From 7d6992f581071051cdeee3b5fd3fbe06cd9fa239 Mon Sep 17 00:00:00 2001
From: Dr Nathan Green <n8thangreen@yahoo.co.uk>
Date: Fri, 16 Feb 2024 08:59:42 +0000
Subject: [PATCH 1/6] update NEWS

---
 NEWS.md   | 1 +
 README.md | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index 438f6a62..1f7c537d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -5,6 +5,7 @@ _February 2024_
 
 Patch fixing small bugs from last CRAN release.
 
+* Moved `{voi}` package to Suggests in DESCRIPTION and added `requireNamespace()` in `evppi()` to avoid error when not installed (e.g. on CRAN) (f3e3e3e)
 * Converted help documentation in `man-roxygen` folder to md (cf858b1)
 * bugfix: line width in CEAC plot. `{ggplot2}` changed in version 3 to `linewidth` from `size` argument and had only changed some of the code. Updated to `scale_linewidth_manual()`. (60bea9c)
 * Using `testdata` folder `{testthat}` unit tests. (cbce0fa)
diff --git a/README.md b/README.md
index 4d6892d7..ef78becc 100644
--- a/README.md
+++ b/README.md
@@ -12,7 +12,7 @@
 
 > Perform Bayesian Cost-Effectiveness Analysis in R.
 
-:rocket: **Version 2.4.5 in development now!** [Check out the release notes here](https://github.com/n8thangreen/BCEA/releases).
+:rocket: **Version 2.4.6 in development now!** [Check out the release notes here](https://github.com/n8thangreen/BCEA/releases).
 
 ## Contents
 

From 3d8a7703bb48e62adefabb525efc8f8569fee566 Mon Sep 17 00:00:00 2001
From: Dr Nathan Green <n8thangreen@yahoo.co.uk>
Date: Thu, 22 Feb 2024 17:46:47 +0000
Subject: [PATCH 2/6] generalised input argument to ceplane.plot for wtp label
 for ggplot

* still need to test
* refactor for base plot version
---
 R/ceplane.plot.R          |  1 -
 R/ceplane_geom_params.R   |  4 ++--
 R/ceplane_ggplot_params.R |  3 ---
 R/ceplane_plot_graph.R    |  6 ++----
 R/prep_ceplane_params.R   | 27 +++++++++++++++++++++------
 5 files changed, 25 insertions(+), 16 deletions(-)

diff --git a/R/ceplane.plot.R b/R/ceplane.plot.R
index a62e9bd1..8fa1ccd0 100644
--- a/R/ceplane.plot.R
+++ b/R/ceplane.plot.R
@@ -120,7 +120,6 @@ ceplane.plot.bcea <- function(he,
   } else if (is_ggplot(graph)) {
     
     ceplane_plot_ggplot(he,
-                        wtp,
                         pos_legend = pos,
                         graph_params, ...)
     
diff --git a/R/ceplane_geom_params.R b/R/ceplane_geom_params.R
index 650cdb6c..f90fb858 100644
--- a/R/ceplane_geom_params.R
+++ b/R/ceplane_geom_params.R
@@ -25,14 +25,14 @@ ceplane_geom_params <- function(...) {
       names(extra_params) %in% c("area_include", "area_color")]
   names(polygon_params) <- gsub("area_", "", names(polygon_params))
   
-  wtp_params <-
+  label.pos <-
     extra_params[
       names(extra_params) %in% "label.pos"]
   
   modifyList(
     list(
       area_include = TRUE,
-      wtp_label.pos = wtp_params),
+      label.pos = label.pos),
     list(
       icer = icer_params,
       point = point_params,
diff --git a/R/ceplane_ggplot_params.R b/R/ceplane_ggplot_params.R
index 5a57d6ee..6ab5bd80 100644
--- a/R/ceplane_ggplot_params.R
+++ b/R/ceplane_ggplot_params.R
@@ -2,7 +2,6 @@
 #' CE-plane ggplot Parameters
 #' 
 #' @template args-he
-#' @param wtp Willingness to pay
 #' @param pos_legend Position of legend
 #' @param graph_params Other graphical parameters
 #' @param ... Additional arguments
@@ -11,7 +10,6 @@
 #' @keywords internal
 #' 
 ceplane_ggplot_params <- function(he,
-                                  wtp,
                                   pos_legend,
                                   graph_params,
                                   ...) {
@@ -33,7 +31,6 @@ ceplane_ggplot_params <- function(he,
         y = graph_params$ylim[1],
         hjust = "inward",
         vjust = "inward",
-        label = paste0("  k = ", format(wtp, digits = 6), "\n"),
         size = convert_pts_to_mm(1),
         colour = "black"),
       icer = list(
diff --git a/R/ceplane_plot_graph.R b/R/ceplane_plot_graph.R
index cbf5e9a3..ca3bf676 100644
--- a/R/ceplane_plot_graph.R
+++ b/R/ceplane_plot_graph.R
@@ -138,10 +138,8 @@ ceplane_plot_base <- function(he, ...) {
 #'              theme = ggplot2::theme_linedraw())
 #'              
 ceplane_plot_ggplot.bcea <- function(he,
-                                     wtp = 25000,
                                      pos_legend,
                                      graph_params, ...) {
-  
   # single long format for ggplot data
   delta_ce <-
     merge(
@@ -160,7 +158,7 @@ ceplane_plot_ggplot.bcea <- function(he,
       by = c("sim", "comparison"))
   
   plot_params <-
-    ceplane_ggplot_params(he, wtp, pos_legend, graph_params, ...)
+    ceplane_ggplot_params(he, pos_legend, graph_params, ...)
   
   theme_add <- purrr::keep(list(...), is.theme)
   
@@ -194,7 +192,7 @@ ceplane_plot_ggplot.bcea <- function(he,
             list(title = plot_params$title,
                  x = plot_params$xlab,
                  y = plot_params$ylab)) +
-    do.call(geom_abline, c(slope = wtp, plot_params$line)) +
+    do.call(geom_abline, c(slope = plot_params$wtp_value, plot_params$line)) +
     do.call(geom_point, plot_params$icer) +
     do.call(annotate, plot_params$wtp) +
     do.call(annotate, plot_params$icer_txt) +
diff --git a/R/prep_ceplane_params.R b/R/prep_ceplane_params.R
index 816009f7..dd5f6829 100644
--- a/R/prep_ceplane_params.R
+++ b/R/prep_ceplane_params.R
@@ -5,7 +5,7 @@
 #' parameters with defaults.
 #'
 #' @template args-he
-#' @param wtp Willingness-to-pay
+#' @param wtp_params Willingness-to-pay threshold. This can be a single value or a list.
 #' @param ... Additional arguments
 #' @importFrom grDevices grey.colors
 #'
@@ -13,11 +13,14 @@
 #' @export
 #' @keywords internal
 #'
-prep_ceplane_params <- function(he, wtp, ...) {
+prep_ceplane_params <- function(he, wtp_params, ...) {
   
   graph_params <- list(...)
   
-  ##TODO: back-compatibility helper..
+  # back compatibility
+  if (!is.list(wtp_params)) {
+    wtp_params <- list(value = wtp_params)
+  }
   
   intervs_in_title <-
     paste("\n",
@@ -32,8 +35,8 @@ prep_ceplane_params <- function(he, wtp, ...) {
       ifelse(he$n_comparisons == 1,  #he$change_comp,
              yes = intervs_in_title,
              no = ""))
-  
-  axes_lim <- xy_params(he, wtp, graph_params)
+  browser()
+  axes_lim <- xy_params(he, wtp_params$value, graph_params)
   
   default_params <-
     list(xlab = "Incremental effectiveness",
@@ -47,6 +50,8 @@ prep_ceplane_params <- function(he, wtp, ...) {
                                alpha = 1),
            size = 0.35,
            shape = rep(20, he$n_comparisons)),
+         wtp = list(
+           value = 25000),
          area_include = TRUE,
          ICER_size = 2,
          area = list(
@@ -54,6 +59,16 @@ prep_ceplane_params <- function(he, wtp, ...) {
            col = "grey95"),
          ref_first = TRUE)
   
-  modifyList(default_params, graph_params)
+  out <- 
+    modifyList(default_params, graph_params) |> 
+    modifyList(list(wtp = wtp_params))
+  
+  out$wtp$label <- paste0("  k = ", format(out$wtp$value, digits = 6), "\n")
+  
+  # move out of wtp list so can pass straight to geom
+  out$wtp_value <- out$wtp$value
+  out$wtp$value <- NULL
+    
+  out
 }
 

From d4467e61044109f3d1c6a4e9352d9ec15a2b44d9 Mon Sep 17 00:00:00 2001
From: Dr Nathan Green <n8thangreen@yahoo.co.uk>
Date: Thu, 22 Feb 2024 20:16:44 +0000
Subject: [PATCH 3/6] fixed bug with wtp in polygon_params()

---
 .Rbuildignore               | 1 +
 R/ceplane.plot.R            | 2 +-
 R/ceplane_base_params.R     | 2 +-
 R/ceplane_base_params_xxx.R | 4 +++-
 R/ceplane_ggplot_params.R   | 4 ++--
 R/ceplane_plot_graph.R      | 1 +
 R/prep_ceplane_params.R     | 4 ++--
 cran-comments.md            | 2 +-
 8 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index 7bb08579..4abe8285 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -25,3 +25,4 @@
 ^CONTRIBUTING\.md$
 ^revdep$
 ^CRAN-SUBMISSION$
+^CITATION\.cff$
diff --git a/R/ceplane.plot.R b/R/ceplane.plot.R
index 8fa1ccd0..70e8989a 100644
--- a/R/ceplane.plot.R
+++ b/R/ceplane.plot.R
@@ -103,7 +103,7 @@ ceplane.plot.bcea <- function(he,
                               pos = c(0, 1),
                               graph = c("base", "ggplot2", "plotly"),
                               ...) {
-  
+  browser()
   graph <- match.arg(graph)
   
   he <- setComparisons(he, comparison)
diff --git a/R/ceplane_base_params.R b/R/ceplane_base_params.R
index 02737f4c..a3c189c5 100644
--- a/R/ceplane_base_params.R
+++ b/R/ceplane_base_params.R
@@ -8,7 +8,7 @@ ceplane_base_params <- function(he,
   c(list(
     setup = setup_params(graph_params),
     points = points_params(graph_params),
-    polygon = polygon_params(graph_params, wtp),
+    polygon = polygon_params(graph_params),
     k_txt = k_text(graph_params, wtp),
     wtp = wtp,
     ref_first = graph_params$ref_first),
diff --git a/R/ceplane_base_params_xxx.R b/R/ceplane_base_params_xxx.R
index 80cb4ffc..8ece3392 100644
--- a/R/ceplane_base_params_xxx.R
+++ b/R/ceplane_base_params_xxx.R
@@ -17,7 +17,9 @@ setup_params <- function(graph_params) {
 
 #' @keywords dplot
 #' 
-polygon_params <- function(graph_params, wtp) {
+polygon_params <- function(graph_params) {
+  
+  wtp <- graph_params$wtp_value
   
   x_max <- graph_params$xlim[2]
   y_min <- graph_params$ylim[1]
diff --git a/R/ceplane_ggplot_params.R b/R/ceplane_ggplot_params.R
index 6ab5bd80..d539e57a 100644
--- a/R/ceplane_ggplot_params.R
+++ b/R/ceplane_ggplot_params.R
@@ -13,11 +13,11 @@ ceplane_ggplot_params <- function(he,
                                   pos_legend,
                                   graph_params,
                                   ...) {
-  
+
   ext_params <- ceplane_geom_params(...)
   
   graph_params$area <-
-    modifyList(polygon_params(graph_params, wtp),
+    modifyList(polygon_params(graph_params),
                graph_params$area)
   
   graph_params$legend <- make_legend_ggplot(he, pos_legend)
diff --git a/R/ceplane_plot_graph.R b/R/ceplane_plot_graph.R
index ca3bf676..c8f8071a 100644
--- a/R/ceplane_plot_graph.R
+++ b/R/ceplane_plot_graph.R
@@ -140,6 +140,7 @@ ceplane_plot_base <- function(he, ...) {
 ceplane_plot_ggplot.bcea <- function(he,
                                      pos_legend,
                                      graph_params, ...) {
+  browser()
   # single long format for ggplot data
   delta_ce <-
     merge(
diff --git a/R/prep_ceplane_params.R b/R/prep_ceplane_params.R
index dd5f6829..ffdfc7c6 100644
--- a/R/prep_ceplane_params.R
+++ b/R/prep_ceplane_params.R
@@ -14,7 +14,7 @@
 #' @keywords internal
 #'
 prep_ceplane_params <- function(he, wtp_params, ...) {
-  
+  browser()
   graph_params <- list(...)
   
   # back compatibility
@@ -35,7 +35,7 @@ prep_ceplane_params <- function(he, wtp_params, ...) {
       ifelse(he$n_comparisons == 1,  #he$change_comp,
              yes = intervs_in_title,
              no = ""))
-  browser()
+  
   axes_lim <- xy_params(he, wtp_params$value, graph_params)
   
   default_params <-
diff --git a/cran-comments.md b/cran-comments.md
index 39b96e6e..be5b6fc1 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,5 +1,5 @@
 ## R CMD check results
 
-0 errors | 0 warnings | 0 note
+0 errors | 0 warnings | 0 notes
 
 * This is an updated release.

From 8a7d01f792ceab360cb62155961a028621966b42 Mon Sep 17 00:00:00 2001
From: Dr Nathan Green <n8thangreen@yahoo.co.uk>
Date: Fri, 23 Feb 2024 09:18:00 +0000
Subject: [PATCH 4/6] updated documentation with new `wtp` argument for ggplot2
 ceplane.plot()

---
 NEWS.md                      |  4 ++++
 R/ceplane.plot.R             | 13 +++++++++----
 R/ceplane_plot_graph.R       |  1 -
 R/prep_ceplane_params.R      |  2 +-
 man/ceplane.plot.Rd          | 12 +++++++++---
 man/ceplane_ggplot_params.Rd |  4 +---
 man/ceplane_plot_graph.Rd    |  2 +-
 man/prep_ceplane_params.Rd   |  4 ++--
 vignettes/ceplane.Rmd        | 34 ++++++++++++++++++++++++++++++++++
 9 files changed, 61 insertions(+), 15 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 1f7c537d..f1f3b137 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,8 @@
 
+# BCEA 2.4.6 (dev)
+
+* In `ceplane.plot()` for `{ggplot2}` version used the ggplot syntax thats already used for other plotting arguments so that we can now pass e.g. `wtp = list(value = 20000, colour = "blue", x = 10, y = 10, size = 4)`. This closes issue #151 so can do something like `wtp = list(size = 0)` to hide the willingness to pay text. (3d8a770)
+
 # BCEA 2.4.6
 
 _February 2024_
diff --git a/R/ceplane.plot.R b/R/ceplane.plot.R
index 70e8989a..bf62d65b 100644
--- a/R/ceplane.plot.R
+++ b/R/ceplane.plot.R
@@ -7,7 +7,8 @@
 #'   comparisons together. Any subset of the possible comparisons can be selected
 #'   (e.g., `comparison = c(1,3)` or `comparison = 2`).
 #' @param wtp The value of the willingness to pay parameter. Not used if
-#'   `graph = "base"` for multiple comparisons.
+#'   `graph = "base"` for multiple comparisons. For \pkg{ggplot2} can also provide
+#'   a list of arguments for more options (see below).
 #' @param pos Parameter to set the position of the legend; for a single
 #'   comparison plot, the ICER legend position. Can be given in form of a string
 #'   `(bottom|top)(right|left)` for base graphics and
@@ -36,12 +37,17 @@
 #'   Should be of length 1 or equal to the number of comparisons.
 #'   \item `icer = list(color)`: a vector of colours specifying the colour(s) of the ICER
 #'   points. Should be of length 1 or equal to the number of comparisons.
-#'   \item `icer = list(size)`: a vector of colours specifying the size(s) of the ICER
+#'   \item `icer = list(size)`: a vector of values specifying the size(s) of the ICER
 #'   points. Should be of length 1 or equal to the number of comparisons.
 #'   \item `area_include`: logical, include or exclude the cost-effectiveness 
-#'   acceptability area (default is TRUE).
+#'   acceptability area (default is `TRUE`).
+#'   \item `wtp = list(value)`: equivalent to simply using `wtp = value` but for when multiple
+#'   arguments are passed in list form.
 #'   \item `area = list(color)`: a colour specifying the colour of the cost-effectiveness
 #'   acceptability area.
+#'   \item `wtp = list(color)`: a colour specifying the colour of the willingness-to-pay text
+#'   \item `wtp = list(size)`: a value specifying the size of the willingness-to-pay text
+#'   \item `wtp = list(x=..., y=...)`: a value specifying the x and y coordinates of the willingness-to-pay text
 #'   \item `currency`: Currency prefix to cost differential values - \pkg{ggplot2} only.
 #'   \item `icer_annot`: Annotate each ICER point with text label - \pkg{ggplot2} only.
 #'  }
@@ -103,7 +109,6 @@ ceplane.plot.bcea <- function(he,
                               pos = c(0, 1),
                               graph = c("base", "ggplot2", "plotly"),
                               ...) {
-  browser()
   graph <- match.arg(graph)
   
   he <- setComparisons(he, comparison)
diff --git a/R/ceplane_plot_graph.R b/R/ceplane_plot_graph.R
index c8f8071a..ca3bf676 100644
--- a/R/ceplane_plot_graph.R
+++ b/R/ceplane_plot_graph.R
@@ -140,7 +140,6 @@ ceplane_plot_base <- function(he, ...) {
 ceplane_plot_ggplot.bcea <- function(he,
                                      pos_legend,
                                      graph_params, ...) {
-  browser()
   # single long format for ggplot data
   delta_ce <-
     merge(
diff --git a/R/prep_ceplane_params.R b/R/prep_ceplane_params.R
index ffdfc7c6..aec58910 100644
--- a/R/prep_ceplane_params.R
+++ b/R/prep_ceplane_params.R
@@ -14,7 +14,7 @@
 #' @keywords internal
 #'
 prep_ceplane_params <- function(he, wtp_params, ...) {
-  browser()
+  
   graph_params <- list(...)
   
   # back compatibility
diff --git a/man/ceplane.plot.Rd b/man/ceplane.plot.Rd
index 8db3a13c..0accf6b1 100644
--- a/man/ceplane.plot.Rd
+++ b/man/ceplane.plot.Rd
@@ -26,7 +26,8 @@ comparisons together. Any subset of the possible comparisons can be selected
 (e.g., \code{comparison = c(1,3)} or \code{comparison = 2}).}
 
 \item{wtp}{The value of the willingness to pay parameter. Not used if
-\code{graph = "base"} for multiple comparisons.}
+\code{graph = "base"} for multiple comparisons. For \pkg{ggplot2} can also provide
+a list of arguments for more options (see below).}
 
 \item{pos}{Parameter to set the position of the legend; for a single
 comparison plot, the ICER legend position. Can be given in form of a string
@@ -58,12 +59,17 @@ Should be of length 1 or equal to the number of comparisons.
 Should be of length 1 or equal to the number of comparisons.
 \item \code{icer = list(color)}: a vector of colours specifying the colour(s) of the ICER
 points. Should be of length 1 or equal to the number of comparisons.
-\item \code{icer = list(size)}: a vector of colours specifying the size(s) of the ICER
+\item \code{icer = list(size)}: a vector of values specifying the size(s) of the ICER
 points. Should be of length 1 or equal to the number of comparisons.
 \item \code{area_include}: logical, include or exclude the cost-effectiveness
-acceptability area (default is TRUE).
+acceptability area (default is \code{TRUE}).
+\item \code{wtp = list(value)}: equivalent to simply using \code{wtp = value} but for when multiple
+arguments are passed in list form.
 \item \code{area = list(color)}: a colour specifying the colour of the cost-effectiveness
 acceptability area.
+\item \code{wtp = list(color)}: a colour specifying the colour of the willingness-to-pay text
+\item \code{wtp = list(size)}: a value specifying the size of the willingness-to-pay text
+\item \code{wtp = list(x=..., y=...)}: a value specifying the x and y coordinates of the willingness-to-pay text
 \item \code{currency}: Currency prefix to cost differential values - \pkg{ggplot2} only.
 \item \code{icer_annot}: Annotate each ICER point with text label - \pkg{ggplot2} only.
 }}
diff --git a/man/ceplane_ggplot_params.Rd b/man/ceplane_ggplot_params.Rd
index 712807cf..0aa3cd57 100644
--- a/man/ceplane_ggplot_params.Rd
+++ b/man/ceplane_ggplot_params.Rd
@@ -4,14 +4,12 @@
 \alias{ceplane_ggplot_params}
 \title{CE-plane ggplot Parameters}
 \usage{
-ceplane_ggplot_params(he, wtp, pos_legend, graph_params, ...)
+ceplane_ggplot_params(he, pos_legend, graph_params, ...)
 }
 \arguments{
 \item{he}{A \code{bcea} object containing the results of the Bayesian
 modelling and the economic evaluation.}
 
-\item{wtp}{Willingness to pay}
-
 \item{pos_legend}{Position of legend}
 
 \item{graph_params}{Other graphical parameters}
diff --git a/man/ceplane_plot_graph.Rd b/man/ceplane_plot_graph.Rd
index 9c8026cf..21d68f22 100644
--- a/man/ceplane_plot_graph.Rd
+++ b/man/ceplane_plot_graph.Rd
@@ -14,7 +14,7 @@
 
 ceplane_plot_base(he, ...)
 
-\method{ceplane_plot_ggplot}{bcea}(he, wtp = 25000, pos_legend, graph_params, ...)
+\method{ceplane_plot_ggplot}{bcea}(he, pos_legend, graph_params, ...)
 
 ceplane_plot_ggplot(he, ...)
 
diff --git a/man/prep_ceplane_params.Rd b/man/prep_ceplane_params.Rd
index 97f30827..151ed979 100644
--- a/man/prep_ceplane_params.Rd
+++ b/man/prep_ceplane_params.Rd
@@ -4,13 +4,13 @@
 \alias{prep_ceplane_params}
 \title{Prepare CE-plane Parameters}
 \usage{
-prep_ceplane_params(he, wtp, ...)
+prep_ceplane_params(he, wtp_params, ...)
 }
 \arguments{
 \item{he}{A \code{bcea} object containing the results of the Bayesian
 modelling and the economic evaluation.}
 
-\item{wtp}{Willingness-to-pay}
+\item{wtp_params}{Willingness-to-pay threshold. This can be a single value or a list.}
 
 \item{...}{Additional arguments}
 }
diff --git a/vignettes/ceplane.Rmd b/vignettes/ceplane.Rmd
index 2d361bd4..55f4d78b 100644
--- a/vignettes/ceplane.Rmd
+++ b/vignettes/ceplane.Rmd
@@ -111,6 +111,40 @@ ceplane.plot(he, pos = c(1, 0))
 ceplane.plot(he, pos = c(1, 1))
 ```
 
+### Willingness-to-pay
+
+For `{ggplot2}`
+
+```{r}
+ceplane.plot(he, graph = "ggplot2")  # default
+ceplane.plot(he, graph = "ggplot2", wtp = 10000)
+ceplane.plot(he, graph = "ggplot2", wtp = list(value = 10000))
+ceplane.plot(he, graph = "ggplot2", wtp = list(value = 10000, colour = "blue"))
+ceplane.plot(he, graph = "ggplot2", wtp = list(colour = "blue"))
+ceplane.plot(he, graph = "ggplot2", wtp = list(y = 8))
+ceplane.plot(he, graph = "ggplot2", wtp = list(size = 5))
+
+# to hide text
+ceplane.plot(he, graph = "ggplot2", wtp = list(size = 0))
+```
+
+For base `R`
+
+```{r}
+ceplane.plot(he)  # default
+
+##TODO: not yet implemented
+# ceplane.plot(he, wtp = 10000)
+# ceplane.plot(he, wtp = list(value = 10000))
+# ceplane.plot(he, wtp = list(value = 10000, colour = "blue"))
+# ceplane.plot(he, wtp = list(colour = "blue"))
+# ceplane.plot(he, wtp = list(y = 8))
+# ceplane.plot(he, wtp = list(size = 5))
+# 
+# # to hide text
+# ceplane.plot(he, wtp = list(size = 0))
+```
+
 <!-- ```{r} -->
 <!-- ceac.plot(he, graph = "ggplot2", pos = c(0, 0)) -->
 <!-- ceac.plot(he, graph = "ggplot2", pos = c(0, 1)) -->

From 4ee271105da7e542a5a8f436a5cd5266cc8a2cde Mon Sep 17 00:00:00 2001
From: Dr Nathan Green <n8thangreen@yahoo.co.uk>
Date: Fri, 23 Feb 2024 11:06:28 +0000
Subject: [PATCH 5/6] premerge

---
 BCEA.Rproj                   |   2 +-
 R/prep_ceplane_params.R      |   4 +-
 man/ceplane_ggplot_params.Rd |  24 -------
 man/ceplane_plot_graph.Rd    | 126 -----------------------------------
 man/prep_ceplane_params.Rd   |  24 -------
 vignettes/ceplane.Rmd        |  23 +++++++
 6 files changed, 26 insertions(+), 177 deletions(-)
 delete mode 100644 man/ceplane_ggplot_params.Rd
 delete mode 100644 man/ceplane_plot_graph.Rd
 delete mode 100644 man/prep_ceplane_params.Rd

diff --git a/BCEA.Rproj b/BCEA.Rproj
index 6843888d..9f964990 100644
--- a/BCEA.Rproj
+++ b/BCEA.Rproj
@@ -15,4 +15,4 @@ LaTeX: pdfLaTeX
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace,vignette
+PackageRoxygenize: rd,collate,namespace
diff --git a/R/prep_ceplane_params.R b/R/prep_ceplane_params.R
index dd5f6829..ebf8c066 100644
--- a/R/prep_ceplane_params.R
+++ b/R/prep_ceplane_params.R
@@ -5,7 +5,7 @@
 #' parameters with defaults.
 #'
 #' @template args-he
-#' @param wtp_params Willingness-to-pay threshold. This can be a single value or a list.
+#' @param wtp_params Willingness-to-pay parameters. This can be a single value or a list.
 #' @param ... Additional arguments
 #' @importFrom grDevices grey.colors
 #'
@@ -35,7 +35,7 @@ prep_ceplane_params <- function(he, wtp_params, ...) {
       ifelse(he$n_comparisons == 1,  #he$change_comp,
              yes = intervs_in_title,
              no = ""))
-  browser()
+
   axes_lim <- xy_params(he, wtp_params$value, graph_params)
   
   default_params <-
diff --git a/man/ceplane_ggplot_params.Rd b/man/ceplane_ggplot_params.Rd
deleted file mode 100644
index 712807cf..00000000
--- a/man/ceplane_ggplot_params.Rd
+++ /dev/null
@@ -1,24 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ceplane_ggplot_params.R
-\name{ceplane_ggplot_params}
-\alias{ceplane_ggplot_params}
-\title{CE-plane ggplot Parameters}
-\usage{
-ceplane_ggplot_params(he, wtp, pos_legend, graph_params, ...)
-}
-\arguments{
-\item{he}{A \code{bcea} object containing the results of the Bayesian
-modelling and the economic evaluation.}
-
-\item{wtp}{Willingness to pay}
-
-\item{pos_legend}{Position of legend}
-
-\item{graph_params}{Other graphical parameters}
-
-\item{...}{Additional arguments}
-}
-\description{
-CE-plane ggplot Parameters
-}
-\keyword{internal}
diff --git a/man/ceplane_plot_graph.Rd b/man/ceplane_plot_graph.Rd
deleted file mode 100644
index 9c8026cf..00000000
--- a/man/ceplane_plot_graph.Rd
+++ /dev/null
@@ -1,126 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ceplane_plot_graph.R
-\name{ceplane_plot_graph}
-\alias{ceplane_plot_graph}
-\alias{ceplane_plot_base.bcea}
-\alias{ceplane_plot_base}
-\alias{ceplane_plot_ggplot.bcea}
-\alias{ceplane_plot_ggplot}
-\alias{ceplane_plot_plotly.bcea}
-\alias{ceplane_plot_plotly}
-\title{Cost-Effectiveness Plane Plot By Graph Device}
-\usage{
-\method{ceplane_plot_base}{bcea}(he, wtp = 25000, pos_legend, graph_params, ...)
-
-ceplane_plot_base(he, ...)
-
-\method{ceplane_plot_ggplot}{bcea}(he, wtp = 25000, pos_legend, graph_params, ...)
-
-ceplane_plot_ggplot(he, ...)
-
-\method{ceplane_plot_plotly}{bcea}(he, wtp = 25000, pos_legend, graph_params, ...)
-
-ceplane_plot_plotly(he, ...)
-}
-\arguments{
-\item{he}{A \code{bcea} object containing the results of the Bayesian
-modelling and the economic evaluation.}
-
-\item{wtp}{Willingness to pay threshold; default 25,000}
-
-\item{pos_legend}{Legend position}
-
-\item{graph_params}{Graph parameters in \pkg{ggplot2} format}
-
-\item{...}{Additional arguments}
-}
-\value{
-For base R returns a plot
-
-For \pkg{ggplot2} returns \pkg{ggplot2} object
-
-For \pkg{plotly} returns a plot in the Viewer
-}
-\description{
-Choice of base R, \pkg{ggplot2} or \pkg{plotly}.
-}
-\examples{
-# single comparator
-data(Vaccine, package = "BCEA")
-
-he <- bcea(eff, cost)
-ceplane.plot(he, graph = "base")
-
-\dontrun{
-# need to provide all the defaults because thats what
-# ceplane.plot() does
-
-graph_params <-  list(xlab = "x-axis label",
-                      ylab = "y-axis label",
-                      title = "my title",
-                      xlim = c(-0.002, 0.001),
-                      ylim = c(-13, 5),
-                      point = list(sizes = 1,
-                                   colors = "darkgrey"),
-                      area = list(color = "lightgrey"))
-                      
-he$delta_e <- as.matrix(he$delta_e)
-he$delta_c <- as.matrix(he$delta_c)
-
-BCEA::ceplane_plot_base(he, graph_params = graph_params)
-
-## single non-default comparator
-
-
-## multiple comparators
-data(Smoking)
-
-graph_params <-  list(xlab = "x-axis label",
-                      ylab = "y-axis label",
-                      title = "my title",
-                      xlim = c(-1, 2.5),
-                      ylim = c(-1, 160),
-                      point = list(sizes = 0.5,
-                                   colors = grey.colors(3, start = 0.1, end = 0.7)),
-                      area = list(color = "lightgrey"))
-                                   
-he <- bcea(eff, cost, ref = 4, Kmax = 500, interventions = treats)
-
-BCEA::ceplane_plot_base(he,
-                        wtp = 200,
-                        pos_legend = FALSE,
-                        graph_params = graph_params)
-}
-
-
-data(Vaccine)
-he <- bcea(eff, cost)
-
-ceplane.plot(he, graph = "ggplot2")
-ceplane.plot(he, wtp=10000, graph = "ggplot2",
-             point = list(colors = "blue", sizes = 2),
-             area = list(col = "springgreen3"))
-
-data(Smoking)
-he <- bcea(eff, cost, ref = 4, Kmax = 500, interventions = treats)
-
-ceplane.plot(he, graph = "ggplot2")
-
-ceplane.plot(he,
-             wtp = 200,
-             pos = "right",
-             ICER_size = 2,
-             graph = "ggplot2")
-   
-ceplane.plot(he,
-             wtp = 200,
-             pos = TRUE,
-             graph = "ggplot2")
-
-ceplane.plot(he,
-             graph = "ggplot2",
-             wtp=200,
-             theme = ggplot2::theme_linedraw())
-             
-}
-\keyword{hplot}
diff --git a/man/prep_ceplane_params.Rd b/man/prep_ceplane_params.Rd
deleted file mode 100644
index 97f30827..00000000
--- a/man/prep_ceplane_params.Rd
+++ /dev/null
@@ -1,24 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/prep_ceplane_params.R
-\name{prep_ceplane_params}
-\alias{prep_ceplane_params}
-\title{Prepare CE-plane Parameters}
-\usage{
-prep_ceplane_params(he, wtp, ...)
-}
-\arguments{
-\item{he}{A \code{bcea} object containing the results of the Bayesian
-modelling and the economic evaluation.}
-
-\item{wtp}{Willingness-to-pay}
-
-\item{...}{Additional arguments}
-}
-\value{
-List pf graph parameters
-}
-\description{
-In ggplot format, combine user-supplied
-parameters with defaults.
-}
-\keyword{internal}
diff --git a/vignettes/ceplane.Rmd b/vignettes/ceplane.Rmd
index 2d361bd4..a7f75632 100644
--- a/vignettes/ceplane.Rmd
+++ b/vignettes/ceplane.Rmd
@@ -111,6 +111,29 @@ ceplane.plot(he, pos = c(1, 0))
 ceplane.plot(he, pos = c(1, 1))
 ```
 
+### Willingness-to-pay label
+
+For `{ggplot2}`
+
+```{r}
+ceplane.plot(he, graph = "ggplot2")
+ceplane.plot(he, graph = "ggplot2", wtp = list(value = 25000, colour = "blue"))
+ceplane.plot(he, graph = "ggplot2", wtp = list(colour = "blue"))
+ceplane.plot(he, graph = "ggplot2", wtp = list(value = 40000, colour = "blue"))
+ceplane.plot(he, graph = "ggplot2", wtp = 40000)
+```
+
+For base `R`
+
+```{r}
+ceplane.plot(he)
+ceplane.plot(he, wtp = list(value = 25000, colour = "blue"))
+ceplane.plot(he, wtp = list(colour = "blue"))
+ceplane.plot(he, wtp = list(value = 40000, colour = "blue"))
+ceplane.plot(he, wtp = 40000)
+```
+
+
 <!-- ```{r} -->
 <!-- ceac.plot(he, graph = "ggplot2", pos = c(0, 0)) -->
 <!-- ceac.plot(he, graph = "ggplot2", pos = c(0, 1)) -->

From c2ea8010d0f1e0809ca143398f1d7f83732a1ef8 Mon Sep 17 00:00:00 2001
From: Dr Nathan Green <n8thangreen@yahoo.co.uk>
Date: Fri, 23 Feb 2024 11:10:28 +0000
Subject: [PATCH 6/6] removed some leftover merge <<< ===

---
 R/prep_ceplane_params.R |  4 ----
 vignettes/ceplane.Rmd   | 23 -----------------------
 2 files changed, 27 deletions(-)

diff --git a/R/prep_ceplane_params.R b/R/prep_ceplane_params.R
index 661ed4b0..ebf8c066 100644
--- a/R/prep_ceplane_params.R
+++ b/R/prep_ceplane_params.R
@@ -35,11 +35,7 @@ prep_ceplane_params <- function(he, wtp_params, ...) {
       ifelse(he$n_comparisons == 1,  #he$change_comp,
              yes = intervs_in_title,
              no = ""))
-<<<<<<< HEAD
 
-=======
-  
->>>>>>> 8a7d01f792ceab360cb62155961a028621966b42
   axes_lim <- xy_params(he, wtp_params$value, graph_params)
   
   default_params <-
diff --git a/vignettes/ceplane.Rmd b/vignettes/ceplane.Rmd
index bf437ed5..f58bf761 100644
--- a/vignettes/ceplane.Rmd
+++ b/vignettes/ceplane.Rmd
@@ -111,22 +111,11 @@ ceplane.plot(he, pos = c(1, 0))
 ceplane.plot(he, pos = c(1, 1))
 ```
 
-<<<<<<< HEAD
 ### Willingness-to-pay label
-=======
-### Willingness-to-pay
->>>>>>> 8a7d01f792ceab360cb62155961a028621966b42
 
 For `{ggplot2}`
 
 ```{r}
-<<<<<<< HEAD
-ceplane.plot(he, graph = "ggplot2")
-ceplane.plot(he, graph = "ggplot2", wtp = list(value = 25000, colour = "blue"))
-ceplane.plot(he, graph = "ggplot2", wtp = list(colour = "blue"))
-ceplane.plot(he, graph = "ggplot2", wtp = list(value = 40000, colour = "blue"))
-ceplane.plot(he, graph = "ggplot2", wtp = 40000)
-=======
 ceplane.plot(he, graph = "ggplot2")  # default
 ceplane.plot(he, graph = "ggplot2", wtp = 10000)
 ceplane.plot(he, graph = "ggplot2", wtp = list(value = 10000))
@@ -137,22 +126,11 @@ ceplane.plot(he, graph = "ggplot2", wtp = list(size = 5))
 
 # to hide text
 ceplane.plot(he, graph = "ggplot2", wtp = list(size = 0))
->>>>>>> 8a7d01f792ceab360cb62155961a028621966b42
 ```
 
 For base `R`
 
 ```{r}
-<<<<<<< HEAD
-ceplane.plot(he)
-ceplane.plot(he, wtp = list(value = 25000, colour = "blue"))
-ceplane.plot(he, wtp = list(colour = "blue"))
-ceplane.plot(he, wtp = list(value = 40000, colour = "blue"))
-ceplane.plot(he, wtp = 40000)
-```
-
-
-=======
 ceplane.plot(he)  # default
 
 ##TODO: not yet implemented
@@ -167,7 +145,6 @@ ceplane.plot(he)  # default
 # ceplane.plot(he, wtp = list(size = 0))
 ```
 
->>>>>>> 8a7d01f792ceab360cb62155961a028621966b42
 <!-- ```{r} -->
 <!-- ceac.plot(he, graph = "ggplot2", pos = c(0, 0)) -->
 <!-- ceac.plot(he, graph = "ggplot2", pos = c(0, 1)) -->