Package: multinma 0.7.2.9009

multinma: Bayesian Network Meta-Analysis of Individual and Aggregate Data

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) <doi:10.1111/rssa.12579>. Models are estimated in a Bayesian framework using 'Stan'.

Authors:David M. Phillippo [aut, cre], Samuel J. Perren [ctb]

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multinma/json (API)
NEWS

# Install 'multinma' in R:

install.packages('multinma', repos = c('https://dmphillippo.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dmphillippo/multinma/issues

Pkgdown site:https://dmphillippo.github.io

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

atrial_fibrillation - Stroke prevention in atrial fibrillation patients
bcg_vaccine - BCG vaccination
blocker - Beta blockers to prevent mortality after MI
diabetes - Incidence of diabetes in trials of antihypertensive drugs
dietary_fat - Reduced dietary fat to prevent mortality
hta_psoriasis - HTA Plaque Psoriasis
ndmm_agd - Newly diagnosed multiple myeloma
ndmm_agd_covs - Newly diagnosed multiple myeloma
ndmm_ipd - Newly diagnosed multiple myeloma
parkinsons - Mean off-time reduction in Parkison's disease
plaque_psoriasis_agd - Plaque psoriasis data
plaque_psoriasis_ipd - Plaque psoriasis data
smoking - Smoking cessation data
social_anxiety - Social Anxiety
statins - Statins for cholesterol lowering
thrombolytics - Thrombolytic treatments data
transfusion - Granulocyte transfusion in patients with neutropenia or neutrophil dysfunction

On CRAN:

statistics cpp

9.34 score 35 stars 163 scripts 514 downloads 1 mentions 64 exports 96 dependencies

Last updated 1 days agofrom:a4db8e4dc1. Checks:5 OK, 7 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 24 2025
R-4.5-win-x86_64	OK	Mar 24 2025
R-4.5-mac-x86_64	OK	Mar 24 2025
R-4.5-mac-aarch64	OK	Mar 24 2025
R-4.5-linux-x86_64	OK	Mar 24 2025
R-4.4-win-x86_64	NOTE	Mar 24 2025
R-4.4-mac-x86_64	NOTE	Mar 24 2025
R-4.4-mac-aarch64	NOTE	Mar 24 2025
R-4.4-linux-x86_64	NOTE	Mar 24 2025
R-4.3-win-x86_64	NOTE	Mar 24 2025
R-4.3-mac-x86_64	NOTE	Mar 24 2025
R-4.3-mac-aarch64	NOTE	Mar 24 2025

Exports:.default .is_default add_integration as.stanfit as.tibble.nodesplit_summary cauchy combine_network dbern dgamma dgent dic distr dlogitnorm dlogt dmspline exponential flat geom_km get_nodesplits half_cauchy half_normal half_student_t has_direct has_indirect hmspline Hmspline inv_softmax is_network_connected log_normal log_student_t make_knots marginal_effects multi nma normal pbern pgamma pgent plogitnorm plogt plot_integration_error plot_prior_posterior pmspline posterior_rank_probs posterior_ranks qbern qgamma qgent qlogitnorm qlogt qmspline RE_cor relative_effects rmst_mspline set_agd_arm set_agd_contrast set_agd_surv set_ipd softmax student_t Surv theme_multinma unnest_integration which_RE

Dependencies:abind ADGofTest backports bayesplot BH cachem callr checkmate cli colorspace copula cpp11 desc distributional dplyr evd fansi farver fastmap forcats generics ggdist ggforce ggplot2 ggraph ggrepel ggridges glue graphlayouts gridExtra gsl gtable igraph inline isoband jsonlite labeling lattice lifecycle loo magrittr MASS Matrix matrixStats memoise mgcv munsell mvtnorm nlme numDeriv pcaPP pillar pkgbuild pkgconfig plyr polyclip posterior processx ps pspline purrr quadprog QuickJSR R6 randtoolbox rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel Rdpack reshape2 rlang rngWELL rstan rstantools scales stabledist StanHeaders stringi stringr survival systemfonts tensorA tibble tidygraph tidyr tidyselect truncdist tweenr utf8 vctrs viridis viridisLite withr

Overview of Examples

Rendered fromvignette_overview.Rmdusingknitr::rmarkdownon Mar 24 2025.

Last update: 2025-03-21
Started: 2020-11-20

Example: Atrial fibrillation

Rendered fromexample_atrial_fibrillation.html.asisusingR.rsp::asison Mar 24 2025.

Last update: 2020-11-26
Started: 2020-06-18

Example: BCG vaccine for tuberculosis

Rendered fromexample_bcg_vaccine.html.asisusingR.rsp::asison Mar 24 2025.

Last update: 2020-11-26
Started: 2020-06-18

Example: Beta blockers

Rendered fromexample_blocker.html.asisusingR.rsp::asison Mar 24 2025.

Last update: 2020-11-26
Started: 2020-06-18

Example: Diabetes

Rendered fromexample_diabetes.html.asisusingR.rsp::asison Mar 24 2025.

Last update: 2020-06-18
Started: 2020-06-18

Example: Dietary fat

Rendered fromexample_dietary_fat.html.asisusingR.rsp::asison Mar 24 2025.

Last update: 2020-11-26
Started: 2020-06-18

Example: Newly diagnosed multiple myeloma

Rendered fromexample_ndmm.html.asisusingR.rsp::asison Mar 24 2025.

Last update: 2023-08-30
Started: 2023-08-30

Example: Parkinson's disease

Rendered fromexample_parkinsons.html.asisusingR.rsp::asison Mar 24 2025.

Last update: 2020-11-26
Started: 2020-06-18

Example: Plaque psoriasis HTA report

Rendered fromexample_hta_psoriasis.html.asisusingR.rsp::asison Mar 24 2025.

Last update: 2020-11-26
Started: 2020-09-11

Example: Plaque psoriasis ML-NMR

Rendered fromexample_plaque_psoriasis.html.asisusingR.rsp::asison Mar 24 2025.

Last update: 2020-11-26
Started: 2020-06-18

Example: Smoking cessation

Rendered fromexample_smoking.html.asisusingR.rsp::asison Mar 24 2025.

Last update: 2020-11-26
Started: 2020-06-18

Example: Social Anxiety

Rendered fromexample_social_anxiety.html.asisusingR.rsp::asison Mar 24 2025.

Last update: 2025-03-21
Started: 2025-03-21

Example: Statins for cholesterol lowering

Rendered fromexample_statins.html.asisusingR.rsp::asison Mar 24 2025.

Last update: 2020-06-18
Started: 2020-06-18

Example: Thrombolytic treatments

Rendered fromexample_thrombolytics.html.asisusingR.rsp::asison Mar 24 2025.

Last update: 2020-11-26
Started: 2020-06-18

Example: White blood cell transfusion

Rendered fromexample_transfusion.html.asisusingR.rsp::asison Mar 24 2025.

Last update: 2020-11-26
Started: 2020-06-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
multinma: A Package for Network Meta-Analysis of Individual and Aggregate Data in Stan	multinma-package multinma
Set default values	.default .is_default
Target average acceptance probability	adapt_delta
Add numerical integration points to aggregate data	add_integration add_integration.data.frame add_integration.default add_integration.nma_data unnest_integration
Convert samples into arrays, matrices, or data frames	as.array.stan_nma as.data.frame.stan_nma as.matrix.stan_nma as.tibble.stan_nma as_tibble.stan_nma
Convert networks to graph objects	as.igraph.nma_data as_tbl_graph.nma_data
as.stanfit	as.stanfit as.stanfit.default as.stanfit.stan_nma
Stroke prevention in atrial fibrillation patients	atrial_fibrillation
BCG vaccination	bcg_vaccine
Beta blockers to prevent mortality after MI	blocker
Combine multiple data sources into one network	combine_network
Generalised Student's t distribution (with location and scale)	dgent pgent qgent
Incidence of diabetes in trials of antihypertensive drugs	diabetes
Deviance Information Criterion (DIC)	dic
Reduced dietary fat to prevent mortality	dietary_fat
Specify a general marginal distribution	distr
The logit Normal distribution	dlogitnorm plogitnorm qlogitnorm
Log Student's t distribution	dlogt plogt qlogt
Distribution functions for M-spline baseline hazards	dmspline Hmspline hmspline pmspline qmspline rmst_mspline
Example newly-diagnosed multiple myeloma	example_ndmm
Example plaque psoriasis ML-NMR	example_pso_mlnmr
Example smoking FE NMA	example_smk_fe
Example smoking node-splitting	example_smk_nodesplit
Example smoking RE NMA	example_smk_re
Example smoking UME NMA	example_smk_ume
Kaplan-Meier curves of survival data	geom_km
Direct and indirect evidence	get_nodesplits has_direct has_indirect
HTA Plaque Psoriasis	hta_psoriasis
Check network connectedness	is_network_connected
Model comparison using the 'loo' package	loo loo.stan_nma waic waic.stan_nma
Knot locations for M-spline baseline hazard models	make_knots
Marginal treatment effects	marginal_effects
Working with 3D MCMC arrays	mcmc_array mcmc_array-class names.mcmc_array names<-.mcmc_array plot.mcmc_array print.mcmc_array summary.mcmc_array
Multinomial outcome data	multi
Newly diagnosed multiple myeloma	ndmm_agd ndmm_agd_covs ndmm_ipd
Network meta-analysis models	nma
The nma_data class	mlnmr_data mlnmr_data-class nma_data nma_data-class
The nma_dic class	nma_dic nma_dic-class
The nma_nodesplit class	nma_nodesplit nma_nodesplit-class nma_nodesplit_df nma_nodesplit_df-class
The nma_prior class	nma_prior nma_prior-class
The 'nma_summary' class	nma_rank_probs nma_summary nma_summary-class
The 'nodesplit_summary' class	nodesplit_summary nodesplit_summary-class
Matrix of plots for a 'stan_nma' object	pairs.stan_nma
Mean off-time reduction in Parkison's disease	parkinsons
Plaque psoriasis data	plaque_psoriasis plaque_psoriasis_agd plaque_psoriasis_ipd
Plot numerical integration error	plot_integration_error
Plot prior vs posterior distribution	plot_prior_posterior
Network plots	plot.nma_data
Plots of model fit diagnostics	plot.nma_dic
Plots of summary results	plot.nma_parameter_summary plot.nma_rank_probs plot.nma_summary plot.surv_nma_summary
Plots of node-splitting models	plot.nodesplit_summary
Treatment rankings and rank probabilities	posterior_ranks posterior_rank_probs
Predictions of absolute effects from NMA models	predict.stan_nma predict.stan_nma_surv
Print 'nma_data' objects	print.mlnmr_data print.nma_data
Methods for 'nma_dic' objects	as.array.nma_dic as.data.frame.nma_dic as.matrix.nma_dic as.tibble.nma_dic as_tibble.nma_dic print.nma_dic
Print 'nma_nodesplit_df' objects	print.nma_nodesplit print.nma_nodesplit_df
Methods for 'nma_summary' objects	as.array.nma_rank_probs as.array.nma_summary as.data.frame.nma_summary as.matrix.nma_rank_probs as.matrix.nma_summary as.tibble.nma_summary as_tibble.nma_summary print.nma_summary
Methods for 'nodesplit_summary' objects	as.data.frame.nodesplit_summary as.tibble.nodesplit_summary as_tibble.nodesplit_summary print.nodesplit_summary
Print 'stan_nma' objects	print.stan_nma
Prior distributions	cauchy exponential flat half_cauchy half_normal half_student_t log_normal log_student_t normal priors student_t
The Bernoulli Distribution	dbern pbern qbern
The Gamma distribution	dgamma pgamma qgamma
Random effects structure	RE_cor which_RE
Relative treatment effects	relative_effects
Set up arm-based aggregate data	set_agd_arm
Set up contrast-based aggregate data	set_agd_contrast
Set up aggregate survival data	set_agd_surv
Set up individual patient data	set_ipd
Smoking cessation data	smoking
Social Anxiety	social_anxiety
Softmax transform	inv_softmax softmax
The stan_nma class	stan_mlnmr stan_nma stan_nma-class
Statins for cholesterol lowering	statins
Summarise the results of node-splitting models	plot.nma_nodesplit plot.nma_nodesplit_df summary.nma_nodesplit summary.nma_nodesplit_df
Summary of prior distributions	summary.nma_prior
Posterior summaries from 'stan_nma' objects	plot.stan_nma summary.stan_nma
Plot theme for multinma plots	theme_multinma
Thrombolytic treatments data	thrombolytics
Granulocyte transfusion in patients with neutropenia or neutrophil dysfunction	transfusion

Package: multinma 0.7.2.9009

multinma: Bayesian Network Meta-Analysis of Individual and Aggregate Data

Overview of Examples

Example: Atrial fibrillation

Example: BCG vaccine for tuberculosis

Example: Beta blockers

Example: Diabetes

Example: Dietary fat

Example: Newly diagnosed multiple myeloma

Example: Parkinson's disease

Example: Plaque psoriasis HTA report

Example: Plaque psoriasis ML-NMR

Example: Smoking cessation

Example: Social Anxiety

Example: Statins for cholesterol lowering

Example: Thrombolytic treatments

Example: White blood cell transfusion

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)