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publipha

An R package for Bayesian meta-analysis that accounts for publication bias or p-hacking.

Overview

publipha is an package for doing Bayesian meta-analysis that accounts for publication bias or p-hacking. Its main functions are:

• psma does random effects meta-analysis under publication bias with a one-sided p-value based selection probability. The model is roughly the same as that of (Hedges, 1992)
• phma does random effects meta-analysis under a certain model of p-hacking with a one-sided p-value based propensity to p-hack. This is based on the forthcoming paper of by Moss and De Bin (2019).
• cma does classical random effects meta-analysis with the same priors as psma and cma.

Installation

Use the following command from inside R:

# install.packages("devtools")
devtools::install_github("JonasMoss/publipha")

Usage

Call the library function and use it like a barebones metafor::rma. The alpha tells psma or phma where they should place the cutoffs for significance.

library("publipha")
# Publication bias model
set.seed(313) # For reproducibility
model_psma = publipha::psma(yi = yi,
                            vi = vi,
                            alpha = c(0, 0.025, 0.05, 1),
                            data = metadat::dat.bangertdrowns2004)

# p-hacking model
set.seed(313)
model_phma = publipha::phma(yi = yi,
                          vi = vi,
                          alpha = c(0, 0.025, 0.05, 1),
                          data = metadat::dat.bangertdrowns2004)

# Classical model
set.seed(313)
model_cma = publipha::cma(yi = yi,
                          vi = vi,
                          alpha = c(0, 0.025, 0.05, 1),
                          data = metadat::dat.bangertdrowns2004)

You can calculate the posterior means of the meta-analytic mean with extract_theta0:

extract_theta0(model_psma)
#> [1] 0.1277197

extract_theta0(model_cma)
#> [1] 0.2212093

If you wish to plot a histogram of the posterior distribution of tau, the standard deviation of the effect size distribution, you can do it like this:

extract_tau(model_psma, hist)

References

• Hedges, Larry V. “Modeling publication selection effects in meta-analysis.” Statistical Science (1992): 246-255.
• Moss, Jonas and De Bin, Riccardo. “Modelling publication bias and p-hacking” (2019)

How to Contribute or Get Help

If you encounter a bug, have a feature request or need some help, open a Github issue. Create a pull requests to contribute.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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