Package: multinma 0.7.2.9003

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]

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multinma.pdf |multinma.html✨
multinma/json (API)
NEWS

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

Peer review:

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

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

statistics

9.19 score 35 stars 159 scripts 583 downloads 1 mentions 62 exports 95 dependencies

Last updated 2 months agofrom:be91d2131a. Checks:OK: 2 NOTE: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 23 2024
R-4.5-win-x86_64NOTENov 23 2024
R-4.5-linux-x86_64OKNov 23 2024
R-4.4-win-x86_64NOTENov 23 2024
R-4.4-mac-x86_64NOTENov 23 2024
R-4.4-mac-aarch64NOTENov 23 2024
R-4.3-win-x86_64NOTENov 23 2024
R-4.3-mac-x86_64NOTENov 23 2024
R-4.3-mac-aarch64NOTENov 23 2024

Exports:.default.is_defaultadd_integrationas.stanfitas.tibble.nodesplit_summarycauchycombine_networkdberndgammadgentdicdistrdlogitnormdlogtdmsplineexponentialflatgeom_kmget_nodesplitshalf_cauchyhalf_normalhalf_student_thas_directhas_indirecthmsplineHmsplineis_network_connectedlog_normallog_student_tmake_knotsmarginal_effectsmultinmanormalpbernpgammapgentplogitnormplogtplot_integration_errorplot_prior_posteriorpmsplineposterior_rank_probsposterior_ranksqbernqgammaqgentqlogitnormqlogtqmsplineRE_correlative_effectsrmst_msplineset_agd_armset_agd_contrastset_agd_survset_ipdstudent_tSurvtheme_multinmaunnest_integrationwhich_RE

Dependencies:abindADGofTestbackportsbayesplotBHcachemcallrcheckmateclicolorspacecopulacpp11descdistributionaldplyrevdfansifarverfastmapforcatsgenericsggdistggforceggplot2ggraphggrepelggridgesgluegraphlayoutsgridExtragslgtableigraphinlineisobandlabelinglatticelifecycleloomagrittrMASSMatrixmatrixStatsmemoisemgcvmunsellmvtnormnlmenumDerivpcaPPpillarpkgbuildpkgconfigplyrpolyclipposteriorprocessxpspsplinepurrrquadprogQuickJSRR6randtoolboxrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRdpackreshape2rlangrngWELLrstanrstantoolsscalesstabledistStanHeadersstringistringrsurvivalsystemfontstensorAtibbletidygraphtidyrtidyselecttruncdisttweenrutf8vctrsviridisviridisLitewithr

Overview of Examples

Rendered fromvignette_overview.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2023-08-30
Started: 2020-11-20

Example: Atrial fibrillation

Rendered fromexample_atrial_fibrillation.html.asisusingR.rsp::asison Nov 23 2024.

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

Example: BCG vaccine for tuberculosis

Rendered fromexample_bcg_vaccine.html.asisusingR.rsp::asison Nov 23 2024.

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

Example: Beta blockers

Rendered fromexample_blocker.html.asisusingR.rsp::asison Nov 23 2024.

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

Example: Diabetes

Rendered fromexample_diabetes.html.asisusingR.rsp::asison Nov 23 2024.

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

Example: Dietary fat

Rendered fromexample_dietary_fat.html.asisusingR.rsp::asison Nov 23 2024.

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

Example: Newly diagnosed multiple myeloma

Rendered fromexample_ndmm.html.asisusingR.rsp::asison Nov 23 2024.

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

Example: Parkinson's disease

Rendered fromexample_parkinsons.html.asisusingR.rsp::asison Nov 23 2024.

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

Example: Plaque psoriasis HTA report

Rendered fromexample_hta_psoriasis.html.asisusingR.rsp::asison Nov 23 2024.

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

Example: Plaque psoriasis ML-NMR

Rendered fromexample_plaque_psoriasis.html.asisusingR.rsp::asison Nov 23 2024.

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

Example: Smoking cessation

Rendered fromexample_smoking.html.asisusingR.rsp::asison Nov 23 2024.

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

Example: Statins for cholesterol lowering

Rendered fromexample_statins.html.asisusingR.rsp::asison Nov 23 2024.

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

Example: Thrombolytic treatments

Rendered fromexample_thrombolytics.html.asisusingR.rsp::asison Nov 23 2024.

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

Example: White blood cell transfusion

Rendered fromexample_transfusion.html.asisusingR.rsp::asison Nov 23 2024.

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

Readme and manuals

Help Manual

Help pageTopics
multinma: A Package for Network Meta-Analysis of Individual and Aggregate Data in Stanmultinma-package multinma
Set default values.default .is_default
Target average acceptance probabilityadapt_delta
Add numerical integration points to aggregate dataadd_integration add_integration.data.frame add_integration.default add_integration.nma_data unnest_integration
Convert samples into arrays, matrices, or data framesas.array.stan_nma as.data.frame.stan_nma as.matrix.stan_nma as.tibble.stan_nma as_tibble.stan_nma
Convert networks to graph objectsas.igraph.nma_data as_tbl_graph.nma_data
as.stanfitas.stanfit as.stanfit.default as.stanfit.stan_nma
Stroke prevention in atrial fibrillation patientsatrial_fibrillation
BCG vaccinationbcg_vaccine
Beta blockers to prevent mortality after MIblocker
Combine multiple data sources into one networkcombine_network
Generalised Student's t distribution (with location and scale)dgent pgent qgent
Incidence of diabetes in trials of antihypertensive drugsdiabetes
Deviance Information Criterion (DIC)dic
Reduced dietary fat to prevent mortalitydietary_fat
Specify a general marginal distributiondistr
Log Student's t distributiondlogt plogt qlogt
Distribution functions for M-spline baseline hazardsdmspline Hmspline hmspline pmspline qmspline rmst_mspline
Example newly-diagnosed multiple myelomaexample_ndmm
Example plaque psoriasis ML-NMRexample_pso_mlnmr
Example smoking FE NMAexample_smk_fe
Example smoking node-splittingexample_smk_nodesplit
Example smoking RE NMAexample_smk_re
Example smoking UME NMAexample_smk_ume
Kaplan-Meier curves of survival datageom_km
Direct and indirect evidenceget_nodesplits has_direct has_indirect
HTA Plaque Psoriasishta_psoriasis
Check network connectednessis_network_connected
Model comparison using the 'loo' packageloo loo.stan_nma waic waic.stan_nma
Knot locations for M-spline baseline hazard modelsmake_knots
Marginal treatment effectsmarginal_effects
Working with 3D MCMC arraysmcmc_array mcmc_array-class names.mcmc_array names<-.mcmc_array plot.mcmc_array print.mcmc_array summary.mcmc_array
Multinomial outcome datamulti
Newly diagnosed multiple myelomandmm_agd ndmm_agd_covs ndmm_ipd
Network meta-analysis modelsnma
The nma_data classmlnmr_data mlnmr_data-class nma_data nma_data-class
The nma_dic classnma_dic nma_dic-class
The nma_nodesplit classnma_nodesplit nma_nodesplit-class nma_nodesplit_df nma_nodesplit_df-class
The nma_prior classnma_prior nma_prior-class
The 'nma_summary' classnma_rank_probs nma_summary nma_summary-class
The 'nodesplit_summary' classnodesplit_summary nodesplit_summary-class
Matrix of plots for a 'stan_nma' objectpairs.stan_nma
Mean off-time reduction in Parkison's diseaseparkinsons
Plaque psoriasis dataplaque_psoriasis plaque_psoriasis_agd plaque_psoriasis_ipd
Plot numerical integration errorplot_integration_error
Plot prior vs posterior distributionplot_prior_posterior
Network plotsplot.nma_data
Plots of model fit diagnosticsplot.nma_dic
Plots of summary resultsplot.nma_parameter_summary plot.nma_rank_probs plot.nma_summary plot.surv_nma_summary
Plots of node-splitting modelsplot.nodesplit_summary
Treatment rankings and rank probabilitiesposterior_ranks posterior_rank_probs
Predictions of absolute effects from NMA modelspredict.stan_nma predict.stan_nma_surv
Print 'nma_data' objectsprint.mlnmr_data print.nma_data
Print DIC detailsprint.nma_dic
Print 'nma_nodesplit_df' objectsprint.nma_nodesplit print.nma_nodesplit_df
Methods for 'nma_summary' objectsas.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' objectsas.data.frame.nodesplit_summary as.tibble.nodesplit_summary as_tibble.nodesplit_summary print.nodesplit_summary
Print 'stan_nma' objectsprint.stan_nma
Prior distributionscauchy exponential flat half_cauchy half_normal half_student_t log_normal log_student_t normal priors student_t
The Bernoulli Distributiondbern pbern qbern
The Gamma distributiondgamma pgamma qgamma
The logit Normal distributiondlogitnorm plogitnorm qlogitnorm
Random effects structureRE_cor which_RE
Relative treatment effectsrelative_effects
Set up arm-based aggregate dataset_agd_arm
Set up contrast-based aggregate dataset_agd_contrast
Set up aggregate survival dataset_agd_surv
Set up individual patient dataset_ipd
Smoking cessation datasmoking
The stan_nma classstan_mlnmr stan_nma stan_nma-class
Statins for cholesterol loweringstatins
Summarise the results of node-splitting modelsplot.nma_nodesplit plot.nma_nodesplit_df summary.nma_nodesplit summary.nma_nodesplit_df
Summary of prior distributionssummary.nma_prior
Posterior summaries from 'stan_nma' objectsplot.stan_nma summary.stan_nma
Plot theme for multinma plotstheme_multinma
Thrombolytic treatments datathrombolytics
Granulocyte transfusion in patients with neutropenia or neutrophil dysfunctiontransfusion