Merge pull request #57 from n8thangreen/dev

CRAN release

.Rbuildignore

@@ -19,6 +19,7 @@
 ^inst/extdata/vaccine_jags\.RData$
 ^inst/extdata/statins_base\.RData$
 ^inst/extdata/statins_HC\.RData$
+^inst/extdata/smoking_output\.RData$
 ^paper\.bib$
 ^paper\.md$
 ^CONTRIBUTING\.md$

.gitignore

@@ -6,4 +6,5 @@ BCEA.Rcheck/
 *.Rproj
 inst/doc
 renv/
-BCEA_book.pdf - Shortcut
+revdep/
+BCEA_book.pdf - Shortcut

DESCRIPTION

@@ -22,7 +22,7 @@ Authors@R: c(
 Imports:
     cli (>= 3.3.0),
     dplyr,
-    ggplot2,
+    ggplot2 (>= 3.4.0),
     graphics,
     gridExtra,
     MASS,
@@ -32,8 +32,9 @@ Imports:
     Rdpack,
     reshape2,
     rlang,
+    rstan,
     scales,
-    voi
+    voi (>= 1.0.1)
 Depends:
     R (>= 3.5.0)
 Suggests:
@@ -47,14 +48,12 @@ Suggests:
     RColorBrewer,
     rjags,
     rmarkdown,
-    rstan,
     splancs,
     testthat (>= 2.1.0),
     vdiffr,
     withr
 RdMacros: Rdpack
 VignetteBuilder: knitr
-Additional_repositories: https://inla.r-inla-download.org/R/testing/
 Description: Produces an economic evaluation of a sample of suitable variables of
              cost and effectiveness / utility for two or more interventions,
              e.g. from a Bayesian model in the form of MCMC simulations.
@@ -69,8 +68,6 @@ NeedsCompilation: no
 RoxygenNote: 7.2.3.9000
 Encoding: UTF-8
 BugReports: https://github.com/n8thangreen/BCEA/issues/
-Remotes: 
-    chjackson/voi,
-    plotrix/plotrix
 LazyData: false
 Roxygen: list(markdown = TRUE)
+

NAMESPACE

@@ -138,6 +138,7 @@ importFrom(purrr,pluck)
 importFrom(reshape2,melt)
 importFrom(rlang,.data)
 importFrom(rlang,int)
+importFrom(rstan,extract)
 importFrom(scales,label_dollar)
 importFrom(stats,as.formula)
 importFrom(stats,cov)

R/add_contour_quadrants.R

@@ -42,7 +42,7 @@ add_contour_quadrants <- function(he, params) {
 #' Geom Quadrant Text
 #' 
 #' @template args-he
-#' @template args-graph
+#' @param graph_params Plot parameters; list
 #' @keywords internal aplot
 #' 
 geom_quad_txt <- function(he, graph_params) {

R/bcea.default.R

@@ -108,6 +108,7 @@ bcea.rjags <- function(eff, ...) {
 
 #' @rdname bcea
 #' @param ... Additional arguments
+#' @importFrom rstan extract
 #' @export
 bcea.rstan <- function(eff, ...) {
 

R/ce_table.R

@@ -49,6 +49,10 @@ ce_table <- function(he,
 #'   comparison label and associated ICER
 #' 
 #' @export
+#' @examples
+#' data("Smoking")
+#' he <- BCEA::bcea(eff, cost)
+#' tabulate_means(he)
 #' 
 tabulate_means <- function(he,
                            comp_label = NULL,

R/ceac_plot_graph.R

@@ -136,7 +136,7 @@ ceac_ggplot <- function(he,
 
   ggplot(data_psa, aes(x = .data$k, y = .data$ceac)) +
     geom_line(aes(linetype = .data$comparison,
-                  size = factor(.data$comparison),
+                  linewidth = factor(.data$comparison),
                   colour = factor(.data$comparison))) +
     theme_ceac() + 
     theme_add +                                            # theme

R/contour_ggplot_params.R

@@ -2,7 +2,6 @@
 #' Contour ggplot Parameters
 #' 
 #' @template args-he
-#' @param pos_legend Position of legend
 #' @param graph_params Other graphical parameters
 #' @param ... Additional arguments
 #'

R/ib.plot.R

@@ -25,14 +25,23 @@
 #' @author Gianluca Baio, Andrea Berardi
 #' @seealso [bcea()],
 #'          [ceplane.plot()]
-#' @importFrom Rdpack reprompt
-#' 
 #' @references
+#' 
 #' \insertRef{Baio2011}{BCEA}
+#' 
 #' \insertRef{Baio2013}{BCEA}
 #' 
+#' @keywords hplot
 #' @export
 #' 
+#' @import ggplot2
+#' @importFrom Rdpack reprompt
+#' 
+#' @examples
+#' data("Vaccine")
+#' he <- BCEA::bcea(eff, cost)
+#' ib.plot(he)
+#' 
 ib.plot.bcea <- function(he,
                          comparison = NULL,
                          wtp = 25000,

cran-comments.md

@@ -1,30 +1,7 @@
-
-# Resubmission (2.4.4)
-
-* Suggested package wasn't used conditionally in unit test causing CRAN check error. `MCMCvis` is now moved to Required packages.
-* Fixed R package CRAN webpage canonical form in README
-
 ## R CMD check results
 
-0 errors | 0 warnings | 1 note
-
-* Any notes about using INLA has been condoned in previous versions, as they are only suggested.
-
-CHECK message:
-
-  Suggests or Enhances not in mainstream repositories:
-    INLA
-  Availability using Additional_repositories specification:
-    INLA   yes   https://inla.r-inla-download.org/R/stable/
-
-Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
-Check: package dependencies, Result: NOTE
-  Package suggested but not available for checking: 'INLA'
-
-## Downstream dependencies
-
-We checked 2 reverse dependencies (missingHE, heesim), comparing R CMD check results across CRAN and dev versions of this package.
+0 errors | 0 warnings | 0 note
 
-* We saw 0 new problems
-* We failed to check 0 packages
+* This is an updated release.
 
+Previous versions depended directly on INLA which is now not the case