Package: RoBMA 3.1.0

RoBMA: Robust Bayesian Meta-Analyses

A framework for estimating ensembles of meta-analytic models (assuming either presence or absence of the effect, heterogeneity, and publication bias). The RoBMA framework uses Bayesian model-averaging to combine the competing meta-analytic models into a model ensemble, weights the posterior parameter distributions based on posterior model probabilities and uses Bayes factors to test for the presence or absence of the individual components (e.g., effect vs. no effect; Bartoš et al., 2022, <doi:10.1002/jrsm.1594>; Maier, Bartoš & Wagenmakers, 2022, <doi:10.1037/met0000405>). Users can define a wide range of non-informative or informative prior distributions for the effect size, heterogeneity, and publication bias components (including selection models and PET-PEESE). The package provides convenient functions for summary, visualizations, and fit diagnostics.

Authors:František Bartoš [aut, cre], Maximilian Maier [aut], Eric-Jan Wagenmakers [ths], Joris Goosen [ctb], Matthew Denwood [cph], Martyn Plummer [cph]

RoBMA_3.1.0.tar.gz
RoBMA_3.1.0.zip(r-4.5)RoBMA_3.1.0.zip(r-4.4)RoBMA_3.1.0.zip(r-4.3)
RoBMA_3.1.0.tgz(r-4.4-x86_64)RoBMA_3.1.0.tgz(r-4.4-arm64)RoBMA_3.1.0.tgz(r-4.3-x86_64)RoBMA_3.1.0.tgz(r-4.3-arm64)
RoBMA_3.1.0.tar.gz(r-4.5-noble)RoBMA_3.1.0.tar.gz(r-4.4-noble)
RoBMA.pdf |RoBMA.html✨
RoBMA/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/fbartos/robma/issues

Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • Anderson2010 - 27 experimental studies from Anderson et al. (2010) that meet the best practice criteria
  • Bem2011 - 9 experimental studies from Bem
  • Kroupova2021 - 881 estimates from 69 studies of a relationship between employment and educational outcomes collected by Kroupova et al.
  • Lui2015 - 18 studies of a relationship between acculturation mismatch and intergenerational cultural conflict collected by Lui
  • Poulsen2006 - 5 studies with a tactile outcome assessment from Poulsen et al. (2006) of the effect of potassium-containing toothpaste on dentine hypersensitivity

On CRAN:

meta-analysismodel-averagingpublication-bias

80 exports 8 stars 1.64 score 41 dependencies 1 mentions 37 scripts 1.0k downloads

Last updated 1 years agofrom:8de6009b50. Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 14 2024
R-4.5-win-x86_64WARNINGSep 14 2024
R-4.5-linux-x86_64WARNINGSep 14 2024
R-4.4-win-x86_64WARNINGSep 14 2024
R-4.4-mac-x86_64WARNINGSep 14 2024
R-4.4-mac-aarch64WARNINGSep 14 2024
R-4.3-win-x86_64WARNINGSep 14 2024
R-4.3-mac-x86_64WARNINGSep 14 2024
R-4.3-mac-aarch64WARNINGSep 14 2024

Exports:BiBMAcheck_RoBMAcheck_setupcheck_setup.BiBMAcheck_setup.regcombine_datacontr.independentcontr.meandifcontr.orthonormald2logORd2ORd2rd2zdiagnosticsdiagnostics_autocorrelationdiagnostics_densitydiagnostics_tracedwnormforestinterpretis.BiBMAis.NoBMAis.NoBMA.regis.RoBMAis.RoBMA.reglogOR2dlogOR2ORlogOR2rlogOR2zmarginal_plotmarginal_summaryn_dn_rn_zNoBMANoBMA.regOR2dOR2logOROR2rOR2zplot_modelspriorprior_factorprior_informedprior_noneprior_PEESEprior_PETprior_weightfunctionpwnormqwnormr2dr2logORr2ORr2zRoBMARoBMA.get_optionRoBMA.optionsRoBMA.regrwnormse_dse_d2se_logORse_d2se_rse_d2se_zse_logOR2se_dse_logOR2se_rse_logOR2se_zse_rse_r2se_dse_r2se_logORse_r2se_zse_zse_z2se_dse_z2se_logORse_z2se_rset_autofit_controlset_convergence_checksz2dz2logORz2ORz2r

Dependencies:BayesToolsbridgesamplingBrobdingnagclicodacolorspaceextraDistrfansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellmvtnormnlmepillarpkgconfigR6rbibutilsRColorBrewerRcppRdpackrjagsrlangrunjagsscalesstringistringrtibbleutf8vctrsviridisLitewithr

Fitting Custom Meta-Analytic Ensembles

František Bartoš

Rendered fromCustomEnsembles.Rmdusingknitr::rmarkdownon Sep 14 2024.

Last update: 2022-03-31
Started: 2020-07-08

Hierarchical Bayesian Model-Averaged Meta-Analysis

František Bartoš

Rendered fromHierarchicalBMA.Rmdusingknitr::rmarkdownon Sep 14 2024.

Last update: 2023-06-01
Started: 2023-05-31

Informed Bayesian Model-Averaged Meta-Analysis in Medicine

František Bartoš

Rendered fromMedicineBMA.Rmdusingknitr::rmarkdownon Sep 14 2024.

Last update: 2023-05-31
Started: 2021-11-03

Reproducing Bayesian Model-Averaged Meta-Analysis

František Bartoš

Rendered fromReproducingBMA.Rmdusingknitr::rmarkdownon Sep 14 2024.

Last update: 2023-05-31
Started: 2020-07-08

Tutorial: Adjusting for Publication Bias in JASP and R - Selection Models, PET-PEESE, and Robust Bayesian Meta-Analysis

František Bartoš, Maximilian Maier, Daniel S. Quintana & Eric-Jan Wagenmakers

Rendered fromTutorial.Rmdusingknitr::rmarkdownon Sep 14 2024.

Last update: 2023-05-31
Started: 2023-05-31

Readme and manuals

Help Manual

Help pageTopics
RoBMA: Robust Bayesian meta-analysisRoBMA-package RoBMA.package RoBMA_package _PACKAGE
27 experimental studies from Anderson et al. (2010) that meet the best practice criteriaAnderson2010
9 experimental studies from Bem (2011) as described in Bem et al. (2011)Bem2011
Estimate a Bayesian Model-Averaged Meta-Analysis of Binomial DataBiBMA
Check fitted RoBMA object for errors and warningscheck_RoBMA
Prints summary of '"RoBMA"' ensemble implied by the specified priorscheck_setup check_setup.RoBMA
Prints summary of '"BiBMA.reg"' ensemble implied by the specified priors and formulacheck_setup.BiBMA
Prints summary of '"RoBMA.reg"' ensemble implied by the specified priors and formulacheck_setup.reg check_setup.RoBMA.reg
Combines different effect sizes into a common metriccombine_data
Independent contrast matrixcontr.independent
Mean difference contrast matrixcontr.meandif
Checks a fitted RoBMA objectdiagnostics diagnostics_autocorrelation diagnostics_density diagnostics_trace
Effect size transformationsd2logOR d2OR d2r d2z effect_sizes logOR2d logOR2OR logOR2r logOR2z OR2d OR2logOR OR2r OR2z r2d r2logOR r2OR r2z z2d z2logOR z2OR z2r
Forest plot for a RoBMA objectforest
Interprets results of a RoBMA model.interpret
Reports whether x is a RoBMA objectis.BiBMA is.NoBMA is.NoBMA.reg is.RoBMA is.RoBMA.reg
881 estimates from 69 studies of a relationship between employment and educational outcomes collected by Kroupova et al. (2021)Kroupova2021
18 studies of a relationship between acculturation mismatch and intergenerational cultural conflict collected by Lui (2015)Lui2015
Plots marginal estimates of a fitted RoBMA regression objectmarginal_plot
Summarize marginal estimates of a fitted RoBMA regression objectmarginal_summary
Estimate a Bayesian Model-Averaged Meta-AnalysisNoBMA
Estimate a Bayesian Model-Averaged Meta-RegressionNoBMA.reg
Models plot for a RoBMA objectplot_models
Plots a fitted RoBMA objectplot.RoBMA
5 studies with a tactile outcome assessment from Poulsen et al. (2006) of the effect of potassium-containing toothpaste on dentine hypersensitivityPoulsen2006
Prints marginal_summary object for RoBMA methodprint.marginal_summary.RoBMA
Prints a fitted RoBMA objectprint.RoBMA
Prints summary object for RoBMA methodprint.summary.RoBMA
Creates a prior distributionprior
Creates a prior distribution for factorsprior_factor
Creates an informed prior distribution based on researchprior_informed
Creates a prior distributionprior_none
Creates a prior distribution for PET or PEESE modelsprior_PEESE
Creates a prior distribution for PET or PEESE modelsprior_PET
Creates a prior distribution for a weight functionprior_weightfunction
Estimate a Robust Bayesian Meta-AnalysisRoBMA
Control MCMC fitting processRoBMA_control set_autofit_control set_autofit_control, set_convergence_checks
Options for the RoBMA packageRoBMA.get_option RoBMA.options RoBMA_options
Estimate a Robust Bayesian Meta-Analysis Meta-RegressionRoBMA.reg
Sample sizes to standard errors calculationsn_d n_r n_z sample_sizes se_d se_r se_z
Standard errors transformationsse_d2se_logOR se_d2se_r se_d2se_z se_logOR2se_d se_logOR2se_r se_logOR2se_z se_r2se_d se_r2se_logOR se_r2se_z se_z2se_d se_z2se_logOR se_z2se_r standard_errors
Summarize fitted RoBMA objectsummary.RoBMA
Updates a fitted BiBMA objectupdate.BiBMA
Updates a fitted RoBMA objectupdate.RoBMA
Weighted multivariate normal distributionweighted_multivariate_normal
Weighted normal distributiondwnorm pwnorm qwnorm rwnorm weighted_normal