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BCEA

Contents

Overview

Perform Bayesian Cost-Effectiveness Analysis in R. 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

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")

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

GPL-3 © G Baio.

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

2.4.1

License

GPL-3

Issues

Pull Requests

Stars

Forks

Maintainer

Gianluca Baio

Last Published

October 28th, 2021

Functions in BCEA (2.4.1)

comp_names_from_

Comparison Names From
Smoking

Data set for the Bayesian model for the cost-effectiveness of smoking cessation interventions
ceplane.plot.bcea

Cost-effectiveness Plane Plot
compute.evppi

Compute EVPPI
ceplane_geom_params

Extract Separate Parameter Sets
compute_ceaf

Compute Cost-Effectiveness Acceptability Frontier
bcea

Create Bayesian Cost-Effectiveness Analysis Object
ceplane_ggplot_params

CE-plane ggplot Parameters
compute_EVI

Compute Expected Value of Information
Vaccine

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

Compute NB for mixture of interventions
ceplane_plot_graph

Cost-Effectiveness Plane Plot By Graph Device
compute_Ustar

Compute Ustar Statistic
contour_graph

Contour Cost-Effectiveness Plane
convert_pts_to_mm

Use from Base R to ggplot
ceac.plot.bcea

Cost-Effectiveness Acceptability Curve (CEAC) Plot
compute_ICER

Compute Incremental Cost-Effectiveness Ratio
best_interv_given_k

Optimal intervention
compute_U

Compute U Statistic
contour.bcea

Contour Plots for the Cost-Effectiveness Plane
compute_eib_cri

Calculate Credible Intervals
compute_kstar

Compute k^*
eib.plot.bcea

Expected Incremental Benefit (EIB) Plot
eib_params_base

EIB parameters specific to base R plot
evi.plot.bcea

Expected Value of Information (EVI) Plot
geom_cri

Credible interval ggplot geom
compute_ol

Compute Opportunity Loss
contour2.bcea

Specialised CE-plane Contour Plot
compute_IB

Compute Incremental Benefit
compute_p_best_interv

Compute Probability Best Intervention
ceaf.plot.pairwise

Cost-Effectiveness Acceptability Frontier (CEAF) plot
eib_plot_graph

Expected Incremental Benefit Plot By Graph Device
evi.plot.mixedAn

EVI Plot of the Health Economic Analysis For Mixed Analysis
kstar_vlines

Prepare K-star vertical lines
is.bcea

Check bcea Class
compute_vi

Compute Value of Information
make.report

Make Report
make_legend_plotly

Legend Positioning
evppi_plot_graph

Plot Expected Value of Partial Information With Respect to a Set of Parameters
ceef.plot.bcea

Cost-Effectiveness Efficiency Frontier (CEAF) Plot
fit.gam

Gaussian Additive Model Fitting
ib_plot_base

IB plot base R version
estimate.hyperparams

Estimate hyperparameters
ceef.summary

Summary table for CEEF
BCEA-package

BCEA: A package for Bayesian Cost-Effectiveness Analysis
CEriskav_assign

Cost-effectiveness Analysis Including a Parameter of Risk Aversion
prepare.output

Prepare output
plot.mesh

Mesh Plot
evi_plot_graph

Expected Value of Information Plot By Graph Device
plot.evppi

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

Cost-effectiveness Efficiency Frontier Plot By Graph Device
evppi

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

Information-Rank Plot for bcea Class
compute_EIB

Compute Expected Incremental Benefit
compute_CEAC

Compute Cost-Effectiveness Acceptability Curve
fit.gp

Fit Gaussian Process
multiplot

Plot Multiple bcea Graphs
fit.inla

Fit INLA
createInputs.default

Create Inputs for EVPI Calculation
mixedAn<-

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

bcea Print Method
line_labels

Create Labels for Plot
plot_eib_cri

Plot Credible Intervals
ib.plot.bcea

Incremental Benefit (IB) Distribution Plot
diag.evppi

Diagnostic Plots For The Results Of The EVPPI
info_rank_graph

Info Rank Plot By Graph Device
new_bcea

Constructor for bcea
multi.ce

Cost-effectiveness Analysis With Multiple Comparison
make.mesh

Make Mesh
inforank_params

Prepare Info Rank plot parameters
make.proj

INLA Fitting
plot.CEriskav

Plots EIB and EVPI for the Risk Aversion Case
loo_rank

Leave-one-out ranking
prep.x

Prepare Delta arrays
prep_ceplane_params

Prepare CE-plane Parameters
plot.bcea

Summary Plot of the Health Economic Analysis
num_lines

Get number of lines
setKmax_assign

Set Maximum Willingness to Pay
post.density

Gaussian Process Fitting
setReferenceGroup_assign

Set Reference Group
openPDF

Automatically open pdf output using default pdf viewer
setComparisons_assign

Set Comparison Group
setComparisons

Set Comparisons Group
sim_table

Table of Simulation Statistics for the Health Economic Model
struct.psa

Structural Probability Sensitivity Analysis
prep_frontier_data

Prepare frontier data
prep_eib_params

Prepare EIB plot parameters
summary.bcea

Summary Method for Objects of Class bcea
summary.mixedAn

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

Allow disabling of the cat messages
select_plot_type

Choose Graphical Engine
validate_bcea

Validate bcea
validate_eib_params

Validate EIB parameters
tabulate_means

Calculate Dataset For ICERs From bcea Object
CEriskav_plot_graph

Cost-effectiveness Plot Including a Parameter of Risk Aversion Choice of base R, ggplot2.
ceac_plot_graph

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

CEAC Matrix Plot