Main CRAN submission

.Rbuildignore

@@ -25,4 +25,5 @@
 ^CONTRIBUTING\.md$
 ^revdep$
 ^CRAN-SUBMISSION$
+^CITATION\.cff$
 ^CITATION.cff

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

.gitignore

@@ -2,9 +2,15 @@
 .Rhistory
 .RData
 .Ruserdata
-BCEA.Rcheck/
+*.html
+*.xml
+*.js
 *.Rproj
+BCEA.Rcheck/
 inst/doc
 renv/
 revdep/
 BCEA_book.pdf - Shortcut
+docs/*/
+docs/
+docs/**

BCEA.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 3d4ed2e6-cc51-4450-bdff-f9b9d46ae254
 
 RestoreWorkspace: Default
 SaveWorkspace: Default
@@ -15,4 +16,4 @@ LaTeX: pdfLaTeX
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace,vignette
+PackageRoxygenize: rd,collate,namespace

CITATION.cff

@@ -14,7 +14,7 @@ authors:
   given-names: "Nathan"
   orcid: https://orcid.org/0000-0003-2745-1736
 title: "BCEA: Bayesian Cost-Effectiveness Analysis"
-version: 2.4-5
+version: 2.4.6
 doi: 10.1007/978-3-319-55718-2
 date-released: 2023-11-20
 url: "https://gianluca.statistica.it/software/bcea/"

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: BCEA
 Type: Package
 Title: Bayesian Cost Effectiveness Analysis
-Version: 2.4.6
+Version: 2.4.7
 Authors@R: c(
     person("Gianluca", "Baio",
             email = "[email protected]",
@@ -22,7 +22,7 @@ Authors@R: c(
 Imports:
     cli (>= 3.3.0),
     dplyr,
-    ggplot2 (>= 3.4.0),
+    ggplot2 (>= 3.5.0),
     graphics,
     gridExtra,
     MASS,
@@ -33,7 +33,7 @@ Imports:
     reshape2,
     rlang,
     rstan,
-    scales,
+    scales
 Depends:
     R (>= 3.5.0)
 Suggests:
@@ -63,11 +63,11 @@ Description: Produces an economic evaluation of a sample of suitable variables o
 License: GPL-3
 URL: https://gianluca.statistica.it/software/bcea/,
      https://gianluca.statistica.it/,
-     https://github.com/giabaio/BCEA/  
+     https://github.com/giabaio/BCEA/,
+     https://n8thangreen.github.io/BCEA/
 NeedsCompilation: no
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Encoding: UTF-8
 BugReports: https://github.com/n8thangreen/BCEA/issues/
 LazyData: false
 Roxygen: list(markdown = TRUE)
-

NAMESPACE

@@ -133,7 +133,6 @@ importFrom(purrr,keep)
 importFrom(purrr,list_cbind)
 importFrom(purrr,map)
 importFrom(purrr,map_int)
-importFrom(purrr,map_lgl)
 importFrom(purrr,pluck)
 importFrom(reshape2,melt)
 importFrom(rlang,.data)

NEWS.md

@@ -1,10 +1,25 @@
 
+# BCEA 2.4.7 (dev)
+
+# BCEA 2.4.7
+
+_January 2025_
+
+* 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)
+* Small features added which were missing for the new edition of the BCEA book:
+  - Extended `ggplot` version legend to take a vertical or horizontal part to the `pos` argument (85ba87f)
+  - Relative font size argument `rel` for ceplane and ceac plot (8d1586f)
+  - Added text size `ggplot` argument to `eib_plot` (1e32788) and `evi_plot` (84aaa2f)
+  - `label.pos` logical argument fixed in `ceplane.plot` for `ggplot` (92e9eb0) and base `R` (c7351e4)
+
+
 # BCEA 2.4.6
 
 _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)
@@ -13,11 +28,11 @@ Patch fixing small bugs from last CRAN release.
 
 _November 2023_
 
-Some cosmetic changes to clean up
+Some cosmetic changes to clean up.
 
 * Removed the (by now, unnecessary) appveyor webhook
-* Added correct 'Remotes' in the 'DESCRIPTION' file to point to the correct GitHub repos for 'voi' and 'plotrix'
-* Changed the class of the object 'smoking_output' to be used in the 'evppi' example avoiding the need for 'rjags'
+* Added correct `Remotes` in the `DESCRIPTION` file to point to the correct GitHub repos for `voi` and `plotrix`
+* Changed the class of the object `smoking_output` to be used in the `evppi` example avoiding the need for `rjags`
 
 _October 2023_
 

R/CEriskav_plot_graph.R

@@ -112,7 +112,7 @@ CEriskav_plot_ggplot <- function(he, pos_legend) {
       legend.direction = legend_params$legend_direction,
       legend.title = element_blank(),
       legend.background = element_blank(),
-      legend.text.align = 0,
+      legend.text = element_text(hjust = 0),
       plot.title = element_text(
         lineheight = 1.05,
         face = "bold",
@@ -146,7 +146,7 @@ CEriskav_plot_ggplot <- function(he, pos_legend) {
       legend.direction = legend_params$legend.direction,
       legend.title = element_blank(),
       legend.background = element_blank(),
-      legend.text.align = 0,
+      legend.text = element_text(hjust = 0),
       plot.title = element_text(
         lineheight = 1.05,
         face = "bold",

R/ceac_plot_graph.R

@@ -111,6 +111,8 @@ ceac_plot_ggplot.bcea <- function(he,
 #' @rdname ceac_plot_graph
 #' @param ceac ceac index in `he`
 #' @importFrom scales label_dollar
+#' @importFrom purrr keep
+#' @import ggplot2
 #' @keywords internal hplot
 #' @md
 ceac_ggplot <- function(he,
@@ -132,7 +134,7 @@ ceac_ggplot <- function(he,
 
   graph_params <- helper_ggplot_params(he, graph_params)
   legend_params <- make_legend_ggplot(he, pos_legend)
-  theme_add <- purrr::keep(extra_params, is.theme)
+  theme_add <- Filter(f = \(val) ggplot2::is.theme(val), x = extra_params)
 
   ggplot(data_psa, aes(x = .data$k, y = .data$ceac)) +
     geom_line(aes(linetype = .data$comparison,
@@ -145,6 +147,10 @@ ceac_ggplot <- function(he,
       labels = scales::label_dollar(prefix = graph_params$currency)) +
     do.call(labs, graph_params$annot) +                    # text
     do.call(theme, legend_params) +                        # legend
+    do.call(theme, list(
+      axis.text = element_text(size = graph_params$text$size),
+      axis.title.x = element_text(size = graph_params$text$size),
+      axis.title.y = element_text(size = graph_params$text$size))) +  # text size
     scale_linetype_manual("",                              # lines
                           labels = graph_params$labels,
                           values = graph_params$line$type) +

R/ceaf.plot.R

@@ -88,11 +88,11 @@ ceaf.plot.pairwise <- function(mce,
          xlab = "Willingness to pay",
          ylab = "Probability of most cost effectiveness",
          main = "Cost-effectiveness acceptability frontier")
-    matplot(x = mce$k,
-            mce$p_best_interv,
-            type = "l",
-            lty = 3,
-            add = TRUE)
+    # matplot(x = mce$k,              # underlying ceac curves
+    #         mce$p_best_interv,
+    #         type = "l",
+    #         lty = 3,
+    #         add = TRUE)
     lines(x = mce$k,
           y = mce$ceaf,
           type = "l",

R/ceef_plot_graph.R

@@ -36,8 +36,7 @@ ceef_plot_ggplot <- function(he,
 
   extra_args <- list(...)
 
-  opt_theme <- purrr::keep(extra_args, is.theme)
-
+  opt_theme <- Filter(f = \(val) ggplot2::is.theme(val), x = extra_args)
   ceplane <- ggplot(ceef.points, aes(x = .data$x, y = .data$y))
 
   if (add_dominance_region) {
@@ -111,7 +110,7 @@ ceef_plot_ggplot <- function(he,
       legend.spacing = grid::unit(-1.25, "line"),
       panel.grid = element_blank(),
       legend.key = element_blank(),
-      legend.text.align = 0,
+      legend.text = element_text(hjust = 0),
       plot.title = element_text(
         hjust = 0.5,
         face = "bold",

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"),
                               ...) {
-
   graph <- match.arg(graph)
 
   he <- setComparisons(he, comparison)
@@ -120,7 +125,6 @@ ceplane.plot.bcea <- function(he,
   } else if (is_ggplot(graph)) {
 
     ceplane_plot_ggplot(he,
-                        wtp,
                         pos_legend = pos,
                         graph_params, ...)
 

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),

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]
@@ -51,7 +53,9 @@ points_params <- function(graph_params) {
 k_text <- function(graph_params, wtp) {
 
   x_k <- graph_params$xlim[1]
-  y_k <- max(x_k*wtp, graph_params$ylim[1])
+  y_k <- ifelse(graph_params$label.pos,
+                max(x_k*wtp, graph_params$ylim[1]),
+                    graph_params$ylim[1])
 
   x_adj <- diff(graph_params$xlim)*0.04
   y_adj <- diff(graph_params$ylim)*0.04