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Changelog

Source: NEWS.md

BCEA 2.4.6

February 2024

Patch fixing small bugs from last CRAN release.

  • Converted help documentation in man-roxygen folder to md (cf858b1)
  • bugfix: line width in CEAC plot. ggplot2 changed in version 3 to linewidth from size argument and had only changed some of the code. Updated to scale_linewidth_manual(). (60bea9c)
  • Using testdata folder testthat unit tests. (cbce0fa)

BCEA 2.4.5

November 2023

Moved internal EVPPI calculation out of BCEA and now uses voi package instead. Refactoring but retaining same interface and functionality.

  • Ensure using latest CRAN release of voi which has a patch so that BCEA can use it without losing functionality
    • Latest version of voi needed when we use check = TRUE in voi::evppi() in order to access fitting data (6e436b5, 94f5fc5)
  • evppi() tested against all use cases in BCEA book (1c1457d2)
  • Select parameters by position (as well as name) in new evppi() (f2e4d005)
  • Use single parameter case only like voi package for methods sal and so (#140)
  • New evppi() matching output of old evppi() (1e2c5e7)
  • Latest development version of voi needed when we use check = TRUE in voi::evppi() in order to access fitting data (6e436b5, 94f5fc5)
  • No longer require INLA package to be available inside of BCEA so can remove direct dependency. This helps with passing CRAN checks and GitHub Actions ()

BCEA 2.4.4

June 2023

  • Patch to fix a CRAN checks error. Suggested package MCMCvis wasn’t used conditionally in unit test. Moved to Required packages in DESCRIPTION.

BCEA 2.4.3

May 2023

Bug fixes

  • Consistent colours across plots for each intervention for grid of plots in plot.bcea() (cf1ee43)
  • make.report() change variable name (f940f2e)
  • Fixed issue with summary table where names of interventions in the wrong order (6a006e3)
  • summary.bcea() now only prints results for chosen comparisons and not always all of them. kstar and best in bcea() object were not updated with subset of interventions (#125)

Refactoring

  • withr::with_par() used in plotting function plot.bcea() to only temporarily change graphics parameters. (725c536)
  • Using @md and markdown syntax in function documentation
  • Update psa.struct() to add the absolute value in the formula to compute the weights (1cea278)
  • Use dplyr piping new syntax from .data$* to simply using speech marks "*" (2b280ad)

Miscellaneous

  • Template added for GitHub Issues (0ea59fa)

BCEA 2.4.2

August 2022

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 ceplane.plot() and ceac.plot() ggplot2 versions (6808aa6)
  • Argument added to ceplane.plot() of icer_annot to annotate each of the ICER points with the text label of the intervention name. Only for ggplot2 at the moment. (a7b4beb)
  • Added pos argument to contour2() so that its consistent with contour() and ceplane.plot(). (50f8f8b)
  • Allow passing ref argument by name as well as index in bcea(). (9eab459)

BCEA 2.4.1.2

April 2022

Bug fixes

  • ceplane_ggplot() missing legend
  • Legend bug in evppi()
  • Arguments in consistent same order as ceplane.plot()
  • ceplane_plot_base() wasn’t showing grey area. Fixed by removing alpha transparency
  • ceac.plot() wasn’t showing confidence interval by default for one comparison
  • Typo fixed in dropping dimension in compute_vi()
  • setReferenceGroup() for CEAC plot legend error; doesn’t use supplied names but generic intervention 1, intervention 2, … (#82)
  • Missing multi.ce() line for reference group (#80)

Miscellaneous

  • Use cli package for warning messages
  • Clean @keywords in Roxygen
    • Removed all the internal helper functions from the Manual by using @keyword internal
  • Refactor contour plots
  • Plot functions take more standard ggplot2 format style arguments e.g. as list
    • Extend some function (ceac.plot()) to take more style arguments than before for e.g. colour of lines, types of points and line thickness.
    • Resuse ceplane.plot() code in contour()
  • goodpractice package suggested changes
  • Contributor guidelines (#93)
  • Deprecated functions document
  • contour2() changed so xlim, ylim arguments are optional; the same as ceplane.plot() since they are passes to it
  • contour() and ceplane.plot() vignettes written

BCEA 2.4.1.1

Oct 2021

Major refactoring

  • Code base improved robustness and extensibility.
  • bcea() is now a helper function which calls the constructor new_bcea(), separating concerns.
  • new_bcea() composed of smaller HEE statistics functions with names starting with compute_* e.g. compute_CEAC(), compute_EIB(),…. This allows us to call and test them individually. It also allows more flexibility in changing or adding functionality to new_bcea().
  • Plotting functions have been rewritten. These functions now simply dispatch to the base R, ggplot2 or plotly versions (think strategy pattern). Internally, these functions, e.g.ceplane_plot_ggplot(), are also split into parameter and data setting and plotting components. This modulisation allows us to add new layers to plots or modify existing parameter sets and defaults. We could also return the data without the plotting step as in e.g. ggplot2::autoplot(). It also means we can reuse some functionality across plots such as axes and legend setting e.g. BCEA:::where_legend().
  • ceac_plot() changes
    • Deprecated mce.plot(). Now dispatched on ceac.plot() for both multi.ce() and bcea() outputs.
    • For a multiple comparison the plot for pairwise comparison over all interventions is returned by default. The alternative version of each comparison against the reference group is still available.
    • Plots and tables using S3 methods for bcea type object.
  • Tables updated. Duplication in summary() and sim_table() removed.
  • createInputs() used for EVPI calculation now dispatches S3 methods by JAGS, BUGS, Stan and other R data types.
  • make.report() rewritten to have separate section files.

New features

  • Extend ways to set comparison interventions. Subsets of comparison can still be set in a call to a plotting function as before. Now subsets can be set in both the original bcea() construction or separately using a setter functions setComparisons().
  • Similarly, maximum willingness to pay and the reference group can be set with setKmax() and setReferenceGroup(), respectively.
  • multi.ce() and CEriskAv() also now work similarly. They operate by modifying the bcea object, rather than creating new one (think decorator pattern).
  • bcea() methods for JAGS, WinBUGS, Stan (#76)

Miscellaneous

  • Additional help documentation and examples.
  • New vignettes about plotting and comparison intervention setting.
  • Testing suite started. This is not comprehensive as of yet.
  • Added a NEWS.md file to track changes to the package. Details about previous releases, such as dates, versions, fixes and enhancements obtained from CRAN and code comments so a little patchy.
  • pkgdown GitHub site made.
  • Cheatsheet written and published on RStudio site (#22).
  • Dependency package ldr removed from BCEA because it was removed from CRAN (#74)

BCEA 2.3-1.1

26 Aug 2019

BCEA 2.3-1

5 Aug 2019

BCEA 2.2-6

11 July 2018

  • Fix in evppi to allow N to be selected in all methods
  • Fix diag.evppi

BCEA 2.2-5

18 Nov 2016

  • Some changes to EVPPI

BCEA 2.2.4

Nov 2016

  • Fixes for new ggplot2 version (legend.spacing() and plot.title hjust argument)

BCEA 2.2-3

22 May 2016

  • Major update for the EVPPI to include PFC
  • Fixed issues with info.rank

BCEA 2.2-2

25 Jan 2016

  • Minor change to ceef.plot to align with ggplot2 v2.0.0

BCEA 2.2.1

Oct 2015

  • Adds the info-rank plot

BCEA 2.2

Oct 2015

  • Cleaned up and aligned with R’s settings
  • EVPPI function polished up

BCEA 2.1-1

6 May 2015 2015

  • New function for EVPPI using SPDE-INLA
  • Modifications to the EVPPI functions
  • Documentation updated
  • Allows xlim & ylim in the ceplane.plot(), contour() and contour2() functions
  • It is now possible to run bcea for a scalar wtp
  • Old evppi() function and method has been renamed evppi0, which means there’s also a new plot.evppi0 method

BCEA 2.1-0

13 Jan 2015

  • Migrated from if (require()) to if (requireNamespace(,quietly=TRUE))
  • Documentation updated
  • Added threshold argument to ceef.plot function

BCEA 2.1.0-pre2

Oct 2014

  • modifications to ceef.plot, createInputs, struct.psa

BCEA 2.1-0-pre1

13 Jan 2015

  • Documentation updated
  • Smoking dataset and ceef.plot function included, additional modifications

BCEA 2.0-2c

2 Dec 2013

BCEA v2.0-2b

2 Dec 2013

  • ceac.plot and eib.plot: option comparison included for base graphics

BCEA 2.0-2

2 Dec 2013

BCEA 2.0-1

31 July 2013

BCEA 2.0

30 July 2013

Feature updates

  • Implements two quick and general methods to compute the EVPPI
  • Function CreateInputs(), which takes as input an object in the class rjags or bugs
  • Compute the EVPPI for one or more parameters calling the function evppi()
  • Results can be visualised using the specific method plot for the class evppi and show the overall EVPI with the EVPPI for the selected parameter(s)

BCEA 1.3-1

BCEA 1.3-0

3 July 2013

BCEA 1.2

17 September 2012

BCEA 1.1.1

22 Feb 2013

BCEA 1.1

15 Sept 2012

BCEA 1.0

13 May 2012