From 057adaff3816a6e95aa494f6b70fdb981b4ad8f8 Mon Sep 17 00:00:00 2001 From: Dr Nathan Green Date: Tue, 2 May 2023 10:35:12 +0100 Subject: [PATCH 01/13] updated NEWS --- NEWS.md | 22 ++++++++++++++++++++-- 1 file changed, 20 insertions(+), 2 deletions(-) diff --git a/NEWS.md b/NEWS.md index 907810a0..547ef225 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,24 @@ -# BCEA 2.4.2.9000 +# 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 @@ -30,7 +49,6 @@ August 2022 * Allow passing `ref` argument by name as well as index in `bcea()`. (9eab459) - # BCEA 2.4.1.2 April 2022 From 1925fc6ef33ed4732fc9432a01916c3188c88c6d Mon Sep 17 00:00:00 2001 From: Dr Nathan Green Date: Tue, 2 May 2023 12:24:24 +0100 Subject: [PATCH 02/13] lots of very minor fixes to pass the CRAN CHECKS --- DESCRIPTION | 6 +-- R/CEriskav_plot_graph.R | 8 ++-- R/bcea.default.R | 2 +- R/ceac_plot_graph.R | 2 +- R/compute_xxx.R | 2 +- R/eib_plot_graph.R | 2 +- README.md | 5 +-- README_dev.md | 60 -------------------------- cran-comments.md | 20 ++++++++- inst/CITATION | 2 +- man/BCEA-package.Rd | 2 +- tests/testthat/test-CEriskav.R | 16 +++---- tests/testthat/test-bcea.R | 19 +++++--- tests/testthat/test-bcea_setters.R | 9 +++- tests/testthat/test-ceac_plot_ggplot.R | 7 +-- tests/testthat/test-compute_U.R | 11 +++-- tests/testthat/test-compute_ol.R | 10 +++-- tests/testthat/test-compute_vi.R | 13 ++++-- vignettes/CEriskav.Rmd | 2 +- vignettes/bcea.Rmd | 2 +- vignettes/ceac.Rmd | 2 +- vignettes/ceef.Rmd | 2 +- vignettes/contour.Rmd | 4 +- vignettes/eib.Rmd | 2 +- 24 files changed, 88 insertions(+), 122 deletions(-) delete mode 100644 README_dev.md diff --git a/DESCRIPTION b/DESCRIPTION index 906976d7..eaf31e57 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,11 +1,11 @@ Package: BCEA Type: Package Title: Bayesian Cost Effectiveness Analysis -Version: 2.4.2.9000 +Version: 2.4.3 Authors@R: c( person("Gianluca", "Baio", email = "gianluca@stats.ucl.ac.uk", - role = c("aut", "cre"), + role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-4314-2570")), person("Andrea", "Berardi", email = "a.berardi@ucl.ac.uk", @@ -65,6 +65,6 @@ URL: https://gianluca.statistica.it/software/bcea/, https://gianluca.statistica.it/, https://github.com/giabaio/BCEA/ NeedsCompilation: no -RoxygenNote: 7.2.3 +RoxygenNote: 7.2.3.9000 Encoding: UTF-8 BugReports: https://github.com/n8thangreen/BCEA/issues/ diff --git a/R/CEriskav_plot_graph.R b/R/CEriskav_plot_graph.R index b213c3ef..389f9e67 100644 --- a/R/CEriskav_plot_graph.R +++ b/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$r)) evir_plot <- diff --git a/R/bcea.default.R b/R/bcea.default.R index 2d6ddd9e..c484c98a 100644 --- a/R/bcea.default.R +++ b/R/bcea.default.R @@ -69,7 +69,7 @@ bcea.default <- function(eff, df_ce <- df_ce %>% select(-ref) %>% - rename(ref = .data$ints) %>% + rename(ref = "ints") %>% merge(df_ce, by = c("ref", "sim"), suffixes = c("0", "1"), diff --git a/R/ceac_plot_graph.R b/R/ceac_plot_graph.R index bbdc9510..d9608ed9 100644 --- a/R/ceac_plot_graph.R +++ b/R/ceac_plot_graph.R @@ -136,7 +136,7 @@ ceac_ggplot <- function(he, ggplot(data_psa, aes(.data$k, .data$ceac)) + geom_line(aes(linetype = .data$comparison, - size = .data$comparison, + linewidth = .data$comparison, colour = factor(.data$comparison))) + theme_ceac() + theme_add + # theme diff --git a/R/compute_xxx.R b/R/compute_xxx.R index 12145a32..e8bf2fb2 100644 --- a/R/compute_xxx.R +++ b/R/compute_xxx.R @@ -264,7 +264,7 @@ compute_IB <- function(df_ce, k) { df_ce <- df_ce %>% filter(ints != .data$ref) %>% - rename(comps = .data$ints) + rename(comps = "ints") ib_df <- data.frame(k = rep(k, each = nrow(df_ce)), diff --git a/R/eib_plot_graph.R b/R/eib_plot_graph.R index 222759dd..d0483b7f 100644 --- a/R/eib_plot_graph.R +++ b/R/eib_plot_graph.R @@ -88,7 +88,7 @@ eib_plot_ggplot <- function(he, data = data.frame("kstar" = he$kstar), colour = "grey50", linetype = 2, - size = 0.5) + + linewidth = 0.5) + scale_linetype_manual( "", labels = graph_params$labels, diff --git a/README.md b/README.md index 3cc80b78..f88be185 100644 --- a/README.md +++ b/README.md @@ -72,14 +72,13 @@ Examples of using specific functions and their different arguments are given in ## Further details The `pkgdown` site is [here](https://n8thangreen.github.io/BCEA/). -More details on `BCEA` are available in our book [_Bayesian Cost-Effectiveness Analysis with the R Package BCEA_](https://gianluca.statistica.it/book/bcea/) (published in the UseR! Springer series). Also, details about the package, including some references and links to a pdf presentation and some posts on my own blog) are given [here](https://gianluca.statistica.it/software/bcea/). +More details on `BCEA` are available in our book [_Bayesian Cost-Effectiveness Analysis with the R Package BCEA_](https://gianluca.statistica.it/books/bcea/) (published in the UseR! Springer series). Also, details about the package, including some references and links to a pdf presentation and some posts on my own blog) are given [here](https://gianluca.statistica.it/software/bcea/). ## License [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) ## Contributing -Please submit contributions through `Pull Requests`, following the [contributing -guidelines](https://github.com/n8thangreen/BCEA/blob/dev/CONTRIBUTING.md). +Please submit contributions through `Pull Requests`, following the [contributing guidelines](https://github.com/n8thangreen/BCEA/blob/dev/CONTRIBUTING.md). To report issues and/or seek support, please file a new ticket in the [issue](https://github.com/n8thangreen/BCEA/issues) tracker. diff --git a/README_dev.md b/README_dev.md deleted file mode 100644 index 62facb3f..00000000 --- a/README_dev.md +++ /dev/null @@ -1,60 +0,0 @@ -# BCEA --- development version - - - -[![Build Status](https://app.travis-ci.com/n8thangreen/BCEA.svg?branch=dev)](https://app.travis-ci.com/n8thangreen/BCEA) -[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/BCEA)](https://cran.r-project.org/package=BCEA) [![CRAN_Download_Badge](http://cranlogs.r-pkg.org/badges/BCEA)](https://cran.r-project.org/package=BCEA) -[![CRAN_Download_Badge](http://cranlogs.r-pkg.org/badges/grand-total/BCEA?color=orange)](https://cran.r-project.org/package=BCEA) -[![CodeFactor](https://www.codefactor.io/repository/github/n8thangreen/bcea/badge)](https://www.codefactor.io/repository/github/n8thangreen/bcea) - - -## Contents - -- [Overview](#introduction) -- [Features](#features) -- [Installation](#installation) -- [Further details](#further-details) - -## Overview - -Perform Bayesian Cost-Effectiveness Analysis in R. -Given the results of a Bayesian model (possibly based on MCMC) in the form of simulations from the posterior distributions of suitable variables of costs and clinical benefits for two or more interventions, produces a health economic evaluation. Compares one of the interventions (the "reference") to the others ("comparators"). - -## Features - -Main features of `BCEA` include: - -* Summary statistics and tables -* Cost-effectiveness analysis plots, such as CE planes and CEAC -* EVPPI calculations and plots - -This is the **development** version of BCEA (currently 2.4). It contains a major refactoring of the code to streamline the functions. - -## Installation -The development version can be installed using this GitHub repository. On Windows machines, you need to install a few dependencies, including [Rtools](https://cran.r-project.org/bin/windows/Rtools/) first, e.g. by running - -```r -pkgs <- c("MASS", "Rtools", "remotes") -repos <- c("https://cran.rstudio.com", "https://inla.r-inla-download.org/R/stable/") -install.packages(pkgs, repos=repos, dependencies = "Depends") -``` -before installing the package using `remotes`: - -```r -remotes::install_github("giabaio/BCEA", ref="dev") -``` -Under Linux or MacOS, it is sufficient to install the package via `remotes`: - -```r -install.packages("remotes") -remotes::install_github("giabaio/BCEA", ref="dev") -``` - -## Further details -The `pkgdown` site is [here](https://n8thangreen.github.io/BCEA/). -More details on `BCEA` are available in our book [_Bayesian Cost-Effectiveness Analysis with the R Package BCEA_](https://gianluca.statistica.it/book/bcea/) (published in the UseR! Springer series). Also, details about the package, including some references and links to a pdf presentation and some posts on my own blog) are given [here](https://gianluca.statistica.it/software/bcea/). - -## Licence -GPL-3 © [G Baio](https://github.com/giabaio/). - -Please note that this project is released with a [Contributor Code of Conduct](https://github.com/n8thangreen/BCEA/blob/dev/CONDUCT.md). By participating in this project you agree to abide by its terms. diff --git a/cran-comments.md b/cran-comments.md index 01fa3693..f45c74ab 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,4 +1,21 @@ -## Resubmission + +# Submission (2.4.3) + +## 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. + +## Downstream dependencies + +We checked 2 reverse dependencies (missingHE, heesim), comparing R CMD check results across CRAN and dev versions of this package. + +* We saw 0 new problems +* We failed to check 0 packages + + +# Resubmission (2.4.2.1) This is a resubmission. In this version I have: * Removed from the build large data files so that not more than 5 MB for a CRAN package. @@ -10,7 +27,6 @@ There were no ERRORs or WARNINGs. * Any notes about using INLA has been condoned in previous versions, as they are only suggested. - ## Downstream dependencies We checked 2 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. diff --git a/inst/CITATION b/inst/CITATION index d3ef2f35..d079d029 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -1,6 +1,6 @@ citHeader("To cite BCEA in publications use:") -citEntry( +bibentry( entry = "Book", title = "Bayesian Cost-Effectiveness Analysis with the R package BCEA", publisher = "Springer", diff --git a/man/BCEA-package.Rd b/man/BCEA-package.Rd index 594e4ab0..d2cff1a0 100644 --- a/man/BCEA-package.Rd +++ b/man/BCEA-package.Rd @@ -21,7 +21,7 @@ Useful links: } \author{ -\strong{Maintainer}: Gianluca Baio \email{gianluca@stats.ucl.ac.uk} (\href{https://orcid.org/0000-0003-4314-2570}{ORCID}) +\strong{Maintainer}: Gianluca Baio \email{gianluca@stats.ucl.ac.uk} (\href{https://orcid.org/0000-0003-4314-2570}{ORCID}) [copyright holder] Authors: \itemize{ diff --git a/tests/testthat/test-CEriskav.R b/tests/testthat/test-CEriskav.R index a81b162b..d02fd226 100644 --- a/tests/testthat/test-CEriskav.R +++ b/tests/testthat/test-CEriskav.R @@ -1,19 +1,18 @@ # risk aversion -# library(BCEA) -library(dplyr) -library(reshape2) +# library(dplyr) +# library(reshape2) ##TODO:... -load(test_path("ce_smoking.RData")) - -treats <- c("No intervention", "Self-help", "Individual counselling", "Group counselling") -bcea_smoke <- bcea(eff, cost, ref = 4, interventions = treats, Kmax = 500) - test_that("zero risk aversion is equal to default", { + load(test_path("ce_smoking.RData")) + + treats <- c("No intervention", "Self-help", "Individual counselling", "Group counselling") + bcea_smoke <- bcea(eff, cost, ref = 4, interventions = treats, Kmax = 500) + r <- 0 CEriskav(bcea_smoke) <- r tol <- 0.0001 @@ -23,4 +22,3 @@ test_that("zero risk aversion is equal to default", { expect_equivalent(bcea_smoke$U[,,3], bcea_smoke$Ur[,,3,1], tolerance = tol) expect_equivalent(bcea_smoke$U[,,4], bcea_smoke$Ur[,,4,1], tolerance = tol) }) - diff --git a/tests/testthat/test-bcea.R b/tests/testthat/test-bcea.R index 6f0ed833..ac1a1814 100644 --- a/tests/testthat/test-bcea.R +++ b/tests/testthat/test-bcea.R @@ -3,16 +3,14 @@ ## names outputs? -# library(BCEA) -library(dplyr) -library(reshape2) - - -load(test_path("ce.RData")) +# library(dplyr) +# library(reshape2) test_that("input errors", { + load(test_path("ce.RData")) + expect_dims_error <- function(x, y) { expect_error( bcea(x, y, @@ -62,6 +60,8 @@ test_that("input errors", { test_that("basic return", { + load(test_path("ce.RData")) + res <- bcea(e = eff, c = cost) @@ -187,6 +187,8 @@ test_that("jags, bugs, stan methods", { test_that("k and wtp arguments", { + load(test_path("ce.RData")) + m <- bcea(eff, cost, plot = FALSE) expect_equal(m$Kmax, 50000) @@ -202,6 +204,9 @@ test_that("k and wtp arguments", { }) test_that("using e and c still works", { + + load(test_path("ce.RData")) + e <- eff c <- cost bcea_res <- bcea(eff = eff, cost = cost) @@ -213,6 +218,8 @@ test_that("using e and c still works", { test_that("named reference", { + load(test_path("ce.RData")) + expect_equal(bcea(eff, cost, ref = 1, interventions = c("a", "b")), bcea(eff, cost, ref = "a", interventions = c("a", "b"))) diff --git a/tests/testthat/test-bcea_setters.R b/tests/testthat/test-bcea_setters.R index 4d96b2e0..4fab4fe7 100644 --- a/tests/testthat/test-bcea_setters.R +++ b/tests/testthat/test-bcea_setters.R @@ -1,10 +1,11 @@ -library(dplyr) +# library(dplyr) # data(Vaccine) -load(test_path("ce.RData")) test_that("setKmax", { + + load(test_path("ce.RData")) m <- bcea(e = eff, c = cost, @@ -22,6 +23,8 @@ test_that("setKmax", { test_that("setReferenceGroup", { + load(test_path("ce.RData")) + m <- bcea(e = eff, c = cost, ref = 2, @@ -37,6 +40,8 @@ test_that("setReferenceGroup", { test_that("setComparison", { + load(test_path("ce.RData")) + m_r1 <- bcea(e = eff, c = cost, Kmax = 50000, diff --git a/tests/testthat/test-ceac_plot_ggplot.R b/tests/testthat/test-ceac_plot_ggplot.R index 2516186d..69083cd5 100644 --- a/tests/testthat/test-ceac_plot_ggplot.R +++ b/tests/testthat/test-ceac_plot_ggplot.R @@ -1,11 +1,6 @@ # vdiffr::manage_cases(filter = "ceac") -# library(ggplot2) -# library(dplyr) -# library(reshape2) -# library(vdiffr) -library(purrr) - +# library(purrr) test_that("ceac.plot_ggplot draws correctly", { load("ce.RData") diff --git a/tests/testthat/test-compute_U.R b/tests/testthat/test-compute_U.R index f6c7e825..b60ab568 100644 --- a/tests/testthat/test-compute_U.R +++ b/tests/testthat/test-compute_U.R @@ -1,14 +1,13 @@ -# library(BCEA) -library(dplyr) -library(reshape2) - - -load("ce.RData") +# library(dplyr) +# library(reshape2) +##TODO: test_that("compute_U", { + load(test_path("ce.RData")) + # single wtp # c_tmp <- matrix(c(0, 0, 100, 10), nrow = 2) diff --git a/tests/testthat/test-compute_ol.R b/tests/testthat/test-compute_ol.R index 9d6c0695..3f79ee39 100644 --- a/tests/testthat/test-compute_ol.R +++ b/tests/testthat/test-compute_ol.R @@ -1,15 +1,15 @@ # opportunity loss -# library(BCEA) -library(dplyr) -library(reshape2) +# library(dplyr) +# library(reshape2) -load(test_path("ce.RData")) test_that("simple data input parameters", { + load(test_path("ce.RData")) + # only one intervention # limiting case @@ -66,6 +66,8 @@ test_that("simple data input parameters", { test_that("call via bcea", { + load(test_path("ce.RData")) + res <- bcea(e = eff, c = cost) diff --git a/tests/testthat/test-compute_vi.R b/tests/testthat/test-compute_vi.R index c2c3cb6e..cf15baad 100644 --- a/tests/testthat/test-compute_vi.R +++ b/tests/testthat/test-compute_vi.R @@ -1,15 +1,15 @@ # value of information -# library(BCEA) -library(dplyr) -library(reshape2) +# library(dplyr) +# library(reshape2) -load(test_path("ce.RData")) test_that("simple data", { + load(test_path("ce.RData")) + # only one intervention # limiting case U <- array(c(1,1,1,1,1,1), @@ -50,6 +50,8 @@ test_that("simple data", { test_that("call via bcea", { + load(test_path("ce.RData")) + res <- bcea(e = eff, c = cost) @@ -83,6 +85,9 @@ test_that("errors in dimensions", { }) test_that("using sim_table", { + + load(test_path("ce.RData")) + res <- bcea(e = eff, c = cost) diff --git a/vignettes/CEriskav.Rmd b/vignettes/CEriskav.Rmd index 7df450fe..d2fbf3b8 100644 --- a/vignettes/CEriskav.Rmd +++ b/vignettes/CEriskav.Rmd @@ -2,7 +2,7 @@ title: "Risk Aversion Analysis" output: rmarkdown::html_vignette vignette: > - %\VignetteIndexEntry{Risk aversion analysis} + %\VignetteIndexEntry{Risk Aversion Analysis} %\VignetteEncoding{UTF-8} %\VignetteEngine{knitr::rmarkdown} editor_options: diff --git a/vignettes/bcea.Rmd b/vignettes/bcea.Rmd index 985d61fc..98bc0112 100644 --- a/vignettes/bcea.Rmd +++ b/vignettes/bcea.Rmd @@ -2,7 +2,7 @@ title: "Getting Started" output: rmarkdown::html_vignette vignette: > - %\VignetteIndexEntry{Getting started} + %\VignetteIndexEntry{Getting Started} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- diff --git a/vignettes/ceac.Rmd b/vignettes/ceac.Rmd index d7e247aa..70fad633 100644 --- a/vignettes/ceac.Rmd +++ b/vignettes/ceac.Rmd @@ -2,7 +2,7 @@ title: "Cost-Effectiveness Acceptability Curve Plots" output: rmarkdown::html_vignette vignette: > - %\VignetteIndexEntry{Cost-effectiveness acceptability curve plots} + %\VignetteIndexEntry{Cost-Effectiveness Acceptability Curve Plots} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- diff --git a/vignettes/ceef.Rmd b/vignettes/ceef.Rmd index f90ecab7..6ad27959 100644 --- a/vignettes/ceef.Rmd +++ b/vignettes/ceef.Rmd @@ -2,7 +2,7 @@ title: "Cost-Effectiveness Efficiency Frontier" output: rmarkdown::html_vignette vignette: > - %\VignetteIndexEntry{Cost-effectiveness efficiency frontier} + %\VignetteIndexEntry{Cost-Effectiveness Efficiency Frontier} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- diff --git a/vignettes/contour.Rmd b/vignettes/contour.Rmd index 8d4a6700..2b4b257f 100644 --- a/vignettes/contour.Rmd +++ b/vignettes/contour.Rmd @@ -1,8 +1,8 @@ --- -title: "Contour plots" +title: "Contour Plots" output: rmarkdown::html_vignette vignette: > - %\VignetteIndexEntry{Contour-plot} + %\VignetteIndexEntry{Contour Plots} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- diff --git a/vignettes/eib.Rmd b/vignettes/eib.Rmd index ab00a72a..a03aa11a 100644 --- a/vignettes/eib.Rmd +++ b/vignettes/eib.Rmd @@ -2,7 +2,7 @@ title: "Expected Incremental Benefit Plot" output: rmarkdown::html_vignette vignette: > - %\VignetteIndexEntry{Expected incremental benefit plot} + %\VignetteIndexEntry{Expected Incremental Benefit Plot} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- From 7a56fbcbf95166ddf159aa337c87b8de764b6942 Mon Sep 17 00:00:00 2001 From: Dr Nathan Green Date: Tue, 2 May 2023 12:46:51 +0100 Subject: [PATCH 03/13] fix bibtype field in CITATION --- cran-comments.md | 20 -------------------- inst/CITATION | 22 ++++++++++------------ vignettes/.gitignore | 1 + vignettes/figure/unnamed-chunk-11-1.png | Bin 6191 -> 0 bytes vignettes/figure/unnamed-chunk-12-1.png | Bin 5529 -> 0 bytes vignettes/figure/unnamed-chunk-13-1.png | Bin 5529 -> 0 bytes vignettes/figure/unnamed-chunk-14-1.png | Bin 5412 -> 0 bytes vignettes/figure/unnamed-chunk-15-1.png | Bin 5412 -> 0 bytes vignettes/figure/unnamed-chunk-16-1.png | Bin 5529 -> 0 bytes vignettes/figure/unnamed-chunk-16-2.png | Bin 5412 -> 0 bytes vignettes/figure/unnamed-chunk-4-1.png | Bin 6048 -> 0 bytes 11 files changed, 11 insertions(+), 32 deletions(-) delete mode 100644 vignettes/figure/unnamed-chunk-11-1.png delete mode 100644 vignettes/figure/unnamed-chunk-12-1.png delete mode 100644 vignettes/figure/unnamed-chunk-13-1.png delete mode 100644 vignettes/figure/unnamed-chunk-14-1.png delete mode 100644 vignettes/figure/unnamed-chunk-15-1.png delete mode 100644 vignettes/figure/unnamed-chunk-16-1.png delete mode 100644 vignettes/figure/unnamed-chunk-16-2.png delete mode 100644 vignettes/figure/unnamed-chunk-4-1.png diff --git a/cran-comments.md b/cran-comments.md index f45c74ab..b3545454 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -13,23 +13,3 @@ We checked 2 reverse dependencies (missingHE, heesim), comparing R CMD check res * We saw 0 new problems * We failed to check 0 packages - - -# Resubmission (2.4.2.1) -This is a resubmission. In this version I have: - -* Removed from the build large data files so that not more than 5 MB for a CRAN package. - -* Reference about the method added in the Description with doi: prefix - -## R CMD check results -There were no ERRORs or WARNINGs. - -* Any notes about using INLA has been condoned in previous versions, as they are only suggested. - -## Downstream dependencies - -We checked 2 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. - -* We saw 0 new problems -* We failed to check 0 packages diff --git a/inst/CITATION b/inst/CITATION index d079d029..f27cd54e 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -1,22 +1,20 @@ citHeader("To cite BCEA in publications use:") -bibentry( - entry = "Book", - title = "Bayesian Cost-Effectiveness Analysis with the R package BCEA", - publisher = "Springer", - year = "2017", +bibentry( + bibtype = "Book", + title = "Bayesian Cost-Effectiveness Analysis with the R package {BCEA}", author = "Baio, G and Berardi, A and Heath, A", + year = "2017", + publisher = "Springer", month = "Jul", address = "New York, NY", url = "https://link.springer.com/book/10.1007/978-3-319-55718-2", doi = "10.1007/978-3-319-55718-2", isbn = "978-3-319-55718-2", - textVersion = - paste("Baio et al (2017).", - "Bayesian Cost Effectiveness Analysis with the R package BCEA.", - "Springer, New York, NY.", - "doi: 10.1007/978-3-319-55718-2,", - "URL: https://link.springer.com/book/10.1007/978-3-319-55718-2" - ) + paste("Baio et al (2017).", + "Bayesian Cost Effectiveness Analysis with the R package BCEA.", + "Springer, New York, NY.", + "doi: 10.1007/978-3-319-55718-2,", + "URL: https://link.springer.com/book/10.1007/978-3-319-55718-2") ) \ No newline at end of file diff --git a/vignettes/.gitignore b/vignettes/.gitignore index 097b2416..003766bd 100644 --- a/vignettes/.gitignore +++ b/vignettes/.gitignore @@ -1,2 +1,3 @@ *.html *.R +figure \ No newline at end of file diff --git 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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: From 0b6afb8512eaa006f5c3d89af3a69376bd7f86ef Mon Sep 17 00:00:00 2001 From: Dr Nathan Green Date: Tue, 2 May 2023 13:27:49 +0100 Subject: [PATCH 05/13] initial CRAN submission attempt --- CRAN-SUBMISSION | 6 +++--- DESCRIPTION | 2 +- NEWS.md | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index 5eddd3d7..8f13b8ad 100644 --- a/CRAN-SUBMISSION +++ b/CRAN-SUBMISSION @@ -1,3 +1,3 @@ -Version: 2.4.2 -Date: 2022-08-23 11:44:30 UTC -SHA: f0469ce213fba001efa2707da7fa79289b337105 +Version: 2.4.3 +Date: 2023-05-02 12:27:02 UTC +SHA: 7d94eddfb7edf7ecd542a9f64a4afe18afd8f57c diff --git a/DESCRIPTION b/DESCRIPTION index eaf31e57..e907bab7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -4,7 +4,7 @@ Title: Bayesian Cost Effectiveness Analysis Version: 2.4.3 Authors@R: c( person("Gianluca", "Baio", - email = "gianluca@stats.ucl.ac.uk", + email = "g.baio@ucl.ac.uk", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-4314-2570")), person("Andrea", "Berardi", diff --git a/NEWS.md b/NEWS.md index 547ef225..0cf2342b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -11,7 +11,7 @@ May 2023 ## Refactoring -* `withr::with_par()` used in plotting function ``plot.bcea()` to only temporarily change graphics parameters. (725c536) +* `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) @@ -43,7 +43,7 @@ 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) +* 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) From 849eaea3529ff1cdbddbd3e537c66e9b2da26194 Mon Sep 17 00:00:00 2001 From: Dr Nathan Green Date: Tue, 2 May 2023 16:54:07 +0100 Subject: [PATCH 06/13] fixed CRAN check notess with compute.evppi() and plot.mesh() --- R/evppi.default.R | 9 ++--- R/evppi_helpers.R | 5 +-- cran-comments.md | 41 +++++++++++++++++++++- man/BCEA-package.Rd | 2 +- man/{compute.evppi.Rd => compute_evppi.Rd} | 6 ++-- man/{plot.mesh.Rd => plot_mesh.Rd} | 8 +++-- 6 files changed, 57 insertions(+), 14 deletions(-) rename man/{compute.evppi.Rd => compute_evppi.Rd} (82%) rename man/{plot.mesh.Rd => plot_mesh.Rd} (75%) diff --git a/R/evppi.default.R b/R/evppi.default.R index ac89cd6e..3ff6f2d9 100644 --- a/R/evppi.default.R +++ b/R/evppi.default.R @@ -515,11 +515,12 @@ evppi.bcea <- function(he, convex.inner = convex.inner, convex.outer = convex.outer, cutoff = cutoff, - max.edge = max.edge - ) - plot.mesh(mesh = mesh$mesh, + max.edge = max.edge) + + plot_mesh(mesh = mesh$mesh, data = data, plot = plot) + if (!suppress.messages) { cat("Calculating fitted values for the GP regression using INLA/SPDE \n") } @@ -579,7 +580,7 @@ evppi.bcea <- function(he, } if (!suppress.messages) cat("Calculating EVPPI \n") - comp <- compute.evppi(he = he, fit.full = fit.full) + comp <- compute_evppi(he = he, fit.full = fit.full) name <- prepare.output(parameters = params, inputs = inputs) diff --git a/R/evppi_helpers.R b/R/evppi_helpers.R index 5ecd7f08..f9cbac7b 100644 --- a/R/evppi_helpers.R +++ b/R/evppi_helpers.R @@ -323,13 +323,14 @@ make.proj <- function(parameter, #' @param mesh Mesh #' @param data Data #' @param plot Create plot? logical +#' @param ... Additional parameters #' #' @importFrom utils select.list #' @importFrom grDevices dev.off #' @seealso \code{\link{evppi}} #' @keywords internal #' -plot.mesh <- function(mesh, data, plot) { +plot_mesh <- function(mesh, data, plot, ...) { if (!plot) return() @@ -510,7 +511,7 @@ fit.inla <- function(parameter, #' @seealso \code{\link{evppi}} #' @keywords internal #' -compute.evppi <- function(he, fit.full) { +compute_evppi <- function(he, fit.full) { EVPPI <- array() tic <- proc.time() for (i in seq_along(he$k)) { diff --git a/cran-comments.md b/cran-comments.md index b3545454..f010148c 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,11 +1,47 @@ -# Submission (2.4.3) +# Resubmission (2.4.3) + +* compute.evppi() was mismatched with the dplyr compute() function. We've changed the +function name to compute_evppi() to avoid confusion since it is only an internal function. + +CHECK message: + +Flavor: r-devel-linux-x86_64-debian-gcc +Check: S3 generic/method consistency, Result: NOTE + Mismatches for apparent methods not registered: + compute: + function(x, ...) + compute.evppi: + function(he, fit.full) + +* Similarly, the internal function plot.mesh() is not a plot method but was being considered so, +so we have renamed to plot_mesh() + +CHECK message: + + plot: + function(x, ...) + plot.mesh: + function(mesh, data, plot) + See section 'Registering S3 methods' in the 'Writing R Extensions' + manual. ## 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 @@ -13,3 +49,6 @@ We checked 2 reverse dependencies (missingHE, heesim), comparing R CMD check res * We saw 0 new problems * We failed to check 0 packages + + + diff --git a/man/BCEA-package.Rd b/man/BCEA-package.Rd index d2cff1a0..dfc99b85 100644 --- a/man/BCEA-package.Rd +++ b/man/BCEA-package.Rd @@ -21,7 +21,7 @@ Useful links: } \author{ -\strong{Maintainer}: Gianluca Baio \email{gianluca@stats.ucl.ac.uk} (\href{https://orcid.org/0000-0003-4314-2570}{ORCID}) [copyright holder] +\strong{Maintainer}: Gianluca Baio \email{g.baio@ucl.ac.uk} (\href{https://orcid.org/0000-0003-4314-2570}{ORCID}) [copyright holder] Authors: \itemize{ diff --git a/man/compute.evppi.Rd b/man/compute_evppi.Rd similarity index 82% rename from man/compute.evppi.Rd rename to man/compute_evppi.Rd index 2726e489..64ac88ad 100644 --- a/man/compute.evppi.Rd +++ b/man/compute_evppi.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/evppi_helpers.R -\name{compute.evppi} -\alias{compute.evppi} +\name{compute_evppi} +\alias{compute_evppi} \title{Compute EVPPI} \usage{ -\method{compute}{evppi}(he, fit.full) +compute_evppi(he, fit.full) } \arguments{ \item{he}{A \code{bcea} object containing the results of the Bayesian diff --git a/man/plot.mesh.Rd b/man/plot_mesh.Rd similarity index 75% rename from man/plot.mesh.Rd rename to man/plot_mesh.Rd index af02b748..4a8b11c4 100644 --- a/man/plot.mesh.Rd +++ b/man/plot_mesh.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/evppi_helpers.R -\name{plot.mesh} -\alias{plot.mesh} +\name{plot_mesh} +\alias{plot_mesh} \title{Mesh Plot} \usage{ -\method{plot}{mesh}(mesh, data, plot) +plot_mesh(mesh, data, plot, ...) } \arguments{ \item{mesh}{Mesh} @@ -12,6 +12,8 @@ \item{data}{Data} \item{plot}{Create plot? logical} + +\item{...}{Additional parameters} } \description{ Option of interactively saving the plot. From 3b5033215fbbb82a23a7e1791a9d458b3a185daf Mon Sep 17 00:00:00 2001 From: Dr Nathan Green Date: Wed, 3 May 2023 09:59:55 +0100 Subject: [PATCH 07/13] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index f88be185..46cc599c 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ > Perform Bayesian Cost-Effectiveness Analysis in R. -:rocket: **Version 2.4.2 out now!** [Check out the release notes here](https://github.com/n8thangreen/BCEA/releases/tag/v2.4.2). +:rocket: **Version 2.4.3 out now!** [Check out the release notes here](https://github.com/n8thangreen/BCEA/releases/tag/v2.4.3). ## Contents From eb8dfcf4ee8e4d79b9896e87156c0bb0418e5d4c Mon Sep 17 00:00:00 2001 From: Dr Nathan Green Date: Wed, 3 May 2023 10:02:31 +0100 Subject: [PATCH 08/13] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 46cc599c..acea5868 100644 --- a/README.md +++ b/README.md @@ -34,7 +34,7 @@ Main features of `BCEA` include: * EVPPI calculations and plots ## Installation -Install the released version from CRAN with +Install the [released version from CRAN](https://cran.r-project.org/web/packages/BCEA/index.html) with ```r install.packages("BCEA") ``` From 5c8a6eb288dabe67f402377f3c8105bacf10d905 Mon Sep 17 00:00:00 2001 From: Dr Nathan Green Date: Wed, 3 May 2023 10:44:49 +0100 Subject: [PATCH 09/13] updatd pkgdown site and added cheatsheet tab --- CRAN-SUBMISSION | 4 +- _pkgdown.yml | 9 + docs/404.html | 59 +- docs/CONDUCT.html | 13 +- docs/CONTRIBUTING.html | 13 +- docs/ISSUE_TEMPLATE.html | 90 ++ docs/LICENSE.html | 13 +- docs/articles/CEriskav.html | 19 +- .../figure-html/unnamed-chunk-6-5.png | Bin 56710 -> 52115 bytes docs/articles/Set_bcea_parameters.html | 19 +- docs/articles/bcea.html | 48 +- .../figure-html/unnamed-chunk-7-1.png | Bin 0 -> 270059 bytes docs/articles/ceac.html | 19 +- docs/articles/ceef.html | 19 +- 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docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js.map create mode 100644 docs/deps/bootstrap-5.2.2/bootstrap.min.css create mode 100644 docs/reference/compute_evppi.html create mode 100644 docs/reference/libs/htmlwidgets-1.6.2/htmlwidgets.js create mode 100644 docs/reference/libs/plotly-binding-4.10.1/plotly.js create mode 100644 docs/reference/libs/plotly-htmlwidgets-css-2.11.1/plotly-htmlwidgets.css create mode 100644 docs/reference/libs/plotly-main-2.11.1/plotly-latest.min.js create mode 100644 docs/reference/plot_mesh.html create mode 100644 pkgdown/assets/bcea_cheatsheet.pdf diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index 8f13b8ad..eefdb54a 100644 --- a/CRAN-SUBMISSION +++ b/CRAN-SUBMISSION @@ -1,3 +1,3 @@ Version: 2.4.3 -Date: 2023-05-02 12:27:02 UTC -SHA: 7d94eddfb7edf7ecd542a9f64a4afe18afd8f57c +Date: 2023-05-02 15:57:14 UTC +SHA: 849eaea3529ff1cdbddbd3e537c66e9b2da26194 diff --git a/_pkgdown.yml b/_pkgdown.yml index e03de6e6..891e1399 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -9,6 +9,15 @@ template: bslib: font_scale: 1.0 +navbar: + structure: + left: [intro, reference, articles, tutorials, news, cheatsheet] + right: [search, github] + components: + cheatsheet: + text: "Cheatsheet" + href: "bcea_cheatsheet.pdf" + reference: - title: "Main" contents: diff --git a/docs/404.html b/docs/404.html index f8bd2dba..04f3b0fa 100644 --- a/docs/404.html +++ b/docs/404.html @@ -6,33 +6,33 @@ Page not found (404) • BCEA - - - - - - - - - + + + + + + + + + - + - + - Skip to contents + Skip to contents
-

Page not found (404)

+

Page not found (404)

@@ -98,7 +101,7 @@

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/CONDUCT.html b/docs/CONDUCT.html index 19005542..21bb32a3 100644 --- a/docs/CONDUCT.html +++ b/docs/CONDUCT.html @@ -1,5 +1,5 @@ -Contributor Code of Conduct • BCEAContributor Code of Conduct • BCEA @@ -10,7 +10,7 @@ BCEA - 2.4.2 + 2.4.3
-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html index 34ad2f1e..1f64b73a 100644 --- a/docs/CONTRIBUTING.html +++ b/docs/CONTRIBUTING.html @@ -1,5 +1,5 @@ -Contributing to BCEA • BCEAContributing to BCEA • BCEA @@ -10,7 +10,7 @@ BCEA - 2.4.2 + 2.4.3 + + + + + +
+
+
+

NA

+ Source: .github/ISSUE_TEMPLATE.md +
+ + +

Please briefly describe your problem and what output you expect. If you have a general question, please don’t use this form. Instead, ask on https://stackoverflow.com/ or https://community.rstudio.com/.

+

Please include a minimal reproducible example (AKA a reprex). If you’ve never heard of a reprex before, start by reading https://www.tidyverse.org/help/#reprex.

+

Brief description of the problem

+
+# insert reprex here
+ + +
+ + +
+

Developed by Gianluca Baio, Andrea Berardi, Anna Heath, Nathan Green.

+
+ +
+

Site built with pkgdown 2.0.7.

+
+ +
+ + + + + + + diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 4cbf2503..a6de75fb 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -1,5 +1,5 @@ -GNU General Public License • BCEAGNU General Public License • BCEA @@ -10,7 +10,7 @@ BCEA - 2.4.2 + 2.4.3 + + + + + +
+
+
+

Compute EVPPI

+ Source: R/evppi_helpers.R +
compute_evppi.Rd
+
+ +
+

Compute EVPPI

+
+ +
+

Usage

+ 
compute_evppi(he, fit.full)
+
+ +
+

Arguments

+
he
+

A bcea object containing the results of the Bayesian +modelling and the economic evaluation.

+ + +
fit.full
+

fit.full

+ +
+
+

Value

+ + +

list

+
+
+

See also

+

evppi

+
+ +
+ + +
+

Developed by Gianluca Baio, Andrea Berardi, Anna Heath, Nathan Green.

+
+ +
+

Site built with pkgdown 2.0.7.

+
+ +
+ + + + + + + diff --git a/docs/reference/compute_kstar.html b/docs/reference/compute_kstar.html index 7e865c7c..8f04bad7 100644 --- a/docs/reference/compute_kstar.html +++ b/docs/reference/compute_kstar.html @@ -1,5 +1,5 @@ -Compute k^* — compute_kstar • BCEACompute k^* — compute_kstar • BCEA @@ -10,7 +10,7 @@ BCEA - 2.4.2 + 2.4.3 + + + + + +
+
+
+

Mesh Plot

+ Source: R/evppi_helpers.R +
plot_mesh.Rd
+
+ +
+

Option of interactively saving the plot.

+
+ +
+

Usage

+ 
plot_mesh(mesh, data, plot, ...)
+
+ +
+

Arguments

+
mesh
+

Mesh

+ + +
data
+

Data

+ + +
plot
+

Create plot? logical

+ + +
...
+

Additional parameters

+ +
+
+

See also

+

evppi

+
+ +
+ + +
+

Developed by Gianluca Baio, Andrea Berardi, Anna Heath, Nathan Green.

+
+ +
+

Site built with pkgdown 2.0.7.

+
+ +
+ + + + + + + diff --git a/docs/reference/post.density.html b/docs/reference/post.density.html index 2337ef05..dc07d746 100644 --- a/docs/reference/post.density.html +++ b/docs/reference/post.density.html @@ -1,5 +1,5 @@ -Gaussian Process Fitting — post.density • BCEAGaussian Process Fitting — post.density • BCEA @@ -10,7 +10,7 @@ BCEA - 2.4.2 + 2.4.3