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bnma (Bayesian network meta analysis)

This Package is quite similar and has been inspired by the popular Bayesian NMA package gemtc. Some additional features of bnma include:

  • bnma allows binomial, normal, and multinomial outcomes.
  • bnma adds modelling baseline risk
  • bnma automatically checks for convergence using gelman-rubin diagnostics before sampling full iteration amount
  • bnma generates reasonable and dispersed initial values if left unspecified
  • bnma adds an option to report relative risk, risk difference, and number needed to treat using external placebo event rate when the outcome is binomial
  • bnma adds new summary plots: rank plots, forest plot, etc

Please see the vignette for detailed examples of using this package.

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Version

Install

install.packages('bnma')

Monthly Downloads

402

Version

1.6.0

License

GPL-3

Maintainer

Michael Seo

Last Published

February 11th, 2024

Functions in bnma (1.6.0)

network.cumrank.tx.plot

Create a treatment cumulative rank plot
network.forest.plot

Draws forest plot
network.autocorr.diag

Generate autocorrelation diagnostics using coda package
network.autocorr.plot

Generate autocorrelation plot using coda package
network.gelman.diag

Use coda package to find Gelman-Rubin diagnostics
draw.network.graph

Draws network graph using igraph package
network.data

Make a network object containing data, priors, and a JAGS model file
network.covariate.plot

Make a covariate plot
network.gelman.plot

Use coda package to plot Gelman-Rubin diagnostic plot
network.inconsistency.plot

Plotting comparison of posterior mean deviance in the consistency model and inconsistency model
nodesplit.network.run

Run the model using the nodesplit network object
nodesplit.network.data

Make a network object containing data, priors, and a JAGS model file
network.leverage.plot

Make a leverage plot
parkinsons

Dopamine agonists as adjunct therapy in Parkinson's disease
rank.tx

Create a treatment rank table
plot.ume.network.result

Plot traceplot and posterior density of the result using contrast data
parkinsons_contrast

Dopamine agonists as adjunct therapy in Parkinson's disease
network.rank.tx.plot

Create a treatment rank plot
network.run

Run the model using the network object
thrombolytic

Thrombolytic drugs and percutaneous transluminal coronary angioplasty
statins

Trials of statins for cholesterol lowering vs. placebo or usual care
smoking

Smoking cessation counseling programs
summary.contrast.network.result

Summarize result run by contrast.network.run
variance.tx.effects

Calculate correlation matrix for multinomial heterogeneity parameter.
plot.network.result

Plot traceplot and posterior density of the result
relative.effects.table

Make a summary table for relative effects
summary.ume.network.result

Summarize result run by ume.network.run
relative.effects

Find relative effects for base treatment and comparison treatments
plot.contrast.network.result

Plot traceplot and posterior density of the result using contrast data
sucra

Calculate SUCRA
summary.nodesplit.network.result

Summarize result run by nodesplit.network.run
summary.network.result

Summarize result run by network.run
ume.network.data

Make a network object for the unrelated mean effects model (inconsistency model) containing data, priors, and a JAGS model file
ume.network.run

Run the model using the network object
cardiovascular

Trials of low dose and high dose statins for cardiovascular disease vs. placebo
bnma-package

bnma: A package for network meta analysis using Bayesian methods
calculate.contrast.deviance

Find deviance statistics such as DIC and pD.
contrast.network.deviance.plot

Make a contrast network deviance plot
contrast.network.data

Make a network object for contrast-level data containing data, priors, and a JAGS model file
calculate.deviance

Find deviance statistics such as DIC and pD.
contrast.network.run

Run the model using the network object
contrast.network.leverage.plot

Make a leverage plot
network.deviance.plot

Make a deviance plot
certolizumab

Trials of certolizumab pegol (CZP) for the treatment of rheumatoid arthritis in patients
blocker

Beta blockers to prevent mortality after myocardial infarction