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belaybbelayb
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unwrap examples
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‎CRAN-SUBMISSION‎

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Version: 1.0.1
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Date: 2025-09-11 15:23:20 UTC
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SHA: a294880155d61ecbee1fc22f127ed598f99ba9e3
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Version: 1.0.2
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Date: 2025-09-16 11:37:13 UTC
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SHA: 4aaea0d89839c008e43b4736b713c1f19204119e

‎DESCRIPTION‎

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Package: BOP2FE
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Type: Package
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Title: Bayesian Optimal Phase II Design with Futility and Efficacy Stopping Boundaries
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Version: 1.0.2
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Version: 1.0.3
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Authors@R: c(
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person("Belay Birlie", "Yimer", email = "belayabyimer@gmail.com", role = c("aut", "cre")),
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person("Xinling", "Xu", role = "aut"),

‎NEWS.md‎

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# BOP2FE 1.0.3
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# BOP2FE 1.0.2
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# BOP2FE 1.0.1

‎R/binary_endpoint.R‎

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#'
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#' @returns A list with the first element corresponding to futility and the second for efficacy boundaries
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#' @examples
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#'\donttest{
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#' H0 <- 0.2
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#' a1 <- H0
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#' b1 <- 1- a1
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#' seed <- 123
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#' n <- c(10, 5, 5, 5, 5, 5, 5)
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#' n <- c(10, 5, 5)
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#' method <- "power"
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#'
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#' boundary_binary<- get_boundary_binary(H0=H0, a1=a1, b1=b1, n =n,
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#' eta = seq(0, 3, l = 301),
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#' method = method,
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#' seed = seed)
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#' }
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#'
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get_boundary_binary <- function(H0, a1, b1, n, lambda, gamma, eta = NULL, method = "power", seed=NULL) {
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set.seed(seed)
@@ -180,12 +178,11 @@ get_boundary_binary <- function(H0, a1, b1, n, lambda, gamma, eta = NULL, method
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#' }
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#'
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#' @examples
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#' \donttest{
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#' H0 <- 0.2
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#' a1 <- H0
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#' b1 <- 1-a1
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#' seed <- 123
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#' n <- c(10, 5, 5, 5, 5, 5, 5)
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#' n <- c(10, 5, 5)
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#' method <- "power"
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#' boundary_tab<- get_boundary_binary(H0=H0, a1=a1, b1=b1, n =n,
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#' lambda = seq(0, 1, l = 11),
@@ -195,13 +192,12 @@ get_boundary_binary <- function(H0, a1, b1, n, lambda, gamma, eta = NULL, method
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#' seed=seed)
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#' test_oc<-get_oc_binary(
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#' p = 0.2,
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#' n = c(10, 5, 5, 5, 5, 5, 5),
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#' n = c(10, 5, 5),
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#' nsim = 1000,
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#' fb = boundary_tab$cnf,
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#' sb = boundary_tab$cns,
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#' seed = seed
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#' )
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#' }
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#'
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get_oc_binary <- function(p, n, nsim, fb, sb, seed = NULL) {
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set.seed(seed)
@@ -374,19 +370,17 @@ get_oc_binary <- function(p, n, nsim, fb, sb, seed = NULL) {
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#' \item{gamma: }{gamma values for cut-off probability}
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#' \item{eta: }{eta values for cut-off probability}}
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#' @examples
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#' \donttest{
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#' oc_binary<-get_boundary_oc_binary(
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#' H0=0.2,
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#' H1= 0.4,
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#' n = c(10, 5, 5, 5, 5, 5, 5),
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#' n = c(10, 5, 5),
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#' nsim = 1000,
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#' lambda = seq(0, 1, l = 11),
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#' gamma = seq(0, 1, l = 11),
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#' eta = seq(0, 3, l = 31),
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#' method = "power",
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#' seed = 1
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#' )
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#' }
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#'
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get_boundary_oc_binary <- function(
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H0, H1, n, nsim, lambda, gamma, eta = NULL, method = "power", seed = NULL
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#' @export
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#' @keywords internal
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#' @examples
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#' \donttest{
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#'test_binary <- search_optimal_pars_binary(
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#' H0=0.2,
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#' H1= 0.4,
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#' n = c(10, 5, 5, 5, 5, 5, 5),
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#' n = c(10, 5, 5),
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#' nsim = 1000,
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#' t1e = 0.1,
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#' method = "power",
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#' grid3 = 31,
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#' seed = 123
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#')
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#'}
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#'
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#'
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search_optimal_pars_binary <- function(

‎R/coprimary_endpoint.R‎

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@@ -22,18 +22,16 @@
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#'
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#' @returns A list with the first element corresponding to futility and the second for efficacy boundaries
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#' @examples
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#' \donttest{
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#' H0=c(0.05,0.05, 0.15, 0.75)
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#' a <- H0
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#' seed <- 123
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#' n <- c(10, 5, 5, 5, 5, 5, 5)
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#' n <- c(10, 5, 5)
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#' method <- "power"
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#' test1<- get_boundary_coprimary(H0=H0, a=a, n =n,
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#' lambda = seq(0, 1, l = 11),
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#' gamma = seq(0, 1, l = 11),
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#' eta = seq(0, 3, l = 31),
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#' method = "power")
36-
#' }
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#'
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get_boundary_coprimary <- function(H0, a, n, lambda, gamma, eta = NULL, method = "power", seed = NULL) {
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set.seed(seed)
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#' }
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#'
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#' @examples
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#' \donttest{
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#' H0=c(0.05,0.05, 0.15, 0.75)
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#' a <- H0
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#' seed <- 123
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#' n <- c(10, 5, 5, 5, 5, 5, 5)
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#' n <- c(10, 5, 5)
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#' method <- "power"
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#' boundary_tab<- get_boundary_coprimary(H0=H0, a=a, n =n,
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#' lambda = seq(0, 1, l = 11),
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#' p2 = 0.05,
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#' p3 = 0.15,
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#' p4 = 0.75,
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#' n = c(10, 5, 5, 5, 5, 5, 5),
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#' n = c(10, 5, 5),
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#' nsim = 1000,
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#' fb = boundary_tab$cnf,
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#' sb = boundary_tab$cns,
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#' seed = seed
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#' )
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#' }
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#'
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get_oc_coprimary <- function(p1, p2, p3, p4, n, nsim, fb, sb, seed = NULL) {
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set.seed(seed)
@@ -516,19 +512,18 @@ get_oc_coprimary <- function(p1, p2, p3, p4, n, nsim, fb, sb, seed = NULL) {
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#' \item{gamma: }{gamma values for cut-off probability}
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#' \item{eta: }{eta values for cut-off probability}}
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#' @examples
519-
#' \donttest{
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#' oc_coprimary<-get_boundary_oc_coprimary(
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#' H0=c(0.15,0.30, 0.15, 0.40),
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#' H1= c(0.18,0.42, 0.02, 0.38),
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#' n = c(10, 5, 5, 5, 5, 5, 5),
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#' n = c(10, 5, 5),
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#' nsim = 1000,
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#' lambda = seq(0, 1, l = 11),
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#' gamma = seq(0, 1, l = 11),
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#' eta = seq(0, 3, l = 31),
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#' method = "power",
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#' seed = 1
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#' )
531-
#' }
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532527
#'
533528
get_boundary_oc_coprimary <- function(
534529
H0, H1, n, nsim, lambda, gamma, eta = NULL, method = "power", seed = NULL
@@ -642,11 +637,10 @@ get_boundary_oc_coprimary <- function(
642637
#' @export
643638
#' @keywords internal
644639
#' @examples
645-
#' \donttest{
646640
#'test_comprimary <- search_optimal_pars_coprimary(
647641
#' H0=c(0.05,0.05, 0.15, 0.75),
648642
#' H1= c(0.15,0.15, 0.20, 0.50),
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#' n = c(10, 5, 5, 5, 5, 5, 5),
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#' n = c(10, 5, 5),
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#' nsim = 1000,
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#' t1e = 0.1,
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#' method = "power",
@@ -661,7 +655,6 @@ get_boundary_oc_coprimary <- function(
661655
#' grid3 = 31,
662656
#' seed = 123
663657
#')
664-
#'}
665658
#'
666659
search_optimal_pars_coprimary <- function(
667660
H0, H1, n, nsim, t1e = NULL, method = "power",

‎R/efftox_endpoint.R‎

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@@ -22,18 +22,16 @@
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#'
2323
#' @returns A list with the first element corresponding to futility and the second for efficacy boundaries
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#' @examples
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#' \donttest{
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#' H0=c(0.15,0.30, 0.15, 0.40)
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#' a <- H0
2827
#' seed <- 123
29-
#' n <- c(10, 5, 5, 5, 5, 5, 5)
28+
#' n <- c(10, 5, 5)
3029
#' method <- "power"
3130
#' test1<- get_boundary_jointefftox(H0=H0, a=a, n =n,
3231
#' lambda = seq(0, 1, l = 11),
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#' gamma = seq(0, 1, l = 11),
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#' eta = seq(0, 3, l = 31),
3534
#' method = "power")
36-
#' }
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#'
3836

3937
get_boundary_jointefftox <- function(H0, a, n, lambda, gamma, eta = NULL, method = "power", seed = NULL) {
@@ -279,11 +277,10 @@ get_boundary_jointefftox <- function(H0, a, n, lambda, gamma, eta = NULL, method
279277
#' }
280278
#'
281279
#' @examples
282-
#' \donttest{
283280
#' H0=c(0.15,0.30, 0.15, 0.40)
284281
#' a <- H0
285282
#' seed <- 123
286-
#' n <- c(10, 5, 5, 5, 5, 5, 5)
283+
#' n <- c(10, 5, 5)
287284
#' method <- "power"
288285
#' boundary_tab<- get_boundary_jointefftox(H0=H0, a=a, n =n,
289286
#' lambda = seq(0, 1, l = 11),
@@ -296,13 +293,12 @@ get_boundary_jointefftox <- function(H0, a, n, lambda, gamma, eta = NULL, method
296293
#' p2 = 0.30,
297294
#' p3 = 0.15,
298295
#' p4 = 0.40,
299-
#' n = c(10, 5, 5, 5, 5, 5, 5),
296+
#' n = c(10, 5, 5),
300297
#' nsim = 1000,
301298
#' fb = boundary_tab$cnf,
302299
#' sb = boundary_tab$cns,
303300
#' seed = seed
304301
#' )
305-
#' }
306302
#'
307303
get_oc_jointefftox <- function(p1, p2, p3, p4, n, nsim, fb, sb, seed = NULL) {
308304
set.seed(seed)
@@ -561,19 +557,17 @@ get_oc_jointefftox <- function(p1, p2, p3, p4, n, nsim, fb, sb, seed = NULL) {
561557
#' \item{gamma: }{gamma values for cut-off probability}
562558
#' \item{eta: }{eta values for cut-off probability}}
563559
#' @examples
564-
#' \donttest{
565560
#' oc_joint<-get_boundary_oc_efftox(
566561
#' H0=c(0.15,0.30, 0.15, 0.40),
567562
#' H1= c(0.18,0.42, 0.02, 0.38),
568-
#' n = c(10, 5, 5, 5, 5, 5, 5),
563+
#' n = c(10, 5, 5),
569564
#' nsim = 1000,
570565
#' lambda = seq(0, 1, l = 11),
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#' gamma = seq(0, 1, l = 11),
572567
#' eta = seq(0, 3, l = 31),
573568
#' method = "power",
574569
#' seed = 1
575570
#' )
576-
#' }
577571
#'
578572
get_boundary_oc_efftox <- function(
579573
H0, H1, n, nsim, lambda, gamma, eta = NULL, method = "power", seed = NULL
@@ -687,11 +681,10 @@ get_boundary_oc_efftox <- function(
687681
#' @export
688682
#' @keywords internal
689683
#' @examples
690-
#' \donttest{
691-
#'test_jointy <- search_optimal_pars_efftox(
684+
#'test_joint <- search_optimal_pars_efftox(
692685
#' H0=c(0.15,0.30, 0.15, 0.40),
693686
#' H1= c(0.18,0.42, 0.02, 0.38),
694-
#' n = c(10, 5, 5, 5, 5, 5, 5),
687+
#' n = c(10, 5, 5),
695688
#' nsim = 1000,
696689
#' t1e = 0.1,
697690
#' method = "power",
@@ -706,7 +699,6 @@ get_boundary_oc_efftox <- function(
706699
#' grid3 = 31,
707700
#' seed = 123
708701
#')
709-
#'}
710702
#'
711703
search_optimal_pars_efftox <- function(
712704
H0, H1, n, nsim, t1e = NULL, method = "power",

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