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'))

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-statistics meta-analysis quantile-regression stan treatment-effects

37 exports 46 stars 3.10 score 79 dependencies 86 scripts 477 downloads

Last updated 7 months agofrom:98e261de4b. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Aug 27 2024
R-4.5-win-x86_64	NOTE	Aug 27 2024
R-4.5-linux-x86_64	NOTE	Aug 27 2024
R-4.4-win-x86_64	NOTE	Aug 27 2024
R-4.4-mac-aarch64	NOTE	Aug 27 2024
R-4.4-mac-x86_64	NOTE	Jul 28 2024
R-4.3-win-x86_64	NOTE	Aug 27 2024
R-4.3-mac-aarch64	NOTE	Aug 27 2024
R-4.3-mac-x86_64	NOTE	Jul 28 2024

Exports:baggr baggr_compare baggr_plot baggr_theme_get baggr_theme_replace baggr_theme_set baggr_theme_update binary_to_individual bubble cauchy convert_inputs effect_draw effect_plot fixed_effects forest_plot group_effects heterogeneity hypermean hypersd labbe lkj lognormal loo_compare loocv mint multinormal mutau_cor normal plot_quantiles pooling prepare_ma random_effects single_comp_plot student_t study_effects treatment_effect uniform

Dependencies:abind backports bayesplot BH brio callr checkmate cli colorspace crayon desc diffobj digest distributional dplyr evaluate fansi farver forestplot fs generics ggplot2 ggplotify ggrepel ggridges glue gridExtra gridGraphics gtable inline isoband jsonlite labeling lattice lifecycle loo magrittr MASS Matrix matrixStats mgcv munsell nlme numDeriv pillar pkgbuild pkgconfig pkgload plyr posterior praise processx ps QuickJSR R6 RColorBrewer Rcpp RcppEigen RcppParallel rematch2 reshape2 rlang rprojroot rstan rstantools scales StanHeaders stringi stringr tensorA testthat tibble tidyselect utf8 vctrs viridisLite waldo withr yulab.utils

Aggregating Average Treatment Effects with baggr

Rachael Meager, Witold Wiecek

Rendered frombaggr.Rmdusingknitr::rmarkdownon Aug 27 2024.

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

Meta-analysis of binary data with baggr

Witold Wiecek

Rendered frombaggr_binary.Rmdusingknitr::rmarkdownon Aug 27 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
baggr - a package for Bayesian meta-analysis	baggr-package
Add colors to baggr plots	add_color_to_plot
Bayesian aggregate treatment effects model	baggr
(Run and) compare multiple baggr models	baggr_compare
Plotting method in baggr package	baggr_plot
Set, get, and replace themes for baggr plots	baggr_theme_get baggr_theme_replace baggr_theme_set baggr_theme_update
Generate individual-level binary outcome data from an aggregate statistics	binary_to_individual
Bubble plots for meta-regression models	bubble
Chickens: impact of electromagnetic field on calcium ion efflux in chicken brains	chicks
Convert inputs for baggr models	convert_inputs
Spike & slab example dataset	data_spike
Make predictive draws from baggr model	effect_draw
Plot predictive draws from baggr model	effect_plot
Effects of covariates on outcome in baggr models	fixed_effects
Draw a forest plot for a baggr model	forest_plot
Separate out ordering so we can test directly	get_order
Extract baggr study/group effects	group_effects study_effects
Check if something is a baggr_cv object	is.baggr_cv
L'Abbe plot for binary data	labbe
Compare LOO CV models	loo_compare
Leave one group out cross-validation for 'baggr' models	loocv
7 studies on effect of microcredit supply	microcredit
Simplified version of the microcredit dataset.	microcredit_simplified
"Mean and interval" function, including other summaries, calculated for matrix (by column) or vector	mint
Correlation between mu and tau in a baggr model	mutau_cor
plot quantiles	plot_quantiles
Plotting method for baggr outputs	plot.baggr
Plot method for baggr_compare models	plot.baggr_compare
Plotting method for results of baggr LOO analyses	plot.baggr_cv
Pooling metrics and related statistics for baggr	heterogeneity pooling weights.baggr
Convert from individual to summary data in meta-analyses	prepare_ma
Prepare prior values for Stan models in baggr	prepare_prior
Output a distribution as a string	print_dist
S3 print method for objects of class 'baggr' (model fits)	print.baggr
Print method for baggr_compare models	print.baggr_compare
Print baggr cv objects nicely	print.baggr_cv
Print baggr_cv comparisons	print.compare_baggr_cv
Prior distributions in baggr	cauchy lkj lognormal multinormal normal priors student_t uniform
Extract only random effects from a baggr model	random_effects
8 schools example	schools
Add prior values to Stan input for baggr	set_prior_val
Plot single comparison ggplot in 'baggr_compare' style	single_comp_plot
Average treatment effects in a baggr model	hypermean hypersd treatment_effect
Yusuf et al: beta-blockers and heart attacks	yusuf