new BCEA

Nathan and I — well the more correct version of this statement is “Nathan”… — have been working on a few relatively major improvements on BCEA and have managed to push all the changes to the main version, which is now available from CRAN.

The changes are mainly of three types — some are probably just “cosmetics”, others are a bit more structural, like new features or just fixing bugs (the weird numbers-letters codes in brackets are pointers to the Git commit in which changes have happened). Some of the new features came out from exposure to people’s requests and comments when we were running our Summer School, but others are directly requests from users, which is pretty cool and we like that sort of thing…

Nathan has been doing a fantastic job in keeping track of all these, so we do have an updated list of all the changes (as below, but also in the NEWS.md file that gets saved into the main package).

Installation is, as usual, from CRAN

install.packages("BCEA")

which gives you the latest version (now 4.2.1).

Bug fixes

• summary.bcea() wasn’t passing wtp argument to sim_table() internally (5440eb3)
• summary() was the same for basic bcea and multi.ce objects. Now has own summary.pairwise() method. (88ade51)
• struct.psa() output now works with summary() and plots all still work without having to use $ to get at bcea object as before. (b014c83)
• Changed wtp argument in bcea() to k because wtp in the plotting functions refers to the wtp line and so is a scalar whereas k is a grid of points. Added an error message to use new argument. (b014c83)
• bcea() still allows a scalar k but added a warning that this will give empty plots.
• Updated GitHub Actions for checking the package to use r-lib/Actions version 2. There was an error with not finding INLA but this was solved by Gabor at RStudio (see thread here https://community.rstudio.com/t/not-finding-inla-package-not-on-cran-in-actions/141398)
• GrassmannOptim package r-release-macos-x86_64 isn’t available resulting in a CRAN check error and doesn’t appear to be maintained. Tried emailing the author but bounced. Removed dependency and copied GrassmannOptim() function inside of package with acknowledgement.

Refactoring

• Now uses Rdpack for bibliography in documentation (229c96d)
• The cost and health values in the Smoking and Vaccine data sets have been renamed from c and e to cost and eff. This is to avoid any conflict with the c() function.
• Changed the axes labels in the cost-effectiveness planes from “differential” to “incremental”. (688d98b)

New features

• Can now specify what order the interventions labels are in the legend for ce plane (and contour plots) for base R and ggplot2 i.e. reference first or second with optional ref_first argument (cc38f07)
• Can specify currency for axes in ce-plane.plot and ceac.plot ggplot2 versions (6808aa6)
• Argument added to ceplane.plot of icer_annot to annotate each of the ICER points with the text label of the intervention name. Only for ggplot2 at the moment. (a7b4beb)
• 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)

If there’s anything else you’d like to change, fiddle with, just shout! 😉