max N`
# table_3$`Constrained design: ESS`[i] <- n1_gs_n2_i$`ESS(piO,piO)`[1]
# message("..Table 3 constrained design ", i, " completed..")
# }
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