multinma

Network meta-analysis of individual and aggregate data in Stan

https://github.com/dmphillippo/multinma

Science Score: 77.0%

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Keywords

r r-package r-stats statistics

Keywords from Contributors

rspatial meshes flux office tide surrogate transformation interpretability standardization hack

Last synced: 6 months ago · JSON representation ·

Repository

Network meta-analysis of individual and aggregate data in Stan

Basic Info

Host: GitHub
Owner: dmphillippo
Language: HTML
Default Branch: develop
Homepage: https://dmphillippo.github.io/multinma
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Stars: 39
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Topics

r r-package r-stats statistics

Created over 6 years ago · Last pushed 9 months ago

Metadata Files

Readme Changelog Citation

README.Rmd

---
output: github_document
bibliography: inst/REFERENCES.bib
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```
# multinma: Network Meta-Analysis of individual and aggregate data in Stan 


[![CRAN status](https://www.r-pkg.org/badges/version/multinma)](https://CRAN.R-project.org/package=multinma)
[![R-universe](https://dmphillippo.r-universe.dev/badges/multinma)](https://dmphillippo.r-universe.dev)
[![R-CMD-check](https://github.com/dmphillippo/multinma/workflows/R-CMD-check/badge.svg)](https://github.com/dmphillippo/multinma/actions)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3904454.svg)](https://doi.org/10.5281/zenodo.3904454)


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 [@methods_paper;@Phillippo_thesis].
Models are estimated in a Bayesian framework using Stan [@Carpenter2017].

## Installation

You can install the released version of `multinma` from [CRAN](https://CRAN.R-project.org/package=multinma) with:

``` r
install.packages("multinma")
```

The development version can be installed from [R-universe](https://dmphillippo.r-universe.dev) with:

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

or from source on [GitHub](https://github.com/dmphillippo/multinma) with:

``` r
# 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](https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started).

## 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](https://doi.org/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](https://arxiv.org/abs/2401.12640).

## Citing multinma
The `multinma` package can be cited as follows:

> Phillippo, D. M. (`r format(Sys.Date(), "%Y")`). _multinma: Bayesian Network Meta-Analysis of Individual and Aggregate Data_. R package version `r getNamespaceVersion("multinma")`, doi: [10.5281/zenodo.3904454](https://doi.org/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](https://doi.org/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](https://arxiv.org/abs/2401.12640).

## References

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
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license: GPL-3.0-only
title: 'multinma: Bayesian Network Meta-Analysis of Individual and Aggregate Data'
version: 0.8.1.9000
doi: 10.5281/zenodo.3904454
identifiers:
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  value: 10.32614/CRAN.package.multinma
abstract: Network meta-analysis and network meta-regression models for aggregate data,
  individual patient data, and mixtures of both individual and aggregate data using
  multilevel network meta-regression as described by Phillippo et al. (2020) <https://doi.org/10.1111/rssa.12579>.
  Models are estimated in a Bayesian framework using 'Stan'.
authors:
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  abstract: 'ggdist: Visualizations of Distributions and Uncertainty'
  notes: Imports
  url: https://mjskay.github.io/ggdist/
  repository: https://CRAN.R-project.org/package=ggdist
  authors:
  - family-names: Kay
    given-names: Matthew
    email: mjskay@northwestern.edu
  year: '2025'
  doi: 10.32614/CRAN.package.ggdist
  version: '>= 2.1.1'
- type: software
  title: truncdist
  abstract: 'truncdist: Truncated Random Variables'
  notes: Imports
  repository: https://CRAN.R-project.org/package=truncdist
  authors:
  - family-names: Novomestky
    given-names: Frederick
    email: fn334@nyu.edu
  - family-names: Nadarajah
    given-names: Saralees
    email: saralees.nadarajah@manchester.ac.uk
  year: '2025'
  doi: 10.32614/CRAN.package.truncdist
- type: software
  title: bayesplot
  abstract: 'bayesplot: Plotting for Bayesian Models'
  notes: Imports
  url: https://mc-stan.org/bayesplot/
  repository: https://CRAN.R-project.org/package=bayesplot
  authors:
  - family-names: Gabry
    given-names: Jonah
    email: jsg2201@columbia.edu
  - family-names: Mahr
    given-names: Tristan
  year: '2025'
  doi: 10.32614/CRAN.package.bayesplot
- type: software
  title: BH
  abstract: 'BH: Boost C++ Header Files'
  notes: LinkingTo
  url: https://dirk.eddelbuettel.com/code/bh.html
  repository: https://CRAN.R-project.org/package=BH
  authors:
  - family-names: Eddelbuettel
    given-names: Dirk
    email: edd@debian.org
    orcid: https://orcid.org/0000-0001-6419-907X
  - family-names: Emerson
    given-names: John W.
  - family-names: Kane
    given-names: Michael J.
    orcid: https://orcid.org/0000-0003-1899-6662
  year: '2025'
  doi: 10.32614/CRAN.package.BH
  version: '>= 1.66.0'
- type: software
  title: RcppEigen
  abstract: 'RcppEigen: ''Rcpp'' Integration for the ''Eigen'' Templated Linear Algebra
    Library'
  notes: LinkingTo
  url: https://dirk.eddelbuettel.com/code/rcpp.eigen.html
  repository: https://CRAN.R-project.org/package=RcppEigen
  authors:
  - family-names: Bates
    given-names: Doug
    orcid: https://orcid.org/0000-0001-8316-9503
  - family-names: Eddelbuettel
    given-names: Dirk
    email: edd@debian.org
    orcid: https://orcid.org/0000-0001-6419-907X
  - family-names: Francois
    given-names: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
  - family-names: Qiu
    given-names: Yixuan
    orcid: https://orcid.org/0000-0003-0109-6692
  year: '2025'
  doi: 10.32614/CRAN.package.RcppEigen
  version: '>= 0.3.3.3.0'
- type: software
  title: StanHeaders
  abstract: 'StanHeaders: C++ Header Files for Stan'
  notes: LinkingTo
  url: https://mc-stan.org/
  repository: https://CRAN.R-project.org/package=StanHeaders
  authors:
  - family-names: Goodrich
    given-names: Ben
    email: benjamin.goodrich@columbia.edu
  - family-names: Gelman
    given-names: Andrew
  - family-names: Carpenter
    given-names: Bob
  - family-names: Hoffman
    given-names: Matt
  - family-names: Lee
    given-names: Daniel
  - family-names: Betancourt
    given-names: Michael
  - family-names: Brubaker
    given-names: Marcus
  - family-names: Guo
    given-names: Jiqiang
  - family-names: Li
    given-names: Peter
  - family-names: Riddell
    given-names: Allen
  - family-names: Inacio
    given-names: Marco
  - family-names: Morris
    given-names: Mitzi
  - family-names: Arnold
    given-names: Jeffrey
  - family-names: Goedman
    given-names: Rob
  - family-names: Lau
    given-names: Brian
  - family-names: Trangucci
    given-names: Rob
  - family-names: Gabry
    given-names: Jonah
  - family-names: Kucukelbir
    given-names: Alp
  - family-names: Grant
    given-names: Robert
  - family-names: Tran
    given-names: Dustin
  - family-names: Malecki
    given-names: Michael
  - family-names: Gao
    given-names: Yuanjun
  - family-names: Badr
    given-names: Hamada S.
    email: badr@jhu.edu
    orcid: https://orcid.org/0000-0002-9808-2344
  year: '2025'
  doi: 10.32614/CRAN.package.StanHeaders
  version: '>= 2.32.9'
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  url: https://testthat.r-lib.org
  repository: https://CRAN.R-project.org/package=testthat
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.testthat
  version: '>= 2.1.0'
- type: software
  title: vdiffr
  abstract: 'vdiffr: Visual Regression Testing and Graphical Diffing'
  notes: Suggests
  url: https://vdiffr.r-lib.org/
  repository: https://CRAN.R-project.org/package=vdiffr
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Luciani
    given-names: T Jake
    email: jake@apache.org
  - family-names: Decorde
    given-names: Matthieu
    email: matthieu.decorde@ens-lyon.fr
  - family-names: Lise
    given-names: Vaudor
    email: lise.vaudor@ens-lyon.fr
  year: '2025'
  doi: 10.32614/CRAN.package.vdiffr
- type: software
  title: withr
  abstract: 'withr: Run Code ''With'' Temporarily Modified Global State'
  notes: Suggests
  url: https://withr.r-lib.org
  repository: https://CRAN.R-project.org/package=withr
  authors:
  - family-names: Hester
    given-names: Jim
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Müller
    given-names: Kirill
    email: krlmlr+r@mailbox.org
  - family-names: Ushey
    given-names: Kevin
    email: kevinushey@gmail.com
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Chang
    given-names: Winston
  year: '2025'
  doi: 10.32614/CRAN.package.withr
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
  repository: https://CRAN.R-project.org/package=knitr
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2025'
  doi: 10.32614/CRAN.package.knitr
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
  url: https://pkgs.rstudio.com/rmarkdown/
  repository: https://CRAN.R-project.org/package=rmarkdown
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: Dervieux
    given-names: Christophe
    email: cderv@posit.co
    orcid: https://orcid.org/0000-0003-4474-2498
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@posit.co
  - family-names: Luraschi
    given-names: Javier
  - family-names: Ushey
    given-names: Kevin
    email: kevin@posit.co
  - family-names: Atkins
    given-names: Aron
    email: aron@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Cheng
    given-names: Joe
    email: joe@posit.co
  - family-names: Chang
    given-names: Winston
    email: winston@posit.co
  - family-names: Iannone
    given-names: Richard
    email: rich@posit.co
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2025'
  doi: 10.32614/CRAN.package.rmarkdown
- type: software
  title: parallel
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Suggests
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
- type: software
  title: R.rsp
  abstract: 'R.rsp: Dynamic Generation of Scientific Reports'
  notes: Suggests
  url: https://henrikbengtsson.github.io/R.rsp/
  repository: https://CRAN.R-project.org/package=R.rsp
  authors:
  - family-names: Bengtsson
    given-names: Henrik
    email: henrikb@braju.com
  year: '2025'
  doi: 10.32614/CRAN.package.R.rsp
- type: software
  title: rprojroot
  abstract: 'rprojroot: Finding Files in Project Subdirectories'
  notes: Suggests
  url: https://rprojroot.r-lib.org/
  repository: https://CRAN.R-project.org/package=rprojroot
  authors:
  - family-names: Müller
    given-names: Kirill
    email: kirill@cynkra.com
    orcid: https://orcid.org/0000-0002-1416-3412
  year: '2025'
  doi: 10.32614/CRAN.package.rprojroot
- type: software
  title: loo
  abstract: 'loo: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models'
  notes: Suggests
  url: https://mc-stan.org/loo/
  repository: https://CRAN.R-project.org/package=loo
  authors:
  - family-names: Vehtari
    given-names: Aki
    email: Aki.Vehtari@aalto.fi
  - family-names: Gabry
    given-names: Jonah
    email: jsg2201@columbia.edu
  - family-names: Magnusson
    given-names: Måns
  - family-names: Yao
    given-names: Yuling
  - family-names: Bürkner
    given-names: Paul-Christian
  - family-names: Paananen
    given-names: Topi
  - family-names: Gelman
    given-names: Andrew
  year: '2025'
  doi: 10.32614/CRAN.package.loo
  version: '>= 2.0.0'
- type: software
  title: crayon
  abstract: 'crayon: Colored Terminal Output'
  notes: Suggests
  url: https://r-lib.github.io/crayon/
  repository: https://CRAN.R-project.org/package=crayon
  authors:
  - family-names: Csárdi
    given-names: Gábor
    email: csardi.gabor@gmail.com
  year: '2025'
  doi: 10.32614/CRAN.package.crayon
- type: software
  title: tidygraph
  abstract: 'tidygraph: A Tidy API for Graph Manipulation'
  notes: Suggests
  url: https://tidygraph.data-imaginist.com
  repository: https://CRAN.R-project.org/package=tidygraph
  authors:
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomasp85@gmail.com
    orcid: https://orcid.org/0000-0002-5147-4711
  year: '2025'
  doi: 10.32614/CRAN.package.tidygraph
- type: software
  title: pkgdown
  abstract: 'pkgdown: Make Static HTML Documentation for a Package'
  notes: Suggests
  url: https://pkgdown.r-lib.org/
  repository: https://CRAN.R-project.org/package=pkgdown
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Hesselberth
    given-names: Jay
    orcid: https://orcid.org/0000-0002-6299-179X
  - family-names: Salmon
    given-names: Maëlle
    orcid: https://orcid.org/0000-0002-2815-0399
  - family-names: Roy
    given-names: Olivier
  - family-names: Brüggemann
    given-names: Salim
    orcid: https://orcid.org/0000-0002-5329-5987
  year: '2025'
  doi: 10.32614/CRAN.package.pkgdown
- type: software
  title: splines2
  abstract: 'splines2: Regression Spline Functions and Classes'
  notes: Suggests
  url: https://wwenjie.org/splines2
  repository: https://CRAN.R-project.org/package=splines2
  authors:
  - family-names: Wang
    given-names: Wenjie
    email: wang@wwenjie.org
    orcid: https://orcid.org/0000-0003-0363-3180
  - family-names: Yan
    given-names: Jun
    orcid: https://orcid.org/0000-0003-4401-7296
  year: '2025'
  doi: 10.32614/CRAN.package.splines2
  version: '>= 0.5.0'
- type: software
  title: flexsurv
  abstract: 'flexsurv: Flexible Parametric Survival and Multi-State Models'
  notes: Suggests
  url: http://chjackson.github.io/flexsurv/
  repository: https://CRAN.R-project.org/package=flexsurv
  authors:
  - family-names: Jackson
    given-names: Christopher
    email: chris.jackson@mrc-bsu.cam.ac.uk
  year: '2025'
  doi: 10.32614/CRAN.package.flexsurv
- type: software
  title: rstpm2
  abstract: 'rstpm2: Smooth Survival Models, Including Generalized Survival Models'
  notes: Suggests
  url: https://github.com/mclements/rstpm2
  repository: https://CRAN.R-project.org/package=rstpm2
  authors:
  - family-names: Clements
    given-names: Mark
    email: mark.clements@ki.se
  - family-names: Liu
    given-names: Xing-Rong
    email: xingrong.liu@ki.se
  - family-names: Christoffersen
    given-names: Benjamin
    email: benjamin.christoffersen@ki.se
  year: '2025'
  doi: 10.32614/CRAN.package.rstpm2

GitHub Events

Total

Create event: 6
Release event: 1
Issues event: 4
Watch event: 5
Issue comment event: 4
Push event: 47
Pull request event: 3
Pull request review comment event: 24
Pull request review event: 6
Fork event: 9

Last Year

Create event: 6
Release event: 1
Issues event: 4
Watch event: 5
Issue comment event: 4
Push event: 47
Pull request event: 3
Pull request review comment event: 24
Pull request review event: 6
Fork event: 9

Committers

Last synced: 12 months ago

All Time

Total Commits: 1,964
Total Committers: 6
Avg Commits per committer: 327.333
Development Distribution Score (DDS): 0.01

Past Year

Commits: 109
Committers: 2
Avg Commits per committer: 54.5
Development Distribution Score (DDS): 0.028

Top Committers

Name	Email	Commits
David Phillippo	d**o@b**k	1,945
Niels Dunnewind	n**s@n**l	8
unknown		5
github-actions[bot]	4****]	3
Andrew Johnson	a**n@a**m	2
David Phillippo	d**9@b**k	1

Committer Domains (Top 20 + Academic)

bristol.ac.uk: 2 arjohnsonau.com: 1 nielsdunnewind.nl: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 37
Total pull requests: 16
Average time to close issues: 5 months
Average time to close pull requests: about 2 months
Total issue authors: 27
Total pull request authors: 4
Average comments per issue: 1.62
Average comments per pull request: 1.5
Merged pull requests: 11
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 8
Pull requests: 4
Average time to close issues: 2 months
Average time to close pull requests: 40 minutes
Issue authors: 7
Pull request authors: 4
Average comments per issue: 0.88
Average comments per pull request: 0.25
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

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Issue Authors

dmphillippo (3)
MilaniC (3)
bct0022 (2)
sunfeng06 (2)
chumbleycode (2)
zhui126 (2)
rogula (2)
bgoodri (1)
ZixiaoChenMcK (1)
ndunnewind (1)
EmmaBenbow (1)
mattknowlesOHG (1)
sjperren (1)
Rednose22 (1)
danjamstat (1)

Pull Request Authors

ndunnewind (14)
sjperren (5)
andrjohns (3)
dkarletsos (1)

Top Labels

Issue Labels

question (2) enhancement (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 993 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 16
Total maintainers: 1

cran.r-project.org: multinma

Bayesian Network Meta-Analysis of Individual and Aggregate Data

Homepage: https://dmphillippo.github.io/multinma/
Documentation: http://cran.r-project.org/web/packages/multinma/multinma.pdf
License: GPL-3
Latest release: 0.8.1
published 9 months ago

Versions: 16
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 993 Last month

Rankings

Forks count: 4.8%

Stargazers count: 11.2%

Average: 18.0%

Downloads: 21.3%

Dependent repos count: 23.8%

Dependent packages count: 28.6%

Maintainers (1)

david.phillippo@bristol.ac.uk

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

R >= 3.4.0 depends
Matrix * imports
Rcpp >= 0.12.0 imports
RcppParallel >= 5.0.1 imports
Rdpack >= 0.7 imports
bayesplot * imports
copula * imports
dplyr >= 0.8.3 imports
forcats * imports
ggdist >= 2.1.1 imports
ggplot2 * imports
ggraph * imports
glue * imports
graphics * imports
igraph * imports
methods * imports
purrr * imports
randtoolbox * imports
rlang * imports
rstan >= 2.19.2 imports
rstantools >= 2.0.0 imports
stats * imports
stringr * imports
tibble >= 2.1.3 imports
tidyr >= 1.0.0 imports
truncdist * imports
R.rsp * suggests
crayon * suggests
knitr * suggests
logitnorm * suggests
loo >= 2.0.0 suggests
parallel * suggests
pkgdown * suggests
rmarkdown * suggests
rprojroot * suggests
testthat >= 2.1.0 suggests
tidygraph * suggests
withr * suggests

.github/workflows/R-CMD-check-HTML5.yaml actions

actions/checkout v2 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/R-CMD-check.yaml actions

actions/checkout v2 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/pkgdown.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

multinma

Science Score: 77.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.Rmd

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

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Past Year

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Committer Domains (Top 20 + Academic)

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cran.r-project.org: multinma

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Maintainers (1)

Dependencies