meta_bma: Model Averaging for Meta-Analysis

Description Usage Arguments Details References See Also Examples

View source: R/meta_bma.R

Description

Fits random- and fixed-effects meta-analyses and performs Bayesian model averaging for H1 (d != 0) vs. H0 (d = 0).

Usage

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meta_bma(
  y,
  SE,
  labels,
  data,
  d = prior("cauchy", c(location = 0, scale = 0.707)),
  tau = prior("invgamma", c(shape = 1, scale = 0.15)),
  rscale_contin = 0.5,
  rscale_discrete = 0.707,
  centering = TRUE,
  prior = c(1, 1, 1, 1),
  logml = "integrate",
  summarize = "stan",
  ci = 0.95,
  rel.tol = .Machine$double.eps^0.3,
  logml_iter = 5000,
  silent_stan = TRUE,
  ...
)

Arguments

y

effect size per study. Can be provided as (1) a numeric vector, (2) the quoted or unquoted name of the variable in data, or (3) a formula to include discrete or continuous moderator variables.

SE

standard error of effect size for each study. Can be a numeric vector or the quoted or unquoted name of the variable in data

labels

optional: character values with study labels. Can be a character vector or the quoted or unquoted name of the variable in data

data

data frame containing the variables for effect size y, standard error SE, labels, and moderators per study.

d

prior distribution on the average effect size d. The prior probability density function is defined via prior.

tau

prior distribution on the between-study heterogeneity tau (i.e., the standard deviation of the study effect sizes dstudy in a random-effects meta-analysis. A (nonnegative) prior probability density function is defined via prior.

rscale_contin

scale parameter of the JZS prior for the continuous covariates.

rscale_discrete

scale parameter of the JZS prior for discrete moderators.

centering

whether continuous moderators are centered.

prior

prior probabilities over models (possibly unnormalized) in the order c(fixed_H0, fixed_H1, random_H0, random_H1). For instance, if we expect fixed effects to be two times as likely as random effects and H0 and H1 to be equally likely: prior = c(2,2,1,1).

logml

how to estimate the log-marginal likelihood: either by numerical integration ("integrate") or by bridge sampling using MCMC/Stan samples ("stan"). To obtain high precision with logml="stan", many MCMC samples are required (e.g., logml_iter=10000, warmup=1000).

summarize

how to estimate parameter summaries (mean, median, SD, etc.): Either by numerical integration (summarize = "integrate") or based on MCMC/Stan samples (summarize = "stan").

ci

probability for the credibility/highest-density intervals.

rel.tol

relative tolerance used for numerical integration using integrate. Use rel.tol=.Machine$double.eps for maximal precision (however, this might be slow).

logml_iter

number of iterations (per chain) from the posterior distribution of d and tau. The samples are used for computing the marginal likelihood of the random-effects model with bridge sampling (if logml="stan") and for obtaining parameter estimates (if summarize="stan"). Note that the argument iter=2000 controls the number of iterations for estimation of the random-effect parameters per study in random-effects meta-analysis.

silent_stan

whether to suppress the Stan progress bar.

...

further arguments passed to rstan::sampling (see stanmodel-method-sampling). Relevant MCMC settings concern the number of warmup samples that are discarded (warmup=500), the total number of iterations per chain (iter=2000), the number of MCMC chains (chains=4), whether multiple cores should be used (cores=4), and control arguments that make the sampling in Stan more robust, for instance: control=list(adapt_delta=.97).

Details

Bayesian model averaging for four meta-analysis models: Fixed- vs. random-effects and H0 (d=0) vs. H1 (e.g., d>0). For a primer on Bayesian model-averaged meta-analysis, see Gronau, Heck, Berkhout, Haaf, and Wagenmakers (2020).

By default, the log-marginal likelihood is computed by numerical integration (logml="integrate"). This is relatively fast and gives precise, reproducible results. However, for extreme priors or data (e.g., very small standard errors), numerical integration is not robust and might provide incorrect results. As an alternative, the log-marginal likelihood can be estimated using MCMC/Stan samples and bridge sampling (logml="stan").

To obtain posterior summary statistics for the average effect size d and the heterogeneity parameter tau, one can also choose between numerical integration (summarize="integrate") or MCMC sampling in Stan (summarize="stan"). If any moderators are included in a model, both the marginal likelihood and posterior summary statistics can only be computed using Stan.

References

Gronau, Q. F., Erp, S. V., Heck, D. W., Cesario, J., Jonas, K. J., & Wagenmakers, E.-J. (2017). A Bayesian model-averaged meta-analysis of the power pose effect with informed and default priors: the case of felt power. Comprehensive Results in Social Psychology, 2(1), 123-138. doi: 10.1080/23743603.2017.1326760

Gronau, Q. F., Heck, D. W., Berkhout, S. W., Haaf, J. M., & Wagenmakers, E.-J. (2020). A primer on Bayesian model-averaged meta-analysis. doi: 10.31234/osf.io/97qup

See Also

meta_fixed, meta_random

Examples

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### Bayesian Model-Averaged Meta-Analysis (H1: d>0)
data(towels)
set.seed(123)
mb <- meta_bma(logOR, SE, study, towels,
  d = prior("norm", c(mean = 0, sd = .3), lower = 0),
  tau = prior("invgamma", c(shape = 1, scale = 0.15))
)
mb
plot_posterior(mb, "d")

metaBMA documentation built on March 17, 2021, 9:06 a.m.