From 26d9870a7520efc11aa3118c9ed040df2fdb7292 Mon Sep 17 00:00:00 2001
From: Yilong Zhang <elong0527@gmail.com>
Date: Sat, 24 Jun 2023 04:08:54 +0000
Subject: [PATCH 01/13] move functions to internal

- h1
- hupdate
- gridpts
---
 NAMESPACE                                     |  3 -
 R/gridpts_h1_hupdate.R                        |  6 +-
 R/gs_spending_bound.R                         | 33 ----------
 _pkgdown.yml                                  |  3 -
 inst/old_function/gs_power_npe_.R             |  5 +-
 man/gridpts.Rd                                | 58 -----------------
 man/gs_spending_bound.Rd                      | 33 ----------
 man/h1.Rd                                     | 53 ----------------
 man/hupdate.Rd                                | 62 -------------------
 vignettes/articles/story-npe-integration.Rmd  | 12 ++--
 .../articles/usage-gs-spending-bound.Rmd      |  4 +-
 11 files changed, 13 insertions(+), 259 deletions(-)
 delete mode 100644 man/gridpts.Rd
 delete mode 100644 man/h1.Rd
 delete mode 100644 man/hupdate.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 44bdd055..1d97215a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -14,7 +14,6 @@ export(expected_accrual)
 export(expected_event)
 export(expected_time)
 export(fixed_design)
-export(gridpts)
 export(gs_b)
 export(gs_create_arm)
 export(gs_design_ahr)
@@ -33,8 +32,6 @@ export(gs_power_rd)
 export(gs_power_wlr)
 export(gs_spending_bound)
 export(gs_spending_combo)
-export(h1)
-export(hupdate)
 export(ppwe)
 export(s2pwe)
 export(to_integer)
diff --git a/R/gridpts_h1_hupdate.R b/R/gridpts_h1_hupdate.R
index 8a5137e3..4d410ed2 100644
--- a/R/gridpts_h1_hupdate.R
+++ b/R/gridpts_h1_hupdate.R
@@ -51,7 +51,7 @@
 #' }
 #' \if{html}{The contents of this section are shown in PDF user manual only.}
 #'
-#' @export
+#' @noRd
 #'
 #' @examples
 #' # Approximate variance of standard normal (i.e., 1)
@@ -93,7 +93,7 @@ gridpts <- function(r = 18, mu = 0, a = -Inf, b = Inf) {
 #' }
 #' \if{html}{The contents of this section are shown in PDF user manual only.}
 #'
-#' @export
+#' @noRd
 #'
 #' @examples
 #' # Replicate variance of 1, mean of 35
@@ -137,7 +137,7 @@ h1 <- function(r = 18, theta = 0, info = 1, a = -Inf, b = Inf) {
 #' }
 #' \if{html}{The contents of this section are shown in PDF user manual only.}
 #'
-#' @export
+#' @noRd
 #'
 #' @examples
 #' # 2nd analysis with no interim bound and drift 0 should have mean 0, variance 1
diff --git a/R/gs_spending_bound.R b/R/gs_spending_bound.R
index 1276b1da..a85d0c54 100644
--- a/R/gs_spending_bound.R
+++ b/R/gs_spending_bound.R
@@ -81,39 +81,6 @@
 #' @importFrom stats qnorm
 #'
 #' @export
-#'
-#' @examples
-#' info <- (1:3) * 10
-#' info_frac <- info / max(info)
-#' k <- length(info_frac)
-#'
-#' # 1st analysis
-#' a1 <- gs_spending_bound(
-#'   k = 1, efficacy = FALSE, theta = 0,
-#'   par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
-#'   hgm1 = NULL
-#' )
-#'
-#' b1 <- gs_spending_bound(
-#'   k = 1, efficacy = TRUE, theta = 0,
-#'   par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
-#'   hgm1 = NULL
-#' )
-#' cat("The (lower, upper) boundary at the 1st analysis is (", a1, ", ", b1, ").\n")
-#'
-#' # 2nd analysis
-#' a2 <- gs_spending_bound(
-#'   k = 2, efficacy = FALSE, theta = 0,
-#'   par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
-#'   hgm1 = h1(r = 18, theta = 0, info = info[1], a = a1, b = b1)
-#' )
-#'
-#' b2 <- gs_spending_bound(
-#'   k = 2, efficacy = TRUE, theta = 0,
-#'   par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
-#'   hgm1 = h1(r = 18, theta = 0, info = info[1], a = a1, b = b1)
-#' )
-#' cat("The upper boundary at the 2nd analysis is (", a2, ", ", b2, ").\n")
 gs_spending_bound <- function(k = 1,
                               par = list(
                                 sf = gsDesign::sfLDOF,
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 2991dd63..386d8d46 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -97,9 +97,6 @@ reference:
     - expected_accrual
     - ppwe
     - s2pwe
-    - gridpts
-    - h1
-    - hupdate
     - gs_create_arm
 
 articles:
diff --git a/inst/old_function/gs_power_npe_.R b/inst/old_function/gs_power_npe_.R
index a8e6112a..e09f1931 100644
--- a/inst/old_function/gs_power_npe_.R
+++ b/inst/old_function/gs_power_npe_.R
@@ -255,15 +255,14 @@ gs_power_npe_ <- function(theta = .1, theta1 = NULL, info = 1, info1 = NULL, inf
         0
       }
 
-      # hgm1_0 <- h1(r = r, theta = 0, info = info0[1], a = if(binding){a[1]}else{-Inf}, b = b[1])
       hgm1_0 <- h1(r = r, theta = 0, info = info0[1], a = if (binding) {
         a[1]
       } else {
         -Inf
       }, b = b[1])
-      # hgm1_1 <- h1(r = r, theta = theta1[1], info = info1[1], a = a[1], b = b[1])
+
       hgm1_1 <- h1(r = r, theta = theta1[1], info = info1[1], a = a[1], b = b[1])
-      # hgm1   <- h1(r = r, theta = theta[1], info = info[1],  a = a[1], b = b[1])
+
       hgm1 <- h1(r = r, theta = theta[1], info = info[1], a = a[1], b = b[1])
     } else {
       # Cross upper bound
diff --git a/man/gridpts.Rd b/man/gridpts.Rd
deleted file mode 100644
index 3d2ccdc6..00000000
--- a/man/gridpts.Rd
+++ /dev/null
@@ -1,58 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/gridpts_h1_hupdate.R
-\name{gridpts}
-\alias{gridpts}
-\title{Grid points for group sequential design numerical integration}
-\usage{
-gridpts(r = 18, mu = 0, a = -Inf, b = Inf)
-}
-\arguments{
-\item{r}{Integer, at least 2; default of 18 recommended by Jennison and Turnbull.}
-
-\item{mu}{Mean of normal distribution (scalar) under consideration.}
-
-\item{a}{Lower limit of integration (scalar).}
-
-\item{b}{Upper limit of integration (scalar \verb{> a}).}
-}
-\value{
-A list with grid points in \code{z} and numerical integration weights in \code{w}.
-}
-\description{
-Points and weights for Simpson's rule numerical integration from
-p 349--350 of Jennison and Turnbull book.
-This is not used for arbitrary integration, but for the canonical form of Jennison and Turnbull.
-mu is computed elsewhere as drift parameter times sqrt of information.
-Since this is a lower-level routine, no checking of input is done; calling routines should
-ensure that input is correct.
-Lower limit of integration can be \code{-Inf} and upper limit of integration can be \code{Inf}.
-}
-\details{
-Jennison and Turnbull (p 350) claims accuracy of \code{10e-6} with \code{r=16}.
-The numerical integration grid spreads out at the tail to enable accurate tail probability calculations.
-}
-\section{Specification}{
-
-\if{latex}{
- \itemize{
-   \item Define odd numbered grid points for real line.
-   \item Trim points outside of $[a, b]$ and include those points.
-   \item If extreme, include only 1 point where density will be essentially 0.
-   \item Define even numbered grid points between the odd ones.
-   \item Compute weights for odd numbered grid points.
-   \item Combine odd- and even-numbered grid points with their corresponding weights.
-   \item Return a tibble of with grid points in z and numerical integration weights in z.
-  }
-}
-\if{html}{The contents of this section are shown in PDF user manual only.}
-}
-
-\examples{
-# Approximate variance of standard normal (i.e., 1)
-g <- gridpts()
-sum((g$z)^2 * g$w * dnorm(g$z))
-
-# Approximate probability above .95 quantile (i.e., 0.05)
-g <- gridpts(a = qnorm(0.95), b = Inf)
-sum(g$w * dnorm(g$z))
-}
diff --git a/man/gs_spending_bound.Rd b/man/gs_spending_bound.Rd
index 2cf99be6..9d4159e1 100644
--- a/man/gs_spending_bound.Rd
+++ b/man/gs_spending_bound.Rd
@@ -85,39 +85,6 @@ that in Chapter 19 of Jennison and Turnbull (2000).
 \if{html}{The contents of this section are shown in PDF user manual only.}
 }
 
-\examples{
-info <- (1:3) * 10
-info_frac <- info / max(info)
-k <- length(info_frac)
-
-# 1st analysis
-a1 <- gs_spending_bound(
-  k = 1, efficacy = FALSE, theta = 0,
-  par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
-  hgm1 = NULL
-)
-
-b1 <- gs_spending_bound(
-  k = 1, efficacy = TRUE, theta = 0,
-  par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
-  hgm1 = NULL
-)
-cat("The (lower, upper) boundary at the 1st analysis is (", a1, ", ", b1, ").\n")
-
-# 2nd analysis
-a2 <- gs_spending_bound(
-  k = 2, efficacy = FALSE, theta = 0,
-  par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
-  hgm1 = h1(r = 18, theta = 0, info = info[1], a = a1, b = b1)
-)
-
-b2 <- gs_spending_bound(
-  k = 2, efficacy = TRUE, theta = 0,
-  par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
-  hgm1 = h1(r = 18, theta = 0, info = info[1], a = a1, b = b1)
-)
-cat("The upper boundary at the 2nd analysis is (", a2, ", ", b2, ").\n")
-}
 \references{
 Jennison C and Turnbull BW (2000),
 \emph{Group Sequential Methods with Applications to Clinical Trials}.
diff --git a/man/h1.Rd b/man/h1.Rd
deleted file mode 100644
index 7fc437e9..00000000
--- a/man/h1.Rd
+++ /dev/null
@@ -1,53 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/gridpts_h1_hupdate.R
-\name{h1}
-\alias{h1}
-\title{Initialize numerical integration for group sequential design}
-\usage{
-h1(r = 18, theta = 0, info = 1, a = -Inf, b = Inf)
-}
-\arguments{
-\item{r}{Integer, at least 2; default of 18 recommended by Jennison and Turnbull.}
-
-\item{theta}{Drift parameter for first analysis.}
-
-\item{info}{Information at first analysis.}
-
-\item{a}{Lower limit of integration (scalar).}
-
-\item{b}{Upper limit of integration (scalar \verb{> a}).}
-}
-\value{
-A list with grid points in \code{z}, numerical integration weights in \code{w},
-and a normal density with mean \verb{mu = theta * sqrt\{I\}}
-and variance 1 times the weight in \code{h}.
-}
-\description{
-Compute grid points for first interim analysis in a group sequential design.
-}
-\details{
-Mean for standard normal distribution under consideration is \code{mu = theta * sqrt(I)}.
-}
-\section{Specification}{
-
-\if{latex}{
- \itemize{
-   \item Compute drift at analysis 1.
-   \item Compute deviation from drift.
-   \item Compute standard normal density, multiply by grid weight.
-   \item Return a tibble of z, w, and h.
-  }
-}
-\if{html}{The contents of this section are shown in PDF user manual only.}
-}
-
-\examples{
-# Replicate variance of 1, mean of 35
-g <- h1(theta = 5, info = 49)
-mu <- sum(g$z * g$h)
-var <- sum((g$z - mu)^2 * g$h)
-
-# Replicate p-value of 0.0001 by numerical integration of tail
-g <- h1(a = qnorm(0.9999))
-sum(g$h)
-}
diff --git a/man/hupdate.Rd b/man/hupdate.Rd
deleted file mode 100644
index fa4203f2..00000000
--- a/man/hupdate.Rd
+++ /dev/null
@@ -1,62 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/gridpts_h1_hupdate.R
-\name{hupdate}
-\alias{hupdate}
-\title{Update numerical integration for group sequential design}
-\usage{
-hupdate(
-  r = 18,
-  theta = 0,
-  info = 2,
-  a = -Inf,
-  b = Inf,
-  thetam1 = 0,
-  im1 = 1,
-  gm1 = h1()
-)
-}
-\arguments{
-\item{r}{Integer, at least 2; default of 18 recommended by Jennison and Turnbull.}
-
-\item{theta}{Drift parameter for current analysis.}
-
-\item{info}{Information at current analysis.}
-
-\item{a}{Lower limit of integration (scalar).}
-
-\item{b}{Upper limit of integration (scalar \verb{> a}).}
-
-\item{thetam1}{Drift parameter for previous analysis.}
-
-\item{im1}{Information at previous analysis.}
-
-\item{gm1}{Numerical integration grid from \code{\link[=h1]{h1()}} or previous run of \code{\link[=hupdate]{hupdate()}}.}
-}
-\value{
-A list with grid points in \code{z},
-numerical integration weights in \code{w},
-a normal density with mean \verb{mu = theta * sqrt\{I\}}
-and variance 1 times the weight in \code{h}.
-}
-\description{
-Update grid points for numerical integration from one analysis to the next.
-}
-\section{Specification}{
-
-\if{latex}{
- \itemize{
-   \item Compute the square root of the change in information.
-   \item Compute the grid points for group sequential design numerical integration.
-   \item Update the integration.
-   \item Return a tibble of z, w, and h.
-  }
-}
-\if{html}{The contents of this section are shown in PDF user manual only.}
-}
-
-\examples{
-# 2nd analysis with no interim bound and drift 0 should have mean 0, variance 1
-g <- hupdate()
-mu <- sum(g$z * g$h)
-var <- sum((g$z - mu)^2 * g$h)
-}
diff --git a/vignettes/articles/story-npe-integration.Rmd b/vignettes/articles/story-npe-integration.Rmd
index 970a5340..f9868695 100644
--- a/vignettes/articles/story-npe-integration.Rmd
+++ b/vignettes/articles/story-npe-integration.Rmd
@@ -195,7 +195,7 @@ The columns in the resulting table are
 ```{r}
 # Set up grid over continuation region
 # Null hypothesis
-grid1_0 <- h1(theta = 0, info = info[1], a = a1, b = b1)
+grid1_0 <- gsDesign2:::h1(theta = 0, info = info[1], a = a1, b = b1)
 grid1_0 %>% head()
 ```
 The probability of not crossing a bound under the null hypothesis is computed as follows:
@@ -212,7 +212,7 @@ cat(
 We now set up numerical integration grid under the alternate hypothesis and the compute continuation probability.
 
 ```{r}
-grid1_1 <- h1(theta = theta[1], info = info[1], a = a1, b = b1)
+grid1_1 <- gsDesign2:::h1(theta = theta[1], info = info[1], a = a1, b = b1)
 prob_h1_continue <- sum(grid1_1$h)
 h1mean <- sqrt(info[1]) * theta[1]
 cat(
@@ -248,7 +248,7 @@ Under the null hypothesis, we need to update to the interval above `b2_0`.
 
 ```{r}
 # Upper rejection region grid under H0
-grid2_0 <- hupdate(theta = 0, info = info[2], a = b2_0, b = Inf, im1 = info[1], gm1 = grid1_0)
+grid2_0 <- gsDesign2:::hupdate(theta = 0, info = info[2], a = b2_0, b = Inf, im1 = info[1], gm1 = grid1_0)
 pupper_0 <- sum(grid2_0$h)
 cat(
   "Upper spending at analysis 2\n Target:", spend0, "\n Using initial bound approximation:",
@@ -272,7 +272,7 @@ cat(
   "Original bound approximation:", b2_0,
   "\nUpdated bound approximation:", b2_1
 )
-grid2_0 <- hupdate(theta = 0, info = info[2], a = b2_1, b = Inf, im1 = info[1], gm1 = grid1_0)
+grid2_0 <- gsDesign2:::hupdate(theta = 0, info = info[2], a = b2_1, b = Inf, im1 = info[1], gm1 = grid1_0)
 pupper_1 <- sum(grid2_0$h)
 cat(
   "\nOriginal boundary crossing probability:", pupper_0,
@@ -286,7 +286,7 @@ We now update the lower bound in an analogous fashion.
 
 ```{r}
 # Lower rejection region grid under H1
-grid2_1 <- hupdate(
+grid2_1 <- gsDesign2:::hupdate(
   theta = theta[2], info = info[2], a = -Inf, b = a2_0,
   thetam1 = theta[1], im1 = info[1], gm1 = grid1_1
 )
@@ -305,7 +305,7 @@ cat(
   "\nUpdated bound approximation:", a2_1
 )
 
-grid2_1 <- hupdate(
+grid2_1 <- gsDesign2:::hupdate(
   theta = theta[2], info = info[2], a = -Inf, b = a2_1,
   thetam1 = theta[1], im1 = info[1], gm1 = grid1_1
 )
diff --git a/vignettes/articles/usage-gs-spending-bound.Rmd b/vignettes/articles/usage-gs-spending-bound.Rmd
index 22ae41c5..a18fce71 100644
--- a/vignettes/articles/usage-gs-spending-bound.Rmd
+++ b/vignettes/articles/usage-gs-spending-bound.Rmd
@@ -61,13 +61,13 @@ cat("The (lower, upper) boundary at the 1st analysis is (", a1, ", ", b1, ").\n"
 a2 <- gs_spending_bound(
   k = 2, efficacy = FALSE, theta = 0,
   par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
-  hgm1 = h1(r = 18, theta = 0, info = info[1], a = a1, b = b1)
+  hgm1 = gsDesign2:::h1(r = 18, theta = 0, info = info[1], a = a1, b = b1)
 )
 
 b2 <- gs_spending_bound(
   k = 2, efficacy = TRUE, theta = 0,
   par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
-  hgm1 = h1(r = 18, theta = 0, info = info[1], a = a1, b = b1)
+  hgm1 = gsDesign2:::h1(r = 18, theta = 0, info = info[1], a = a1, b = b1)
 )
 cat("The upper boundary at the 2nd analysis is (", a2, ", ", b2, ").\n")
 ```

From 4f58c51b1750f505b3b6074c7e15205f1bc255e1 Mon Sep 17 00:00:00 2001
From: yilong zhang <elong0527@gmail.com>
Date: Fri, 14 Jul 2023 19:44:24 +0000
Subject: [PATCH 02/13] add examples back in `gs_spending_bound`

---
 R/gs_spending_bound.R    | 33 +++++++++++++++++++++++++++++++++
 man/gs_spending_bound.Rd | 34 ++++++++++++++++++++++++++++++++++
 2 files changed, 67 insertions(+)

diff --git a/R/gs_spending_bound.R b/R/gs_spending_bound.R
index a85d0c54..ed9104ac 100644
--- a/R/gs_spending_bound.R
+++ b/R/gs_spending_bound.R
@@ -79,7 +79,40 @@
 #'
 #' @importFrom gsDesign gsDesign sfLDOF
 #' @importFrom stats qnorm
+#' 
+#' @examples
+#' info <- (1:3) * 10
+#' info_frac <- info / max(info)
+#' k <- length(info_frac)
 #'
+#' # 1st analysis
+#' a1 <- gs_spending_bound(
+#'   k = 1, efficacy = FALSE, theta = 0,
+#'   par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
+#'   hgm1 = NULL
+#' )
+#'
+#' b1 <- gs_spending_bound(
+#'   k = 1, efficacy = TRUE, theta = 0,
+#'   par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
+#'   hgm1 = NULL
+#' )
+#' cat("The (lower, upper) boundary at the 1st analysis is (", a1, ", ", b1, ").\n")
+#'
+#' # 2nd analysis
+#' # a2 <- gs_spending_bound(
+#' #     k = 2, efficacy = FALSE, theta = 0,
+#' #   par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
+#' #   hgm1 = gsDesign2:::h1(r = 18, theta = 0, info = info[1], a = a1, b = b1)
+#' # )
+#'
+#' # b2 <- gs_spending_bound(
+#' #    k = 2, efficacy = TRUE, theta = 0,
+#' #    par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
+#' #    hgm1 = gsDesign2:::h1(r = 18, theta = 0, info = info[1], a = a1, b = b1)
+#' # )
+#' # cat("The upper boundary at the 2nd analysis is (", a2, ", ", b2, ").\n")
+#' 
 #' @export
 gs_spending_bound <- function(k = 1,
                               par = list(
diff --git a/man/gs_spending_bound.Rd b/man/gs_spending_bound.Rd
index 9d4159e1..84ae9411 100644
--- a/man/gs_spending_bound.Rd
+++ b/man/gs_spending_bound.Rd
@@ -85,6 +85,40 @@ that in Chapter 19 of Jennison and Turnbull (2000).
 \if{html}{The contents of this section are shown in PDF user manual only.}
 }
 
+\examples{
+info <- (1:3) * 10
+info_frac <- info / max(info)
+k <- length(info_frac)
+
+# 1st analysis
+a1 <- gs_spending_bound(
+  k = 1, efficacy = FALSE, theta = 0,
+  par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
+  hgm1 = NULL
+)
+
+b1 <- gs_spending_bound(
+  k = 1, efficacy = TRUE, theta = 0,
+  par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
+  hgm1 = NULL
+)
+cat("The (lower, upper) boundary at the 1st analysis is (", a1, ", ", b1, ").\n")
+
+# 2nd analysis
+# a2 <- gs_spending_bound(
+#     k = 2, efficacy = FALSE, theta = 0,
+#   par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
+#   hgm1 = gsDesign2:::h1(r = 18, theta = 0, info = info[1], a = a1, b = b1)
+# )
+
+# b2 <- gs_spending_bound(
+#    k = 2, efficacy = TRUE, theta = 0,
+#    par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
+#    hgm1 = gsDesign2:::h1(r = 18, theta = 0, info = info[1], a = a1, b = b1)
+# )
+# cat("The upper boundary at the 2nd analysis is (", a2, ", ", b2, ").\n")
+
+}
 \references{
 Jennison C and Turnbull BW (2000),
 \emph{Group Sequential Methods with Applications to Clinical Trials}.

From 1198152c05042e32daeed0b869ffb88b901d24ad Mon Sep 17 00:00:00 2001
From: yilong zhang <elong0527@gmail.com>
Date: Sat, 15 Jul 2023 02:55:36 +0000
Subject: [PATCH 03/13] address warning in test

---
 R/utility_tidy_tbl.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/utility_tidy_tbl.R b/R/utility_tidy_tbl.R
index 1d706338..7889f522 100644
--- a/R/utility_tidy_tbl.R
+++ b/R/utility_tidy_tbl.R
@@ -75,7 +75,7 @@ table_ab <- function(table_a, table_b, byvar, decimals = 1, aname = names(table_
   # Get order of names to unite table_a columns together with names into a string
   col_order <- c(rbind(names(anames), names(table_a)))
   # Now unite columns of table_a into a string
-  astring <- xx %>% tidyr::unite("_alab", col_order, sep = " ")
+  astring <- xx %>% tidyr::unite("_alab", all_of(col_order), sep = " ")
   # Bind this together with the byvar column
   astring <- cbind(table_a %>% select(all_of(byvar)), astring)
   # Now merge with table_b

From df9f441225b31c2d6a48bf56e88d131ba31ab684 Mon Sep 17 00:00:00 2001
From: yilong zhang <elong0527@gmail.com>
Date: Sat, 15 Jul 2023 03:17:37 +0000
Subject: [PATCH 04/13] apply ::: to internal functions

---
 .../test-developer-gs_spending_bound.R        |  4 +--
 tests/testthat/test-independent-gridpts.R     |  4 +--
 .../test-independent-gs_spending_bound.R      | 16 ++++++------
 tests/testthat/test-independent-h1.R          | 18 ++++++-------
 tests/testthat/test-independent-hupdate.R     | 26 +++++++++----------
 tests/testthat/test-oldversion-gridpts.R      |  6 ++---
 6 files changed, 37 insertions(+), 37 deletions(-)

diff --git a/tests/testthat/test-developer-gs_spending_bound.R b/tests/testthat/test-developer-gs_spending_bound.R
index 134cacf7..9ff70efd 100644
--- a/tests/testthat/test-developer-gs_spending_bound.R
+++ b/tests/testthat/test-developer-gs_spending_bound.R
@@ -1,8 +1,8 @@
 test_that("gs_spending_bound() does not execute as expected", {
   expect_true(is.numeric(b <- gs_spending_bound()))
   expect_true(is.numeric(a <- gs_spending_bound(efficacy = FALSE)))
-  hgm1_0 <- h1(theta = 0, info = 1, a = a, b = b)
-  hgm1_1 <- h1(theta = .1, info = 1, a = a, b = b)
+  hgm1_0 <- gsDesign2:::h1(theta = 0, info = 1, a = a, b = b)
+  hgm1_1 <- gsDesign2:::h1(theta = .1, info = 1, a = a, b = b)
   expect_true(is.numeric(b2 <- gs_spending_bound(k = 2, theta = 0, hgm1 = hgm1_0)))
   expect_true(is.numeric(a2 <- gs_spending_bound(k = 2, theta = .1, hgm1 = hgm1_1, efficacy = FALSE)))
 })
diff --git a/tests/testthat/test-independent-gridpts.R b/tests/testthat/test-independent-gridpts.R
index 42c448a3..d701965f 100644
--- a/tests/testthat/test-independent-gridpts.R
+++ b/tests/testthat/test-independent-gridpts.R
@@ -1,10 +1,10 @@
 test_that("compare gridpts results with gsDesign::normalGrid results", {
-  x1 <- gridpts(r = 18, mu = 4, a = -Inf, b = Inf)
+  x1 <- gsDesign2:::gridpts(r = 18, mu = 4, a = -Inf, b = Inf)
   x2 <- gsDesign::normalGrid(r = 18, bounds = c(-40, 40), mu = 4, sigma = 1)
   expect_equal(x1$w, x2$gridwgts)
   expect_equal(x1$z, x2$z)
 
-  x1 <- gridpts(r = 18, mu = 2, a = -Inf, b = Inf)
+  x1 <- gsDesign2:::gridpts(r = 18, mu = 2, a = -Inf, b = Inf)
   x2 <- gsDesign::normalGrid(r = 18, bounds = c(-40, 40), mu = 2, sigma = 1)
   expect_equal(x1$w, x2$gridwgts)
   expect_equal(x1$z, x2$z)
diff --git a/tests/testthat/test-independent-gs_spending_bound.R b/tests/testthat/test-independent-gs_spending_bound.R
index 0f6cb055..3b98e8ae 100644
--- a/tests/testthat/test-independent-gs_spending_bound.R
+++ b/tests/testthat/test-independent-gs_spending_bound.R
@@ -25,7 +25,7 @@ test_that("compare gs_spending_bound with gsDesign results with equal IA timing
   a <- -Inf
   b <- Inf
   b <- gs_spending_bound()
-  hgm1_0 <- h1(
+  hgm1_0 <- gsDesign2:::h1(
     theta = 0,
     info = info[1],
     a = a,
@@ -37,7 +37,7 @@ test_that("compare gs_spending_bound with gsDesign results with equal IA timing
     hgm1 = hgm1_0,
     info = info
   )
-  hgm2_0 <- hupdate(
+  hgm2_0 <- gsDesign2:::hupdate(
     theta = 0,
     info = info[2],
     a = a,
@@ -61,7 +61,7 @@ test_that("compare gs_spending_bound with gsDesign results with equal IA timing
     efficacy = FALSE,
     info = info
   )
-  hgm1_1 <- h1(theta = x$theta[2], info = info[1], a = a, b = b)
+  hgm1_1 <- gsDesign2:::h1(theta = x$theta[2], info = info[1], a = a, b = b)
 
   a2 <- gs_spending_bound(
     k = 2,
@@ -72,7 +72,7 @@ test_that("compare gs_spending_bound with gsDesign results with equal IA timing
     info = info
   )
 
-  hgm2_1 <- hupdate(
+  hgm2_1 <- gsDesign2:::hupdate(
     theta = x$theta[2],
     info = info[2],
     a = a2,
@@ -129,7 +129,7 @@ test_that("compare gs_spending_bound with gsDesign results with unequal IA timin
     hgm1 = NULL,
     info = info
   )
-  hgm1_0 <- h1(
+  hgm1_0 <- gsDesign2:::h1(
     theta = 0,
     info = info[1],
     a = a,
@@ -141,7 +141,7 @@ test_that("compare gs_spending_bound with gsDesign results with unequal IA timin
     hgm1 = hgm1_0,
     info = info
   )
-  hgm2_0 <- hupdate(
+  hgm2_0 <- gsDesign2:::hupdate(
     theta = 0,
     info = info[2],
     a = a,
@@ -166,7 +166,7 @@ test_that("compare gs_spending_bound with gsDesign results with unequal IA timin
     info = info
   )
 
-  hgm1_1 <- h1(theta = y$theta[2], info = info[1], a = a, b = b)
+  hgm1_1 <- gsDesign2:::h1(theta = y$theta[2], info = info[1], a = a, b = b)
 
   a2 <- gs_spending_bound(
     k = 2,
@@ -177,7 +177,7 @@ test_that("compare gs_spending_bound with gsDesign results with unequal IA timin
     info = info
   )
 
-  hgm2_1 <- hupdate(
+  hgm2_1 <- gsDesign2:::hupdate(
     theta = y$theta[2],
     info = info[2],
     a = a2,
diff --git a/tests/testthat/test-independent-h1.R b/tests/testthat/test-independent-h1.R
index 5739415e..b4fa9e3a 100644
--- a/tests/testthat/test-independent-h1.R
+++ b/tests/testthat/test-independent-h1.R
@@ -1,30 +1,30 @@
-test_that("h1() returns results as expected ", {
+test_that("gsDesign2:::h1() returns results as expected ", {
   # the design
   gstry <- gsDesign::gsDesign(
     k = 3,
     sfl = gsDesign::sfLDOF,
     delta = 0
   )
-  # probabilities calculated based on function h1()
-  upper.null <- sum(h1(
+  # probabilities calculated based on function gsDesign2:::h1()
+  upper.null <- sum(gsDesign2:::h1(
     theta = gstry$theta[1],
     info = gstry$n.I[1],
     a = gstry$upper$bound[1],
     b = Inf
   )$h)
-  upper.alt <- sum(h1(
+  upper.alt <- sum(gsDesign2:::h1(
     theta = gstry$theta[2],
     info = gstry$n.I[1],
     a = gstry$upper$bound[1],
     b = Inf
   )$h)
-  lower.null <- sum(h1(
+  lower.null <- sum(gsDesign2:::h1(
     theta = gstry$theta[1],
     info = gstry$n.I[1],
     a = -Inf,
     b = gstry$lower$bound[1]
   )$h)
-  lower.alt <- sum(h1(
+  lower.alt <- sum(gsDesign2:::h1(
     theta = gstry$theta[2],
     info = gstry$n.I[1],
     a = -Inf,
@@ -41,8 +41,8 @@ test_that("h1() returns results as expected ", {
   expect_equal(object = as.numeric(c(lower.null, lower.alt)), expected = x$lower$prob[1, ], tolerance = 0.0001)
 })
 
-test_that("h1() returns probability almost zero for extreme case", {
-  exmtest1 <- sum(h1(theta = 9, info = 0.5, a = -Inf, b = 0)$h)
-  exmtest2 <- sum(h1(theta = 1, info = 0.5, a = 9, b = Inf)$h)
+test_that("gsDesign2:::h1() returns probability almost zero for extreme case", {
+  exmtest1 <- sum(gsDesign2:::h1(theta = 9, info = 0.5, a = -Inf, b = 0)$h)
+  exmtest2 <- sum(gsDesign2:::h1(theta = 1, info = 0.5, a = 9, b = Inf)$h)
   expect_equal(object = as.numeric(c(exmtest1, exmtest2)), expected = c(0, 0), tolerance = 0.0001)
 })
diff --git a/tests/testthat/test-independent-hupdate.R b/tests/testthat/test-independent-hupdate.R
index 0b5337ae..dd144a47 100644
--- a/tests/testthat/test-independent-hupdate.R
+++ b/tests/testthat/test-independent-hupdate.R
@@ -1,20 +1,20 @@
-test_that("hupdate() returns results as expected ", {
+test_that("gsDesign2:::hupdate() returns results as expected ", {
   # the design
   gstry <- gsDesign::gsDesign(
     k = 3,
     sfl = gsDesign::sfLDOF,
     delta = 0
   )
-  # probabilities calculated based on function h1(), IA1 needs to full between low and upper bound
+  # probabilities calculated based on function gsDesign2:::h1(), IA1 needs to full between low and upper bound
   # in order to continue to IA2
-  null.01 <- h1(
+  null.01 <- gsDesign2:::h1(
     theta = gstry$theta[1],
     info = gstry$n.I[1],
     a = gstry$lower$bound[1],
     b = gstry$upper$bound[1]
   )
   # IA2 to reject H0, we integrate from upper bound to Inf
-  upper.null.02 <- sum(hupdate(
+  upper.null.02 <- sum(gsDesign2:::hupdate(
     theta = gstry$theta[1],
     thetam1 = gstry$theta[1],
     info = gstry$n.I[2],
@@ -24,7 +24,7 @@ test_that("hupdate() returns results as expected ", {
     b = Inf
   )$h)
   # IA2 to accept H0, we integrate from -Inf to lower bound
-  lower.null.02 <- sum(hupdate(
+  lower.null.02 <- sum(gsDesign2:::hupdate(
     theta = gstry$theta[1],
     thetam1 = gstry$theta[1],
     info = gstry$n.I[2],
@@ -34,14 +34,14 @@ test_that("hupdate() returns results as expected ", {
     b = gstry$lower$bound[2]
   )$h)
 
-  alt.01 <- h1(
+  alt.01 <- gsDesign2:::h1(
     theta = gstry$theta[2],
     info = gstry$n.I[1],
     a = gstry$lower$bound[1],
     b = gstry$upper$bound[1]
   )
   # IA2 to reject H0, we integrate from upper bound to Inf
-  upper.alt.02 <- sum(hupdate(
+  upper.alt.02 <- sum(gsDesign2:::hupdate(
     theta = gstry$theta[2],
     thetam1 = gstry$theta[2],
     info = gstry$n.I[2],
@@ -51,7 +51,7 @@ test_that("hupdate() returns results as expected ", {
     b = Inf
   )$h)
   # IA2 to accept H0, we integrate from -Inf to lower bound
-  lower.alt.02 <- sum(hupdate(
+  lower.alt.02 <- sum(gsDesign2:::hupdate(
     theta = gstry$theta[2],
     thetam1 = gstry$theta[2],
     info = gstry$n.I[2],
@@ -72,19 +72,19 @@ test_that("hupdate() returns results as expected ", {
   expect_equal(object = as.numeric(c(lower.null.02, lower.alt.02)), expected = x$lower$prob[2, ], tolerance = 0.0001)
   expect_equal(object = as.numeric(c(upper.null.02, upper.alt.02)), expected = x$upper$prob[2, ], tolerance = 0.0001)
   # problem with below code on extreme case:
-  # hupdate(theta = gstry$theta[1], thetam1= gstry$theta[1],
+  # gsDesign2:::theta = gstry$theta[1], thetam1= gstry$theta[1],
   #     info=gstry$n.I[1]+0.00000000000001,im1=gstry$n.I[1],gm1=null.01,
   #     a = gstry$upper$bound[2],b=Inf) %>% summarise(p = sum(h))
 })
 
-test_that("hupdate() returns probability almost zero for extreme case", {
+test_that("gsDesign2:::) returns probability almost zero for extreme case", {
   # the design
   gstry <- gsDesign::gsDesign(
     k = 3,
     sfl = gsDesign::sfLDOF,
     delta = 0
   )
-  null.01 <- h1(
+  null.01 <- gsDesign2:::h1(
     theta = gstry$theta[1],
     info = gstry$n.I[1],
     a = gstry$lower$bound[1],
@@ -92,7 +92,7 @@ test_that("hupdate() returns probability almost zero for extreme case", {
   )
   # IA2 to reject H0, we integrate from upper bound to Inf
   #-8 is an arbitrary extreme case for theta
-  poor.02 <- sum(hupdate(
+  poor.02 <- sum(gsDesign2:::hupdate(
     theta = -8,
     thetam1 = gstry$theta[1],
     info = gstry$n.I[2],
@@ -103,7 +103,7 @@ test_that("hupdate() returns probability almost zero for extreme case", {
   )$h)
   # IA2 to accept H0, we integrate from -Inf to lower bound
   #-8 is an arbitrary extreme case for the bound
-  high.02 <- sum(hupdate(
+  high.02 <- sum(gsDesign2:::hupdate(
     theta = gstry$theta[2],
     thetam1 = gstry$theta[2],
     info = gstry$n.I[2],
diff --git a/tests/testthat/test-oldversion-gridpts.R b/tests/testthat/test-oldversion-gridpts.R
index f70eecde..0c25a659 100644
--- a/tests/testthat/test-oldversion-gridpts.R
+++ b/tests/testthat/test-oldversion-gridpts.R
@@ -6,21 +6,21 @@ library(dplyr)
 
 test_that("Default (N(0,1)) - approximate variance of standard normal (i.e., 1)", {
   x1 <- gridpts_(mu = 0, a = -20, b = 20, r = 18)  # gsDesign2 old version
-  x2 <- gridpts(mu = 0, a = -20, b = 20, r = 18)   # gsDesign2 latest version
+  x2 <- gsDesign2:::gridpts(mu = 0, a = -20, b = 20, r = 18)   # gsDesign2 latest version
   expect_equal(x1$z, x2$z)
   expect_equal(x1$w, x2$w)
 })
 
 test_that("Approximate probability of N(0,1) above .95 quantile (i.e., .05)", {
   x1 <- gridpts_(mu = 0, a = qnorm(0.95), b = Inf, r = 18)
-  x2 <- gridpts(mu = 0, a = qnorm(0.95), b = Inf, r = 18)
+  x2 <- gsDesign2:::gridpts(mu = 0, a = qnorm(0.95), b = Inf, r = 18)
   expect_equal(x1$z, x2$z)
   expect_equal(x1$w, x2$w)
 })
 
 test_that("Approximate probability of N(0.5, 1) above .95 quantile (i.e., .05)", {
   x1 <- gridpts_(mu = 0.5, a = qnorm(0.95), b = Inf, r = 18)
-  x2 <- gridpts(mu = 0.5, a = qnorm(0.95), b = Inf, r = 18)
+  x2 <- gsDesign2:::gridpts(mu = 0.5, a = qnorm(0.95), b = Inf, r = 18)
   expect_equal(x1$z, x2$z)
   expect_equal(x1$w, x2$w)
 })

From c78be2422a78bd736e7e3a01c92f9da44a490af4 Mon Sep 17 00:00:00 2001
From: yilong zhang <elong0527@gmail.com>
Date: Sat, 15 Jul 2023 06:01:44 +0000
Subject: [PATCH 05/13] use old `h1_` function instead of `h1`.

---
 inst/old_function/gridpts_h1_hupdate_oldR.R | 2 +-
 inst/old_function/gs_power_npe_.R           | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/inst/old_function/gridpts_h1_hupdate_oldR.R b/inst/old_function/gridpts_h1_hupdate_oldR.R
index 26607aa5..f65e741e 100644
--- a/inst/old_function/gridpts_h1_hupdate_oldR.R
+++ b/inst/old_function/gridpts_h1_hupdate_oldR.R
@@ -188,7 +188,7 @@ NULL
 #' gsDesign2:::hupdate_() %>% summarise(mu = sum(z * h), var = sum((z - mu)^2 * h))
 #'
 #' @noRd
-hupdate_ <- function(r = 18, theta = 0, I = 2, a = -Inf, b = Inf, thetam1 = 0, Im1 = 1, gm1 = h1()) {
+hupdate_ <- function(r = 18, theta = 0, I = 2, a = -Inf, b = Inf, thetam1 = 0, Im1 = 1, gm1 = h1_()) {
   # sqrt of change in information
   rtdelta <- sqrt(I - Im1)
   rtI <- sqrt(I)
diff --git a/inst/old_function/gs_power_npe_.R b/inst/old_function/gs_power_npe_.R
index e09f1931..2dc8ae8e 100644
--- a/inst/old_function/gs_power_npe_.R
+++ b/inst/old_function/gs_power_npe_.R
@@ -255,15 +255,15 @@ gs_power_npe_ <- function(theta = .1, theta1 = NULL, info = 1, info1 = NULL, inf
         0
       }
 
-      hgm1_0 <- h1(r = r, theta = 0, info = info0[1], a = if (binding) {
+      hgm1_0 <- h1_(r = r, theta = 0, info = info0[1], a = if (binding) {
         a[1]
       } else {
         -Inf
       }, b = b[1])
 
-      hgm1_1 <- h1(r = r, theta = theta1[1], info = info1[1], a = a[1], b = b[1])
+      hgm1_1 <- h1_(r = r, theta = theta1[1], info = info1[1], a = a[1], b = b[1])
 
-      hgm1 <- h1(r = r, theta = theta[1], info = info[1], a = a[1], b = b[1])
+      hgm1 <- h1_(r = r, theta = theta[1], info = info[1], a = a[1], b = b[1])
     } else {
       # Cross upper bound
       upperProb[k] <- if (b[k] < Inf) {

From c282f328bccccb4d5d503916ff6d9a0a0941f024 Mon Sep 17 00:00:00 2001
From: yilong zhang <elong0527@gmail.com>
Date: Sun, 16 Jul 2023 16:40:49 +0000
Subject: [PATCH 06/13] using gsDesign2:::h1()

---
 inst/old_function/gridpts_h1_hupdate_oldR.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/old_function/gridpts_h1_hupdate_oldR.R b/inst/old_function/gridpts_h1_hupdate_oldR.R
index f65e741e..b04b3519 100644
--- a/inst/old_function/gridpts_h1_hupdate_oldR.R
+++ b/inst/old_function/gridpts_h1_hupdate_oldR.R
@@ -188,7 +188,7 @@ NULL
 #' gsDesign2:::hupdate_() %>% summarise(mu = sum(z * h), var = sum((z - mu)^2 * h))
 #'
 #' @noRd
-hupdate_ <- function(r = 18, theta = 0, I = 2, a = -Inf, b = Inf, thetam1 = 0, Im1 = 1, gm1 = h1_()) {
+hupdate_ <- function(r = 18, theta = 0, I = 2, a = -Inf, b = Inf, thetam1 = 0, Im1 = 1, gm1 = gsDesign2:::h1()) {
   # sqrt of change in information
   rtdelta <- sqrt(I - Im1)
   rtI <- sqrt(I)

From d0798c6a25f964130fc4b3f1e2b1c466062d956e Mon Sep 17 00:00:00 2001
From: yilong zhang <elong0527@gmail.com>
Date: Sun, 16 Jul 2023 17:17:02 +0000
Subject: [PATCH 07/13] using `gsDesign2:::`

---
 inst/old_function/gs_power_npe_.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/inst/old_function/gs_power_npe_.R b/inst/old_function/gs_power_npe_.R
index 2dc8ae8e..208031d9 100644
--- a/inst/old_function/gs_power_npe_.R
+++ b/inst/old_function/gs_power_npe_.R
@@ -255,15 +255,15 @@ gs_power_npe_ <- function(theta = .1, theta1 = NULL, info = 1, info1 = NULL, inf
         0
       }
 
-      hgm1_0 <- h1_(r = r, theta = 0, info = info0[1], a = if (binding) {
+      hgm1_0 <- gsDesign2:::h1(r = r, theta = 0, info = info0[1], a = if (binding) {
         a[1]
       } else {
         -Inf
       }, b = b[1])
 
-      hgm1_1 <- h1_(r = r, theta = theta1[1], info = info1[1], a = a[1], b = b[1])
+      hgm1_1 <- gsDesign2:::h1(r = r, theta = theta1[1], info = info1[1], a = a[1], b = b[1])
 
-      hgm1 <- h1_(r = r, theta = theta[1], info = info[1], a = a[1], b = b[1])
+      hgm1 <- gsDesign2:::h1(r = r, theta = theta[1], info = info[1], a = a[1], b = b[1])
     } else {
       # Cross upper bound
       upperProb[k] <- if (b[k] < Inf) {

From 2471a53da77f32bca748ecc7f28f6299fa9785d2 Mon Sep 17 00:00:00 2001
From: yilong zhang <elong0527@gmail.com>
Date: Sun, 16 Jul 2023 17:41:56 +0000
Subject: [PATCH 08/13] using gsDesign2:::hupdate

---
 inst/old_function/gs_power_npe_.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/inst/old_function/gs_power_npe_.R b/inst/old_function/gs_power_npe_.R
index 208031d9..d5caf8a1 100644
--- a/inst/old_function/gs_power_npe_.R
+++ b/inst/old_function/gs_power_npe_.R
@@ -292,7 +292,7 @@ gs_power_npe_ <- function(theta = .1, theta1 = NULL, info = 1, info1 = NULL, inf
       if (k < K) {
         # hgm1_0 <- hupdate(r = r, theta = 0, info = info0[k], a = if(binding){a[k]}else{-Inf}, b = b[k],
         #                   thetam1 = 0, im1 = info0[k-1], gm1 = hgm1_0)
-        hgm1_0 <- hupdate(
+        hgm1_0 <- gsDesign2:::hupdate(
           r = r, theta = 0, info = info0[k], a = if (binding) {
             a[k]
           } else {
@@ -302,13 +302,13 @@ gs_power_npe_ <- function(theta = .1, theta1 = NULL, info = 1, info1 = NULL, inf
         )
         # hgm1_1 <- hupdate(r = r, theta = theta1[k], info = info1[k], a = a[k], b = b[k],
         #                   thetam1 = theta1[k-1], im1 = info1[k-1], gm1 = hgm1_1)
-        hgm1_1 <- hupdate(
+        hgm1_1 <- gsDesign2:::(
           r = r, theta = theta1[k], info = info1[k], a = a[k], b = b[k],
           thetam1 = theta1[k - 1], im1 = info1[k - 1], gm1 = hgm1_1
         )
         # hgm1   <- hupdate(r = r, theta = theta[k], info = info[k], a = a[k], b = b[k],
         #                   thetam1 = theta[k-1], im1 = info[k-1], gm1 = hgm1)
-        hgm1 <- hupdate(
+        hgm1 <- gsDesign2:::(
           r = r, theta = theta[k], info = info[k], a = a[k], b = b[k],
           thetam1 = theta[k - 1], im1 = info[k - 1], gm1 = hgm1
         )

From 4736a698d71d0f2ac0a6de2342cf2f4dab9432c9 Mon Sep 17 00:00:00 2001
From: yilong zhang <elong0527@gmail.com>
Date: Sun, 16 Jul 2023 17:42:42 +0000
Subject: [PATCH 09/13] using gsDesign2:::gridpts

---
 inst/old_function/gridpts_h1_hupdate_oldR.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/inst/old_function/gridpts_h1_hupdate_oldR.R b/inst/old_function/gridpts_h1_hupdate_oldR.R
index b04b3519..2aac01f1 100644
--- a/inst/old_function/gridpts_h1_hupdate_oldR.R
+++ b/inst/old_function/gridpts_h1_hupdate_oldR.R
@@ -144,7 +144,7 @@ h1_ <- function(r = 18, theta = 0, I = 1, a = -Inf, b = Inf) {
   z <- w <- h <- NULL
   # compute drift at analysis 1
   mu <- theta * sqrt(I)
-  g <- gridpts(r, mu, a, b)
+  g <- gsDesign2:::gridpts(r, mu, a, b)
   # compute deviation from drift
   x <- g$z - mu
   # compute standard normal density, multiply by grid weight and return
@@ -193,7 +193,7 @@ hupdate_ <- function(r = 18, theta = 0, I = 2, a = -Inf, b = Inf, thetam1 = 0, I
   rtdelta <- sqrt(I - Im1)
   rtI <- sqrt(I)
   rtIm1 <- sqrt(Im1)
-  g <- gridpts(r = r, mu = theta * rtI, a = a, b = b)
+  g <- gsDesign2:::gridpts(r = r, mu = theta * rtI, a = a, b = b)
   # update integration
   mu <- theta * I - thetam1 * Im1
   h <- rep(0, length(g$z))

From 61938bbb986a6b6d03e4a1f8201bd49eb0fc0b01 Mon Sep 17 00:00:00 2001
From: yilong zhang <elong0527@gmail.com>
Date: Sun, 16 Jul 2023 17:54:10 +0000
Subject: [PATCH 10/13] fix typo

---
 inst/old_function/gs_power_npe_.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/inst/old_function/gs_power_npe_.R b/inst/old_function/gs_power_npe_.R
index d5caf8a1..16f97f4a 100644
--- a/inst/old_function/gs_power_npe_.R
+++ b/inst/old_function/gs_power_npe_.R
@@ -302,13 +302,13 @@ gs_power_npe_ <- function(theta = .1, theta1 = NULL, info = 1, info1 = NULL, inf
         )
         # hgm1_1 <- hupdate(r = r, theta = theta1[k], info = info1[k], a = a[k], b = b[k],
         #                   thetam1 = theta1[k-1], im1 = info1[k-1], gm1 = hgm1_1)
-        hgm1_1 <- gsDesign2:::(
+        hgm1_1 <- gsDesign2:::hupdate(
           r = r, theta = theta1[k], info = info1[k], a = a[k], b = b[k],
           thetam1 = theta1[k - 1], im1 = info1[k - 1], gm1 = hgm1_1
         )
         # hgm1   <- hupdate(r = r, theta = theta[k], info = info[k], a = a[k], b = b[k],
         #                   thetam1 = theta[k-1], im1 = info[k-1], gm1 = hgm1)
-        hgm1 <- gsDesign2:::(
+        hgm1 <- gsDesign2:::hupdate(
           r = r, theta = theta[k], info = info[k], a = a[k], b = b[k],
           thetam1 = theta[k - 1], im1 = info[k - 1], gm1 = hgm1
         )

From 9903a133d8c45f8c582a1cd918ca2fcfefd04cdc Mon Sep 17 00:00:00 2001
From: yilong zhang <elong0527@gmail.com>
Date: Sun, 16 Jul 2023 18:07:37 +0000
Subject: [PATCH 11/13] using gsDesign2:::hupdate

---
 inst/old_function/gs_power_npe_.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/inst/old_function/gs_power_npe_.R b/inst/old_function/gs_power_npe_.R
index 16f97f4a..6a0357b0 100644
--- a/inst/old_function/gs_power_npe_.R
+++ b/inst/old_function/gs_power_npe_.R
@@ -270,7 +270,7 @@ gs_power_npe_ <- function(theta = .1, theta1 = NULL, info = 1, info1 = NULL, inf
         # hupdate(r = r, theta = theta[k], info = info[k], a = b[k], b = Inf,
         #         thetam1 = theta[k - 1], im1 = info[k - 1], gm1 = hgm1) %>%
         #   summarise(sum(h)) %>% as.numeric()
-        sum(hupdate(
+        sum(gsDesign2:::hupdate(
           r = r, theta = theta[k], info = info[k], a = b[k], b = Inf,
           thetam1 = theta[k - 1], im1 = info[k - 1], gm1 = hgm1
         )$h)
@@ -282,7 +282,7 @@ gs_power_npe_ <- function(theta = .1, theta1 = NULL, info = 1, info1 = NULL, inf
         # hupdate(r = r, theta = theta[k], info = info[k], a = -Inf, b = a[k],
         #         thetam1 = theta[k - 1], im1 = info[k - 1], gm1 = hgm1) %>%
         #   summarise(sum(h)) %>% as.numeric()
-        sum(hupdate(
+        sum(gsDesign2:::hupdate(
           r = r, theta = theta[k], info = info[k], a = -Inf, b = a[k],
           thetam1 = theta[k - 1], im1 = info[k - 1], gm1 = hgm1
         )$h)

From af743f76e07005df791784737c7c6e0f70c7273d Mon Sep 17 00:00:00 2001
From: yilong zhang <elong0527@gmail.com>
Date: Sun, 16 Jul 2023 18:30:47 +0000
Subject: [PATCH 12/13] run styler

---
 R/gs_spending_bound.R                         |  4 ++--
 tests/testthat/test-oldversion-ahr.R          | 24 ++++++++++++-------
 .../testthat/test-oldversion-expected_event.R | 13 ++++++----
 .../testthat/test-oldversion-expected_time.R  | 18 +++++++++-----
 tests/testthat/test-oldversion-gridpts.R      |  4 ++--
 .../testthat/test-oldversion-gs_design_ahr.R  | 12 ++++++----
 .../testthat/test-oldversion-gs_design_npe.R  | 16 ++++++++-----
 tests/testthat/test-oldversion-gs_power_npe.R | 15 ++++++++----
 8 files changed, 68 insertions(+), 38 deletions(-)

diff --git a/R/gs_spending_bound.R b/R/gs_spending_bound.R
index ed9104ac..025f4632 100644
--- a/R/gs_spending_bound.R
+++ b/R/gs_spending_bound.R
@@ -79,7 +79,7 @@
 #'
 #' @importFrom gsDesign gsDesign sfLDOF
 #' @importFrom stats qnorm
-#' 
+#'
 #' @examples
 #' info <- (1:3) * 10
 #' info_frac <- info / max(info)
@@ -112,7 +112,7 @@
 #' #    hgm1 = gsDesign2:::h1(r = 18, theta = 0, info = info[1], a = a1, b = b1)
 #' # )
 #' # cat("The upper boundary at the 2nd analysis is (", a2, ", ", b2, ").\n")
-#' 
+#'
 #' @export
 gs_spending_bound <- function(k = 1,
                               par = list(
diff --git a/tests/testthat/test-oldversion-ahr.R b/tests/testthat/test-oldversion-ahr.R
index 89dc7bfd..e96e64ff 100644
--- a/tests/testthat/test-oldversion-ahr.R
+++ b/tests/testthat/test-oldversion-ahr.R
@@ -7,21 +7,25 @@ library(dplyr)
 test_that("unstratified population", {
   enroll_rate <- define_enroll_rate(
     duration = c(2, 10, 4, 4, 8),
-    rate = c(5, 10, 0, 3, 6))
+    rate = c(5, 10, 0, 3, 6)
+  )
   fail_rate <- define_fail_rate(
     stratum = "All",
     duration = 1,
     fail_rate = c(.1, .2, .3, .4),
     hr = c(.9, .75, .8, .6),
-    dropout_rate = .001)
+    dropout_rate = .001
+  )
   x1 <- ahr( # latest version
     enroll_rate = enroll_rate,
     fail_rate = fail_rate,
-    total_duration = c(15, 30))
+    total_duration = c(15, 30)
+  )
   x2 <- AHR_( # old version
     enrollRates = enroll_rate %>% rename(Stratum = stratum),
     failRates = fail_rate %>% rename(Stratum = stratum, failRate = fail_rate, dropoutRate = dropout_rate),
-    totalDuration = c(15, 30)) %>%
+    totalDuration = c(15, 30)
+  ) %>%
     rename(time = Time, ahr = AHR, event = Events)
   expect_equal(x1, x2)
 })
@@ -30,21 +34,25 @@ test_that("stratified population", {
   enroll_rate <- define_enroll_rate(
     stratum = c(rep("Low", 2), rep("High", 3)),
     duration = c(2, 10, 4, 4, 8),
-    rate = c(5, 10, 0, 3, 6))
+    rate = c(5, 10, 0, 3, 6)
+  )
   fail_rate <- define_fail_rate(
     stratum = c(rep("Low", 2), rep("High", 2)),
     duration = 1,
     fail_rate = c(.1, .2, .3, .4),
     hr = c(.9, .75, .8, .6),
-    dropout_rate = .001)
+    dropout_rate = .001
+  )
   x1 <- ahr( # latest version
     enroll_rate = enroll_rate,
     fail_rate = fail_rate,
-    total_duration = c(15, 30))
+    total_duration = c(15, 30)
+  )
   x2 <- AHR_( # old version
     enrollRates = enroll_rate %>% rename(Stratum = stratum),
     failRates = fail_rate %>% rename(Stratum = stratum, failRate = fail_rate, dropoutRate = dropout_rate),
-    totalDuration = c(15, 30)) %>%
+    totalDuration = c(15, 30)
+  ) %>%
     rename(time = Time, ahr = AHR, event = Events)
   expect_equal(x1, x2)
 })
diff --git a/tests/testthat/test-oldversion-expected_event.R b/tests/testthat/test-oldversion-expected_event.R
index 5f07f74a..b4c698d7 100644
--- a/tests/testthat/test-oldversion-expected_event.R
+++ b/tests/testthat/test-oldversion-expected_event.R
@@ -8,7 +8,7 @@ test_that("expected event vs gsDesign", {
   enroll_rate <- define_enroll_rate(duration = c(2, 1, 2), rate = c(5, 10, 20))
   fail_rate <- define_fail_rate(duration = c(1, 1, 1), fail_rate = c(.05, .02, .01), dropout_rate = .01)
   total_duration <- 20
-  x1 <- gsDesign::eEvents(  # gsDesign
+  x1 <- gsDesign::eEvents( # gsDesign
     lambda = fail_rate$fail_rate,
     S = fail_rate$duration[1:(nrow(fail_rate) - 1)],
     eta = fail_rate$dropout_rate,
@@ -16,13 +16,16 @@ test_that("expected event vs gsDesign", {
     R = enroll_rate$duration,
     T = total_duration
   )$d
-  x2 <- eEvents_df_(      # gsDesign2 old version
+  x2 <- eEvents_df_( # gsDesign2 old version
     enrollRates = enroll_rate %>% rename(Stratum = stratum),
     failRates = fail_rate %>% rename(Stratum = stratum, failRate = fail_rate, dropoutRate = dropout_rate),
     total_duration,
-    simple = TRUE)
-  x3 <- expected_event(   # gsDesign2 latest version
-    enroll_rate, fail_rate, total_duration, simple = TRUE)
+    simple = TRUE
+  )
+  x3 <- expected_event( # gsDesign2 latest version
+    enroll_rate, fail_rate, total_duration,
+    simple = TRUE
+  )
   expect(x1, x2)
   expect(x2, x3)
 })
diff --git a/tests/testthat/test-oldversion-expected_time.R b/tests/testthat/test-oldversion-expected_time.R
index 2075123c..34dafe66 100644
--- a/tests/testthat/test-oldversion-expected_time.R
+++ b/tests/testthat/test-oldversion-expected_time.R
@@ -8,18 +8,21 @@ test_that("time to targeted events", {
   enroll_rate <- define_enroll_rate(stratum = "All", duration = c(2, 2, 10), rate = c(3, 6, 9) * 5)
   fail_rate <- define_fail_rate(
     stratum = "All", duration = c(3, 100), fail_rate = log(2) / c(9, 18),
-    hr = c(.9, .6), dropout_rate = rep(.001, 2))
+    hr = c(.9, .6), dropout_rate = rep(.001, 2)
+  )
   ratio <- 1
   x <- AHR_(
     enrollRates = enroll_rate %>% rename(Stratum = stratum),
     failRates = fail_rate %>% rename(Stratum = stratum, failRate = fail_rate, dropoutRate = dropout_rate),
     ratio = ratio,
-    totalDuration = 20)
+    totalDuration = 20
+  )
   y <- expected_time(
     enroll_rate = enroll_rate,
     fail_rate = fail_rate,
     ratio = ratio,
-    target_event = x$Events)
+    target_event = x$Events
+  )
   expect_equal(20, y$time)
 })
 
@@ -34,18 +37,21 @@ test_that("time to targeted events by new/old version", {
   fail_rate <- define_fail_rate(
     stratum = "All", duration = c(3, 100),
     fail_rate = log(2) / c(9, 18), hr = c(.9, .6),
-    dropout_rate = rep(.001, 2))
+    dropout_rate = rep(.001, 2)
+  )
   ratio <- 1
   x1 <- expected_time(
     enroll_rate = enroll_rate,
     fail_rate = fail_rate,
     ratio = ratio,
-    target_event = 200)
+    target_event = 200
+  )
   x2 <- tEvents_(
     enrollRates = enroll_rate %>% rename(Stratum = stratum),
     failRates = fail_rate %>% rename(Stratum = stratum, failRate = fail_rate, dropoutRate = dropout_rate),
     ratio = ratio,
-    targetEvents = 200) %>%
+    targetEvents = 200
+  ) %>%
     rename(time = Time, ahr = AHR, event = Events)
   expect_equal(x1, x2)
 })
diff --git a/tests/testthat/test-oldversion-gridpts.R b/tests/testthat/test-oldversion-gridpts.R
index 0c25a659..5063274a 100644
--- a/tests/testthat/test-oldversion-gridpts.R
+++ b/tests/testthat/test-oldversion-gridpts.R
@@ -5,8 +5,8 @@ sapply(paste0(my_path, source_files), source)
 library(dplyr)
 
 test_that("Default (N(0,1)) - approximate variance of standard normal (i.e., 1)", {
-  x1 <- gridpts_(mu = 0, a = -20, b = 20, r = 18)  # gsDesign2 old version
-  x2 <- gsDesign2:::gridpts(mu = 0, a = -20, b = 20, r = 18)   # gsDesign2 latest version
+  x1 <- gridpts_(mu = 0, a = -20, b = 20, r = 18) # gsDesign2 old version
+  x2 <- gsDesign2:::gridpts(mu = 0, a = -20, b = 20, r = 18) # gsDesign2 latest version
   expect_equal(x1$z, x2$z)
   expect_equal(x1$w, x2$w)
 })
diff --git a/tests/testthat/test-oldversion-gs_design_ahr.R b/tests/testthat/test-oldversion-gs_design_ahr.R
index 2857b245..08506913 100644
--- a/tests/testthat/test-oldversion-gs_design_ahr.R
+++ b/tests/testthat/test-oldversion-gs_design_ahr.R
@@ -97,14 +97,16 @@ test_that("2-sided symmetric design with O'Brien-Fleming spending", {
     upar = list(sf = gsDesign::sfLDOF, total_spend = 0.025, param = NULL, timing = NULL),
     lower = gs_spending_bound,
     lpar = list(sf = gsDesign::sfLDOF, total_spend = 0.025, param = NULL, timing = NULL),
-    h1_spending = FALSE)
+    h1_spending = FALSE
+  )
   x2 <- gs_design_ahr_(
     analysisTimes = c(12, 24, 36), binding = TRUE,
     upper = gs_spending_bound,
     upar = list(sf = gsDesign::sfLDOF, total_spend = 0.025, param = NULL, timing = NULL),
     lower = gs_spending_bound,
     lpar = list(sf = gsDesign::sfLDOF, total_spend = 0.025, param = NULL, timing = NULL),
-    h1_spending = FALSE)
+    h1_spending = FALSE
+  )
   expect_equal(x1$analysis$time, x2$bounds$Time[x2$bounds$Bound == "Upper"])
   expect_equal(x1$analysis$event, x2$bounds$Events[x2$bounds$Bound == "Upper"])
   expect_equal(x1$bound$z[x1$bound$bound == "upper"], x2$bounds$Z[x2$bounds$Bound == "Upper"])
@@ -124,14 +126,16 @@ test_that("Pocock lower spending under H1 (NPH)", {
     upar = list(sf = gsDesign::sfLDOF, total_spend = 0.025, param = NULL, timing = NULL),
     lower = gs_spending_bound,
     lpar = list(sf = gsDesign::sfLDPocock, total_spend = 0.1, param = NULL, timing = NULL),
-    h1_spending = TRUE)
+    h1_spending = TRUE
+  )
   x2 <- gs_design_ahr_(
     analysisTimes = c(12, 24, 36), binding = TRUE,
     upper = gs_spending_bound,
     upar = list(sf = gsDesign::sfLDOF, total_spend = 0.025, param = NULL, timing = NULL),
     lower = gs_spending_bound,
     lpar = list(sf = gsDesign::sfLDPocock, total_spend = 0.1, param = NULL, timing = NULL),
-    h1_spending = TRUE)
+    h1_spending = TRUE
+  )
   expect_equal(x1$analysis$time, x2$bounds$Time[x2$bounds$Bound == "Upper"])
   expect_equal(x1$analysis$event, x2$bounds$Events[x2$bounds$Bound == "Upper"])
   expect_equal(x1$bound$z[x1$bound$bound == "upper"], x2$bounds$Z[x2$bounds$Bound == "Upper"])
diff --git a/tests/testthat/test-oldversion-gs_design_npe.R b/tests/testthat/test-oldversion-gs_design_npe.R
index eaa0ee8f..253f7476 100644
--- a/tests/testthat/test-oldversion-gs_design_npe.R
+++ b/tests/testthat/test-oldversion-gs_design_npe.R
@@ -28,7 +28,8 @@ test_that("verify by gs_power_npe", {
     upper = gs_spending_bound,
     upar = list(sf = gsDesign::sfLDOF, total_spend = 0.025, param = NULL, timing = NULL),
     lower = gs_spending_bound,
-    lpar = list(sf = gsDesign::sfLDOF, total_spend = 0.025, param = NULL, timing = NULL), binding = TRUE)
+    lpar = list(sf = gsDesign::sfLDOF, total_spend = 0.025, param = NULL, timing = NULL), binding = TRUE
+  )
   # The power is 0.9. If we re-use these bounds under alternate hypothesis, then we can get a power close to 0.9.
   y <- gs_power_npe_(
     theta = c(.1, .2, .3), info = (1:3) * 40,
@@ -36,7 +37,7 @@ test_that("verify by gs_power_npe", {
     lower = gs_b, lpar = -(x %>% filter(Bound == "Upper"))$Z,
     binding = TRUE # Always use binding = TRUE for power calculations
   )
-  expect_equal(y$Probability [y$Analysis == 3 & y$Bound == "Upper"], 1 - beta, tolerance = 1e-2)
+  expect_equal(y$Probability[y$Analysis == 3 & y$Bound == "Upper"], 1 - beta, tolerance = 1e-2)
 })
 
 test_that("examples in spec - Lachin book p71", {
@@ -89,7 +90,8 @@ test_that("fixed design with 3 equal info", {
     theta = c(.1, .2, .3),
     info = (1:3) * 80,
     upper = gs_b, upar = gsDesign::gsDesign(k = 3, sfu = gsDesign::sfLDOF)$upper$bound,
-    lower = gs_b, lpar = c(-1, 0, 0)) %>%
+    lower = gs_b, lpar = c(-1, 0, 0)
+  ) %>%
     rename(analysis = Analysis, bound = Bound, z = Z, probability = Probability) %>%
     mutate(bound = tolower(bound)) %>%
     select(-c(theta1, info1)) %>%
@@ -126,7 +128,8 @@ test_that("fixed design with 3 unequal info", {
     theta = c(.1, .2, .3),
     info = (1:3) * 80, info0 = (1:3) * 90 + 10, info1 = (1:3) * 70 - 5,
     upper = gs_b, upar = gsDesign::gsDesign(k = 3, sfu = gsDesign::sfLDOF)$upper$bound,
-    lower = gs_b, lpar = c(-1, 0, 0)) %>%
+    lower = gs_b, lpar = c(-1, 0, 0)
+  ) %>%
     rename(analysis = Analysis, bound = Bound, z = Z, probability = Probability) %>%
     mutate(bound = tolower(bound)) %>%
     select(-c(theta1, info1)) %>%
@@ -167,10 +170,11 @@ test_that("futility at IA1; efficacy only at IA2 +FA", {
     info = (1:3) * 40, info0 = (1:3) * 40,
     upper = gs_spending_bound, upar = list(sf = gsDesign::sfLDOF, total_spend = 0.025, param = NULL, timing = NULL),
     lower = gs_b, lpar = c(-1, -Inf, -Inf),
-    test_upper = c(FALSE, TRUE, TRUE)) %>%
+    test_upper = c(FALSE, TRUE, TRUE)
+  ) %>%
     rename(analysis = Analysis, bound = Bound, z = Z, probability = Probability) %>%
     mutate(bound = tolower(bound)) %>%
-    select(- c(theta1, info1)) %>%
+    select(-c(theta1, info1)) %>%
     arrange(analysis, bound)
   expect_equal(x1_c, x2)
 })
diff --git a/tests/testthat/test-oldversion-gs_power_npe.R b/tests/testthat/test-oldversion-gs_power_npe.R
index 15934f75..b2a8aec2 100644
--- a/tests/testthat/test-oldversion-gs_power_npe.R
+++ b/tests/testthat/test-oldversion-gs_power_npe.R
@@ -281,11 +281,13 @@ test_that("Independent Tests - Expect equal with mvtnorm for efficacy and futili
   expect_equal(
     object = test1$z,
     expected = c(qnorm(1 - alpha_ia), b$root),
-    tolerance = 0.001)
+    tolerance = 0.001
+  )
   expect_equal(
     object = test1$probability,
     expected = cumsum(c(b_ia$spend, pb)),
-    tolerance = 0.001)
+    tolerance = 0.001
+  )
   beta_t <- 0.02
   a_ia <- gsDesign::sfLDOF(alpha = beta_t, t = r)
   beta_ia <- a_ia$spend
@@ -302,11 +304,13 @@ test_that("Independent Tests - Expect equal with mvtnorm for efficacy and futili
   expect_equal(
     object = test2$z,
     expected = c(qnorm(beta_ia), a$root),
-    tolerance = 0.001)
+    tolerance = 0.001
+  )
   expect_equal(
     object = test2$probability,
     expected = cumsum(c(a_ia$spend, pa)),
-    tolerance = 0.001)
+    tolerance = 0.001
+  )
 })
 
 test_that("Expect equal with gsDesign::gsProbability outcome for efficacy bounds", {
@@ -333,7 +337,8 @@ test_that("Expect equal with gsDesign::gsProbability outcome for efficacy bounds
     k = 3, theta = .1,
     n.I = info,
     a = rep(-20, 3),
-    b = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, n.I = info)$upper$bound)
+    b = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, n.I = info)$upper$bound
+  )
   expect_equal(x, y)
   expect_equal(x$z[x$bound == "upper"], z$upper$bound, tolerance = 1e-5)
   expect_equal(x$probability[x$bound == "upper"], cumsum(z$upper$prob), tolerance = 1e-5)

From 4330455bc3e1f2d09086d016deb45184f79f3cee Mon Sep 17 00:00:00 2001
From: "Zhao, Yujie" <yujie.zhao@merck.com>
Date: Tue, 18 Jul 2023 09:48:40 -0400
Subject: [PATCH 13/13] add example to gs_spending_bound per keaven's
 suggestion

---
 R/gs_spending_bound.R    | 39 ++++++++-------------------------------
 man/gs_spending_bound.Rd | 39 ++++++++-------------------------------
 2 files changed, 16 insertions(+), 62 deletions(-)

diff --git a/R/gs_spending_bound.R b/R/gs_spending_bound.R
index 025f4632..ed89ad01 100644
--- a/R/gs_spending_bound.R
+++ b/R/gs_spending_bound.R
@@ -81,38 +81,15 @@
 #' @importFrom stats qnorm
 #'
 #' @examples
-#' info <- (1:3) * 10
-#' info_frac <- info / max(info)
-#' k <- length(info_frac)
-#'
-#' # 1st analysis
-#' a1 <- gs_spending_bound(
-#'   k = 1, efficacy = FALSE, theta = 0,
-#'   par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
-#'   hgm1 = NULL
-#' )
-#'
-#' b1 <- gs_spending_bound(
-#'   k = 1, efficacy = TRUE, theta = 0,
-#'   par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
-#'   hgm1 = NULL
+#' gs_power_ahr(
+#'   analysis_time = c(12, 24, 36),
+#'   event = c(30, 40, 50),
+#'   binding = TRUE,
+#'   upper = gs_spending_bound,
+#'   upar = list(sf = gsDesign::sfLDOF, total_spend = 0.025, param = NULL, timing = NULL),
+#'   lower = gs_spending_bound,
+#'   lpar = list(sf = gsDesign::sfLDOF, total_spend = 0.025, param = NULL, timing = NULL)
 #' )
-#' cat("The (lower, upper) boundary at the 1st analysis is (", a1, ", ", b1, ").\n")
-#'
-#' # 2nd analysis
-#' # a2 <- gs_spending_bound(
-#' #     k = 2, efficacy = FALSE, theta = 0,
-#' #   par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
-#' #   hgm1 = gsDesign2:::h1(r = 18, theta = 0, info = info[1], a = a1, b = b1)
-#' # )
-#'
-#' # b2 <- gs_spending_bound(
-#' #    k = 2, efficacy = TRUE, theta = 0,
-#' #    par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
-#' #    hgm1 = gsDesign2:::h1(r = 18, theta = 0, info = info[1], a = a1, b = b1)
-#' # )
-#' # cat("The upper boundary at the 2nd analysis is (", a2, ", ", b2, ").\n")
-#'
 #' @export
 gs_spending_bound <- function(k = 1,
                               par = list(
diff --git a/man/gs_spending_bound.Rd b/man/gs_spending_bound.Rd
index 84ae9411..bc33323d 100644
--- a/man/gs_spending_bound.Rd
+++ b/man/gs_spending_bound.Rd
@@ -86,38 +86,15 @@ that in Chapter 19 of Jennison and Turnbull (2000).
 }
 
 \examples{
-info <- (1:3) * 10
-info_frac <- info / max(info)
-k <- length(info_frac)
-
-# 1st analysis
-a1 <- gs_spending_bound(
-  k = 1, efficacy = FALSE, theta = 0,
-  par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
-  hgm1 = NULL
-)
-
-b1 <- gs_spending_bound(
-  k = 1, efficacy = TRUE, theta = 0,
-  par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
-  hgm1 = NULL
+gs_power_ahr(
+  analysis_time = c(12, 24, 36),
+  event = c(30, 40, 50),
+  binding = TRUE,
+  upper = gs_spending_bound,
+  upar = list(sf = gsDesign::sfLDOF, total_spend = 0.025, param = NULL, timing = NULL),
+  lower = gs_spending_bound,
+  lpar = list(sf = gsDesign::sfLDOF, total_spend = 0.025, param = NULL, timing = NULL)
 )
-cat("The (lower, upper) boundary at the 1st analysis is (", a1, ", ", b1, ").\n")
-
-# 2nd analysis
-# a2 <- gs_spending_bound(
-#     k = 2, efficacy = FALSE, theta = 0,
-#   par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
-#   hgm1 = gsDesign2:::h1(r = 18, theta = 0, info = info[1], a = a1, b = b1)
-# )
-
-# b2 <- gs_spending_bound(
-#    k = 2, efficacy = TRUE, theta = 0,
-#    par = list(sf = gsDesign::sfLDOF, total_spend = 0.025, timing = info_frac, param = NULL),
-#    hgm1 = gsDesign2:::h1(r = 18, theta = 0, info = info[1], a = a1, b = b1)
-# )
-# cat("The upper boundary at the 2nd analysis is (", a2, ", ", b2, ").\n")
-
 }
 \references{
 Jennison C and Turnbull BW (2000),