meta_fixed: Bayesian Fixed-Effects Meta-Analysis

Description Usage Arguments Examples

View source: R/meta_fixed.R

Description

Runs a Bayesian meta-analysis assuming that the mean effect d in each study is identical (i.e., a fixed-effects analysis).

Usage

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meta_fixed(
  y,
  SE,
  labels,
  data,
  d = prior("cauchy", c(location = 0, scale = 0.707)),
  rscale_contin = 1/2,
  rscale_discrete = 0.707,
  centering = TRUE,
  logml = "integrate",
  summarize = "integrate",
  ci = 0.95,
  rel.tol = .Machine$double.eps^0.3,
  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.

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.

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).

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).

Examples

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### Bayesian Fixed-Effects Meta-Analysis (H1: d>0)
data(towels)
mf <- meta_fixed(logOR, SE, study,
  data = towels,
  d = prior("norm", c(mean = 0, sd = .3), lower = 0)
)
mf
plot_posterior(mf)
plot_forest(mf)

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