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rnmamod (version 0.4.0)

Bayesian Network Meta-Analysis with Missing Participants

Description

A comprehensive suite of functions to perform and visualise pairwise and network meta-analysis with aggregate binary or continuous missing participant outcome data. The package covers core Bayesian one-stage models implemented in a systematic review with multiple interventions, including fixed-effect and random-effects network meta-analysis, meta-regression, evaluation of the consistency assumption via the node-splitting approach and the unrelated mean effects model, and sensitivity analysis. Missing participant outcome data are addressed in all models of the package. The robustness to primary analysis results can also be investigated using a novel intuitive index. Methods to evaluate the transitivity assumption quantitatively are provided. The package also offers a rich, user-friendly visualisation toolkit that aids in appraising and interpreting the results thoroughly and preparing the manuscript for journal submission. The visualisation tools comprise the network plot, forest plots, panel of diagnostic plots, heatmaps on the extent of missing participant outcome data in the network, league heatmaps on estimation and prediction, rankograms, Bland-Altman plot, leverage plot, deviance scatterplot, heatmap of robustness, barplot of Kullback-Leibler divergence, heatmap of comparison dissimilarities and dendrogram of comparison clustering. The package also allows the user to export the results to an Excel file at the working directory.

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install.packages('rnmamod')

Monthly Downloads

325

Version

0.4.0

License

GPL (>= 3)

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Maintainer

Loukia Spineli

Last Published

March 24th, 2024

Functions in rnmamod (0.4.0)

bland_altman_plot

The Bland-Altman plot
comp_clustering

End-user-ready results for comparison dissimilarity and hierarchical clustering (Comparisons' comparability for transitivity evaluation)
describe_network

A function to describe the evidence base
distr_characteristics

Visualising the distribution of characteristics (Comparisons' comparability for transitivity evaluation)
dendro_heatmap

Dendrogram with amalgamated heatmap (Comparisons' comparability for transitivity evaluation)
forestplot_metareg

Comparator-specific forest plot for network meta-regression
forestplot

Comparator-specific forest plot for network meta-analysis
balloon_plot

Enhanced balloon plot
baseline_model

The baseline model for binary outcome
data_preparation

Prepare the dataset in the proper format for R2jags
heterogeneity_param_prior

Determine the prior distribution for the heterogeneity parameter
improved_ume

Detect the frail comparisons in multi-arm trials
league_heatmap

League heatmap for estimation
intervalplot_panel_ume

A panel of interval plots for the unrelated mean effects model
heatmap_missing_dataset

Heatmap of proportion of missing participants in the dataset
heatmap_robustness

Heatmap of robustness
internal_measures_plot

Internal measures for cluster validation (Comparisons' comparability for transitivity evaluation)
heatmap_missing_network

Heatmap of proportion of missing participants in the network
gower_distance

Gower's dissimilarity measure (Trials' comparability for transitivity evaluation)
kld_barplot

Barplot for the Kullback-Leibler divergence measure
netplot

Network plot
nma.baker2009

Pharmacological interventions for chronic obstructive pulmonary disease
leverage_plot

Leverage plot
league_table_absolute_user

League table for relative and absolute effects (user defined)
missingness_param_prior

Define the mean value of the normal distribution of the missingness parameter
miss_characteristics

Visualising missing data in characteristics (Comparisons' comparability for transitivity evaluation)
nma.liu2013

Antidepressants in Parkinson's disease
nodesplit_plot

End-user-ready results for the node-splitting approach
metareg_plot

End-user-ready results for network meta-regression
mcmc_diagnostics

Markov Chain Monte Carlo diagnostics
nma.schwingshackl2014

Training modalities for patients with type 2 diabetes
nma.stowe2011

Antiparkinsonian interventions for later Parkinson's disease
league_table_absolute

League table for relative and absolute effects
league_heatmap_pred

League heatmap for prediction
nma.bottomley2011

Pharmacological interventions for moderately severe scalp psoriasis
pma.hetrick2012

Paroxetine versus placebo for depressive disorders
nma.dogliotti2014

Oral antithrombotics for stroke episode
prepare_nodesplit

WinBUGS code for the node-splitting approach
prepare_model

WinBUGS code for Bayesian pairwise or network meta-analysis and meta-regression
pma.taylor2004

Inositol versus glucose for depressive episode
run_sensitivity

Perform sensitivity analysis for missing participant outcome data
run_series_meta

Perform a series of Bayesian pairwise meta-analyses
robustness_index

Robustness index
rnmamod-package

rnmamod: Bayesian Network Meta-analysis with Missing Participants
robustness_index_user

Robustness index when 'metafor' or 'netmeta' are used
rankosucra_plot

Rankograms and SUCRA curves
prepare_ume

WinBUGS code for the unrelated mean effects model
ume_plot

End-user-ready results for the unrelated mean effects model
trans_quality

Rating the quality of transitivity evaluation
taylor_continuous

Pattern-mixture model with Taylor series for continuous outcome
taylor_imor

Pattern-mixture model with Taylor series for a binary outcome
unrelated_effects_plot

End-user-ready results for unrelated trial effects model
run_model

Perform Bayesian pairwise or network meta-analysis
scatterplots_dev

Deviance scatterplots
run_nodesplit

Perform the node-splitting approach
series_meta_plot

End-user-ready results for a series of pairwise meta-analyses
run_ume

Perform the unrelated mean effects model
run_metareg

Perform Bayesian pairwise or network meta-regression
scatterplot_sucra

Scatterplot of SUCRA values