# Bayesian Network Meta-Analysis of Individual and Aggregate Data

## Documentation for package ‘multinma’ version 0.9.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I K L M N P Q R S T U W misc

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

## -- A --

adapt_delta | Target average acceptance probability
add_integration | Add numerical integration points to aggregate data
add_integration.data.frame | Add numerical integration points to aggregate data
add_integration.default | Add numerical integration points to aggregate data
add_integration.nma_data | Add numerical integration points to aggregate data
as.array.nma_dic | Methods for 'nma_dic' objects
as.array.nma_rank_probs | Methods for 'nma_summary' objects
as.array.nma_summary | Methods for 'nma_summary' objects
as.array.stan_nma | Convert samples into arrays, matrices, or data frames
as.data.frame.nma_dic | Methods for 'nma_dic' objects
as.data.frame.nma_summary | Methods for 'nma_summary' objects
as.data.frame.nodesplit_summary | Methods for 'nodesplit_summary' objects
as.data.frame.stan_nma | Convert samples into arrays, matrices, or data frames
as.igraph.nma_data | Convert networks to graph objects
as.matrix.nma_dic | Methods for 'nma_dic' objects
as.matrix.nma_rank_probs | Methods for 'nma_summary' objects
as.matrix.nma_summary | Methods for 'nma_summary' objects
as.matrix.stan_nma | Convert samples into arrays, matrices, or data frames
as.stanfit | as.stanfit
as.stanfit.default | as.stanfit
as.stanfit.stan_nma | as.stanfit
as.tibble.nma_dic | Methods for 'nma_dic' objects
as.tibble.nma_summary | Methods for 'nma_summary' objects
as.tibble.nodesplit_summary | Methods for 'nodesplit_summary' objects
as.tibble.stan_nma | Convert samples into arrays, matrices, or data frames
as_tbl_graph.nma_data | Convert networks to graph objects
as_tibble.nma_dic | Methods for 'nma_dic' objects
as_tibble.nma_summary | Methods for 'nma_summary' objects
as_tibble.nodesplit_summary | Methods for 'nodesplit_summary' objects
as_tibble.stan_nma | Convert samples into arrays, matrices, or data frames
atrial_fibrillation | Stroke prevention in atrial fibrillation patients

## -- B --

bcg_vaccine | BCG vaccination
blocker | Beta blockers to prevent mortality after MI

## -- C --

cauchy | Prior distributions
certolizumab | Certolizumab
combine_network | Combine multiple data sources into one network

## -- D --

dbern | The Bernoulli Distribution
dgamma | The Gamma distribution
dgent | Generalised Student's t distribution (with location and scale)
diabetes | Incidence of diabetes in trials of antihypertensive drugs
dic | Deviance Information Criterion (DIC)
dietary_fat | Reduced dietary fat to prevent mortality
distr | Specify a general marginal distribution
dlogitnorm | The logit Normal distribution
dlogt | Log Student's t distribution
dmspline | Distribution functions for M-spline baseline hazards

## -- E --

example_ndmm | Example newly-diagnosed multiple myeloma
example_pso_mlnmr | Example plaque psoriasis ML-NMR
example_smk_fe | Example smoking FE NMA
example_smk_nodesplit | Example smoking node-splitting
example_smk_re | Example smoking RE NMA
example_smk_ume | Example smoking UME NMA
exponential | Prior distributions

## -- F --

flat | Prior distributions

## -- G --

geom_km | Kaplan-Meier curves of survival data
get_nodesplits | Direct and indirect evidence

## -- H --

half_cauchy | Prior distributions
half_normal | Prior distributions
half_student_t | Prior distributions
has_direct | Direct and indirect evidence
has_indirect | Direct and indirect evidence
Hmspline | Distribution functions for M-spline baseline hazards
hmspline | Distribution functions for M-spline baseline hazards
hta_psoriasis | HTA Plaque Psoriasis

## -- I --

inv_softmax | Softmax transform
is_network_connected | Check network connectedness

## -- K --

knots.stan_nma | Knot locations for a fitted model

## -- L --

log_normal | Prior distributions
log_student_t | Prior distributions
loo | Model comparison using the 'loo' package
loo.stan_nma | Model comparison using the 'loo' package

## -- M --

make_knots | Knot locations for M-spline baseline hazard models
marginal_effects | Marginal treatment effects
mcmc_array | Working with 3D MCMC arrays
mcmc_array-class | Working with 3D MCMC arrays
mlnmr_data | The nma_data class
mlnmr_data-class | The nma_data class
multi | Multinomial outcome data
multinma | multinma: A Package for Network Meta-Analysis of Individual and Aggregate Data in Stan

## -- N --

names.mcmc_array | Working with 3D MCMC arrays
names<-.mcmc_array | Working with 3D MCMC arrays
ndmm_agd | Newly diagnosed multiple myeloma
ndmm_agd_covs | Newly diagnosed multiple myeloma
ndmm_ipd | Newly diagnosed multiple myeloma
nma | Network meta-analysis models
nma_data | The nma_data class
nma_data-class | The nma_data class
nma_dic | The nma_dic class
nma_dic-class | The nma_dic class
nma_nodesplit | The nma_nodesplit class
nma_nodesplit-class | The nma_nodesplit class
nma_nodesplit_df | The nma_nodesplit class
nma_nodesplit_df-class | The nma_nodesplit class
nma_prior | The nma_prior class
nma_prior-class | The nma_prior class
nma_rank_probs | The 'nma_summary' class
nma_summary | The 'nma_summary' class
nma_summary-class | The 'nma_summary' class
nodesplit_summary | The 'nodesplit_summary' class
nodesplit_summary-class | The 'nodesplit_summary' class
normal | Prior distributions

## -- P --

pairs.stan_nma | Matrix of plots for a 'stan_nma' object
parkinsons | Mean off-time reduction in Parkison's disease
pbern | The Bernoulli Distribution
pgamma | The Gamma distribution
pgent | Generalised Student's t distribution (with location and scale)
plaque_psoriasis | Plaque psoriasis data
plaque_psoriasis_agd | Plaque psoriasis data
plaque_psoriasis_ipd | Plaque psoriasis data
plogitnorm | The logit Normal distribution
plogt | Log Student's t distribution
plot.mcmc_array | Working with 3D MCMC arrays
plot.nma_data | Network plots
plot.nma_dic | Plots of model fit diagnostics
plot.nma_nodesplit | Summarise the results of node-splitting models
plot.nma_nodesplit_df | Summarise the results of node-splitting models
plot.nma_parameter_summary | Plots of summary results
plot.nma_rank_probs | Plots of summary results
plot.nma_summary | Plots of summary results
plot.nodesplit_summary | Plots of node-splitting models
plot.stan_nma | Posterior summaries from 'stan_nma' objects
plot.surv_nma_summary | Plots of summary results
plot_integration_error | Plot numerical integration error
plot_prior_posterior | Plot prior vs posterior distribution
pmspline | Distribution functions for M-spline baseline hazards
posterior_ranks | Treatment rankings and rank probabilities
posterior_rank_probs | Treatment rankings and rank probabilities
predict.stan_nma | Predictions of absolute effects from NMA models
predict.stan_nma_surv | Predictions of absolute effects from NMA models
print.mcmc_array | Working with 3D MCMC arrays
print.mlnmr_data | Print 'nma_data' objects
print.nma_data | Print 'nma_data' objects
print.nma_dic | Methods for 'nma_dic' objects
print.nma_nodesplit | Print 'nma_nodesplit_df' objects
print.nma_nodesplit_df | Print 'nma_nodesplit_df' objects
print.nma_summary | Methods for 'nma_summary' objects
print.nodesplit_summary | Methods for 'nodesplit_summary' objects
print.stan_nma | Print 'stan_nma' objects
priors | Prior distributions

## -- Q --

qbern | The Bernoulli Distribution
qgamma | The Gamma distribution
qgent | Generalised Student's t distribution (with location and scale)
qlogitnorm | The logit Normal distribution
qlogt | Log Student's t distribution
qmspline | Distribution functions for M-spline baseline hazards

## -- R --

relative_effects | Relative treatment effects
RE_cor | Random effects structure
rmst_mspline | Distribution functions for M-spline baseline hazards

## -- S --

set_agd_arm | Set up arm-based aggregate data
set_agd_contrast | Set up contrast-based aggregate data
set_agd_surv | Set up aggregate survival data
set_ipd | Set up individual patient data
smoking | Smoking cessation data
social_anxiety | Social Anxiety
softmax | Softmax transform
stan_mlnmr | The stan_nma class
stan_nma | The stan_nma class
stan_nma-class | The stan_nma class
statins | Statins for cholesterol lowering
student_t | Prior distributions
summary.mcmc_array | Working with 3D MCMC arrays
summary.nma_nodesplit | Summarise the results of node-splitting models
summary.nma_nodesplit_df | Summarise the results of node-splitting models
summary.nma_prior | Summary of prior distributions
summary.stan_nma | Posterior summaries from 'stan_nma' objects

## -- T --

theme_multinma | Plot theme for multinma plots
thrombolytics | Thrombolytic treatments data
transfusion | Granulocyte transfusion in patients with neutropenia or neutrophil dysfunction

## -- U --

unnest_integration | Add numerical integration points to aggregate data

## -- W --

waic | Model comparison using the 'loo' package
waic.stan_nma | Model comparison using the 'loo' package
which_RE | Random effects structure

## -- misc --

.default | Set default values
.is_default | Set default values