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 tolinewidth
fromsize
argument and had only changed some of the code. Updated toscale_linewidth_manual()
. (60bea9c) - Using
testdata
folder{testthat}
unit tests. (cbce0fa)
November 2023
Some cosmetic changes to clean up
- Removed the (by now, unnecessary) appveyor webhook
- Added correct 'Remotes' in the 'DESCRIPTION' file to point to the correct GitHub repos for 'voi' and 'plotrix'
- Changed the class of the object 'smoking_output' to be used in the 'evppi' example avoiding the need for 'rjags'
October 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 usecheck = TRUE
invoi::evppi()
in order to access fitting data (6e436b5, 94f5fc5)
- Latest version of
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 methodssal
andso
(#140) - New
evppi()
matching output of oldevppi()
(1e2c5e7) - Latest development version of
voi
needed when we usecheck = TRUE
invoi::evppi()
in order to access fitting data (6e436b5, 94f5fc5) - No longer require
INLA
package to be available inside ofBCEA
so can remove direct dependency. This helps with passing CRAN checks and GitHub Actions ()
June 2023
- Patch to fix a CRAN checks error. Suggested package
{MCMCvis}
wasn't used conditionally in unit test. Moved to Required packages inDESCRIPTION
.
May 2023
- 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
andbest
inbcea()
object were not updated with subset of interventions (#125)
withr::with_par()
used in plotting functionplot.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)
- Template added for GitHub Issues (0ea59fa)
August 2022
summary.bcea()
wasn't passingwtp
argument tosim_table()
internally (5440eb3)summary()
was the same for basicbcea
andmulti.ce
objects. Now has ownsummary.pairwise()
method. (88ade51)struct.psa()
output now works withsummary()
and plots all still work without having to use $ to get atbcea
object as before. (b014c83)- Changed
wtp
argument inbcea()
tok
becausewtp
in the plotting functions refers to the wtp line and so is a scalar whereask
is a grid of points. Added an error message to use new argument. (b014c83) bcea()
still allows a scalark
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.
- Now uses
Rdpack
for bibliography in documentation (229c96d) - The cost and health values in the
Smoking
andVaccine
data sets have been renamed fromc
ande
tocost
andeff
. This is to avoid any conflict with thec()
function. - Changed the axes labels in the cost-effectiveness planes from "differential" to "incremental". (688d98b)
- 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()
andceac.plot()
ggplot2
versions (6808aa6) - Argument added to
ceplane.plot()
oficer_annot
to annotate each of the ICER points with the text label of the intervention name. Only forggplot2
at the moment. (a7b4beb) - Added
pos
argument tocontour2()
so that its consistent withcontour()
andceplane.plot()
. (50f8f8b) - Allow passing
ref
argument by name as well as index inbcea()
. (9eab459)
April 2022
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 removingalpha
transparencyceac.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)
- 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 incontour()
- Extend some function (
goodpractice
package suggested changes- line length,
seq_len()
, remove;
- line length,
- Contributor guidelines (#93)
- Deprecated functions document
contour2()
changed soxlim
,ylim
arguments are optional; the same asceplane.plot()
since they are passes to itcontour()
andceplane.plot()
vignettes written
Oct 2021
- Code base improved robustness and extensibility.
bcea()
is now a helper function which calls the constructornew_bcea()
, separating concerns.new_bcea()
composed of smaller HEE statistics functions with names starting withcompute_*
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 tonew_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 onceac.plot()
for bothmulti.ce()
andbcea()
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.
- Deprecated
- Tables updated. Duplication in
summary()
andsim_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.
- 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 functionssetComparisons()
. - Similarly, maximum willingness to pay and the reference group can be set with
setKmax()
andsetReferenceGroup()
, respectively. multi.ce()
andCEriskAv()
also now work similarly. They operate by modifying thebcea
object, rather than creating new one (think decorator pattern).bcea()
methods for JAGS, WinBUGS, Stan (#76)
- 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)
26 Aug 2019
5 Aug 2019
11 July 2018
- Fix in
evppi
to allowN
to be selected in all methods - Fix
diag.evppi
18 Nov 2016
- Some changes to EVPPI
Nov 2016
- Fixes for new ggplot2 version (
legend.spacing()
andplot.title
hjust
argument)
22 May 2016
- Major update for the EVPPI to include PFC
- Fixed issues with
info.rank
25 Jan 2016
- Minor change to
ceef.plot
to align with ggplot2 v2.0.0
Oct 2015
- Adds the info-rank plot
Oct 2015
- Cleaned up and aligned with R's settings
EVPPI
function polished up
6 May 2015 2015
- New function for EVPPI using SPDE-INLA
- Modifications to the EVPPI functions
- Documentation updated
- Allows
xlim
&ylim
in theceplane.plot()
,contour()
andcontour2()
functions - It is now possible to run
bcea
for a scalar wtp - Old
evppi()
function and method has been renamedevppi0
, which means there's also a newplot.evppi0
method
13 Jan 2015
- Migrated from
if (require())
toif (requireNamespace(,quietly=TRUE))
- Documentation updated
- Added threshold argument to
ceef.plot
function
Oct 2014
- modifications to
ceef.plot
,createInputs
,struct.psa
13 Jan 2015
- Documentation updated
- Smoking dataset and
ceef.plot
function included, additional modifications
2 Dec 2013
2 Dec 2013
ceac.plot
andeib.plot
: option comparison included for base graphics
2 Dec 2013
31 July 2013
30 July 2013
- 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)
3 July 2013
17 September 2012
22 Feb 2013
15 Sept 2012
13 May 2012