Package: jarbes 2.5.0

Pablo Emilio Verde

jarbes: Just a Rather Bayesian Evidence Synthesis

Provides a new class of Bayesian meta-analysis models that incorporates a model for internal and external validity bias. In this way, it is possible to combine studies of diverse quality and different types. For example, we can combine the results of randomized control trials (RCTs) with the results of observational studies (OS).

Authors:Pablo Emilio Verde [aut, cre]

jarbes_2.5.0.tar.gz
jarbes_2.5.0.tar.gz(r-4.7-any)jarbes_2.5.0.tar.gz(r-4.6-any)
jarbes_2.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
jarbes/json (API)

# Install 'jarbes' in R:
install.packages('jarbes', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC - binary JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. JAGS was written with three aims in mind: * To have an engine for the BUGS language that runs on Unix * To be extensible, allowing users to write their own functions, distributions and samplers. * To be a plaftorm for experimentation with ideas in Bayesian modelling This package contains the 'jags' binary as well as the associated shared library modules loaded by the binary.
  • c++– GNU Standard C++ Library v3
Datasets:
  • acupuncture - Meta-analysis: 29 randomized controlled studies (RCT) assessing the efficacy of acupuncture treatments as complementary treatment in depression patients
  • ai_distress - Meta-analysis of RCTs evaluating the effect of AI agents to reduce psychological distress effects
  • colon_cancer - Meta-analysis: Real World Evidence in metastatic colorectal cancer, comparing antiangiogenic treatments with chemotherapy
  • covid19 - Meta-analysis: Observational studies assessing the impact of risk factors on the severity and mortality of COVID-19 cases
  • diabetes_eyes - Individual Participant Data: Diabetic Eyes Data
  • fnrpcr - Meta-Analysis: Variation in False-Negative Rate of Reverse Transcriptase Polymerase Chain Reaction–Based SARS-CoV-2 Tests by Time Since Exposure
  • ganzfeld - Meta-Analysis of Free-Response Studies, 1992–2008: Assessing the Noise Reduction Model in Parapsychology
  • healing - Efficacy of diabetic foot healing using adjuvant treatments
  • healingipd - Individual participant data for diabetic patients
  • hips - Meta-analysis: generalized evidence synthesis of total hip replacement
  • longcovid - Meta-analysis: Long-COVID Health Outcomes
  • macula_rwe - Meta-analysis: 83 observational studies assessing the effectiveness of intravitreal therapy for diabetic maculaedema
  • personality - Meta-Analysis: Evolution of Personality Traits over time
  • ppvcap - Efficacy of Pneumococcal Polysaccharide Vaccine in Preventing Community Acquired Pneumonia
  • ppvipd - Efficacy of Pneumococcal Polysaccharide Vaccine in Preventing Invasive Pneumococcal Disease
  • preterm - Meta-analysis of Cognitive Outcomes in Very Preterm Children
  • stemcells - Meta-analysis: 31 randomized controled trials (RCTs) with reported discrepancies
  • trisomy21 - Meta-analysis: Observational studies assessing the relationship of a positive ICPC (Isolated Choroid Plexus Cyst) on Trisomy 21
  • tyge_2011 - Mortality data from the tigecycline meta-analysis

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

jagscpp

2.13 score 1 stars 34 scripts 311 downloads 1 mentions 20 exports 92 dependencies

Last updated from:01c1f61690. Checks:4 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK195
source / vignettesOK199
linux-release-x86_64OK158
wasm-releaseOK135

Exports:b3lmetabcbnpbcbnp_0bcdpmetabchmrbcmetabcmixmetabmetacocluster_plotdiagnosticdpmetadpmetaregdpmmetaeffectforestplot_comparehmrmetariskplot_dataplotdata_reg.bcbnpsimData

Dependencies:abindaskpassbase64encbookdownbootbslibcachemclicodacolourpickercommonmarkcpp11crayoncurldigestdplyrevaluatefarverfastmapfontawesomeforcatsfsgenericsGGallyggExtraggplot2ggstatsgluegridExtragtablehighrhmshtmltoolshtmlwidgetshttpuvisobandjquerylibjsonlitekableExtraknitrlabelinglaterlatticelifecyclemagrittrMASSmemoisemimeminiUIotelpatchworkpillarpkgconfigprettyunitsprogresspromisespurrrqpdfR2jagsR2WinBUGSR6rappdirsRColorBrewerRcpprjagsrlangrmarkdownrstudioapiS7sassscalesshinyshinyjssourcetoolsstringistringrsvglitesyssystemfontstextshapingtibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunxml2xtableyaml

Readme and manuals

Help Manual

Help pageTopics
Meta-analysis: 29 randomized controlled studies (RCT) assessing the efficacy of acupuncture treatments as complementary treatment in depression patientsacupuncture
Meta-analysis of RCTs evaluating the effect of AI agents to reduce psychological distress effectsai_distress
Bayesian Meta-Analysis for Combining Studiesb3lmeta
Bias Corrected Meta-Analysis and Meta-Regression with Dirichlet Process Mixture of normal distributionsbcbnp
Bias Corrected Meta-Analysis and Meta-Regression with Dirichlet Mixture Process of normal distributionsbcbnp_0
Bias Corrected Meta-Analysis with Dirichlet Process Priorsbcdpmeta
Bias-Corrected Bayesian Nonparametric Model to combine aggregated and individual participant data for cross design synthesis.bchmr
Bias-Corrected Meta-Analysis for Combining Studies of Different Types and Qualitybcmeta
Bias Corrected Meta-Analysis with Dirichlet Mixture Process Priors for the biased componentbcmixmeta
Bayesian Meta-Analysis for Combining Studiesbmeta
Co-Clustering Heatmap from a Numeric Matrixcocluster_plot
Meta-analysis: Real World Evidence in metastatic colorectal cancer, comparing antiangiogenic treatments with chemotherapycolon_cancer
Meta-analysis: Observational studies assessing the impact of risk factors on the severity and mortality of COVID-19 casescovid19
Individual Participant Data: Diabetic Eyes Datadiabetes_eyes
Generic diagnostic function.diagnostic
Diagnostic function for b3lmeta object in jarbesdiagnostic.b3lmeta
Diagnostic function for bcdpmeta object in jarbesdiagnostic.bcdpmeta
Diagnostic function for bcmeta object in jarbesdiagnostic.bcmeta
Diagnostic function for bcmixmeta object in jarbesdiagnostic.bcmixmeta
Diagnostic function for bmeta object in jarbesdiagnostic.bmeta
Diagnostic function for hmr object in jarbesdiagnostic.hmr
Diagnostic function for metarisk object in jarbesdiagnostic.metarisk
Bayesian Meta-Analysis with Dirichlet Process Priorsdpmeta
Bayesian Meta-Analysis with Dirichlet Process Priorsdpmetareg
Bayesian Meta-Analysis with Dirichlet Process Mixtures Priorsdpmmeta
Generic effect function.effect
Posterior distribution of Effectiveness for a subgroup of patientseffect.hmr
Meta-Analysis: Variation in False-Negative Rate of Reverse Transcriptase Polymerase Chain Reaction–Based SARS-CoV-2 Tests by Time Since Exposurefnrpcr
Forest Plot Comparison for One or Two Modelsforestplot_compare
Meta-Analysis of Free-Response Studies, 1992–2008: Assessing the Noise Reduction Model in Parapsychologyganzfeld
Efficacy of diabetic foot healing using adjuvant treatmentshealing
Individual participant data for diabetic patientshealingipd
Meta-analysis: generalized evidence synthesis of total hip replacementhips
Bayesian meta-analysis to combine aggregated and individual participant data for cross design synthesis.hmr
Meta-analysis: Long-COVID Health Outcomeslongcovid
Meta-analysis: 83 observational studies assessing the effectiveness of intravitreal therapy for diabetic maculaedemamacula_rwe
Bayesian meta-analysis for using baseline risk adjustmentmetarisk
Meta-Analysis: Evolution of Personality Traits over timepersonality
Plot Data Functionplot_data
Generic plot function for b3lmeta object in jarbes.plot.b3lmeta
Generic plot function for bcbnp object.plot.bcbnp
Generic plot function for bcbnp_0 object.plot.bcbnp_0
Generic plot function for bcdpmeta object in jarbes.plot.bcdpmeta
Generic plot function for bcmeta object.plot.bcmeta
Generic plot function for bcmixmeta object.plot.bcmixmeta
Generic plot function for bmeta object in jarbes.plot.bmeta
Generic plot function for dpmeta object.plot.dpmeta
Generic plot function for bmeta object in jarbes.plot.dpmmeta
Generic plot function for hmr object in jarbes.plot.hmr
Generic plot function for metarisk object in jarbes.plot.metarisk
Forest Plot for simData Objectsplot.simData
Plot Meta-Regression Results from a BCBNP Modelplotdata_reg.bcbnp
Efficacy of Pneumococcal Polysaccharide Vaccine in Preventing Community Acquired Pneumoniappvcap
Efficacy of Pneumococcal Polysaccharide Vaccine in Preventing Invasive Pneumococcal Diseaseppvipd
Meta-analysis of Cognitive Outcomes in Very Preterm Childrenpreterm
Generic print function for b3lmeta object in jarbes.print.b3lmeta
Generic print function for bcbnp object in jarbes.print.bcbnp_0
Generic print function for bcdpmeta object in jarbes.print.bcdpmeta
Generic print function for hmr object in jarbes.print.bchmr
Generic print function for bcmeta object in jarbes.print.bcmeta
Generic print function for bcmixmeta object in jarbes.print.bcmixmeta
Generic print function for dpmeta object in jarbes.print.dpmeta
Generic print function for dpmeta object in jarbes.print.dpmetareg
Generic print function for dpmmeta object in jarbes.print.dpmmeta
Generic print function for hmr object in jarbes.print.hmr
Generic print function for metarisk object in jarbes.print.metarisk
Generic print function for simData object.print.simData
Simulate Data for Meta-AnalysissimData
Meta-analysis: 31 randomized controled trials (RCTs) with reported discrepanciesstemcells
Generic summary function for bmeta object in jarbessummary.b3lmeta
Generic summary function for bcbnp object in jarbes.summary.bcbnp
Generic summary function for bcbnp_0 object in jarbes.summary.bcbnp_0
Generic summary function for bcdpmeta object in jarbessummary.bcdpmeta
Generic summary function for bcmeta object.summary.bcmeta
Generic summary function for bcmixmeta object in jarbes.summary.bcmixmeta
Generic summary function for bmeta object in jarbessummary.bmeta
Generic summary function for dpmeta object in jarbes.summary.dpmeta
Generic summary function for dpmmeta object in jarbessummary.dpmmeta
Generic summary function for hmr object in jarbessummary.hmr
Generic summary function for metarisk object in jarbessummary.metarisk
Summary method for simData objectssummary.simData
Meta-analysis: Observational studies assessing the relationship of a positive ICPC (Isolated Choroid Plexus Cyst) on Trisomy 21trisomy21
Mortality data from the tigecycline meta-analysis (Curcio & Verde, 2011)tyge_2011