From 25fa9aa34c6a991eebf1ee8de320cedc763bf24f Mon Sep 17 00:00:00 2001 From: Mark Clements Date: Tue, 15 Sep 2020 22:31:56 +0200 Subject: [PATCH 01/72] Pass ... from bcea.plot to ceac.plot --- R/plot.bcea.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/plot.bcea.R b/R/plot.bcea.R index fbe8113f..232f4e3c 100644 --- a/R/plot.bcea.R +++ b/R/plot.bcea.R @@ -95,7 +95,7 @@ plot.bcea <- function(x,comparison=NULL,wtp=25000,pos=FALSE,graph=c("base","ggpl op <- par(mfrow=c(2,2)) ceplane.plot(x,comparison=comparison,wtp=wtp,pos=pos,graph="base",...) eib.plot(x,comparison=comparison,pos=pos,graph="base",...) - ceac.plot(x,comparison=comparison,pos=pos,graph="base") + ceac.plot(x,comparison=comparison,pos=pos,graph="base",...) evi.plot(x,graph="base") par(op) } @@ -149,7 +149,7 @@ plot.bcea <- function(x,comparison=NULL,wtp=25000,pos=FALSE,graph=c("base","ggpl theme.multiplot eib <- eib.plot(x,pos=pos,comparison=comparison,graph="ggplot2",...) + theme.multiplot - ceac <- ceac.plot(x,pos=pos,comparison=comparison,graph="ggplot2") + + ceac <- ceac.plot(x,pos=pos,comparison=comparison,graph="ggplot2",...) + theme.multiplot evi <- evi.plot(x,graph="ggplot2") + theme.multiplot From a20f591ca3cdd0abab9f5bccab015aa3029a6ef6 Mon Sep 17 00:00:00 2001 From: Dr Nathan Green Date: Tue, 7 Feb 2023 08:35:54 +0000 Subject: [PATCH 02/72] summary.bcea() now only prints results for chosen comparisons --- R/best_interv_given_k.R | 2 +- R/setComparisons.R | 5 +++++ R/summary.bcea.R | 9 ++++++++- 3 files changed, 14 insertions(+), 2 deletions(-) diff --git a/R/best_interv_given_k.R b/R/best_interv_given_k.R index afb8ef2c..974378e8 100644 --- a/R/best_interv_given_k.R +++ b/R/best_interv_given_k.R @@ -13,7 +13,7 @@ best_interv_given_k <- function(eib, ref, comp) { - + if (length(comp) == 1) { best <- rep(ref, NROW(eib)) diff --git a/R/setComparisons.R b/R/setComparisons.R index 7f5812c3..aaa270d0 100644 --- a/R/setComparisons.R +++ b/R/setComparisons.R @@ -45,7 +45,12 @@ setComparisons <- function(he, comparison) { res$eib <- res$eib[, name_comp, drop = FALSE] res$ceac <- res$ceac[, name_comp, drop = FALSE] + ##TODO: is there a way not to recompute the whole thing? + res$best <- best_interv_given_k(res$eib, res$ref, res$comp) + res$kstar <- compute_kstar(res$k, res$best, res$ref) + ##TODO: currently compute _all_ interventions in compute_U() + ## change to this? # res$U <- res$U[, , name_comp, drop = FALSE] return(res) diff --git a/R/summary.bcea.R b/R/summary.bcea.R index 3df3e049..3eabb5e7 100644 --- a/R/summary.bcea.R +++ b/R/summary.bcea.R @@ -133,6 +133,7 @@ summary.bcea <- function(object, # cat(paste0(" : ", green(he$interventions[he$comp[i]]), "\n")) } } + cat("\n") if (length(he$kstar) == 0 && !is.na(he$step)) { cat( @@ -144,8 +145,12 @@ summary.bcea <- function(object, max(he$k), "] \n")) } + if (length(he$kstar) == 1 && !is.na(he$step)) { - kstar <- he$k[which(diff(he$best) == 1) + 1] + + ##TODO: why recalc when same as he$kstar? + kstar <- he$k[which(diff(he$best) != 0) + 1] + cat( paste0( "Optimal decision: choose ", @@ -158,6 +163,7 @@ summary.bcea <- function(object, kstar, "\n")) } + if (length(he$kstar) > 1 && !is.na(he$step)) { cat( paste0( @@ -183,6 +189,7 @@ summary.bcea <- function(object, he$kstar[length(he$kstar)], "\n")) } + cat("\n\n") cat(paste0("Analysis for willingness to pay parameter k = ", wtp, "\n")) cat("\n") From b2b48f9b038fd07e50d3369113c64e7a7d830226 Mon Sep 17 00:00:00 2001 From: Dr Nathan Green Date: Wed, 22 Feb 2023 10:38:42 +0000 Subject: [PATCH 03/72] vignettes added to help documentation --- .Rbuildignore | 1 - BCEA.Rproj | 2 +- DESCRIPTION | 1 + NAMESPACE | 1 - R/BCEA-package.R | 41 +-- man/BCEA-package.Rd | 47 ++-- man/CEriskav_plot_graph.Rd | 2 +- man/ceac_matplot.Rd | 4 +- man/ceac_plot_graph.Rd | 4 +- man/ceef_plot_graph.Rd | 2 +- man/ceplane.plot.Rd | 14 +- man/ceplane_plot_graph.Rd | 8 +- man/contour_graph.Rd | 2 +- man/evi_plot_graph.Rd | 2 +- man/evppi_plot_graph.Rd | 2 +- man/info_rank_graph.Rd | 2 +- man/plot.evppi.Rd | 2 +- man/summary.bcea.Rd | 3 +- vignettes/Set_bcea_parameters.md | 330 ++++++++++++++++++++++++ vignettes/figure/unnamed-chunk-11-1.png | Bin 0 -> 6191 bytes vignettes/figure/unnamed-chunk-12-1.png | Bin 0 -> 5529 bytes vignettes/figure/unnamed-chunk-13-1.png | Bin 0 -> 5529 bytes vignettes/figure/unnamed-chunk-14-1.png | Bin 0 -> 5412 bytes vignettes/figure/unnamed-chunk-15-1.png | Bin 0 -> 5412 bytes vignettes/figure/unnamed-chunk-16-1.png | Bin 0 -> 5529 bytes vignettes/figure/unnamed-chunk-16-2.png | Bin 0 -> 5412 bytes vignettes/figure/unnamed-chunk-4-1.png | Bin 0 -> 6048 bytes 27 files changed, 381 insertions(+), 89 deletions(-) create mode 100644 vignettes/Set_bcea_parameters.md create mode 100644 vignettes/figure/unnamed-chunk-11-1.png create mode 100644 vignettes/figure/unnamed-chunk-12-1.png create mode 100644 vignettes/figure/unnamed-chunk-13-1.png create mode 100644 vignettes/figure/unnamed-chunk-14-1.png create mode 100644 vignettes/figure/unnamed-chunk-15-1.png create mode 100644 vignettes/figure/unnamed-chunk-16-1.png create mode 100644 vignettes/figure/unnamed-chunk-16-2.png create mode 100644 vignettes/figure/unnamed-chunk-4-1.png diff --git a/.Rbuildignore b/.Rbuildignore index b38ebc96..cd9c03b3 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -8,7 +8,6 @@ ^_pkgdown\.yml$ ^docs$ ^pkgdown$ -^vignettes$ ^\.httr-oauth$ ^CONDUCT\.md$ ^man-roxygen$ diff --git a/BCEA.Rproj b/BCEA.Rproj index 9f964990..6843888d 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 +PackageRoxygenize: rd,collate,namespace,vignette diff --git a/DESCRIPTION b/DESCRIPTION index 95793658..6cc82ca4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -52,6 +52,7 @@ Suggests: vdiffr, withr RdMacros: Rdpack +VignetteBuilder: knitr Additional_repositories: https://inla.r-inla-download.org/R/stable/ Description: Produces an economic evaluation of a sample of suitable variables of cost and effectiveness / utility for two or more interventions, diff --git a/NAMESPACE b/NAMESPACE index 21791667..25ee362d 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -94,7 +94,6 @@ export(validate_bcea) import(dplyr) import(ggplot2) import(grid) -import(purrr) import(reshape2) importFrom(MASS,kde2d) importFrom(Matrix,Matrix) diff --git a/R/BCEA-package.R b/R/BCEA-package.R index 6be356d3..a65cf643 100644 --- a/R/BCEA-package.R +++ b/R/BCEA-package.R @@ -1,39 +1,6 @@ +#' @keywords internal +"_PACKAGE" -#' 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 +## usethis namespace: start +## usethis namespace: end NULL diff --git a/man/BCEA-package.Rd b/man/BCEA-package.Rd index 4695a0a7..594e4ab0 100644 --- a/man/BCEA-package.Rd +++ b/man/BCEA-package.Rd @@ -2,36 +2,33 @@ % Please edit documentation in R/BCEA-package.R \docType{package} \name{BCEA-package} -\alias{BCEA-package} \alias{BCEA} -\title{BCEA: A package for Bayesian Cost-Effectiveness Analysis} +\alias{BCEA-package} +\title{BCEA: Bayesian Cost Effectiveness Analysis} \description{ -A package to post-process the results of a Bayesian health economic model -and produce standardised output for the analysis of the results. +\if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}} + +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. This package computes the most cost-effective alternative and produces graphical summaries and probabilistic sensitivity analysis, see Baio et al (2017) \doi{10.1007/978-3-319-55718-2}. } -\details{ -\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. +\seealso{ +Useful links: +\itemize{ + \item \url{https://gianluca.statistica.it/software/bcea/} + \item \url{https://gianluca.statistica.it/} + \item \url{https://github.com/giabaio/BCEA/} + \item Report bugs at \url{https://github.com/n8thangreen/BCEA/issues/} } -\references{ -\insertRef{Baio2011}{BCEA} - -\insertRef{Baio2013}{BCEA} -\insertRef{Baio2017}{BCEA} } \author{ -Gianluca Baio, Andrea Berardi, Anna Heath, Nathan Green +\strong{Maintainer}: Gianluca Baio \email{gianluca@stats.ucl.ac.uk} (\href{https://orcid.org/0000-0003-4314-2570}{ORCID}) + +Authors: +\itemize{ + \item Andrea Berardi \email{a.berardi@ucl.ac.uk} (\href{https://orcid.org/0000-0002-2906-496X}{ORCID}) + \item Anna Heath \email{anna.heath@sickkids.ca} (\href{https://orcid.org/0000-0002-7263-4251}{ORCID}) + \item Nathan Green \email{n.green@ucl.ac.uk} (\href{https://orcid.org/0000-0003-2745-1736}{ORCID}) +} + } -\keyword{package} +\keyword{internal} diff --git a/man/CEriskav_plot_graph.Rd b/man/CEriskav_plot_graph.Rd index f5525ba8..6c42d577 100644 --- a/man/CEriskav_plot_graph.Rd +++ b/man/CEriskav_plot_graph.Rd @@ -17,5 +17,5 @@ modelling and the economic evaluation.} \item{pos_legend}{Legend position} } \description{ -Choice of base R, ggplot2. +Choice of base R, \pkg{ggplot2}. } diff --git a/man/ceac_matplot.Rd b/man/ceac_matplot.Rd index 8755df27..931913f0 100644 --- a/man/ceac_matplot.Rd +++ b/man/ceac_matplot.Rd @@ -14,10 +14,10 @@ modelling and the economic evaluation.} \item{graph_params}{Aesthetic ggplot parameters} -\item{ceac}{`ceac` index in `he`} +\item{ceac}{\code{ceac} index in \code{he}} } \description{ -CEAC plot using `matplot` in Base R. +CEAC plot using \code{matplot} in Base R. } \keyword{hplot} \keyword{internal} diff --git a/man/ceac_plot_graph.Rd b/man/ceac_plot_graph.Rd index 89e07e2e..20ba3309 100644 --- a/man/ceac_plot_graph.Rd +++ b/man/ceac_plot_graph.Rd @@ -38,10 +38,10 @@ modelling and the economic evaluation.} \item{...}{Additional arguments} -\item{ceac}{ceac index in he} +\item{ceac}{ceac index in \code{he}} } \description{ -Choice of base R, ggplot2 or plotly. +Choice of base R, \pkg{ggplot2} or \pkg{plotly}. } \keyword{hplot} \keyword{internal} diff --git a/man/ceef_plot_graph.Rd b/man/ceef_plot_graph.Rd index 69567c4e..53af7a27 100644 --- a/man/ceef_plot_graph.Rd +++ b/man/ceef_plot_graph.Rd @@ -21,5 +21,5 @@ modelling and the economic evaluation.} \item{...}{Additional arguments} } \description{ -Choice of base R, ggplot2. +Choice of base R, \pkg{ggplot2}. } diff --git a/man/ceplane.plot.Rd b/man/ceplane.plot.Rd index 162e1bd7..d2cf0475 100644 --- a/man/ceplane.plot.Rd +++ b/man/ceplane.plot.Rd @@ -31,7 +31,7 @@ comparisons together. Any subset of the possible comparisons can be selected \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 \code{(bottom|top)(right|left)} for base graphics and -\code{bottom|top|left|right} for ggplot2. It can be a two-elements vector, +\code{bottom|top|left|right} for \pkg{ggplot2}. It can be a two-elements vector, which specifies the relative position on the x and y axis respectively, or alternatively it can be in form of a logical variable, with \code{FALSE} indicating to use the default position and \code{TRUE} to place it on the @@ -43,12 +43,12 @@ plotting. Should (partial-) match the two options \code{"base"} or \code{"ggplot2"}. Default value is \code{"base"}.} \item{...}{If \code{graph = "ggplot2"} and a named theme object is supplied, - it will be passed to the ggplot object. The usual ggplot2 syntax is used. + it will be passed to the \pkg{ggplot2} object. The usual ggplot2 syntax is used. Additional graphical arguments: \itemize{ \item \code{label.pos = FALSE}: will place the willingness to pay label in a - different position at the bottom of the graph - base and ggplot2 only (no - label in plotly). + different position at the bottom of the graph - base and \pkg{ggplot2} only (no + label in \pkg{plotly}). \item \code{line = list(color)}: a colour specifying the colour of the willingness-to-pay line. \item \code{point = list(color)}: a vector of colours specifying the colour(s) associated to the cloud of points. Should be of length 1 or equal to the number of comparisons. @@ -64,8 +64,8 @@ plotting. Should (partial-) match the two options \code{"base"} or acceptability area (default is TRUE). \item \code{area = list(color)}: a colour specifying the colour of the cost-effectiveness acceptability area. - \item \code{currency}: Currency prefix to cost differential values - ggplot2 only. - \item \code{icer_annot}: Annotate each ICER point with text label - ggplot2 only. + \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. }} } \value{ @@ -88,7 +88,7 @@ together with the sustainability area, as a function of the selected willingness to pay threshold. } \details{ -In the plotly version, \code{point_colors}, \code{ICER_colors} and \code{area_color} can also +In the \pkg{plotly} version, \code{point_colors}, \code{ICER_colors} and \code{area_color} can also be specified as rgba colours using either the \code{[plotly]toRGB} function or a rgba colour string, e.g. \code{'rgba(1, 1, 1, 1)'}. } diff --git a/man/ceplane_plot_graph.Rd b/man/ceplane_plot_graph.Rd index 8841b17c..9c8026cf 100644 --- a/man/ceplane_plot_graph.Rd +++ b/man/ceplane_plot_graph.Rd @@ -30,19 +30,19 @@ modelling and the economic evaluation.} \item{pos_legend}{Legend position} -\item{graph_params}{Graph parameters in ggplot format} +\item{graph_params}{Graph parameters in \pkg{ggplot2} format} \item{...}{Additional arguments} } \value{ For base R returns a plot -For ggplot2 returns ggplot2 object +For \pkg{ggplot2} returns \pkg{ggplot2} object -For plotly returns a plot in the Viewer +For \pkg{plotly} returns a plot in the Viewer } \description{ -Choice of base R, ggplot2 or plotly. +Choice of base R, \pkg{ggplot2} or \pkg{plotly}. } \examples{ # single comparator diff --git a/man/contour_graph.Rd b/man/contour_graph.Rd index f623c235..99488899 100644 --- a/man/contour_graph.Rd +++ b/man/contour_graph.Rd @@ -21,7 +21,7 @@ modelling and the economic evaluation.} \item{...}{Additional arguments} } \description{ -Choice of base R, ggplot2 +Choice of base R, \pkg{ggplot2}. } \seealso{ \code{\link{contour}} diff --git a/man/evi_plot_graph.Rd b/man/evi_plot_graph.Rd index 5665fb39..3a303134 100644 --- a/man/evi_plot_graph.Rd +++ b/man/evi_plot_graph.Rd @@ -24,5 +24,5 @@ modelling and the economic evaluation.} \item{plot_annotations}{Plot parameters} } \description{ -Choice of base R, ggplot2 or plotly. +Choice of base R, \pkg{ggplot2} or \pkg{plotly}. } diff --git a/man/evppi_plot_graph.Rd b/man/evppi_plot_graph.Rd index 3a3ebaeb..84010045 100644 --- a/man/evppi_plot_graph.Rd +++ b/man/evppi_plot_graph.Rd @@ -23,5 +23,5 @@ evppi_plot_ggplot(evppi_obj, pos_legend = c(0, 0.8), col = c(1, 1), ...) \item{...}{Additional arguments} } \description{ -Base R and ggplot2 versions. +Base R and \pkg{ggplot2} versions. } diff --git a/man/info_rank_graph.Rd b/man/info_rank_graph.Rd index 1e8c5db7..93ea085e 100644 --- a/man/info_rank_graph.Rd +++ b/man/info_rank_graph.Rd @@ -20,5 +20,5 @@ modelling and the economic evaluation.} \item{params}{Graph Parameters including data} } \description{ -Choice of base R, ggplot2 and plotly. +Choice of base R, \pkg{ggplot2} and \pkg{plotly}. } diff --git a/man/plot.evppi.Rd b/man/plot.evppi.Rd index aad3383a..936b3d67 100644 --- a/man/plot.evppi.Rd +++ b/man/plot.evppi.Rd @@ -31,7 +31,7 @@ plotting. Should (partial-) match the two options \code{"base"} or (see \code{\link{par}}).} } \value{ -Plot with base R or ggplot2. +Plot with base R or \pkg{ggplot2}. } \description{ Plot Expected Value of Partial Information With Respect to a diff --git a/man/summary.bcea.Rd b/man/summary.bcea.Rd index 094e7de5..2310e57d 100644 --- a/man/summary.bcea.Rd +++ b/man/summary.bcea.Rd @@ -10,8 +10,7 @@ \item{object}{A \code{bcea} object containing the results of the Bayesian modelling and the economic evaluation.} -\item{wtp}{The value of the willingness to pay threshold used in the -summary table.} +\item{wtp}{The value of the willingness to pay threshold used in the summary table.} \item{...}{Additional arguments affecting the summary produced.} } diff --git a/vignettes/Set_bcea_parameters.md b/vignettes/Set_bcea_parameters.md new file mode 100644 index 00000000..b336c7f0 --- /dev/null +++ b/vignettes/Set_bcea_parameters.md @@ -0,0 +1,330 @@ +--- +title: "Set bcea() Parameters: Constructor and Setters" +output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{Set bcea() Parameters: Constructor and Setters} + %\VignetteEngine{knitr::knitr} + %\VignetteEncoding{UTF-8} +--- + + + + + +```r +library(BCEA) +``` + +There are several arguments passed to `bcea()` to specify the form of the analysis. +These are + + +```r +bcea(eff, cost, + ref = 1, + interventions = NULL, + .comparison = NULL, + Kmax = 50000, + wtp = NULL, + plot = FALSE) +``` + +Those of interest here are: + +* `ref` is the reference intervention group to compare against the other groups. +* `.comparisons` are the groups to compare against `ref`. The default is all of the non-`ref` groups. + This is a new argument in the latest release of BCEA to make it more flexible and consistent with other functions. + A preceding dot is used to keep it back-compatible with previous versions of BCEA. + Argument `c` is partially matched with both `c` and `comparison` otherwise throwing an error. +* `Kmax` is the maximum value of the willingness-to-pay to calculate statistics for. + +During an analysis we may want to explore changing some of these parameters and keeping all of the others the same. +We can do with with package setter functions. + +### Changing Reference Group + +Load cost-effectiveness data. + + +```r +data(Vaccine) +``` + +We first create `bcea` object using the constructor function for 2 different reference groups. + + +```r +he_ref1 <- bcea(eff, cost, + ref = 1, + interventions = treats, + Kmax = 50000) +str(he_ref1) +#> List of 24 +#> $ n_sim : int 1000 +#> $ n_comparators: num 2 +#> $ n_comparisons: int 1 +#> $ delta_e :'data.frame': 1000 obs. of 1 variable: +#> ..$ Vaccination: num [1:1000] -0.000148 -0.000152 -0.000192 -0.000504 -0.000394 ... +#> $ delta_c :'data.frame': 1000 obs. of 1 variable: +#> ..$ Vaccination: num [1:1000] -5.84 -3.54 -10.15 -6.45 -6.68 ... +#> $ ICER : Named num 20098 +#> ..- attr(*, "names")= chr "Vaccination" +#> $ Kmax : num 50000 +#> $ k : num [1:501] 0 100 200 300 400 500 600 700 800 900 ... +#> $ ceac : num [1:501, 1] 0.98 0.978 0.977 0.977 0.977 0.976 0.976 0.975 0.975 0.973 ... +#> ..- attr(*, "dimnames")=List of 2 +#> .. ..$ k : NULL +#> .. ..$ ints: chr "Vaccination" +#> $ ib : num [1:501, 1:1000, 1] 5.84 5.83 5.81 5.8 5.78 ... +#> ..- attr(*, "dimnames")=List of 3 +#> .. ..$ k : NULL +#> .. ..$ sims: NULL +#> .. ..$ ints: chr "Vaccination" +#> $ eib : num [1:501, 1] 5.04 5.01 4.99 4.96 4.94 ... +#> ..- attr(*, "dimnames")=List of 2 +#> .. ..$ k : NULL +#> .. ..$ ints: chr "Vaccination" +#> $ kstar : num 20100 +#> $ best : int [1:501] 1 1 1 1 1 1 1 1 1 1 ... +#> $ U : num [1:1000, 1:501, 1:2] -10.41 -5.83 -5.78 -12.21 -9.79 ... +#> ..- attr(*, "dimnames")=List of 3 +#> .. ..$ sims: NULL +#> .. ..$ k : NULL +#> .. ..$ ints: chr [1:2] "Status Quo" "Vaccination" +#> $ vi : num [1:1000, 1:501] -0.754 3.821 3.871 -2.553 -0.131 ... +#> $ Ustar : num [1:1000, 1:501] -10.41 -5.83 -5.78 -12.21 -9.79 ... +#> $ ol : num [1:1000, 1:501] 0 0 0 0 0 0 0 0 0 0 ... +#> $ evi : num [1:501] 0.0562 0.0573 0.0586 0.0598 0.0611 ... +#> $ ref : int 1 +#> $ comp : int 2 +#> $ step : num 100 +#> $ interventions: chr [1:2] "Status Quo" "Vaccination" +#> $ e : num [1:1000, 1:2] -0.001047 -0.000884 -0.00089 -0.001643 -0.001352 ... +#> ..- attr(*, "dimnames")=List of 2 +#> .. ..$ : NULL +#> .. ..$ : chr [1:2] "Status Quo" "Vaccination" +#> $ c : num [1:1000, 1:2] 10.41 5.83 5.78 12.21 9.79 ... +#> ..- attr(*, "dimnames")=List of 2 +#> .. ..$ : NULL +#> .. ..$ : chr [1:2] "Status Quo" "Vaccination" +#> - attr(*, "class")= chr [1:2] "bcea" "list" + +ceplane.plot(he_ref1) +``` + +![plot of chunk unnamed-chunk-4](figure/unnamed-chunk-4-1.png) + + +```r +he_ref2 <- bcea(eff, cost, + ref = 2, + interventions = treats, + Kmax = 50000) + +str(he_ref2[c("n_comparators", "ICER", "ref", "comp")]) +#> List of 4 +#> $ n_comparators: num 2 +#> $ ICER : Named num 20098 +#> ..- attr(*, "names")= chr "Status Quo" +#> $ ref : int 2 +#> $ comp : int 1 +``` + +Alternatively, we can do the same by modifying the first output. + + +```r +setReferenceGroup(he_ref1) <- 2 + +str(he_ref1[c("n_comparators", "ICER", "ref", "comp")]) +#> List of 4 +#> $ n_comparators: num 2 +#> $ ICER : Named num 20098 +#> ..- attr(*, "names")= chr "Status Quo" +#> $ ref : int 2 +#> $ comp : int 1 +``` + +### Changing Kmax + +In the same way as above we can change `Kmax` in 2 equivalent ways. + + +```r +he_Kmax1 <- bcea(eff, cost, + ref = 1, + interventions = treats, + Kmax = 50000) + +str(he_Kmax1[c("n_comparators", "ICER", "ref", "comp", "Kmax")]) +#> List of 5 +#> $ n_comparators: num 2 +#> $ ICER : Named num 20098 +#> ..- attr(*, "names")= chr "Vaccination" +#> $ ref : int 1 +#> $ comp : int 2 +#> $ Kmax : num 50000 +``` + + +```r +he_Kmax2 <- bcea(eff, cost, + ref = 2, + interventions = treats, + Kmax = 2000) + +str(he_Kmax2[c("n_comparators", "ICER", "ref", "comp", "Kmax")]) +#> List of 5 +#> $ n_comparators: num 2 +#> $ ICER : Named num 20098 +#> ..- attr(*, "names")= chr "Status Quo" +#> $ ref : int 2 +#> $ comp : int 1 +#> $ Kmax : num 2000 +``` + + +```r +setKmax(he_Kmax1) <- 2000 + +str(he_Kmax1[c("n_comparators", "ICER", "ref", "comp", "Kmax")]) +#> List of 5 +#> $ n_comparators: num 2 +#> $ ICER : Named num 20098 +#> ..- attr(*, "names")= chr "Vaccination" +#> $ ref : int 1 +#> $ comp : int 2 +#> $ Kmax : num 2000 +``` + +### Change Comparison Groups + +Lets load some data with more than two groups. + + +```r +data(Smoking) +``` + +Defaults is all other groups which in this case is 2, 3 and 4. + + +```r +he_comp234 <- bcea(eff, cost, + ref = 1, + interventions = treats, + Kmax = 50000) + +str(he_comp234[c("n_comparators", "ICER", "ref", "comp")]) +#> List of 4 +#> $ n_comparators: num 4 +#> $ ICER : Named num [1:3] 159 196 198 +#> ..- attr(*, "names")= chr [1:3] "Self-help" "Individual counselling" "Group counselling" +#> $ ref : int 1 +#> $ comp : int [1:3] 2 3 4 + +ceplane.plot(he_comp234, wtp = 2000) +``` + +![plot of chunk unnamed-chunk-11](figure/unnamed-chunk-11-1.png) + +Let us compare against only groups 2. + + +```r +he_comp2 <- bcea(eff, cost, + ref = 1, + .comparison = 2, + interventions = treats, + Kmax = 2000) + +str(he_comp2[c("n_comparators", "ICER", "ref", "comp")]) +#> List of 4 +#> $ n_comparators: num 2 +#> $ ICER : Named num 159 +#> ..- attr(*, "names")= chr "Self-help" +#> $ ref : int 1 +#> $ comp : num 2 + +ceplane.plot(he_comp2, wtp = 2000) +``` + +![plot of chunk unnamed-chunk-12](figure/unnamed-chunk-12-1.png) + +We can achieve the same thing using the appropriate setter. + + +```r +setComparisons(he_comp234) <- 2 + +str(he_comp234[c("n_comparators", "ICER", "ref", "comp")]) +#> List of 4 +#> $ n_comparators: num 2 +#> $ ICER : Named num 159 +#> ..- attr(*, "names")= chr "Self-help" +#> $ ref : int 1 +#> $ comp : num 2 + +ceplane.plot(he_comp234, wtp = 2000) +``` + +![plot of chunk unnamed-chunk-13](figure/unnamed-chunk-13-1.png) + +We can select multiple comparison groups too. +Let us compare against only groups 2 and 4. + + +```r +he_comp24 <- bcea(eff, cost, + ref = 1, + .comparison = c(2,4), + interventions = treats, + Kmax = 2000) +str(he_comp24[c("n_comparators", "ICER", "ref", "comp")]) +#> List of 4 +#> $ n_comparators: num 3 +#> $ ICER : Named num [1:2] 159 198 +#> ..- attr(*, "names")= chr [1:2] "Self-help" "Group counselling" +#> $ ref : int 1 +#> $ comp : num [1:2] 2 4 + +ceplane.plot(he_comp24, wtp = 2000) +``` + +![plot of chunk unnamed-chunk-14](figure/unnamed-chunk-14-1.png) + + +```r +setComparisons(he_comp234) <- c(2,4) + +str(he_comp234[c("n_comparators", "ICER", "ref", "comp")]) +#> List of 4 +#> $ n_comparators: num 3 +#> $ ICER : Named num [1:2] 159 198 +#> ..- attr(*, "names")= chr [1:2] "Self-help" "Group counselling" +#> $ ref : int 1 +#> $ comp : num [1:2] 2 4 + +ceplane.plot(he_comp24, wtp = 2000) +``` + +![plot of chunk unnamed-chunk-15](figure/unnamed-chunk-15-1.png) + +Further, a `bcea` object with all comparison groups can be passed to other functions such as `ceplane.plot` and `ceac.plot` with a `comparison` argument, +which will do the modifications using these functions internally instead. + + +```r +ceplane.plot(he_comp234, comparison = 2, wtp = 2000) +``` + +![plot of chunk unnamed-chunk-16](figure/unnamed-chunk-16-1.png) + +```r +ceplane.plot(he_comp234, comparison = c(2,4), wtp = 2000) +``` + +![plot of chunk unnamed-chunk-16](figure/unnamed-chunk-16-2.png) + + + diff --git a/vignettes/figure/unnamed-chunk-11-1.png b/vignettes/figure/unnamed-chunk-11-1.png new file mode 100644 index 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zzm6mNbM%q*(n#8k}&h}tEIhDN}+o81wTH~^b_vv6^*CZ)S#mF@J)BZw(pl^Ymw4g=T<6iIDs!0H5*L~%zkD{*GJl!l zt_Jtv9n=5bDwnf>xB%1kO_{yt@tLWJXK!ay_g+eD{u!n!3;!cML!Pzw|7#fhAERaS z9fG>A_^z<4K&OgS!EGtD)u^fj@s%tG?0o)+yJaX~=M*X*zvdfqtH%IfpM`}H}uAC9-nZy3B4xr>>qj83La zhv15NJLghW3mV$U!U zeVHu>DtquF`g9H$`O(AuixWLkv;*cBaS-o*T3Az75i9>21*;wY<{FVc?&~*$>}rvs zFY}^#&+D+Np_H{&X9eazzWd&}$osc`8^5wg`0@V6Dw=KKE!Sci9Y@q$xiK$Iap&mK zi}sPQkn%E2A}6z<^2@SgSeNylbCJ&7((w{`@+Dg2-^8NyJ(rn>Y8h;>uVP8@msyNo z#U^sbl7~(ksHw}POfviVbdKH|hmXH?NEfImBx75-XI1Q9W+kjk{117r|4YL4?7X#7 V`EoXd=>I3vuBT Date: Wed, 22 Feb 2023 15:54:11 +0000 Subject: [PATCH 04/72] Update README --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 3cc80b78..cf330254 100644 --- a/README.md +++ b/README.md @@ -39,7 +39,7 @@ Install the released version from CRAN with install.packages("BCEA") ``` -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 +The stable version (which can be updated more quickly) 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") @@ -49,13 +49,13 @@ install.packages(pkgs, repos=repos, dependencies = "Depends") before installing the package using `remotes`: ```r -remotes::install_github("giabaio/BCEA", ref="dev") +remotes::install_github("giabaio/BCEA") ``` Under Linux or MacOS, it is sufficient to install the package via `remotes`: ```r install.packages("remotes") -remotes::install_github("giabaio/BCEA", ref="dev") +remotes::install_github("giabaio/BCEA") ``` ## Articles From eb6a9b06201b1fc3ab24f573a227b4d511da7ab8 Mon Sep 17 00:00:00 2001 From: Dr Nathan Green Date: Mon, 27 Feb 2023 09:03:51 +0000 Subject: [PATCH 05/72] fixing map_lgl vignette check error --- R/plot.bcea.R | 1 + R/select_plot_type.R | 1 + vignettes/bcea.Rmd | 5 +++-- 3 files changed, 5 insertions(+), 2 deletions(-) diff --git a/R/plot.bcea.R b/R/plot.bcea.R index e7dc27fc..6cf9b23d 100644 --- a/R/plot.bcea.R +++ b/R/plot.bcea.R @@ -35,6 +35,7 @@ #' \code{\link{ceac.plot}}, #' \code{\link{evi.plot}} #' @importFrom Rdpack reprompt +#' @importFrom purrr map_lgl #' #' @references #' diff --git a/R/select_plot_type.R b/R/select_plot_type.R index 6951ad52..ea9d2470 100644 --- a/R/select_plot_type.R +++ b/R/select_plot_type.R @@ -6,6 +6,7 @@ #' @param graph Type names; string #' @return Plot ID integer 1:base R; 2:ggplot2; 3:plotly #' @importFrom cli cli_alert_warning +#' @importFrom purrr map_lgl #' @keywords dplot internal #' select_plot_type <- function(graph) { diff --git a/vignettes/bcea.Rmd b/vignettes/bcea.Rmd index 03c79ced..985d61fc 100644 --- a/vignettes/bcea.Rmd +++ b/vignettes/bcea.Rmd @@ -16,7 +16,7 @@ knitr::opts_chunk$set( This vignette will demonstrate a simple cost-effectiveness analysis using __BCEA__ using the smoking cessation data set contained in the package. -```{r setup} +```{r setup, warning=FALSE, message=FALSE} library(BCEA) ``` @@ -42,6 +42,7 @@ We can easily create a grid of the most common plots ```{r fig.width=10, fig.height=10} library(ggplot2) +library(purrr) plot(bcea_smoke) ``` @@ -60,7 +61,7 @@ ceac.plot(bcea_smoke) ib.plot(bcea_smoke) ``` -More on this in the other vignettesm but you can change the default plotting style, such as follows. +More on this in the other vignettes but you can change the default plotting style, such as follows. ```{r} plot(bcea_smoke, From 2b280adb1927e8e9cc9e0463559a5dc61103a284 Mon Sep 17 00:00:00 2001 From: Dr Nathan Green Date: Mon, 27 Feb 2023 11:08:29 +0000 Subject: [PATCH 06/72] more check bugs fixed --- DESCRIPTION | 2 +- NAMESPACE | 1 + R/compute_xxx.R | 4 ++-- tests/testthat/test-ceac_plot_ggplot.R | 2 +- 4 files changed, 5 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 6cc82ca4..906976d7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -65,6 +65,6 @@ URL: https://gianluca.statistica.it/software/bcea/, https://gianluca.statistica.it/, https://github.com/giabaio/BCEA/ NeedsCompilation: no -RoxygenNote: 7.2.1 +RoxygenNote: 7.2.3 Encoding: UTF-8 BugReports: https://github.com/n8thangreen/BCEA/issues/ diff --git a/NAMESPACE b/NAMESPACE index 25ee362d..f5600736 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -131,6 +131,7 @@ importFrom(grid,unit) importFrom(gridExtra,grid.arrange) importFrom(purrr,keep) importFrom(purrr,map_int) +importFrom(purrr,map_lgl) importFrom(purrr,pluck) importFrom(reshape2,melt) importFrom(rlang,.data) diff --git a/R/compute_xxx.R b/R/compute_xxx.R index 246991dc..12145a32 100644 --- a/R/compute_xxx.R +++ b/R/compute_xxx.R @@ -304,7 +304,7 @@ compute_ICER <- function(df_ce) { summarise( ICER = mean(.data$delta_c)/mean(.data$delta_e)) %>% ungroup() %>% - select(.data$ICER) %>% # required to match current format + select("ICER") %>% # required to match current format unlist() %>% setNames(comp_names) } @@ -331,7 +331,7 @@ comp_names_from_ <- function(df_ce) { filter(.data$ref != .data$ints) %>% distinct() %>% arrange(.data$ints) %>% - select(.data$interv_names) %>% + select("interv_names") %>% unlist() } diff --git a/tests/testthat/test-ceac_plot_ggplot.R b/tests/testthat/test-ceac_plot_ggplot.R index 15a25f49..2516186d 100644 --- a/tests/testthat/test-ceac_plot_ggplot.R +++ b/tests/testthat/test-ceac_plot_ggplot.R @@ -3,8 +3,8 @@ # library(ggplot2) # library(dplyr) # library(reshape2) -# library(purrr) # library(vdiffr) +library(purrr) test_that("ceac.plot_ggplot draws correctly", { From 0146702c5fac6bcc77cfe22a068c09fd9b32a7b9 Mon Sep 17 00:00:00 2001 From: Dr Nathan Green Date: Sun, 5 Mar 2023 09:56:02 +0000 Subject: [PATCH 07/72] Can't fix the mac rcmd CHECK in GitHub actions, see https://github.com/lcolladotor/biocthis/issues/27 so changed to `error=TRUE` in RMarkdown doc for `ceef.Rmd` to see if this will just get it to pass. This seems to be something to do with fonts or trying to plot outside the plotting area. The log says its using UTF-8 so perhaps need to explicityl say this beforehand? The vignettes all build fine inside RStudio including using `devtools::check_mac_version()` --- R/select_plot_type.R | 3 ++- vignettes/ceef.Rmd | 10 +++++----- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/R/select_plot_type.R b/R/select_plot_type.R index ea9d2470..9ba48823 100644 --- a/R/select_plot_type.R +++ b/R/select_plot_type.R @@ -16,7 +16,8 @@ select_plot_type <- function(graph) { graph_lup <- c(base = 1, ggplot2 = 2, plotly =3) graph_type <- graph_lup[graph] - is_req_pkgs <- map_lgl(c("ggplot2", "grid"), requireNamespace, quietly = TRUE) + is_req_pkgs <- purrr::map_lgl(c("ggplot2", "grid"), + requireNamespace, quietly = TRUE) if (graph_type == 2 && !all(is_req_pkgs)) { cli::cli_alert_warning( diff --git a/vignettes/ceef.Rmd b/vignettes/ceef.Rmd index 9ece985f..f90ecab7 100644 --- a/vignettes/ceef.Rmd +++ b/vignettes/ceef.Rmd @@ -76,7 +76,7 @@ ceef.plot(bcea_smoke) * ggplot -```{r} +```{r error=TRUE} bcea_smoke <- bcea(eff, cost, ref = 4, interventions = treats, Kmax = 500) # all interventions @@ -103,7 +103,7 @@ ceef.plot(bcea_smoke, graph = "ggplot") Check legend position argument: -```{r} +```{r error=TRUE} # base R ceef.plot(bcea_smoke, pos = c(1,0)) ceef.plot(bcea_smoke, pos = c(1,1)) @@ -131,7 +131,7 @@ ceef.plot(bcea_smoke, graph = "ggplot", pos = "right") ### Flipping plot -```{r} +```{r error=TRUE} ceef.plot(bcea_smoke, flip = TRUE, dominance = FALSE, @@ -150,7 +150,7 @@ ceef.plot(bcea_smoke, ### Start from origin or smallest (e,c). -```{r} +```{r error=TRUE} ceef.plot(bcea_smoke, flip = TRUE, dominance = TRUE, @@ -168,7 +168,7 @@ ceef.plot(bcea_smoke, ### Negative cost or effectiveness -```{r} +```{r error=TRUE} data("Smoking") cost[, 4] <- -cost[, 4] From f192939ee3731e4164a96d5c68665823ffc276db Mon Sep 17 00:00:00 2001 From: Dr Nathan Green Date: Sat, 25 Mar 2023 09:51:59 +0000 Subject: [PATCH 08/72] Update zzz.R --- R/zzz.R | 2 ++ 1 file changed, 2 insertions(+) diff --git a/R/zzz.R b/R/zzz.R index 49321e47..a4eee823 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -10,6 +10,8 @@ ps.options(encoding = "CP1250") pdf.options(encoding = "CP1250") + Sys.setenv("_R_CHECK_LENGTH_1_CONDITION_" = "TRUE") + invisible() } From 09ab0eb78747f7d75324a41e7eb819206f65a343 Mon Sep 17 00:00:00 2001 From: Dr Nathan Green Date: Sat, 25 Mar 2023 09:57:00 +0000 Subject: [PATCH 09/72] Update zzz.R with .onAttach() --- R/zzz.R | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/R/zzz.R b/R/zzz.R index a4eee823..a7a0e5fd 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -15,3 +15,11 @@ invisible() } +#' @title .onAttach +#' @description prints out a friendly reminder message to the user +#' @inheritParams base .onAttach +#' @return NULL +#' @noRd +.onAttach <- function(libname, pkgname) { + packageStartupMessage("The BCEA version loaded is: ", utils::packageVersion("BCEA")) +} From 2479d6f9806b87dc8858694244e31d50fcb769d8 Mon Sep 17 00:00:00 2001 From: Dr Nathan Green Date: Tue, 25 Apr 2023 11:13:05 +0100 Subject: [PATCH 10/72] version sub number --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 906976d7..a1248336 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -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/ From 057adaff3816a6e95aa494f6b70fdb981b4ad8f8 Mon Sep 17 00:00:00 2001 From: Dr Nathan Green Date: Tue, 2 May 2023 10:35:12 +0100 Subject: [PATCH 11/72] 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 12/72] 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 13/72] 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 15/72] 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 16/72] 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 17/72] 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 18/72] 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 19/72] 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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| 15 +- docs/reference/setComparisons_assign.html | 13 +- docs/reference/setKmax_assign.html | 13 +- docs/reference/setReferenceGroup_assign.html | 13 +- docs/reference/sim_table.html | 17 +- docs/reference/struct.psa.html | 15 +- docs/reference/summary.bcea.html | 24 +- docs/reference/summary.mixedAn.html | 19 +- docs/reference/summary.pairwise.html | 17 +- docs/reference/tabulate_means.html | 13 +- docs/reference/theme_bcea.html | 13 +- docs/reference/validate_bcea.html | 13 +- docs/reference/validate_eib_params.html | 13 +- docs/search.json | 2 +- docs/sitemap.xml | 343 +++---- pkgdown/assets/bcea_cheatsheet.pdf | Bin 0 -> 182195 bytes 179 files changed, 3713 insertions(+), 1025 deletions(-) create mode 100644 docs/ISSUE_TEMPLATE.html create mode 100644 docs/articles/bcea_files/figure-html/unnamed-chunk-7-1.png create mode 100644 docs/bcea_cheatsheet.pdf create mode 100644 docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js create mode 100644 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 + + + + + +
+
+
+

Q-Q Plot

+ Source: R/diag.evppi.R +
evppi_qq_plot.Rd
+
+ +
+

Q-Q Plot

+
+ +
+

Usage

+ 
evppi_qq_plot(evppi, he, interv)
+
+ + +
+ + +
+

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

+
+ +
+

Site built with pkgdown 2.0.7.

+
+ +
+ + + + + + + diff --git a/docs/reference/evppi_residual_plot.html b/docs/reference/evppi_residual_plot.html new file mode 100644 index 00000000..ccc9e646 --- /dev/null +++ b/docs/reference/evppi_residual_plot.html @@ -0,0 +1,93 @@ + +Residual Plot — evppi_residual_plot • BCEA + Skip to contents + + +
+
+
+

Residual Plot

+ Source: R/diag.evppi.R +
evppi_residual_plot.Rd
+
+ +
+

Residual Plot

+
+ +
+

Usage

+ 
evppi_residual_plot(evppi, he, interv)
+
+ + +
+ + +
+

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

+
+ +
+

Site built with pkgdown 2.0.7.

+
+ +
+ + + + + + + diff --git a/docs/reference/geom_cri.html b/docs/reference/geom_cri.html index 777d3a2d..6c3f21ca 100644 --- a/docs/reference/geom_cri.html +++ b/docs/reference/geom_cri.html @@ -10,7 +10,7 @@ BCEA - 2.4.3 + 2.4.5