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BCEA

Perform Bayesian Cost-Effectiveness Analysis in R.

:rocket: Version 2.4.1 out 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 development version 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", ref="dev")

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

install.packages("remotes")
remotes::install_github("giabaio/BCEA", ref="dev")

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.

Licence

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.

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Version

Install

install.packages('BCEA')

Monthly Downloads

3,822

Version

2.4.2

License

GPL-3

Issues

15

Pull Requests

0

Stars

48

Forks

17

Maintainer

Gianluca Baio

Last Published

August 23rd, 2022

Functions in BCEA (2.4.2)

CEriskav_assign

Cost-effectiveness Analysis Including a Parameter of Risk Aversion
Vaccine

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

Create Bayesian Cost-Effectiveness Analysis Object
BCEA-package

BCEA: A package for Bayesian Cost-Effectiveness Analysis
GrassmannOptim

GrassmannOptim
CEriskav_plot_graph

Cost-effectiveness Plot Including a Parameter of Risk Aversion
BCEA-deprecated

Deprecated functions in package BCEA.
add_contours

Add Contours to Base R Plot
add_contour_quadrants

Add Contour Quadrants
Smoking

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

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

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

Cost-Effectiveness Acceptability Curve (CEAC) Plot
ceef.summary

Summary table for CEEF
ceaf.plot.pairwise

Cost-Effectiveness Acceptability Frontier (CEAF) plot
ceac_plot_graph

Cost-Effectiveness Acceptability Curve (CEAC) Plot By Graph Device
ceplane.plot.bcea

Cost-effectiveness Plane Plot
best_interv_given_k

Optimal intervention
comp_names_from_

Comparison Names From
ceplane_plot_graph

Cost-Effectiveness Plane Plot By Graph Device
compute_IB

Compute Incremental Benefit
compute_vi

Compute Value of Information
compute_ICER

Compute Incremental Cost-Effectiveness Ratio
contour.bcea

Contour Plots for the Cost-Effectiveness Plane
compute_p_best_interv

Compute Probability Best Intervention
compute_ol

Compute Opportunity Loss
contour_graph

Contour Cost-Effectiveness Plane
ce_table

Cost-effectiveness summary statistics table
ceac_matplot

CEAC Matrix Plot
ceplane_geom_params

Extract Separate Parameter Sets
compute_EIB

Compute Expected Incremental Benefit
eib.plot.bcea

Expected Incremental Benefit (EIB) Plot
convert_pts_to_mm

Use from Base R to ggplot
ceplane_ggplot_params

CE-plane ggplot Parameters
is.bcea

Check bcea Class
fit.gp

Fit Gaussian Process
kstar_vlines

Prepare K-star vertical lines
eib_params_base

EIB parameters specific to base R plot
fit.gam

Gaussian Additive Model Fitting
compute.evppi

Compute EVPPI
compute_EVI

Compute Expected Value of Information
compute_CEAC

Compute Cost-Effectiveness Acceptability Curve
openPDF

Automatically open pdf output using default pdf viewer
fit.inla

Fit INLA
compute_ceaf

Compute Cost-Effectiveness Acceptability Frontier
mixedAn<-

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

Compute Ustar Statistic
eib_plot_graph

Expected Incremental Benefit Plot By Graph Device
geom_cri

Credible interval ggplot geom
ib.plot.bcea

Incremental Benefit (IB) Distribution Plot
compute_U

Compute U Statistic
mce.plot

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

EIB Parameters CrI
geom_quad_txt

Geom Quadrant Text
plot.CEriskav

Plots EIB and EVPI for the Risk Aversion Case
compute_eib_cri

Calculate Credible Intervals
make.mesh

Make Mesh
diag.evppi

Diagnostic Plots For The Results Of The EVPPI
evi.plot.mixedAn

EVI Plot of the Health Economic Analysis For Mixed Analysis
compute_kstar

Compute k^*
createInputs.default

Create Inputs for EVPI Calculation
evi_plot_graph

Expected Value of Information Plot By Graph Device
setComparisons

Set Comparisons Group
make.proj

INLA Fitting
line_labels

Create Labels for Plot
make_legend_plotly

Legend Positioning
make.report

Make Report
plot.mesh

Mesh Plot
prep_ceplane_params

Prepare CE-plane Parameters
plot.bcea

Summary Plot of the Health Economic Analysis
loo_rank

Leave-one-out ranking
plot.evppi

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

Prepare EIB plot parameters
compute_Ubar

Compute NB for mixture of interventions
plot_eib_cri

Plot Credible Intervals
contour2.bcea

Specialised CE-plane Contour Plot
contour_ggplot_params

Contour ggplot Parameters
evppi_plot_graph

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

Expected Value of Perfect Partial Information (EVPPI) for Selected Parameters
summary.bcea

Summary Method for Objects of Class bcea
setComparisons_assign

Set Comparison Group
summary.mixedAn

Summary Methods For Objects in the Class mixedAn (Mixed Analysis)
prepare.output

Prepare output
validate_eib_params

Validate EIB parameters
prep_frontier_data

Prepare frontier data
info.rank.bcea

Information-Rank Plot for bcea Class
ib_plot_base

IB plot base R version
print.bcea

bcea Print Method
quadrant_params

Quadrant Parameters requires just a single comparison group
setKmax_assign

Set Maximum Willingness to Pay
setReferenceGroup_assign

Set Reference Group
multiplot

Plot Multiple bcea Graphs
estimate.hyperparams

Estimate hyperparameters
multi.ce

Cost-effectiveness Analysis With Multiple Comparison
sim_table

Table of Simulation Statistics for the Health Economic Model
evi.plot.bcea

Expected Value of Information (EVI) Plot
tabulate_means

Calculate Dataset For ICERs From bcea Object
summary.pairwise

Summary Method for Objects of Class pairwise
struct.psa

Structural Probability Sensitivity Analysis
info_rank_graph

Info Rank Plot By Graph Device
inforank_params

Prepare Info Rank plot parameters
quiet

Allow disabling of the cat messages
prep.x

Prepare Delta arrays
num_lines

Get number of lines
new_bcea

Constructor for bcea
post.density

Gaussian Process Fitting
select_plot_type

Choose Graphical Engine
theme_bcea

bcea theme ggplot2
validate_bcea

Validate bcea