Merge pull request #54 from n8thangreen/dev

refactored evppi and fixed some small bugs

.Rbuildignore

@@ -8,7 +8,6 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
-^vignettes$
 ^\.httr-oauth$
 ^CONDUCT\.md$
 ^man-roxygen$

.github/workflows/check-standard.yaml

@@ -34,7 +34,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          extra-repositories: 'https://inla.r-inla-download.org/R/stable'
+          extra-repositories: 'https://inla.r-inla-download.org/R/testing'
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
@@ -43,7 +43,7 @@ jobs:
 
       - name: Add inla repo
         run: |
-          cat('options(repos = c(INLA = "https://inla.r-inla-download.org/R/stable/", getOption("repos")))', file = "~/.Rprofile", append = TRUE)
+          cat('options(repos = c(INLA = "https://inla.r-inla-download.org/R/testing/", getOption("repos")))', file = "~/.Rprofile", append = TRUE)
         # cat("\noptions(tinytex.verbose = TRUE)\n", file = "~/.Rprofile", append = TRUE)
         shell: Rscript {0}
 
@@ -53,7 +53,7 @@ jobs:
         shell: Rscript {0}
 
 #      - name: Install JAGS
-#       run: |
+#        run: |
 #          sudo apt-get update -y
 #          sudo apt-get install -y jags
 
@@ -67,15 +67,13 @@ jobs:
 
       - name: Install jags (macOS-latest)
         if: runner.os == 'macOS'
-        run : |
-              rm '/usr/local/bin/gfortran'
-              brew install jags
+        run : brew install jags
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages:
-            any::rcmdcheck, local::.
-          needs: check
+          dependencies: '"all"'
+          extra-packages: |
+             rcmdcheck
           
       - uses: r-lib/actions/check-r-package@v2
         with:

BCEA.Rproj

@@ -15,4 +15,4 @@ LaTeX: pdfLaTeX
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace
+PackageRoxygenize: rd,collate,namespace,vignette

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 2.4.2
-Date: 2022-08-23 11:44:30 UTC
-SHA: f0469ce213fba001efa2707da7fa79289b337105
+Version: 2.4.4
+Date: 2023-06-05 12:52:55 UTC
+SHA: 770d3d2d910eca75ebaaccf4c290c20e4668a95a

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: BCEA
 Type: Package
 Title: Bayesian Cost Effectiveness Analysis
-Version: 2.4.2.9000
+Version: 2.4.5
 Authors@R: c(
     person("Gianluca", "Baio",
-            email = "gianluca@stats.ucl.ac.uk",
-            role = c("aut", "cre"),
+            email = "g.baio@ucl.ac.uk",
+            role = c("aut", "cre", "cph"),
             comment = c(ORCID = "0000-0003-4314-2570")),
     person("Andrea", "Berardi",
             email = "a.berardi@ucl.ac.uk",
@@ -23,36 +23,38 @@ Imports:
     cli (>= 3.3.0),
     dplyr,
     ggplot2,
-    gridExtra,
     graphics,
+    gridExtra,
     MASS,
     Matrix,
+    MCMCvis,
     purrr,
     Rdpack,
     reshape2,
     rlang,
-    scales
+    scales,
+    voi
 Depends:
     R (>= 3.5.0)
 Suggests:
     coda,
     grid,
-    INLA,
     knitr,
     markdown,
-    MCMCvis,
     mgcv,
     plotly,
+    plotrix,
+    RColorBrewer,
     rjags,
     rmarkdown,
     rstan,
-    RColorBrewer,
     splancs,
     testthat (>= 2.1.0),
     vdiffr,
     withr
 RdMacros: Rdpack
-Additional_repositories: https://inla.r-inla-download.org/R/stable/
+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.
@@ -64,6 +66,9 @@ URL: https://gianluca.statistica.it/software/bcea/,
      https://gianluca.statistica.it/,
      https://github.com/giabaio/BCEA/  
 NeedsCompilation: no
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3.9000
 Encoding: UTF-8
 BugReports: https://github.com/n8thangreen/BCEA/issues/
+Remotes: 
+    chjackson/voi
+LazyData: false

NAMESPACE

@@ -94,9 +94,9 @@ export(validate_bcea)
 import(dplyr)
 import(ggplot2)
 import(grid)
-import(purrr)
 import(reshape2)
 importFrom(MASS,kde2d)
+importFrom(MCMCvis,MCMCchains)
 importFrom(Matrix,Matrix)
 importFrom(Matrix,expm)
 importFrom(Rdpack,reprompt)
@@ -109,7 +109,6 @@ importFrom(dplyr,slice)
 importFrom(grDevices,colors)
 importFrom(grDevices,colours)
 importFrom(grDevices,dev.new)
-importFrom(grDevices,dev.off)
 importFrom(grDevices,devAskNewPage)
 importFrom(grDevices,grey.colors)
 importFrom(grDevices,pdf.options)
@@ -131,7 +130,10 @@ importFrom(graphics,text)
 importFrom(grid,unit)
 importFrom(gridExtra,grid.arrange)
 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)
@@ -140,10 +142,7 @@ importFrom(scales,label_dollar)
 importFrom(stats,as.formula)
 importFrom(stats,cov)
 importFrom(stats,density)
-importFrom(stats,dist)
-importFrom(stats,dnorm)
 importFrom(stats,lm)
-importFrom(stats,optim)
 importFrom(stats,qnorm)
 importFrom(stats,qqline)
 importFrom(stats,qqnorm)
@@ -153,9 +152,8 @@ importFrom(stats,rnorm)
 importFrom(stats,runif)
 importFrom(stats,sd)
 importFrom(stats,setNames)
-importFrom(stats,update)
 importFrom(utils,methods)
 importFrom(utils,modifyList)
-importFrom(utils,select.list)
 importFrom(utils,str)
 importFrom(utils,tail)
+importFrom(voi,evppi)

NEWS.md

@@ -1,9 +1,47 @@
 
-# BCEA 2.4.2.9000
+# BCEA 2.4.5
+
+_October 2023_
+
+Moved internal EVPPI calculation out of `BCEA` and now uses `voi` package instead. 
+Refactoring but retaining same interface and functionality.
+
+* `evppi()` tested against all use cases in BCEA book (1c1457d2)
+* Select parameters by position (as well as name) in new `evppi()` (f2e4d005)
+* Use single parameter case only like `voi` package for methods `sal` and `so` (#140)
+* New `evppi()` matching output of old `evppi()` (1e2c5e7)
+* Latest development version of `voi` needed when we use `check = TRUE` in `voi::evppi()` in order to access fitting data (6e436b5, 94f5fc5)
+* No longer require `INLA` package to be available inside of `BCEA` so can remove direct dependency. This helps with passing CRAN checks and GitHub Actions ()
+
+# BCEA 2.4.4
+_June 2023_
+
+* Patch to fix a CRAN checks error. Suggested package `MCMCvis` wasn't used conditionally in unit test. Moved to Required packages in `DESCRIPTION`.
+
+# BCEA 2.4.3
+_May 2023_
+
+## Bug fixes
+
+* Consistent colours across plots for each intervention for grid of plots in `plot.bcea()` (cf1ee43)
+* `make.report()` change variable name (f940f2e)
+* Fixed issue with summary table where names of interventions in the wrong order (6a006e3)
+* `summary.bcea()` now only prints results for chosen comparisons and not always all of them. `kstar` and `best` in `bcea()` object were not updated with subset of interventions (#125)
+
+## Refactoring
+
+* `withr::with_par()` used in plotting function `plot.bcea()` to only temporarily change graphics parameters. (725c536)
+* Using `@md` and markdown syntax in function documentation
+* Update `psa.struct()` to add the absolute value in the formula to compute the weights (1cea278)
+* Use `dplyr` piping new syntax from `.data$*` to simply using speech marks `"*"` (2b280ad)
+
+## Miscellaneous
+
+* Template added for GitHub Issues (0ea59fa)
 
 
 # BCEA 2.4.2
-August 2022
+_August 2022_
 
 ## Bug fixes
 
@@ -24,15 +62,14 @@ August 2022
 ## New features
 
 * Can now specify what order the interventions labels are in the legend for ce plane (and contour plots) for base R and ggplot2 i.e. reference first or second with optional `ref_first` argument (cc38f07)
-* Can specify currency for axes in `ce-plane.plot` and `ceac.plot` `ggplot2` versions (6808aa6)
-* Argument added to `ceplane.plot` of `icer_annot` to annotate each of the ICER points with the text label of the intervention name. Only for `ggplot2` at the moment. (a7b4beb)
+* Can specify currency for axes in `ceplane.plot()` and `ceac.plot()` `ggplot2` versions (6808aa6)
+* Argument added to `ceplane.plot()` of `icer_annot` to annotate each of the ICER points with the text label of the intervention name. Only for `ggplot2` at the moment. (a7b4beb)
 * Added `pos` argument to `contour2()` so that its consistent with `contour()` and `ceplane.plot()`. (50f8f8b)
 * Allow passing `ref` argument by name as well as index in `bcea()`. (9eab459)
 
 
-
 # BCEA 2.4.1.2
-April 2022
+_April 2022_
 
 ## Bug fixes
 
@@ -64,7 +101,7 @@ April 2022
 
 
 # BCEA 2.4.1.1
-Oct 2021
+_Oct 2021_
 
 ## Major refactoring
 
@@ -156,9 +193,9 @@ Oct 2015
 * New function for EVPPI using SPDE-INLA
 * Modifications to the EVPPI functions
 * Documentation updated
-* Allows `xlim` & `ylim` in the `ceplane.plot`, `contour` and `contour2` functions
+* Allows `xlim` & `ylim` in the `ceplane.plot()`, `contour()` and `contour2()` functions
 * It is now possible to run `bcea` for a scalar wtp
-* Old `evppi` function and method has been renamed `evppi0`, which means there's also a new `plot.evppi0` method
+* Old `evppi()` function and method has been renamed `evppi0`, which means there's also a new `plot.evppi0` method
 
 # BCEA 2.1-0
 13 Jan 2015

R/BCEA-package.R

@@ -1,39 +1,23 @@
+#------------------------------------------------------------------------------#
+#
+#                        ___           ___           ___     
+#         _____         /  /\         /  /\         /  /\    
+#        /  /::\       /  /:/        /  /:/_       /  /::\   
+#       /  /:/\:\     /  /:/        /  /:/ /\     /  /:/\:\  
+#      /  /:/~/::\   /  /:/  ___   /  /:/ /:/_   /  /:/~/::\ 
+#     /__/:/ /:/\:| /__/:/  /  /\ /__/:/ /:/ /\ /__/:/ /:/\:\
+#     \  \:\/:/~/:/ \  \:\ /  /:/ \  \:\/:/ /:/ \  \:\/:/__\/
+#      \  \::/ /:/   \  \:\  /:/   \  \::/ /:/   \  \::/     
+#       \  \:\/:/     \  \:\/:/     \  \:\/:/     \  \:\     
+#        \  \::/       \  \::/       \  \::/       \  \:\    
+#         \__\/         \__\/         \__\/         \__\/    
+#
+#
+#------------------------------------------------------------------------------#
 
-#' BCEA: A package for Bayesian Cost-Effectiveness Analysis
-#' 
-#' A package to post-process the results of a Bayesian health economic model
-#' and produce standardised output for the analysis of the results.
-#' 
-#' \tabular{ll}{ Package: \tab BCEA\cr
-#'               Type: \tab Package\cr
-#'               Version: \tab 2.4.2\cr
-#'               Date: \tab 2022-09-03\cr
-#'               License: \tab GPL2 \cr
-#'               LazyLoad: \tab Yes\cr }
-#'               
-#' BCEA produces a health economic evaluation given a random sample of
-#' suitable variables of costs and clinical benefits for two or more
-#' interventions, e.g. using results of a Bayesian model (possibly based on
-#' MCMC) in the form of simulations from the posterior distributions.
-#' Compares one of the interventions (the "reference") to the others
-#' ("comparators"). Produces many summaries and plots to analyse the results.
-#' 
-#' @aliases BCEA-package BCEA
-#' 
-#' @author Gianluca Baio, Andrea Berardi, Anna Heath, Nathan Green
-#' 
-#' @references
-#' \insertRef{Baio2011}{BCEA}
-#' 
-#' \insertRef{Baio2013}{BCEA}
-#' 
-#' \insertRef{Baio2017}{BCEA}
-#'  
-#' @keywords package
-#' 
-#' @docType package
-#' @name BCEA-package
-#' 
-#' @import dplyr ggplot2 purrr reshape2
-#' @importFrom Rdpack reprompt
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
 NULL

R/CEriskav_plot_graph.R

@@ -88,8 +88,8 @@ CEriskav_plot_ggplot <- function(he, pos_legend) {
   eib_dat <-
     melt(he$eibr[, default_comp, , drop = FALSE],
          value.name = "eibr") %>%
-    rename(k = .data$Var1,
-           r = .data$Var3) %>%
+    rename(k = "Var1",
+           r = "Var3") %>%
     mutate(r = as.factor(.data$r))
 
   eibr_plot <-
@@ -122,8 +122,8 @@ CEriskav_plot_ggplot <- function(he, pos_legend) {
   evi_dat <-
     melt(he$evir,
          value.name = "evir") %>%
-    rename(r = .data$Var2,
-           k = .data$Var1) %>%
+    rename(r = "Var2",
+           k = "Var1") %>%
     mutate(r = as.factor(.data$r))
 
   evir_plot <-

R/CreateInputs.R

@@ -14,6 +14,12 @@
 createInputs.default <- function(inputs,
                                  print_is_linear_comb = TRUE) {
 
+  # remove NA columns
+  if (sum(is.na(inputs)) > 0) {
+    inputs <- inputs[ , colSums(is.na(inputs)) == 0]
+    message("Dropped any columns containing NAs")
+  }
+
   if (!is.logical(print_is_linear_comb))
     stop("print_is_linear_comb must be logical.", call. = FALSE)