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multinma: Network Meta-Analysis of individual and aggregate data in Stan

The multinma package implements network meta-analysis, network meta-regression, and multilevel network meta-regression models which combine evidence from a network of studies and treatments using either aggregate data or individual patient data from each study (Phillippo et al. 2020; Phillippo 2019). Models are estimated in a Bayesian framework using Stan (Carpenter et al. 2017).

Installation

You can install the released version of multinma from CRAN with:

install.packages("multinma")

The development version can be installed from R-universe with:

install.packages("multinma", repos = c("https://dmphillippo.r-universe.dev", getOption("repos")))

or from source on GitHub with:

# install.packages("devtools")
devtools::install_github("dmphillippo/multinma")

Installing from source requires that the rstan package is installed and configured. See the installation guide here.

Getting started

A good place to start is with the package vignettes which walk through example analyses, see vignette("vignette_overview") for an overview. The series of NICE Technical Support Documents on evidence synthesis gives a detailed introduction to network meta-analysis:

Dias, S. et al. (2011). “NICE DSU Technical Support Documents 1-7: Evidence Synthesis for Decision Making.” National Institute for Health and Care Excellence. Available from https://www.sheffield.ac.uk/nice-dsu/tsds.

Multilevel network meta-regression is set out in the following methods papers:

Phillippo, D. M. et al. (2020). “Multilevel Network Meta-Regression for population-adjusted treatment comparisons.” Journal of the Royal Statistical Society: Series A (Statistics in Society), 183(3):1189-1210. doi: 10.1111/rssa.12579.

Phillippo, D. M. et al. (2024). “Multilevel network meta-regression for general likelihoods: synthesis of individual and aggregate data with applications to survival analysis”. arXiv:2401.12640.

Citing multinma

The multinma package can be cited as follows:

Phillippo, D. M. (2024). multinma: Bayesian Network Meta-Analysis of Individual and Aggregate Data. R package version 0.6.1, doi: 10.5281/zenodo.3904454.

When fitting ML-NMR models, please cite the methods paper:

Phillippo, D. M. et al. (2020). “Multilevel Network Meta-Regression for population-adjusted treatment comparisons.” Journal of the Royal Statistical Society: Series A (Statistics in Society), 183(3):1189-1210. doi: 10.1111/rssa.12579.

For ML-NMR models with time-to-event outcomes, please cite:

Phillippo, D. M. et al. (2024). “Multilevel network meta-regression for general likelihoods: synthesis of individual and aggregate data with applications to survival analysis”. arXiv:2401.12640.

References

Carpenter, B., A. Gelman, M. D. Hoffman, D. Lee, B. Goodrich, M. Betancourt, M. Brubaker, J. Guo, P. Li, and A. Riddell. 2017. “Stan: A Probabilistic Programming Language.” Journal of Statistical Software 76 (1). https://doi.org/10.18637/jss.v076.i01.

Phillippo, D. M. 2019. “Calibration of Treatment Effects in Network Meta-Analysis Using Individual Patient Data.” PhD thesis, University of Bristol.

Phillippo, D. M., S. Dias, A. E. Ades, M. Belger, A. Brnabic, A. Schacht, D. Saure, Z. Kadziola, and N. J. Welton. 2020. “Multilevel Network Meta-Regression for Population-Adjusted Treatment Comparisons.” Journal of the Royal Statistical Society: Series A (Statistics in Society) 183 (3): 1189–1210. https://doi.org/10.1111/rssa.12579.

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Version

Install

install.packages('multinma')

Monthly Downloads

919

Version

0.6.1

License

GPL-3

Issues

17

Pull Requests

4

Stars

35

Forks

23

Maintainer

David Phillippo

Last Published

March 6th, 2024

Functions in multinma (0.6.1)

example_smk_fe

Example smoking FE NMA
example_smk_nodesplit

Example smoking node-splitting
qbern

The Bernoulli Distribution
qlogitnorm

The logit Normal distribution
qgamma

The Gamma distribution
adapt_delta

Target average acceptance probability
blocker

Beta blockers to prevent mortality after MI
example_smk_ume

Example smoking UME NMA
loo.stan_nma

Model comparison using the loo package
combine_network

Combine multiple data sources into one network
plot.nma_data

Network plots
plot.nma_dic

Plots of model fit diagnostics
as.igraph.nma_data

Convert networks to graph objects
as.array.stan_nma

Convert samples into arrays, matrices, or data frames
hta_psoriasis

HTA Plaque Psoriasis
as.stanfit

as.stanfit
add_integration

Add numerical integration points to aggregate data
geom_km

Kaplan-Meier curves of survival data
dic

Deviance Information Criterion (DIC)
dmspline

Distribution functions for M-spline baseline hazards
dietary_fat

Reduced dietary fat to prevent mortality
get_nodesplits

Direct and indirect evidence
multi

Multinomial outcome data
print.nma_data

Print nma_data objects
nma_dic-class

The nma_dic class
print.nma_dic

Print DIC details
nma

Network meta-analysis models
nma_nodesplit-class

The nma_nodesplit class
print.nodesplit_summary

Methods for nodesplit_summary objects
.default

Set default values
nma_data-class

The nma_data class
example_ndmm

Example newly-diagnosed multiple myeloma
priors

Prior distributions
print.nma_summary

Methods for nma_summary objects
RE_cor

Random effects structure
theme_multinma

Plot theme for multinma plots
nodesplit_summary-class

The nodesplit_summary class
example_pso_mlnmr

Example plaque psoriasis ML-NMR
diabetes

Incidence of diabetes in trials of antihypertensive drugs
pairs.stan_nma

Matrix of plots for a stan_nma object
thrombolytics

Thrombolytic treatments data
print.nma_nodesplit_df

Print nma_nodesplit_df objects
transfusion

Granulocyte transfusion in patients with neutropenia or neutrophil dysfunction
print.stan_nma

Print stan_nma objects
atrial_fibrillation

Stroke prevention in atrial fibrillation patients
posterior_ranks

Treatment rankings and rank probabilities
is_network_connected

Check network connectedness
predict.stan_nma

Predictions of absolute effects from NMA models
bcg_vaccine

BCG vaccination
set_agd_arm

Set up arm-based aggregate data
set_agd_contrast

Set up contrast-based aggregate data
distr

Specify a general marginal distribution
dlogt

Log Student's t distribution
multinma-package

multinma: A Package for Network Meta-Analysis of Individual and Aggregate Data in Stan
ndmm_ipd

Newly diagnosed multiple myeloma
smoking

Smoking cessation data
nma_prior-class

The nma_prior class
stan_nma-class

The stan_nma class
dgent

Generalised Student's t distribution (with location and scale)
make_knots

Knot locations for M-spline baseline hazard models
statins

Statins for cholesterol lowering
summary.nma_nodesplit_df

Summarise the results of node-splitting models
mcmc_array-class

Working with 3D MCMC arrays
parkinsons

Mean off-time reduction in Parkison's disease
plaque_psoriasis_ipd

Plaque psoriasis data
plot.nma_summary

Plots of summary results
plot.nodesplit_summary

Plots of node-splitting models
reexports

Objects exported from other packages
nma_summary-class

The nma_summary class
relative_effects

Relative treatment effects
plot_integration_error

Plot numerical integration error
plot_prior_posterior

Plot prior vs posterior distribution
summary.nma_prior

Summary of prior distributions
set_agd_surv

Set up aggregate survival data
summary.stan_nma

Posterior summaries from stan_nma objects
set_ipd

Set up individual patient data
example_smk_re

Example smoking RE NMA