Learn R Programming
⚠️There's a newer version (2.4.83) of this package.Take me there.

BCEA: Bayesian cost-effectiveness analysis

Perform Bayesian Cost-Effectiveness Analysis in R.

:rocket: Version 2.4.6 in development now! Check out the release notes here.

Contents

Overview

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:

  • Cost-effectiveness analysis plots, such as CE planes and CEAC
  • Summary statistics and tables
  • EVPPI calculations and plots

Installation

Install the released version from CRAN with

install.packages("BCEA")

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 first, e.g. by running

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:

remotes::install_github("giabaio/BCEA")

Under Linux or MacOS, it is sufficient to install the package via remotes:

install.packages("remotes")
remotes::install_github("giabaio/BCEA")

Articles

Examples of using specific functions and their different arguments are given in these articles:

Further details

The pkgdown site is here. More details on BCEA are available in our book Bayesian Cost-Effectiveness Analysis with the R Package 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.

License

Contributing

Please submit contributions through Pull Requests, following the contributing guidelines. To report issues and/or seek support, please file a new ticket in the issue tracker.

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

Copy Link

Version

Install

install.packages('BCEA')

Monthly Downloads

545

Version

2.4.6

License

GPL-3

Issues

15

Pull Requests

0

Stars

50

Forks

17

Maintainer

Gianluca Baio

Last Published

February 16th, 2024

Functions in BCEA (2.4.6)

ceef.plot.bcea

Cost-Effectiveness Efficiency Frontier (CEEF) Plot
ceac.plot.bcea

Cost-Effectiveness Acceptability Curve (CEAC) Plot
ceplane_plot_graph

Cost-Effectiveness Plane Plot By Graph Device
compute_ICER

Compute Incremental Cost-Effectiveness Ratio
comp_names_from_

Comparison Names From
compute_CEAC

Compute Cost-Effectiveness Acceptability Curve
compute_EIB

Compute Expected Incremental Benefit
compute_EVI

Compute Expected Value of Information
compute_IB

Compute Incremental Benefit
ceef.summary

Summary table for CEEF
compute_eib_cri

Calculate Credible Intervals
compute_kstar

Compute k^*
compute_Ubar

Compute NB for mixture of interventions
compute_ceaf

Compute Cost-Effectiveness Acceptability Frontier
compute_Ustar

Compute Ustar Statistic
ceplane_ggplot_params

CE-plane ggplot Parameters
ceplane_geom_params

Extract Separate Parameter Sets
compute_p_best_interv

Compute Probability Best Intervention
compute_U

Compute U Statistic
compute_vi

Compute Value of Information
contour_ggplot_params

Contour ggplot Parameters
contour.bcea

Contour Plots for the Cost-Effectiveness Plane
contour2.bcea

Specialised CE-plane Contour Plot
contour_graph

Contour Cost-Effectiveness Plane
diag.evppi

Diagnostic Plots For The Results Of The EVPPI
compute_ol

Compute Opportunity Loss
eib.plot.bcea

Expected Incremental Benefit (EIB) Plot
convert_pts_to_mm

Use from Base R to ggplot
createInputs.default

Create Inputs for EVPI Calculation
ib.plot.bcea

Incremental Benefit (IB) Distribution Plot
eib_params_base

EIB parameters specific to base R plot
get_fitted_

Get fitted values from evppi object
eib_params_cri

EIB Parameters CrI
is.bcea

Check bcea Class
evppi

Expected Value of Perfect Partial Information (EVPPI) for Selected Parameters
make.report

Make Report
eib_plot_graph

Expected Incremental Benefit Plot By Graph Device
geom_cri

Credible interval ggplot geom
evppi_plot_graph

Plot Expected Value of Partial Information With Respect to a Set of Parameters
ib_plot_base

IB plot base R version
geom_quad_txt

Geom Quadrant Text
line_labels

Create Labels for Plot
kstar_vlines

Prepare K-star vertical lines
make_legend_plotly

Legend Positioning
new_bcea

Constructor for bcea
info_rank_graph

Info Rank Plot By Graph Device
evppi_residual_plot

Residual Plot
evppi_qq_plot

Q-Q Plot
evi.plot.bcea

Expected Value of Information (EVI) Plot
loo_rank

Leave-one-out ranking
mixedAn<-

Cost-Effectiveness Analysis When Multiple (Possibly Non-Cost-Effective) Interventions are Present on the Market
mce.plot

Plots the probability that each intervention is the most cost-effective
setReferenceGroup_assign

Set Reference Group
prep_ceplane_params

Prepare CE-plane Parameters
quiet

Allow disabling of the cat messages
plot_eib_cri

Plot Credible Intervals
summary.bcea

Summary Method for Objects of Class bcea
setKmax_assign

Set Maximum Willingness to Pay
info.rank.bcea

Information-Rank Plot for bcea Class
plot.evppi

Plot Expected Value of Partial Information With Respect to a Set of Parameters
inforank_params

Prepare Info Rank plot parameters
plot.CEriskav

Plots EIB and EVPI for the Risk Aversion Case
num_lines

Get number of lines
plot.bcea

Summary Plot of the Health Economic Analysis
evi.plot.mixedAn

EVI Plot of the Health Economic Analysis For Mixed Analysis
select_plot_type

Choose Graphical Engine
evi_plot_graph

Expected Value of Information Plot By Graph Device
prep_eib_params

Prepare EIB plot parameters
validate_eib_params

Validate EIB parameters
openPDF

Automatically open pdf output using default pdf viewer
struct.psa

Structural Probability Sensitivity Analysis
sim_table

Table of Simulation Statistics for the Health Economic Model
summary.mixedAn

Summary Methods For Objects in the Class mixedAn (Mixed Analysis)
prep_frontier_data

Prepare frontier data
multi.ce

Cost-effectiveness Analysis With Multiple Comparison
validate_bcea

Validate bcea
theme_bcea

bcea theme ggplot2
tabulate_means

Calculate Dataset For ICERs From bcea Object
summary.pairwise

Summary Method for Objects of Class pairwise
multiplot

Plot Multiple bcea Graphs
print.bcea

bcea Print Method
setComparisons_assign

Set Comparison Group
setComparisons

Set Comparisons Group
quadrant_params

Quadrant Parameters requires just a single comparison group
BCEA-package

BCEA: Bayesian Cost Effectiveness Analysis
CEriskav_assign

Cost-effectiveness Analysis Including a Parameter of Risk Aversion
Smoking

Data set for the Bayesian model for the cost-effectiveness of smoking cessation interventions
Vaccine

Data set for the Bayesian model for the cost-effectiveness of influenza vaccination
BCEA-deprecated

Deprecated functions in package BCEA.
GrassmannOptim

GrassmannOptim
bcea

Create Bayesian Cost-Effectiveness Analysis Object
add_contours

Add Contours to Base R Plot
add_contour_quadrants

Add Contour Quadrants
CEriskav_plot_graph

Cost-effectiveness Plot Including a Parameter of Risk Aversion
ceef_plot_graph

Cost-effectiveness Efficiency Frontier Plot By Graph Device
ceplane.plot.bcea

Cost-effectiveness Plane Plot
ceaf.plot.pairwise

Cost-Effectiveness Acceptability Frontier (CEAF) plot
ceac_matplot

CEAC Matrix Plot
ceac_plot_graph

Cost-Effectiveness Acceptability Curve (CEAC) Plot By Graph Device
best_interv_given_k

Optimal intervention
ce_table

Cost-effectiveness summary statistics table