new BCEA
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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 passingwtpargument tosim_table()internally (5440eb3)summary()was the same for basicbceaandmulti.ceobjects. Now has ownsummary.pairwise()method. (88ade51)struct.psa()output now works withsummary()and plots all still work without having to use $ to get atbceaobject as before. (b014c83)- Changed
wtpargument inbcea()tokbecausewtpin the plotting functions refers to the wtp line and so is a scalar whereaskis a grid of points. Added an error message to use new argument. (b014c83) bcea()still allows a scalarkbut added a warning that this will give empty plots.- Updated GitHub Actions for checking the package to use
r-lib/Actionsversion 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
Rdpackfor bibliography in documentation (229c96d) - The cost and health values in the
SmokingandVaccinedata sets have been renamed fromcandetocostandeff. This is to avoid any conflict with thec()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_firstargument (cc38f07) - Can specify currency for axes in
ce-plane.plotandceac.plotggplot2versions (6808aa6) - Argument added to
ceplane.plotoficer_annotto annotate each of the ICER points with the text label of the intervention name. Only forggplot2at the moment. (a7b4beb) - Added
posargument tocontour2()so that its consistent withcontour()andceplane.plot(). (50f8f8b) - Allow passing
refargument by name as well as index inbcea(). (9eab459)
If there’s anything else you’d like to change, fiddle with, just shout! 😉
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