From f15a2942eeabe338dc73891fd4e316e9bc4bd0f9 Mon Sep 17 00:00:00 2001
From: Audrey Yeo <comptesaudrey@gmail.com>
Date: Fri, 10 Oct 2025 09:14:18 +0200
Subject: [PATCH 01/17] first edits on documentation

---
 R/plotBounds.R     | 113 ++++++++++++++++++++++++++++++---------------
 man/plotBounds.Rd  |  31 ++-----------
 man/sumBetaDiff.Rd |  11 +++++
 3 files changed, 92 insertions(+), 63 deletions(-)

diff --git a/R/plotBounds.R b/R/plotBounds.R
index 4e956771..2b0bdbd8 100644
--- a/R/plotBounds.R
+++ b/R/plotBounds.R
@@ -1,24 +1,24 @@
 #' Plot the boundary decision cutpoints
 #'
 #' This function will plot the response rate on the futility and efficacy
-#' boundaries, and is used together with \code{\link{boundsPredprob}}
-#' and \code{\link{boundsPostprob}}
+#' boundaries, and is used together with [boundsPredprob()]
+#' and [boundsPostprob()] for Decision 1. See `boundsPredprob()` for rules.
 #'
-#' @param z an output of \code{\link{boundsPredprob}} and
-#' \code{\link{boundsPostprob}}
-#' @param area color the futility/efficacy stop area
-#' @param grid show the grid of y-axis or not
-#' @param yt  indicate the y axis: response rate is "p", number of responses
+#' @typed z an output of [boundsPredprob()] and
+#' [boundsPostprob()]
+#' @typed area color the futility/efficacy stop area
+#' @typed grid show the grid of y-axis or not
+#' @typed yt  indicate the y axis: response rate is "p", number of responses
 #' is "x"
-#' @param add  add the boundary lines or not
-#' @param cols specific the color of `[1]` efficacy area `[2]` futility area
+#' @typed add  add the boundary lines or not
+#' @typed cols specific the color of `[1]` efficacy area `[2]` futility area
 #' `[3]` efficacy boundary `[4]` futility boundary
-#' @param lwds line width (a two dimensional vector)
-#' @param ltype line type
-#' @param lpch  a value of plotting characters or symbols
-#' @param lcex a value giving the amount by which plotting characters and
+#' @typed lwds line width (a two dimensional vector)
+#' @typed ltype line type
+#' @typed lpch  a value of plotting characters or symbols
+#' @typed lcex a value giving the amount by which plotting characters and
 #' symbols should be scaled relative to the default.
-#' @param gy a value to adjust the gray level of the plot (default 20),
+#' @typed gy a value to adjust the gray level of the plot (default 20),
 #' applies when \code{grid==TRUE}
 #' @return nothing, only produces the plot as side effect
 #'
@@ -27,9 +27,19 @@
 #' @example examples/plotBounds.R
 #' @export
 #' @keywords graphics
-plotBounds <- function(z, area = TRUE, grid = TRUE, yt = "x", add = FALSE,
-                       cols = c("green", "red", "darkgreen", "orange"),
-                       lwds = c(3, 3), ltype = "l", lpch = 16, lcex = 1, gy = 20) {
+plotBounds <- function(
+  z,
+  area = TRUE,
+  grid = TRUE,
+  yt = "x",
+  add = FALSE,
+  cols = c("green", "red", "darkgreen", "orange"),
+  lwds = c(3, 3),
+  ltype = "l",
+  lpch = 16,
+  lcex = 1,
+  gy = 20
+) {
   n <- nrow(z)
   nmin <- min(z$looks)
   nmax <- max(z$looks)
@@ -51,40 +61,71 @@ plotBounds <- function(z, area = TRUE, grid = TRUE, yt = "x", add = FALSE,
     stop("yt can only be x or p")
   }
   if (add) {
-    graphics::lines(z$looks, z2,
-      lwd = lwds[1], col = cols[3], type = ltype,
-      pch = lpch, cex = lcex
+    graphics::lines(
+      z$looks,
+      z2,
+      lwd = lwds[1],
+      col = cols[3],
+      type = ltype,
+      pch = lpch,
+      cex = lcex
     )
-    graphics::lines(z$looks, z1,
-      lwd = lwds[2], col = cols[4], type = ltype,
-      pch = lpch, cex = lcex
+    graphics::lines(
+      z$looks,
+      z1,
+      lwd = lwds[2],
+      col = cols[4],
+      type = ltype,
+      pch = lpch,
+      cex = lcex
     )
     return(invisible())
   }
-  graphics::plot(z$looks, rep(0, n),
-    xlim = c(0, max(z$looks)), ylim = c(0, yU), type = "n",
-    xlab = "n", ylab = ylabel
+  graphics::plot(
+    z$looks,
+    rep(0, n),
+    xlim = c(0, max(z$looks)),
+    ylim = c(0, yU),
+    type = "n",
+    xlab = "n",
+    ylab = ylabel
   )
   if (grid) {
     graphics::abline(h = gridy, col = "gray")
   }
   if (area) {
-    graphics::polygon(c(z$looks, nmax, nmin), c(z2, yU, yU2),
+    graphics::polygon(
+      c(z$looks, nmax, nmin),
+      c(z2, yU, yU2),
       lwd = lwds[1],
-      col = cols[1], border = cols[1]
+      col = cols[1],
+      border = cols[1]
     )
-    graphics::polygon(c(z$looks, nmax, nmin), c(z1, 0, 0),
+    graphics::polygon(
+      c(z$looks, nmax, nmin),
+      c(z1, 0, 0),
       lwd = lwds[2],
-      col = cols[2], border = cols[2]
+      col = cols[2],
+      border = cols[2]
     )
   } else {
-    graphics::lines(z$looks, z2,
-      lwd = lwds[1], col = cols[1], type = ltype,
-      pch = lpch, cex = lcex
+    graphics::lines(
+      z$looks,
+      z2,
+      lwd = lwds[1],
+      col = cols[1],
+      type = ltype,
+      pch = lpch,
+      cex = lcex
     )
-    graphics::lines(z$looks, z1,
-      lwd = lwds[2], col = cols[2], type = ltype,
-      pch = lpch, cex = lcex
+    graphics::lines(
+      z$looks,
+      z1,
+      lwd = lwds[2],
+      col = cols[2],
+      type = ltype,
+      pch = lpch,
+      cex = lcex
     )
   }
   return(invisible())
diff --git a/man/plotBounds.Rd b/man/plotBounds.Rd
index 0caf508c..9511770f 100644
--- a/man/plotBounds.Rd
+++ b/man/plotBounds.Rd
@@ -19,40 +19,17 @@ plotBounds(
 )
 }
 \arguments{
-\item{z}{an output of \code{\link{boundsPredprob}} and
-\code{\link{boundsPostprob}}}
+\item{yt  indicate the y axis}{(\verb{response rate is "p", number of responses}):\cr is "x"}
 
-\item{area}{color the futility/efficacy stop area}
-
-\item{grid}{show the grid of y-axis or not}
-
-\item{yt}{indicate the y axis: response rate is "p", number of responses
-is "x"}
-
-\item{add}{add the boundary lines or not}
-
-\item{cols}{specific the color of \verb{[1]} efficacy area \verb{[2]} futility area
-\verb{[3]} efficacy boundary \verb{[4]} futility boundary}
-
-\item{lwds}{line width (a two dimensional vector)}
-
-\item{ltype}{line type}
-
-\item{lpch}{a value of plotting characters or symbols}
-
-\item{lcex}{a value giving the amount by which plotting characters and
-symbols should be scaled relative to the default.}
-
-\item{gy}{a value to adjust the gray level of the plot (default 20),
-applies when \code{grid==TRUE}}
+\item{<parse error>}{(\if{html}{\out{<parse error>}}):\cr \if{html}{\out{<parse error>}}}
 }
 \value{
 nothing, only produces the plot as side effect
 }
 \description{
 This function will plot the response rate on the futility and efficacy
-boundaries, and is used together with \code{\link{boundsPredprob}}
-and \code{\link{boundsPostprob}}
+boundaries, and is used together with \code{\link[=boundsPredprob]{boundsPredprob()}}
+and \code{\link[=boundsPostprob]{boundsPostprob()}} for Decision 1. See \code{boundsPredprob()} for rules.
 }
 \examples{
 # examples
diff --git a/man/sumBetaDiff.Rd b/man/sumBetaDiff.Rd
index 5cc1ae5e..130dde7c 100644
--- a/man/sumBetaDiff.Rd
+++ b/man/sumBetaDiff.Rd
@@ -27,3 +27,14 @@ along with the \code{go} and \code{stop} probabilities.
 A function to summarize the characters of a betadiff distribution \code{\link[=dbetadiff]{dbetadiff()}}.
 May require use of random sample generator to calculate, use \code{\link[=set.seed]{set.seed()}} to reproduce results.
 }
+\examples{
+parX <- c(1, 52) # Control group's parameters
+parY <- c(5.5, 20.5) # Treatment group's parameters
+sumBetaDiff(
+  parX = parX,
+  parY = parY,
+  ci_level = 0.9,
+  go_cut = 0.6,
+  stop_cut = 0.2
+)
+}

From 9c0c4d2720f9977d0ae1e070754c512baa4d8a5a Mon Sep 17 00:00:00 2001
From: Audrey Yeo <comptesaudrey@gmail.com>
Date: Fri, 10 Oct 2025 15:11:21 +0200
Subject: [PATCH 02/17] clean

---
 R/plotBounds.R                   |   4 +-
 design/design_doc_plotBounds.qmd | 328 +++++++++++++++++++++++++++++++
 examples/plotBounds.R            |  38 ++--
 3 files changed, 357 insertions(+), 13 deletions(-)
 create mode 100644 design/design_doc_plotBounds.qmd

diff --git a/R/plotBounds.R b/R/plotBounds.R
index 2b0bdbd8..a7a0c09d 100644
--- a/R/plotBounds.R
+++ b/R/plotBounds.R
@@ -2,7 +2,7 @@
 #'
 #' This function will plot the response rate on the futility and efficacy
 #' boundaries, and is used together with [boundsPredprob()]
-#' and [boundsPostprob()] for Decision 1. See `boundsPredprob()` for rules.
+#' and [boundsPostprob()] for Decision 1. See `boundsPredprob()` for.
 #'
 #' @typed z an output of [boundsPredprob()] and
 #' [boundsPostprob()]
@@ -33,7 +33,7 @@ plotBounds <- function(
   grid = TRUE,
   yt = "x",
   add = FALSE,
-  cols = c("green", "red", "darkgreen", "orange"),
+  cols = c("#009E73", "#FF0046", "#7F55B1", "#F0A04B"),
   lwds = c(3, 3),
   ltype = "l",
   lpch = 16,
diff --git a/design/design_doc_plotBounds.qmd b/design/design_doc_plotBounds.qmd
new file mode 100644
index 00000000..f36dbf83
--- /dev/null
+++ b/design/design_doc_plotBounds.qmd
@@ -0,0 +1,328 @@
+---
+title: "Design Doc for plotBounds"
+format: revealjs
+editor: visual
+---
+
+Statisticians can display boundaries of Go, Stop and GreyZone decisions graphically in terms of response rates required by desired samples sizes or looks. This is such purpose of `plotBounds`. Note that for the predictive probability case, decision 1 rules are chosen. See `ocPredprob` for rules. 
+
+# packages that aid
+
+```{r}
+library(flextable)
+library(ggplot2)
+```
+
+# input
+
+```{r}
+boundsPostprob(
+    looks = c(10, 20, 30, 40),
+    p0 = 0.20,
+    tL = 0.10,
+    tU = 0.90,
+    parE = c(1, 1)
+  )
+```
+
+```{r}
+boundsPredprob(
+    looks = c(10, 20, 30, 40),
+    p0 = 0.20,
+    tT = 0.80,
+    phiL = 0.10,
+    phiU = 0.90,
+  )
+```
+
+# vintage function
+
+```{r}
+vintage_plotBounds <- function(
+  z,
+  area = TRUE,
+  grid = TRUE,
+  yt = "x",
+  add = FALSE,
+  cols = c("#009E73", "#FF0046", "#7F55B1", "#F0A04B"),
+  lwds = c(3, 3),
+  ltype = "l",
+  lpch = 16,
+  lcex = 1,
+  gy = 20
+) {
+  n <- nrow(z)
+  nmin <- min(z$looks)
+  nmax <- max(z$looks)
+  if (yt == "x") {
+    z1 <- z$xL
+    z2 <- z$xU
+    yU <- nmax
+    yU2 <- nmin
+    ylabel <- "Number of Responses"
+    gridy <- seq(0, yU, by = floor(yU / gy))
+  } else if (yt == "p") {
+    z1 <- z$pL
+    z2 <- z$pU
+    yU <- 1
+    yU2 <- 1
+    ylabel <- "Response Rate"
+    gridy <- seq(0, yU, by = yU / gy)
+  } else {
+    stop("yt can only be x or p")
+  }
+  if (add) {
+    graphics::lines(
+      z$looks,
+      z2,
+      lwd = lwds[1],
+      col = cols[3],
+      type = ltype,
+      pch = lpch,
+      cex = lcex
+    )
+    graphics::lines(
+      z$looks,
+      z1,
+      lwd = lwds[2],
+      col = cols[4],
+      type = ltype,
+      pch = lpch,
+      cex = lcex
+    )
+    return(invisible())
+  }
+  graphics::plot(
+    z$looks,
+    rep(0, n),
+    xlim = c(0, max(z$looks)),
+    ylim = c(0, yU),
+    type = "n",
+    xlab = "n",
+    ylab = ylabel
+  )
+  if (grid) {
+    graphics::abline(h = gridy, col = "gray")
+  }
+  if (area) {
+    graphics::polygon(
+      c(z$looks, nmax, nmin),
+      c(z2, yU, yU2),
+      lwd = lwds[1],
+      col = cols[1],
+      border = cols[1]
+    )
+    graphics::polygon(
+      c(z$looks, nmax, nmin),
+      c(z1, 0, 0),
+      lwd = lwds[2],
+      col = cols[2],
+      border = cols[2]
+    )
+  } else {
+    graphics::lines(
+      z$looks,
+      z2,
+      lwd = lwds[1],
+      col = cols[1],
+      type = ltype,
+      pch = lpch,
+      cex = lcex
+    )
+    graphics::lines(
+      z$looks,
+      z1,
+      lwd = lwds[2],
+      col = cols[2],
+      type = ltype,
+      pch = lpch,
+      cex = lcex
+    )
+  }
+  return(invisible())
+}
+
+```
+
+# vintage example that should work with new function
+```{r}
+plotBounds(
+  boundsPostprob(
+    looks = c(10, 20, 30, 40),
+    p0 = 0.20,
+    tL = 0.10,
+    tU = 0.90,
+    parE = c(1, 1)
+  ),
+  yt = "p",
+  add = TRUE
+)
+
+```
+
+# creating polygons with new function
+
+The following output show that important coordinates needed as input to create these polygons. 
+
+As a premise, we establish the criteria:
+Interim
+Go : P(success) > 90 %
+Stop : P(success) > 10 %
+Final
+Go : P(RR > 0.20 | data) > 80 %
+Stop : P(RR > 0.20 | data) < 10 %
+
+The criteria for interim analyses are from predictive probability calculation.
+
+The criteria for final analyses are from posterior probability calculation. 
+
+which translates to boundaries :
+When n = 10, 4 responders and above is a Go, 0 responders and below is a stop.
+When n = 20, 7 responders and above is a Go, 2 responders and below is a stop
+When n = 30, 9 responders and above is a Go, 5 responders and below is a stop
+When n = 40, 10 responders and above is a Go, 9 responders and below is a stop
+
+```{r}
+vintage_plotBounds(
+  boundsPredprob(
+    looks = c(10, 20, 30, 40),
+    p0 = 0.20,
+    tT = 0.80,
+    phiL = 0.10,
+    phiU = 0.90,
+  ),
+  yt = "x"
+)
+```
+
+```{r}
+coords <- boundsPredprob(
+    looks = c(10, 20, 30, 40),
+    p0 = 0.20,
+    tT = 0.80,
+    phiL = 0.10,
+    phiU = 0.90,
+  )
+```
+
+```{r}
+new_plotBounds <- function(coords, 
+                           postprob = TRUE, 
+                           go_colour = "#1B9E77",
+                           stop_colour = "#E41A1C",
+                           alpha = 1) {
+  go_data <- data.frame(
+    n = coords$looks,
+    ymin_go = coords$xU,  
+    ymax_go = coords$looks 
+  )
+  stop_data <- data.frame(
+    n = coords$looks,
+    ymin_stop = c(0, 0, 0, 0),     
+    ymax_stop = coords$xL      
+  )
+  plot <- ggplot2::ggplot() +
+    ggplot2::geom_ribbon(
+      data = stop_data,
+      ggplot2::aes(x = n, ymin = ymin_stop, ymax = ymax_stop),
+      fill = stop_colour, alpha = alpha
+    ) +
+    ggplot2::geom_ribbon(
+      data = go_data,
+      ggplot2::aes(x = n, ymin = ymin_go, ymax = ymax_go),
+      fill = go_colour , alpha = alpha
+    ) +
+    ggplot2::scale_x_continuous(
+      name = "n",
+      breaks = go_data$n
+    ) +
+    ggplot2::scale_y_continuous(
+      breaks = seq(from = 0, to = max(go_data$n), by = 2)
+    ) +
+     ggplot2::geom_point(
+    data = go_data,
+     ggplot2::aes(x = n, y = ymin_go),
+    size = 3,       
+    shape = 16,
+    colour = "#16C47F", 
+  ) +
+     ggplot2::geom_point(
+    data = stop_data,
+     ggplot2::aes(x = n, y = ymax_stop),
+    size = 3,       
+    shape = 16,
+    colour = "#FF748B", #"#DC3C22",FF748B 
+  ) +
+    ggplot2::xlab("Sample Size (n)") +
+    ggplot2::ylab("Number of Responders") +
+    ggplot2::theme_minimal() 
+  
+  if (postprob) {
+    plot +  ggplot2::ggtitle(
+      "Boundaries of responder numbers per sample size"
+    )
+  } else {
+    plot + ggplot2::ggtitle(
+      "Boundaries of responder rates per sample size"
+    ) 
+  }
+}
+```
+```{r}
+coords <- boundsPredprob(
+    looks = c(10, 20, 30, 40),
+    p0 = 0.20,
+    tT = 0.80,
+    phiL = 0.10,
+    phiU = 0.90,
+  )
+new_plotBounds(coords)
+```
+
+
+
+# creating polygons with new function
+
+The following output show that important coordinates needed as input to create these polygons. 
+
+As a premise, we establish the criteria:
+Go : P(RR > 0.20 | data) > 90 %
+Stop : P(RR > 0.20 | data) > 10 %
+which translates to boundaries :
+When n = 10, 4 responders and above is a Go, 3 responders and below is a stop.
+When n = 20, 7 responders and above is a Go, 6 responders and below is a stop
+When n = 30, 9 responders and above is a Go, 8 responders and below is a stop
+When n = 40, 12 responders and above is a Go, 11 responders and below is a stop
+
+
+```{r}
+coords1 <- boundsPostprob(
+    looks = c(10, 20, 30, 40),
+    p0 = 0.20,
+    tL = 0.10,
+    tU = 0.90,
+    parE = c(1, 1)
+  )
+new_plotBounds(coords1)
+```
+
+We extract these coordinates but carefully assign which are Go, Stop and GreyZones.
+
+```{r}
+
+```
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/examples/plotBounds.R b/examples/plotBounds.R
index c39fc05b..4c84dbd5 100644
--- a/examples/plotBounds.R
+++ b/examples/plotBounds.R
@@ -1,16 +1,32 @@
 # examples
 plotBounds(
   boundsPostprob(
-    looks = c(10, 20, 30, 40), p0 = 0.20,
-    tL = 0.10, tU = 0.90, parE = c(1, 1)
+    looks = c(10, 20, 30, 40),
+    p0 = 0.20,
+    tL = 0.10,
+    tU = 0.90,
+    parE = c(1, 1)
   ),
-  yt = "p", add = TRUE
+  yt = "p",
+  add = TRUE
+)
+plotBounds(
+  boundsPredprob(
+    looks = c(10, 20, 30, 40),
+    p0 = 0.20,
+    tT = 0.80,
+    phiL = 0.10,
+    phiU = 0.90,
+  ),
+  yt = "x"
+)
+plotBounds(
+  boundsPredprob(
+    looks = c(10, 20, 30, 40),
+    p0 = 0.20,
+    tT = 0.80,
+    phiL = 0.10,
+    phiU = 0.90,
+  ),
+  yt = "p"
 )
-plotBounds(boundsPredprob(
-  looks = c(10, 20, 30, 40), p0 = 0.20, tT = 0.80,
-  phiL = 0.10, phiU = 0.90,
-), yt = "x")
-plotBounds(boundsPredprob(
-  looks = c(10, 20, 30, 40), p0 = 0.20, tT = 0.80,
-  phiL = 0.10, phiU = 0.90,
-), yt = "p")

From 13a8dbf51cfa5eecffbdd394a0f4df9c4c69e0fe Mon Sep 17 00:00:00 2001
From: Audrey Yeo <comptesaudrey@gmail.com>
Date: Fri, 10 Oct 2025 15:17:50 +0200
Subject: [PATCH 03/17] clean

---
 design/design_doc_plotBounds.qmd | 85 +++++++++++++++-----------------
 1 file changed, 40 insertions(+), 45 deletions(-)

diff --git a/design/design_doc_plotBounds.qmd b/design/design_doc_plotBounds.qmd
index f36dbf83..67dd4f16 100644
--- a/design/design_doc_plotBounds.qmd
+++ b/design/design_doc_plotBounds.qmd
@@ -145,6 +145,7 @@ vintage_plotBounds <- function(
 ```
 
 # vintage example that should work with new function
+
 ```{r}
 plotBounds(
   boundsPostprob(
@@ -160,27 +161,7 @@ plotBounds(
 
 ```
 
-# creating polygons with new function
-
-The following output show that important coordinates needed as input to create these polygons. 
-
-As a premise, we establish the criteria:
-Interim
-Go : P(success) > 90 %
-Stop : P(success) > 10 %
-Final
-Go : P(RR > 0.20 | data) > 80 %
-Stop : P(RR > 0.20 | data) < 10 %
-
-The criteria for interim analyses are from predictive probability calculation.
-
-The criteria for final analyses are from posterior probability calculation. 
-
-which translates to boundaries :
-When n = 10, 4 responders and above is a Go, 0 responders and below is a stop.
-When n = 20, 7 responders and above is a Go, 2 responders and below is a stop
-When n = 30, 9 responders and above is a Go, 5 responders and below is a stop
-When n = 40, 10 responders and above is a Go, 9 responders and below is a stop
+# vintage function
 
 ```{r}
 vintage_plotBounds(
@@ -195,15 +176,6 @@ vintage_plotBounds(
 )
 ```
 
-```{r}
-coords <- boundsPredprob(
-    looks = c(10, 20, 30, 40),
-    p0 = 0.20,
-    tT = 0.80,
-    phiL = 0.10,
-    phiU = 0.90,
-  )
-```
 
 ```{r}
 new_plotBounds <- function(coords, 
@@ -257,17 +229,35 @@ new_plotBounds <- function(coords,
     ggplot2::ylab("Number of Responders") +
     ggplot2::theme_minimal() 
   
-  if (postprob) {
-    plot +  ggplot2::ggtitle(
-      "Boundaries of responder numbers per sample size"
-    )
-  } else {
     plot + ggplot2::ggtitle(
-      "Boundaries of responder rates per sample size"
-    ) 
-  }
+      "Boundaries of Go and Stop Responders per sample size")
 }
 ```
+
+# creating polygons with new function with `boundsPredprob()`
+
+The following output show that important coordinates needed as input to create these polygons. 
+
+As a premise, we establish the criteria:
+
+Interim
+Go : P(success) > 90 %
+Stop : P(success) > 10 %
+
+Final
+Go : P(RR > 0.20 | data) > 80 %
+Stop : P(RR > 0.20 | data) < 10 %
+
+The criteria for interim analyses are from predictive probability calculation.
+
+The criteria for final analyses are from posterior probability calculation. 
+
+which translates to boundaries :
+When n = 10, 4 responders and above is a Go, 0 responders and below is a stop.
+When n = 20, 7 responders and above is a Go, 2 responders and below is a stop
+When n = 30, 9 responders and above is a Go, 5 responders and below is a stop
+When n = 40, 10 responders and above is a Go, 9 responders and below is a stop
+
 ```{r}
 coords <- boundsPredprob(
     looks = c(10, 20, 30, 40),
@@ -276,12 +266,22 @@ coords <- boundsPredprob(
     phiL = 0.10,
     phiU = 0.90,
   )
-new_plotBounds(coords)
+print(coords)
 ```
 
 
+```{r}
+coords <- boundsPredprob(
+    looks = c(10, 20, 30, 40),
+    p0 = 0.20,
+    tT = 0.80,
+    phiL = 0.10,
+    phiU = 0.90,
+  )
+new_plotBounds(coords)
+```
 
-# creating polygons with new function
+# creating polygons with new function with `boundsPostprob()`
 
 The following output show that important coordinates needed as input to create these polygons. 
 
@@ -306,11 +306,6 @@ coords1 <- boundsPostprob(
 new_plotBounds(coords1)
 ```
 
-We extract these coordinates but carefully assign which are Go, Stop and GreyZones.
-
-```{r}
-
-```
 
 
 

From 459b7c920ff816603cae4d818b2c144a1840f8f4 Mon Sep 17 00:00:00 2001
From: Audrey Yeo <comptesaudrey@gmail.com>
Date: Fri, 10 Oct 2025 15:27:59 +0200
Subject: [PATCH 04/17] clean

---
 design/design_doc_plotBounds.qmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/design/design_doc_plotBounds.qmd b/design/design_doc_plotBounds.qmd
index 67dd4f16..34c6034c 100644
--- a/design/design_doc_plotBounds.qmd
+++ b/design/design_doc_plotBounds.qmd
@@ -190,7 +190,7 @@ new_plotBounds <- function(coords,
   )
   stop_data <- data.frame(
     n = coords$looks,
-    ymin_stop = c(0, 0, 0, 0),     
+    ymin_stop = c(rep(0, length(coords$looks))),     
     ymax_stop = coords$xL      
   )
   plot <- ggplot2::ggplot() +

From 4ff49b735e886d4ddda25e2dc0956b08ed0c56bd Mon Sep 17 00:00:00 2001
From: Audrey Yeo <comptesaudrey@gmail.com>
Date: Sat, 11 Oct 2025 10:17:29 +0200
Subject: [PATCH 05/17] clean

---
 R/plotBounds.R                   | 30 +++++++-------
 design/design_doc_plotBounds.qmd | 43 +++++++-------------
 man/plotBounds.Rd                | 69 +++++++++++++++++++++++++-------
 3 files changed, 84 insertions(+), 58 deletions(-)

diff --git a/R/plotBounds.R b/R/plotBounds.R
index a7a0c09d..082a55b6 100644
--- a/R/plotBounds.R
+++ b/R/plotBounds.R
@@ -1,24 +1,24 @@
 #' Plot the boundary decision cutpoints
 #'
 #' This function will plot the response rate on the futility and efficacy
-#' boundaries, and is used together with [boundsPredprob()]
-#' and [boundsPostprob()] for Decision 1. See `boundsPredprob()` for.
+#' boundaries, and is used together with \code{\link{boundsPredprob}}
+#' and \code{\link{boundsPostprob}}
 #'
-#' @typed z an output of [boundsPredprob()] and
-#' [boundsPostprob()]
-#' @typed area color the futility/efficacy stop area
-#' @typed grid show the grid of y-axis or not
-#' @typed yt  indicate the y axis: response rate is "p", number of responses
+#' @param z an output of \code{\link{boundsPredprob}} and
+#' \code{\link{boundsPostprob}}
+#' @param area color the futility/efficacy stop area
+#' @param grid show the grid of y-axis or not
+#' @param yt  indicate the y axis: response rate is "p", number of responses
 #' is "x"
-#' @typed add  add the boundary lines or not
-#' @typed cols specific the color of `[1]` efficacy area `[2]` futility area
+#' @param add  add the boundary lines or not
+#' @param cols specific the color of `[1]` efficacy area `[2]` futility area
 #' `[3]` efficacy boundary `[4]` futility boundary
-#' @typed lwds line width (a two dimensional vector)
-#' @typed ltype line type
-#' @typed lpch  a value of plotting characters or symbols
-#' @typed lcex a value giving the amount by which plotting characters and
+#' @param lwds line width (a two dimensional vector)
+#' @param ltype line type
+#' @param lpch  a value of plotting characters or symbols
+#' @param lcex a value giving the amount by which plotting characters and
 #' symbols should be scaled relative to the default.
-#' @typed gy a value to adjust the gray level of the plot (default 20),
+#' @param gy a value to adjust the gray level of the plot (default 20),
 #' applies when \code{grid==TRUE}
 #' @return nothing, only produces the plot as side effect
 #'
@@ -33,7 +33,7 @@ plotBounds <- function(
   grid = TRUE,
   yt = "x",
   add = FALSE,
-  cols = c("#009E73", "#FF0046", "#7F55B1", "#F0A04B"),
+  cols = c("green", "red", "darkgreen", "orange"),
   lwds = c(3, 3),
   ltype = "l",
   lpch = 16,
diff --git a/design/design_doc_plotBounds.qmd b/design/design_doc_plotBounds.qmd
index 34c6034c..17537ca0 100644
--- a/design/design_doc_plotBounds.qmd
+++ b/design/design_doc_plotBounds.qmd
@@ -4,7 +4,7 @@ format: revealjs
 editor: visual
 ---
 
-Statisticians can display boundaries of Go, Stop and GreyZone decisions graphically in terms of response rates required by desired samples sizes or looks. This is such purpose of `plotBounds`. Note that for the predictive probability case, decision 1 rules are chosen. See `ocPredprob` for rules. 
+Statisticians can display boundaries of Go, Stop and GreyZone decisions graphically in terms of response rates required by desired samples sizes or looks. This is such purpose of `plotBounds`. Note that for the predictive probability case, decision 1 rules are chosen. See `ocPredprob` for rules. Design document aims to translate previous call function to use of more common packages such as `ggplot2` and reduce number of lines. 
 
 # packages that aid
 
@@ -13,28 +13,6 @@ library(flextable)
 library(ggplot2)
 ```
 
-# input
-
-```{r}
-boundsPostprob(
-    looks = c(10, 20, 30, 40),
-    p0 = 0.20,
-    tL = 0.10,
-    tU = 0.90,
-    parE = c(1, 1)
-  )
-```
-
-```{r}
-boundsPredprob(
-    looks = c(10, 20, 30, 40),
-    p0 = 0.20,
-    tT = 0.80,
-    phiL = 0.10,
-    phiU = 0.90,
-  )
-```
-
 # vintage function
 
 ```{r}
@@ -161,7 +139,7 @@ plotBounds(
 
 ```
 
-# vintage function
+# vintage function output
 
 ```{r}
 vintage_plotBounds(
@@ -176,6 +154,7 @@ vintage_plotBounds(
 )
 ```
 
+# new call function
 
 ```{r}
 new_plotBounds <- function(coords, 
@@ -183,6 +162,12 @@ new_plotBounds <- function(coords,
                            go_colour = "#1B9E77",
                            stop_colour = "#E41A1C",
                            alpha = 1) {
+  assert_data_frame(coords, any.missing = FALSE, types = "numeric")
+  assert_flag(postprob)
+  assert_character(go_colour)
+  assert_character(stop_colour)
+  assert_number(alpha, lower = 0, upper = 1)
+  
   go_data <- data.frame(
     n = coords$looks,
     ymin_go = coords$xU,  
@@ -234,9 +219,9 @@ new_plotBounds <- function(coords,
 }
 ```
 
-# creating polygons with new function with `boundsPredprob()`
+# creating plot using new function with output from `boundsPredprob()`
 
-The following output show that important coordinates needed as input to create these polygons. 
+The following output show that important coordinates needed as input to create these plots. 
 
 As a premise, we establish the criteria:
 
@@ -278,10 +263,12 @@ coords <- boundsPredprob(
     phiL = 0.10,
     phiU = 0.90,
   )
-new_plotBounds(coords)
+new_plotBounds(coords = coords,
+               go_colour = "blue",
+               alpha = 1)
 ```
 
-# creating polygons with new function with `boundsPostprob()`
+# creating plots with new function with output from `boundsPostprob()`
 
 The following output show that important coordinates needed as input to create these polygons. 
 
diff --git a/man/plotBounds.Rd b/man/plotBounds.Rd
index 9511770f..5b6ab385 100644
--- a/man/plotBounds.Rd
+++ b/man/plotBounds.Rd
@@ -19,34 +19,73 @@ plotBounds(
 )
 }
 \arguments{
-\item{yt  indicate the y axis}{(\verb{response rate is "p", number of responses}):\cr is "x"}
+\item{z}{an output of \code{\link{boundsPredprob}} and
+\code{\link{boundsPostprob}}}
 
-\item{<parse error>}{(\if{html}{\out{<parse error>}}):\cr \if{html}{\out{<parse error>}}}
+\item{area}{color the futility/efficacy stop area}
+
+\item{grid}{show the grid of y-axis or not}
+
+\item{yt}{indicate the y axis: response rate is "p", number of responses
+is "x"}
+
+\item{add}{add the boundary lines or not}
+
+\item{cols}{specific the color of \verb{[1]} efficacy area \verb{[2]} futility area
+\verb{[3]} efficacy boundary \verb{[4]} futility boundary}
+
+\item{lwds}{line width (a two dimensional vector)}
+
+\item{ltype}{line type}
+
+\item{lpch}{a value of plotting characters or symbols}
+
+\item{lcex}{a value giving the amount by which plotting characters and
+symbols should be scaled relative to the default.}
+
+\item{gy}{a value to adjust the gray level of the plot (default 20),
+applies when \code{grid==TRUE}}
 }
 \value{
 nothing, only produces the plot as side effect
 }
 \description{
 This function will plot the response rate on the futility and efficacy
-boundaries, and is used together with \code{\link[=boundsPredprob]{boundsPredprob()}}
-and \code{\link[=boundsPostprob]{boundsPostprob()}} for Decision 1. See \code{boundsPredprob()} for rules.
+boundaries, and is used together with \code{\link{boundsPredprob}}
+and \code{\link{boundsPostprob}}
 }
 \examples{
 # examples
 plotBounds(
   boundsPostprob(
-    looks = c(10, 20, 30, 40), p0 = 0.20,
-    tL = 0.10, tU = 0.90, parE = c(1, 1)
+    looks = c(10, 20, 30, 40),
+    p0 = 0.20,
+    tL = 0.10,
+    tU = 0.90,
+    parE = c(1, 1)
+  ),
+  yt = "p",
+  add = TRUE
+)
+plotBounds(
+  boundsPredprob(
+    looks = c(10, 20, 30, 40),
+    p0 = 0.20,
+    tT = 0.80,
+    phiL = 0.10,
+    phiU = 0.90,
+  ),
+  yt = "x"
+)
+plotBounds(
+  boundsPredprob(
+    looks = c(10, 20, 30, 40),
+    p0 = 0.20,
+    tT = 0.80,
+    phiL = 0.10,
+    phiU = 0.90,
   ),
-  yt = "p", add = TRUE
+  yt = "p"
 )
-plotBounds(boundsPredprob(
-  looks = c(10, 20, 30, 40), p0 = 0.20, tT = 0.80,
-  phiL = 0.10, phiU = 0.90,
-), yt = "x")
-plotBounds(boundsPredprob(
-  looks = c(10, 20, 30, 40), p0 = 0.20, tT = 0.80,
-  phiL = 0.10, phiU = 0.90,
-), yt = "p")
 }
 \keyword{graphics}

From dbe99e2f19cce929b5e2fa7f73771f9396962703 Mon Sep 17 00:00:00 2001
From: Audrey Yeo <comptesaudrey@gmail.com>
Date: Sat, 11 Oct 2025 10:19:41 +0200
Subject: [PATCH 06/17] clean

---
 design/design_doc_plotBounds.qmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/design/design_doc_plotBounds.qmd b/design/design_doc_plotBounds.qmd
index 17537ca0..2c9fac37 100644
--- a/design/design_doc_plotBounds.qmd
+++ b/design/design_doc_plotBounds.qmd
@@ -270,7 +270,7 @@ new_plotBounds(coords = coords,
 
 # creating plots with new function with output from `boundsPostprob()`
 
-The following output show that important coordinates needed as input to create these polygons. 
+The following output show that important coordinates needed as input to create these plots. Coordinates are the points where the polygon should be drawn and reflect the possible values for a go and stop decision respectively.
 
 As a premise, we establish the criteria:
 Go : P(RR > 0.20 | data) > 90 %

From 2770b1687115e7a611a8e9715af1cfa9f8a8d51d Mon Sep 17 00:00:00 2001
From: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Date: Sat, 11 Oct 2025 11:39:42 +0000
Subject: [PATCH 07/17] [skip style] [skip vbump] Restyle files

---
 R/plotBounds.R                   |  23 +++---
 design/design_doc_plotBounds.qmd | 122 +++++++++++++++----------------
 2 files changed, 72 insertions(+), 73 deletions(-)

diff --git a/R/plotBounds.R b/R/plotBounds.R
index 082a55b6..4b5e9794 100644
--- a/R/plotBounds.R
+++ b/R/plotBounds.R
@@ -28,18 +28,17 @@
 #' @export
 #' @keywords graphics
 plotBounds <- function(
-  z,
-  area = TRUE,
-  grid = TRUE,
-  yt = "x",
-  add = FALSE,
-  cols = c("green", "red", "darkgreen", "orange"),
-  lwds = c(3, 3),
-  ltype = "l",
-  lpch = 16,
-  lcex = 1,
-  gy = 20
-) {
+    z,
+    area = TRUE,
+    grid = TRUE,
+    yt = "x",
+    add = FALSE,
+    cols = c("green", "red", "darkgreen", "orange"),
+    lwds = c(3, 3),
+    ltype = "l",
+    lpch = 16,
+    lcex = 1,
+    gy = 20) {
   n <- nrow(z)
   nmin <- min(z$looks)
   nmax <- max(z$looks)
diff --git a/design/design_doc_plotBounds.qmd b/design/design_doc_plotBounds.qmd
index 2c9fac37..16febfff 100644
--- a/design/design_doc_plotBounds.qmd
+++ b/design/design_doc_plotBounds.qmd
@@ -17,18 +17,17 @@ library(ggplot2)
 
 ```{r}
 vintage_plotBounds <- function(
-  z,
-  area = TRUE,
-  grid = TRUE,
-  yt = "x",
-  add = FALSE,
-  cols = c("#009E73", "#FF0046", "#7F55B1", "#F0A04B"),
-  lwds = c(3, 3),
-  ltype = "l",
-  lpch = 16,
-  lcex = 1,
-  gy = 20
-) {
+    z,
+    area = TRUE,
+    grid = TRUE,
+    yt = "x",
+    add = FALSE,
+    cols = c("#009E73", "#FF0046", "#7F55B1", "#F0A04B"),
+    lwds = c(3, 3),
+    ltype = "l",
+    lpch = 16,
+    lcex = 1,
+    gy = 20) {
   n <- nrow(z)
   nmin <- min(z$looks)
   nmax <- max(z$looks)
@@ -119,7 +118,6 @@ vintage_plotBounds <- function(
   }
   return(invisible())
 }
-
 ```
 
 # vintage example that should work with new function
@@ -136,7 +134,6 @@ plotBounds(
   yt = "p",
   add = TRUE
 )
-
 ```
 
 # vintage function output
@@ -157,8 +154,8 @@ vintage_plotBounds(
 # new call function
 
 ```{r}
-new_plotBounds <- function(coords, 
-                           postprob = TRUE, 
+new_plotBounds <- function(coords,
+                           postprob = TRUE,
                            go_colour = "#1B9E77",
                            stop_colour = "#E41A1C",
                            alpha = 1) {
@@ -167,16 +164,16 @@ new_plotBounds <- function(coords,
   assert_character(go_colour)
   assert_character(stop_colour)
   assert_number(alpha, lower = 0, upper = 1)
-  
+
   go_data <- data.frame(
     n = coords$looks,
-    ymin_go = coords$xU,  
-    ymax_go = coords$looks 
+    ymin_go = coords$xU,
+    ymax_go = coords$looks
   )
   stop_data <- data.frame(
     n = coords$looks,
-    ymin_stop = c(rep(0, length(coords$looks))),     
-    ymax_stop = coords$xL      
+    ymin_stop = c(rep(0, length(coords$looks))),
+    ymax_stop = coords$xL
   )
   plot <- ggplot2::ggplot() +
     ggplot2::geom_ribbon(
@@ -187,7 +184,7 @@ new_plotBounds <- function(coords,
     ggplot2::geom_ribbon(
       data = go_data,
       ggplot2::aes(x = n, ymin = ymin_go, ymax = ymax_go),
-      fill = go_colour , alpha = alpha
+      fill = go_colour, alpha = alpha
     ) +
     ggplot2::scale_x_continuous(
       name = "n",
@@ -196,26 +193,27 @@ new_plotBounds <- function(coords,
     ggplot2::scale_y_continuous(
       breaks = seq(from = 0, to = max(go_data$n), by = 2)
     ) +
-     ggplot2::geom_point(
-    data = go_data,
-     ggplot2::aes(x = n, y = ymin_go),
-    size = 3,       
-    shape = 16,
-    colour = "#16C47F", 
-  ) +
-     ggplot2::geom_point(
-    data = stop_data,
-     ggplot2::aes(x = n, y = ymax_stop),
-    size = 3,       
-    shape = 16,
-    colour = "#FF748B", #"#DC3C22",FF748B 
-  ) +
+    ggplot2::geom_point(
+      data = go_data,
+      ggplot2::aes(x = n, y = ymin_go),
+      size = 3,
+      shape = 16,
+      colour = "#16C47F",
+    ) +
+    ggplot2::geom_point(
+      data = stop_data,
+      ggplot2::aes(x = n, y = ymax_stop),
+      size = 3,
+      shape = 16,
+      colour = "#FF748B", # "#DC3C22",FF748B
+    ) +
     ggplot2::xlab("Sample Size (n)") +
     ggplot2::ylab("Number of Responders") +
-    ggplot2::theme_minimal() 
-  
-    plot + ggplot2::ggtitle(
-      "Boundaries of Go and Stop Responders per sample size")
+    ggplot2::theme_minimal()
+
+  plot + ggplot2::ggtitle(
+    "Boundaries of Go and Stop Responders per sample size"
+  )
 }
 ```
 
@@ -245,27 +243,29 @@ When n = 40, 10 responders and above is a Go, 9 responders and below is a stop
 
 ```{r}
 coords <- boundsPredprob(
-    looks = c(10, 20, 30, 40),
-    p0 = 0.20,
-    tT = 0.80,
-    phiL = 0.10,
-    phiU = 0.90,
-  )
+  looks = c(10, 20, 30, 40),
+  p0 = 0.20,
+  tT = 0.80,
+  phiL = 0.10,
+  phiU = 0.90,
+)
 print(coords)
 ```
 
 
 ```{r}
 coords <- boundsPredprob(
-    looks = c(10, 20, 30, 40),
-    p0 = 0.20,
-    tT = 0.80,
-    phiL = 0.10,
-    phiU = 0.90,
-  )
-new_plotBounds(coords = coords,
-               go_colour = "blue",
-               alpha = 1)
+  looks = c(10, 20, 30, 40),
+  p0 = 0.20,
+  tT = 0.80,
+  phiL = 0.10,
+  phiU = 0.90,
+)
+new_plotBounds(
+  coords = coords,
+  go_colour = "blue",
+  alpha = 1
+)
 ```
 
 # creating plots with new function with output from `boundsPostprob()`
@@ -284,12 +284,12 @@ When n = 40, 12 responders and above is a Go, 11 responders and below is a stop
 
 ```{r}
 coords1 <- boundsPostprob(
-    looks = c(10, 20, 30, 40),
-    p0 = 0.20,
-    tL = 0.10,
-    tU = 0.90,
-    parE = c(1, 1)
-  )
+  looks = c(10, 20, 30, 40),
+  p0 = 0.20,
+  tL = 0.10,
+  tU = 0.90,
+  parE = c(1, 1)
+)
 new_plotBounds(coords1)
 ```
 

From e2398b8127f14d8ca7c5f444e262bf6f142671f8 Mon Sep 17 00:00:00 2001
From: "27856297+dependabot-preview[bot]@users.noreply.github.com"
 <27856297+dependabot-preview[bot]@users.noreply.github.com>
Date: Sat, 11 Oct 2025 11:40:08 +0000
Subject: [PATCH 08/17] [skip roxygen] [skip vbump] Roxygen Man Pages Auto
 Update

---
 man/sumBetaDiff.Rd | 11 -----------
 1 file changed, 11 deletions(-)

diff --git a/man/sumBetaDiff.Rd b/man/sumBetaDiff.Rd
index 130dde7c..5cc1ae5e 100644
--- a/man/sumBetaDiff.Rd
+++ b/man/sumBetaDiff.Rd
@@ -27,14 +27,3 @@ along with the \code{go} and \code{stop} probabilities.
 A function to summarize the characters of a betadiff distribution \code{\link[=dbetadiff]{dbetadiff()}}.
 May require use of random sample generator to calculate, use \code{\link[=set.seed]{set.seed()}} to reproduce results.
 }
-\examples{
-parX <- c(1, 52) # Control group's parameters
-parY <- c(5.5, 20.5) # Treatment group's parameters
-sumBetaDiff(
-  parX = parX,
-  parY = parY,
-  ci_level = 0.9,
-  go_cut = 0.6,
-  stop_cut = 0.2
-)
-}

From 6593aec23ba7463885a47b7461de008df28d71bb Mon Sep 17 00:00:00 2001
From: Audrey Yeo <comptesaudrey@gmail.com>
Date: Sat, 11 Oct 2025 13:41:23 +0200
Subject: [PATCH 09/17] empty commit


From 3d3055dd8cc5e497f0585d442695e4938263ff54 Mon Sep 17 00:00:00 2001
From: Audrey Yeo <comptesaudrey@gmail.com>
Date: Sat, 11 Oct 2025 19:22:05 +0200
Subject: [PATCH 10/17] remove flag

---
 design/design_doc_plotBounds.qmd | 2 --
 1 file changed, 2 deletions(-)

diff --git a/design/design_doc_plotBounds.qmd b/design/design_doc_plotBounds.qmd
index 16febfff..524ed18e 100644
--- a/design/design_doc_plotBounds.qmd
+++ b/design/design_doc_plotBounds.qmd
@@ -155,12 +155,10 @@ vintage_plotBounds(
 
 ```{r}
 new_plotBounds <- function(coords,
-                           postprob = TRUE,
                            go_colour = "#1B9E77",
                            stop_colour = "#E41A1C",
                            alpha = 1) {
   assert_data_frame(coords, any.missing = FALSE, types = "numeric")
-  assert_flag(postprob)
   assert_character(go_colour)
   assert_character(stop_colour)
   assert_number(alpha, lower = 0, upper = 1)

From 3a5eb921795c63128aee0e18a6441a8f9fae026c Mon Sep 17 00:00:00 2001
From: Audrey Yeo <comptesaudrey@gmail.com>
Date: Sun, 12 Oct 2025 16:13:02 +0200
Subject: [PATCH 11/17] Update design/design_doc_plotBounds.qmd

Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com>
---
 design/design_doc_plotBounds.qmd | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/design/design_doc_plotBounds.qmd b/design/design_doc_plotBounds.qmd
index 524ed18e..f4a4f982 100644
--- a/design/design_doc_plotBounds.qmd
+++ b/design/design_doc_plotBounds.qmd
@@ -4,7 +4,9 @@ format: revealjs
 editor: visual
 ---
 
-Statisticians can display boundaries of Go, Stop and GreyZone decisions graphically in terms of response rates required by desired samples sizes or looks. This is such purpose of `plotBounds`. Note that for the predictive probability case, decision 1 rules are chosen. See `ocPredprob` for rules. Design document aims to translate previous call function to use of more common packages such as `ggplot2` and reduce number of lines. 
+Statisticians can display boundaries of Go, Stop and GreyZone decisions graphically in terms of response rates required by desired samples sizes or looks. This is the purpose of the  `plotBounds` function. Coordinates are the points where the polygon should be drawn and reflect the possible values for a go and stop decision respectively.
+
+ Note that for the predictive probability case, decision 1 rules are chosen. See `ocPredprob` for rules. This design document aims to refactor the previous function, in particular to use `ggplot2` and reduce the length of the function. 
 
 # packages that aid
 

From e01e036f1c2fc41f7fde81854d5f8ec3680836c1 Mon Sep 17 00:00:00 2001
From: Audrey Yeo <comptesaudrey@gmail.com>
Date: Sun, 12 Oct 2025 16:13:28 +0200
Subject: [PATCH 12/17] Update design/design_doc_plotBounds.qmd

Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com>
---
 design/design_doc_plotBounds.qmd | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/design/design_doc_plotBounds.qmd b/design/design_doc_plotBounds.qmd
index f4a4f982..713b8392 100644
--- a/design/design_doc_plotBounds.qmd
+++ b/design/design_doc_plotBounds.qmd
@@ -236,10 +236,11 @@ The criteria for interim analyses are from predictive probability calculation.
 The criteria for final analyses are from posterior probability calculation. 
 
 which translates to boundaries :
-When n = 10, 4 responders and above is a Go, 0 responders and below is a stop.
-When n = 20, 7 responders and above is a Go, 2 responders and below is a stop
-When n = 30, 9 responders and above is a Go, 5 responders and below is a stop
-When n = 40, 10 responders and above is a Go, 9 responders and below is a stop
+
+- When n = 10, 4 responders and above is a Go, 0 responders and below is a stop.
+- When n = 20, 7 responders and above is a Go, 2 responders and below is a stop
+- When n = 30, 9 responders and above is a Go, 5 responders and below is a stop
+- When n = 40, 10 responders and above is a Go, 9 responders and below is a stop
 
 ```{r}
 coords <- boundsPredprob(

From b3a0255d6275fbe0e51381b14fe3a5077a7009d9 Mon Sep 17 00:00:00 2001
From: Audrey Yeo <comptesaudrey@gmail.com>
Date: Sun, 12 Oct 2025 16:13:41 +0200
Subject: [PATCH 13/17] Update design/design_doc_plotBounds.qmd

Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com>
---
 design/design_doc_plotBounds.qmd | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/design/design_doc_plotBounds.qmd b/design/design_doc_plotBounds.qmd
index 713b8392..7c200b8f 100644
--- a/design/design_doc_plotBounds.qmd
+++ b/design/design_doc_plotBounds.qmd
@@ -277,10 +277,11 @@ As a premise, we establish the criteria:
 Go : P(RR > 0.20 | data) > 90 %
 Stop : P(RR > 0.20 | data) > 10 %
 which translates to boundaries :
-When n = 10, 4 responders and above is a Go, 3 responders and below is a stop.
-When n = 20, 7 responders and above is a Go, 6 responders and below is a stop
-When n = 30, 9 responders and above is a Go, 8 responders and below is a stop
-When n = 40, 12 responders and above is a Go, 11 responders and below is a stop
+
+- When n = 10, 4 responders and above is a Go, 3 responders and below is a stop.
+- When n = 20, 7 responders and above is a Go, 6 responders and below is a stop
+- When n = 30, 9 responders and above is a Go, 8 responders and below is a stop
+- When n = 40, 12 responders and above is a Go, 11 responders and below is a stop
 
 
 ```{r}

From 16aafbdd59b6024fe16b7d722cd43777abb37b37 Mon Sep 17 00:00:00 2001
From: Audrey Yeo <comptesaudrey@gmail.com>
Date: Sun, 12 Oct 2025 16:31:48 +0200
Subject: [PATCH 14/17] Update design/design_doc_plotBounds.qmd

Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com>
---
 design/design_doc_plotBounds.qmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/design/design_doc_plotBounds.qmd b/design/design_doc_plotBounds.qmd
index 7c200b8f..2794058e 100644
--- a/design/design_doc_plotBounds.qmd
+++ b/design/design_doc_plotBounds.qmd
@@ -271,7 +271,7 @@ new_plotBounds(
 
 # creating plots with new function with output from `boundsPostprob()`
 
-The following output show that important coordinates needed as input to create these plots. Coordinates are the points where the polygon should be drawn and reflect the possible values for a go and stop decision respectively.
+The following output show which inputs from a posterior probability design are needed to create these plots.
 
 As a premise, we establish the criteria:
 Go : P(RR > 0.20 | data) > 90 %

From 155d3effa47eeecd1d2f07a2406e8fdbd1d20604 Mon Sep 17 00:00:00 2001
From: Audrey Yeo <comptesaudrey@gmail.com>
Date: Sun, 12 Oct 2025 19:55:21 +0200
Subject: [PATCH 15/17] clean

---
 design/design_doc_plotBounds.qmd | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/design/design_doc_plotBounds.qmd b/design/design_doc_plotBounds.qmd
index 2794058e..6cc2a0eb 100644
--- a/design/design_doc_plotBounds.qmd
+++ b/design/design_doc_plotBounds.qmd
@@ -8,14 +8,14 @@ Statisticians can display boundaries of Go, Stop and GreyZone decisions graphica
 
  Note that for the predictive probability case, decision 1 rules are chosen. See `ocPredprob` for rules. This design document aims to refactor the previous function, in particular to use `ggplot2` and reduce the length of the function. 
 
-# packages that aid
+# Packages that aid
 
 ```{r}
 library(flextable)
 library(ggplot2)
 ```
 
-# vintage function
+# Vintage function
 
 ```{r}
 vintage_plotBounds <- function(
@@ -122,7 +122,7 @@ vintage_plotBounds <- function(
 }
 ```
 
-# vintage example that should work with new function
+# Vintage example that should work with new function
 
 ```{r}
 plotBounds(
@@ -138,7 +138,7 @@ plotBounds(
 )
 ```
 
-# vintage function output
+# Vintage function output
 
 ```{r}
 vintage_plotBounds(
@@ -153,7 +153,9 @@ vintage_plotBounds(
 )
 ```
 
-# new call function
+# New call function
+
+There are two good options to graph polygons to reflect the purpose of this function. The use of base r's `polygon()` is slightly more laborious; once minimum and maximum coordinates are established, approximation of these points are then required to draw the borders of this polygon. This step can be removed using the `geom_ribbon` call from the package `ggplot2`. Furthermore, the base r approach require the initial plot area to be created, and axes, axes labels, and points to be overlayed. There are additional steps that are also taken in the `ggplot2` approach, however done within a code chunk rather than separated calls. While it can be argued that these additional calls from the base r approach would anyway be encapsulated in one function, that is `plotbound`, the number of code lines is substantially reduced using the `ggplot` approach. 
 
 ```{r}
 new_plotBounds <- function(coords,
@@ -295,7 +297,8 @@ coords1 <- boundsPostprob(
 new_plotBounds(coords1)
 ```
 
-
++ggplot2 vs base R
++https://r-graphics.org/CHAPTER-GGPLOT2.html
 
 
 

From 6a8d1c71c5b179d4f043325a6d1eaac33900e989 Mon Sep 17 00:00:00 2001
From: Audrey Yeo <comptesaudrey@gmail.com>
Date: Wed, 10 Dec 2025 12:28:53 +0100
Subject: [PATCH 16/17] fix error

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

diff --git a/R/ocPredprob.R b/R/ocPredprob.R
index a436ac59..1ceb08c3 100644
--- a/R/ocPredprob.R
+++ b/R/ocPredprob.R
@@ -58,7 +58,7 @@ h_get_decision_one_predprob <- function(nnr, truep, p0, parE = c(1, 1), nnE, nnF
         thetaT = tT,
         parE = parE
       )$result
-      decision <- ifelse(interim_qU > phiU, FALSE, decision)
+      decision <- ifelse(interim_qU > phiU, TRUE, decision)
       all_looks <- orig_nnr[index_look]
     }
     if (size_look %in% nnF) {

From fdaad5bf5ace5caea963ef68004131a05641c02e Mon Sep 17 00:00:00 2001
From: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Date: Wed, 10 Dec 2025 06:16:02 +0000
Subject: [PATCH 17/17] [skip style] [skip vbump] Restyle files

---
 R/plotBounds.R                   | 23 ++++++++++++-----------
 design/design_doc_plotBounds.qmd | 23 ++++++++++++-----------
 2 files changed, 24 insertions(+), 22 deletions(-)

diff --git a/R/plotBounds.R b/R/plotBounds.R
index 4b5e9794..082a55b6 100644
--- a/R/plotBounds.R
+++ b/R/plotBounds.R
@@ -28,17 +28,18 @@
 #' @export
 #' @keywords graphics
 plotBounds <- function(
-    z,
-    area = TRUE,
-    grid = TRUE,
-    yt = "x",
-    add = FALSE,
-    cols = c("green", "red", "darkgreen", "orange"),
-    lwds = c(3, 3),
-    ltype = "l",
-    lpch = 16,
-    lcex = 1,
-    gy = 20) {
+  z,
+  area = TRUE,
+  grid = TRUE,
+  yt = "x",
+  add = FALSE,
+  cols = c("green", "red", "darkgreen", "orange"),
+  lwds = c(3, 3),
+  ltype = "l",
+  lpch = 16,
+  lcex = 1,
+  gy = 20
+) {
   n <- nrow(z)
   nmin <- min(z$looks)
   nmax <- max(z$looks)
diff --git a/design/design_doc_plotBounds.qmd b/design/design_doc_plotBounds.qmd
index 6cc2a0eb..6f8a73a3 100644
--- a/design/design_doc_plotBounds.qmd
+++ b/design/design_doc_plotBounds.qmd
@@ -19,17 +19,18 @@ library(ggplot2)
 
 ```{r}
 vintage_plotBounds <- function(
-    z,
-    area = TRUE,
-    grid = TRUE,
-    yt = "x",
-    add = FALSE,
-    cols = c("#009E73", "#FF0046", "#7F55B1", "#F0A04B"),
-    lwds = c(3, 3),
-    ltype = "l",
-    lpch = 16,
-    lcex = 1,
-    gy = 20) {
+  z,
+  area = TRUE,
+  grid = TRUE,
+  yt = "x",
+  add = FALSE,
+  cols = c("#009E73", "#FF0046", "#7F55B1", "#F0A04B"),
+  lwds = c(3, 3),
+  ltype = "l",
+  lpch = 16,
+  lcex = 1,
+  gy = 20
+) {
   n <- nrow(z)
   nmin <- min(z$looks)
   nmax <- max(z$looks)