Features
- binomial-normal models for binary data via the
BiBMA function
-
NoBMA and NoBMA.reg() functions as wrappers around RoBMA RoBMA.reg() functions for simpler specification of publication bias unadjusted Bayesian model-averaged meta-analysis
- adding odds ratios output transformation`
- extending (instead of a complete refitting) of models via the
update.RoBMA() function (only non-converged models by default or all by setting extend_all = TRUE)
Fixes
- handling of non-converged models
Fixes (thanks to Don & Rens)
Features
- meta-regression with
RoBMA.reg() function
- posterior marginal summary and plots for the
RoBMA.reg models with summary_marginal() and plot_marginal() functions
- new vignette on hierarchical Bayesian model-averaged meta-analysis
- new vignette on robust Bayesian model-averaged meta-regression
- adding vignette from AMPPS tutorial
- faster implementation of JAGS multivariate normal distribution (based on the BUGS JAGS module)
- incorporating
weight argument in the RoBMA and combine_data functions in order to pass custom likelihood weights
- ability to use inverse square weights in the weighted meta-analysis by setting a
weighted_type = "inverse_sqrt" argument
Changes
- reworked interface for the hierarchical models. Prior distributions are now specified via the
priors_hierarchical and priors_hierarchical_null arguments instead of priors_rho and priors_rho_null. The model summary now shows Hierarchical component summary.
Fixes
- suppressing start-up message
- cleaning up imports
Fixes
- fixing weighted meta-analysis parameterization
Features
- weighted meta-analysis by specifying
study_ids argument in RoBMA() and setting weighted = TRUE. The likelihood contribution of estimates from each study is down-weighted proportionally to the number of estimates in that study. Note that this experimental feature is supposed to provide a conservative alternative for estimating RoBMA in cases with multiple estimates from a study where the multivariate option is not computationally feasible.
Fixes
- updating the Makevars to install with R 4.2 and JAGS 4.3.1
Fixes
- updating the C++ to compile on M1 Mac
Changes
- message about the effect size scale of parameter estimates is always shown
- compatibility with BayesTools 0.2.0+
Features
- three-level meta-analysis by specifying
study_ids argument in RoBMA. However, note that this is (1) an experimental feature and (2) the computational expense of fitting selection models with clustering is extreme. As of now, it is almost impossible to have more than 2-3 estimates clustered within a single study).
Fixes
- adding Windows ucrt patch (thanks to Tomas Kalibera)
- adding BayesTools version check
Fixes
- incorrectly formatted citations in vignettes and capitalization
Features
- adding
informed_prior() function (from the BayesTools package) that allows specification of various informed prior distributions from the field of medicine and psychology
- adding a vignette reproducing the example of dentine sensitivity with the informed Bayesian model-averaged meta-analysis from Bartoš et al., 2021 (open-access),
- further reductions of fitted object size when setting
save = "min"
Fixes
- more informative error message when the JAGS module fails to load
- correcting wrong PEESE transformation for the individual models summaries (issue #12)
- fixing error message for missing conditional PET-PEESE
- fixing incorrect lower bound check for log(OR)
Features
- adding
interpret() function (issue #11)
- adding effect size transformation via
output_scale argument to plot() and plot_models() functions
- better handling of effect size transformations and scaling - BayesTools style back-end functions with Jacobian transformations
Please notice that this is a major release that breaks backwards compatibility.
Changes
- naming of the arguments specifying prior distributions for the different parameters/components of the models changed (
priors_mu -> priors_effect, priors_tau -> priors_heterogeneity, and priors_omega -> priors_bias),
- prior distributions for specifying weight functions now use a dedicated function (
prior(distribution = "two.sided", parameters = ...) -> prior_weightfunction(distribution = "two.sided", parameters = ...)),
- new dedicated function for specifying no publication bias adjustment component / no heterogeneity component (
prior_none()),
- new dedicated functions for specifying models with the PET and PEESE publication bias adjustments (
prior_PET(distribution = "Cauchy", parameters = ...) and prior_PEESE(distribution = "Cauchy", parameters = ...)),
- new default prior distribution specification for the publication bias adjustment part of the models (corresponding to the RoBMA-PSMA model from Bartoš et al., 2021 preprint),
- new
model_type argument allowing to specify different “pre-canned” models ("PSMA" = RoBMA-PSMA, "PP" = RoBMA-PP, "2w" = corresponding to Maier et al., in press , manuscript),
-
combine_data function allows combination of different effect sizes / variability measures into a common effect size measure (also used from within the RoBMA function),
- better and improved automatic fitting procedure now enabled by default (can be turned of with
autofit = FALSE)
- prior distributions can be specified on the different scale than the supplied effect sizes (the package fits the model on Fisher’s z scale and back transforms the results back to the scale that was used for prior distributions specification, Cohen’s d by default, but both of them can be overwritten with the
prior_scale and transformation arguments),
- new prior distributions, e.g., beta or fixed weight functions,
- estimates from individual models are now plotted with the
plot_models() function and the forest plot can be obtained with the forest() function,
- the posterior distribution plots for the individual weights are no able supported, however, the weightfunction and the PET-PEESE publication bias adjustments can be visualized with the
plot.RoBMA() function and parameter = "weightfunction" and parameter = "PET-PEESE".
Fixes
- check_setup function not working at all
Changes
- the studies’s true effects are now marginalized out of the random effects models and are no longer estimated (see Appendix A of our prerint for more details). As a results, arguments referring to the true effects are now disabled.
- all models are now being estimated using the likelihood of effect sizes (instead of test-statistics as usually defined). We reproduced the simulation study that we used to evaluate the method performance and it achieved identical results (up to MCMC error, before marginalizing out the true effects). A big advantage of using the normal likelihood for effect sizes is a considerable speed up of the whole estimation process.
- as a results of these two changes, the results of the models will differ to those of pre 1.2.0 version
Fixes
- autofit being turn on if any control argument was specified
Fixes
- vdiffr not being used conditionally in unit tests
Fixes
- inability to fit a model without specifying a seed
- inability to produce individual model plots due to incompatibility with the newer versions of ggplot2
Features
- parallel within and between model fitting using the parallel package with ‘parallel = TRUE’ argument
Fixes:
- models being fitted automatically until reaching R-hat lower than 1.05 without setting max_rhat and autofit control parameters
- bug preventing to draw a bivariate plot of mu and tau
- range for parameter estimates from individual models no containing 0 (or 1 in case of OR measured effect sizes)
- inability to fit a model with only null mu distributions if correlation or OR measured effect sizes were specified
- ordering of the estimated and observed effects when both of them are requested simultaneously
- formatting of this file (NEWS.md)
Improvements:
- priors plot: parameter specification, default plotting range, clearer x-axis labels in cases when the parameter is defined on transformed scale
- parameters plots: probability scale always ends at the same spot as is the last tick on the density scale
- adding warnings if any of the specified models has Rhat higher than 1.05 or the specified value
- grouping the same warnings messages together
Fixes:
- inability to run models without the silent = TRUE control
Features:
- x-axis rescaling for the weight function plot (by setting ‘rescale_x = TRUE’ in the ‘plot.RoBMA’ function)
- setting expected direction of the effect in for RoBMA function
Fixes:
- marginal likelihood calculation for models with spike prior distribution on mean parameter which location was not set to 0
- some additional error messages
CRAM requested changes:
- changing information messages from ‘cat’ to ‘message’ from plot related functions
- saving and returning the ‘par’ settings to the user defined one in the base plot functions
Fixes:
- the summary and plot function now shows quantile based confidence intervals for individual models instead of the HPD provided before (this affects only ‘summary’/‘plot’ with ‘type = “individual”’, all other confidence intervals were quantile based before)
Fixes:
- summary function returning median instead of mean
Fixes:
- incorrectly weighted theta estimates
- models with non-zero point prior distribution incorrectly plotted using when “models” option in case that the mu parameter was transformed
Additional features:
- analyzing OR
- distributions implemented using boost library (helps with convergence issues)
- ability to mute the non-suppressible “precision not achieved” warning messages by using “silent” = TRUE inside of the control argument
- vignettes
Notable changes:
- the way how the seed is set before model fitting (the simulation study will not be reproducible with the new version of the package)