Package: baggr 0.7.8

baggr: Bayesian Aggregate Treatment Effects

Running and comparing meta-analyses of data with hierarchical Bayesian models in Stan, including convenience functions for formatting data, plotting and pooling measures specific to meta-analysis. This implements many models from Meager (2019) <doi:10.1257/app.20170299>.

Authors:Witold Wiecek [cre, aut], Rachael Meager [aut], Brice Green [ctb], Danny Toomey [ctb], Trustees of Columbia University [cph]

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baggr/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/wwiecek/baggr/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • chicks - Chickens: impact of electromagnetic field on calcium ion efflux in chicken brains
  • data_spike - Spike & slab example dataset
  • microcredit - 7 studies on effect of microcredit supply
  • microcredit_simplified - Simplified version of the microcredit dataset.
  • schools - 8 schools example
  • yusuf - Yusuf et al: beta-blockers and heart attacks

On CRAN:

bayesian-statisticsmeta-analysisquantile-regressionstantreatment-effects

7.19 score 46 stars 84 scripts 467 downloads 37 exports 79 dependencies

Last updated 9 months agofrom:98e261de4b. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 26 2024
R-4.5-win-x86_64NOTEOct 26 2024
R-4.5-linux-x86_64NOTEOct 26 2024
R-4.4-win-x86_64NOTEOct 26 2024
R-4.4-mac-x86_64NOTEOct 26 2024
R-4.4-mac-aarch64NOTEOct 26 2024
R-4.3-win-x86_64NOTEOct 26 2024
R-4.3-mac-x86_64NOTEOct 26 2024
R-4.3-mac-aarch64NOTEOct 26 2024

Exports:baggrbaggr_comparebaggr_plotbaggr_theme_getbaggr_theme_replacebaggr_theme_setbaggr_theme_updatebinary_to_individualbubblecauchyconvert_inputseffect_draweffect_plotfixed_effectsforest_plotgroup_effectsheterogeneityhypermeanhypersdlabbelkjlognormalloo_compareloocvmintmultinormalmutau_cornormalplot_quantilespoolingprepare_marandom_effectssingle_comp_plotstudent_tstudy_effectstreatment_effectuniform

Dependencies:abindbackportsbayesplotBHbriocallrcheckmateclicolorspacecrayondescdiffobjdigestdistributionaldplyrevaluatefansifarverforestplotfsgenericsggplot2ggplotifyggrepelggridgesgluegridExtragridGraphicsgtableinlineisobandjsonlitelabelinglatticelifecycleloomagrittrMASSMatrixmatrixStatsmgcvmunsellnlmenumDerivpillarpkgbuildpkgconfigpkgloadplyrposteriorpraiseprocessxpsQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrematch2reshape2rlangrprojrootrstanrstantoolsscalesStanHeadersstringistringrtensorAtestthattibbletidyselectutf8vctrsviridisLitewaldowithryulab.utils

Aggregating Average Treatment Effects with baggr

Rachael Meager, Witold Wiecek

Rendered frombaggr.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2023-02-09
Started: 2018-06-25

Meta-analysis of binary data with baggr

Witold Wiecek

Rendered frombaggr_binary.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2023-02-09
Started: 2019-12-13

Readme and manuals

Help Manual

Help pageTopics
baggr - a package for Bayesian meta-analysisbaggr-package
Add colors to baggr plotsadd_color_to_plot
Bayesian aggregate treatment effects modelbaggr
(Run and) compare multiple baggr modelsbaggr_compare
Plotting method in baggr packagebaggr_plot
Set, get, and replace themes for baggr plotsbaggr_theme_get baggr_theme_replace baggr_theme_set baggr_theme_update
Generate individual-level binary outcome data from an aggregate statisticsbinary_to_individual
Bubble plots for meta-regression modelsbubble
Chickens: impact of electromagnetic field on calcium ion efflux in chicken brainschicks
Convert inputs for baggr modelsconvert_inputs
Spike & slab example datasetdata_spike
Make predictive draws from baggr modeleffect_draw
Plot predictive draws from baggr modeleffect_plot
Effects of covariates on outcome in baggr modelsfixed_effects
Draw a forest plot for a baggr modelforest_plot
Separate out ordering so we can test directlyget_order
Extract baggr study/group effectsgroup_effects study_effects
Check if something is a baggr_cv objectis.baggr_cv
L'Abbe plot for binary datalabbe
Compare LOO CV modelsloo_compare
Leave one group out cross-validation for 'baggr' modelsloocv
7 studies on effect of microcredit supplymicrocredit
Simplified version of the microcredit dataset.microcredit_simplified
"Mean and interval" function, including other summaries, calculated for matrix (by column) or vectormint
Correlation between mu and tau in a baggr modelmutau_cor
plot quantilesplot_quantiles
Plotting method for baggr outputsplot.baggr
Plot method for baggr_compare modelsplot.baggr_compare
Plotting method for results of baggr LOO analysesplot.baggr_cv
Pooling metrics and related statistics for baggrheterogeneity pooling weights.baggr
Convert from individual to summary data in meta-analysesprepare_ma
Prepare prior values for Stan models in baggrprepare_prior
Output a distribution as a stringprint_dist
S3 print method for objects of class 'baggr' (model fits)print.baggr
Print method for baggr_compare modelsprint.baggr_compare
Print baggr cv objects nicelyprint.baggr_cv
Print baggr_cv comparisonsprint.compare_baggr_cv
Prior distributions in baggrcauchy lkj lognormal multinormal normal priors student_t uniform
Extract only random effects from a baggr modelrandom_effects
8 schools exampleschools
Add prior values to Stan input for baggrset_prior_val
Plot single comparison ggplot in 'baggr_compare' stylesingle_comp_plot
Average treatment effects in a baggr modelhypermean hypersd treatment_effect
Yusuf et al: beta-blockers and heart attacksyusuf