The metafor Package

A Meta-Analysis Package for R

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features [2021/06/09 14:32] – [Models and Analysis Approaches] Wolfgang Viechtbauerfeatures [2023/09/05 16:43] (current) – [Publication Bias] Wolfgang Viechtbauer
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 ==== Calculation of Effect Sizes and Outcome Measures ==== ==== Calculation of Effect Sizes and Outcome Measures ====
  
-The package allows the user to calculate various effect sizes and outcome measures frequently used in meta-analyses (''escalc()'' function), including:+The package allows the user to calculate various effect sizes and outcome measures frequently used in meta-analyses (''[[https://wviechtb.github.io/metafor/reference/escalc.html|escalc()]]'' function), including:
  
   * risk differences, risk ratios, and odds ratios for 2×2 table data,   * risk differences, risk ratios, and odds ratios for 2×2 table data,
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   * raw and standardized mean differences and response ratios (ratios of means),   * raw and standardized mean differences and response ratios (ratios of means),
   * raw and Fisher's r-to-z transformed correlation coefficients,   * raw and Fisher's r-to-z transformed correlation coefficients,
 +  * point-biserial and biserial correlation coefficients,
   * raw, log, logit, arcsine, and Freeman-Tukey double arcsine transformed proportions,   * raw, log, logit, arcsine, and Freeman-Tukey double arcsine transformed proportions,
   * raw, log, and square-root transformed incidence rates,   * raw, log, and square-root transformed incidence rates,
   * raw means, mean changes, and standardized mean changes,   * raw means, mean changes, and standardized mean changes,
-  * raw and transformed Cronbach's alpha values.+  * coefficients of variation and standard deviations and ratios thereof, 
 +  * raw and transformed Cronbach's alpha values, 
 +  * partial and semi-partial correlation coefficients. 
 + 
 +For raw and Fisher's r-to-z transformed correlation coefficients, ''[[https://wviechtb.github.io/metafor/reference/rcalc.html|rcalc()]]'' can construct the entire var-cov matrix of (partially) overlapping correlations. The var-cov matrix of dependent estimates more generally can also be constructed with the ''[[https://wviechtb.github.io/metafor/reference/vcalc.html|vcalc()]]'' function.
  
 ==== Models and Analysis Approaches ==== ==== Models and Analysis Approaches ====
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 The package provides a variety of models and analysis approaches, including: The package provides a variety of models and analysis approaches, including:
  
-  * fixed-, random-, and mixed-effects models using the inverse-variance method (''rma()'' function), +  * equal/fixed/random-effects models using the inverse-variance method (''[[https://wviechtb.github.io/metafor/reference/rma.uni.html|rma()]]'' function), 
-  * the Mantel-Haenszel and Peto's (one-step) method for 2×2 table and two-group person-time data (''rma.mh()'' and ''rma.peto()'' functions), +  * the Mantel-Haenszel and Peto's (one-step) method for 2×2 table and two-group person-time data (''[[https://wviechtb.github.io/metafor/reference/rma.mh.html|rma.mh()]]'' and ''[[https://wviechtb.github.io/metafor/reference/rma.peto.html|rma.peto()]]'' functions), 
-  * generalized linear (mixed-effects) models (i.e., mixed-effects (conditional) logistic and Poisson regression models) for the analysis of 2×2 table data, two-group person-time data, proportions, and incidence rates (''rma.glmm()'' function), +  * generalized linear (mixed-effects) models (i.e., mixed-effects (conditional) logistic and Poisson regression models) for the analysis of 2×2 table data, two-group person-time data, proportions, and incidence rates (''[[https://wviechtb.github.io/metafor/reference/rma.glmm.html|rma.glmm()]]'' function), 
-  * models for multilevel and multivariate meta-analyses (''rma.mv()'' function), +  * models for multilevel and multivariate meta-analyses (''[[https://wviechtb.github.io/metafor/reference/rma.mv.html|rma.mv()]]'' function), 
-  * models for network meta-analyses and mixed treatment comparisons (''rma.mv()'' function), +  * models for network meta-analyses and mixed treatment comparisons (''[[https://wviechtb.github.io/metafor/reference/rma.mv.html|rma.mv()]]'' function), 
-  * models for phylogenetic meta-analyses (''rma.mv()'' function), +  * models for phylogenetic meta-analyses (''[[https://wviechtb.github.io/metafor/reference/rma.mv.html|rma.mv()]]'' function), 
-  * spatio-temporal meta-analytic models (''rma.mv()'' function),+  * spatio-temporal meta-analytic models (''[[https://wviechtb.github.io/metafor/reference/rma.mv.html|rma.mv()]]'' function),
   * subgrouping and (mixed-effects) meta-regression analyses,   * subgrouping and (mixed-effects) meta-regression analyses,
-  * location-scale models (''rma()'' function using the ''scale'' argument),+  * location-scale models (''[[https://wviechtb.github.io/metafor/reference/rma.uni.html|rma()]]'' function using the ''scale'' argument),
   * models with user-defined weights.   * models with user-defined weights.
  
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 The package provides functions for creating a variety of meta-analytic plots and figures, including: The package provides functions for creating a variety of meta-analytic plots and figures, including:
  
-  * funnel plots (''funnel()'' function), +  * forest plots (''[[https://wviechtb.github.io/metafor/reference/forest.html|forest()]]'' and ''[[https://wviechtb.github.io/metafor/reference/addpoly.html|addpoly()]]'' functions), 
-  * forest plots (''forest()'' and ''addpoly()'' functions), +  * funnel plots (''[[https://wviechtb.github.io/metafor/reference/funnel.html|funnel()]]'' function), 
-  * scatter plots / bubble plots (''regplot()'' function), +  * scatter plots / bubble plots (''[[https://wviechtb.github.io/metafor/reference/regplot.html|regplot()]]'' function), 
-  * Baujat plots (''baujat()'' function), +  * Baujat plots (''[[https://wviechtb.github.io/metafor/reference/baujat.html|baujat()]]'' function), 
-  * L'Abbé plots (''labbe()'' function), +  * L'Abbé plots (''[[https://wviechtb.github.io/metafor/reference/labbe.html|labbe()]]'' function), 
-  * radial (Galbraith) plots (''radial()'' function), +  * radial (Galbraith) plots (''[[https://wviechtb.github.io/metafor/reference/radial.html|radial()]]'' function), 
-  * GOSH plots (''gosh()'' function), +  * GOSH plots (''[[https://wviechtb.github.io/metafor/reference/gosh.html|gosh()]]'' function), 
-  * profile likelihood plots (''profile()'' function), +  * profile likelihood plots (''[[https://wviechtb.github.io/metafor/reference/profile.rma.html|profile()]]'' function), 
-  * normal quantile-quantile (QQ) plots (''qqnorm()'' function).+  * normal quantile-quantile (QQ) plots (''[[https://wviechtb.github.io/metafor/reference/qqnorm.rma.html|qqnorm()]]'' function).
  
 R itself also provides extensive and very flexible graphing and plotting capabilities that can be easily adapted to create further plots and figures. R itself also provides extensive and very flexible graphing and plotting capabilities that can be easily adapted to create further plots and figures.
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 The presence of publication bias (or more accurately, funnel plot asymmetry or "small-study effects") and its potential impact on the results can be examined via a variety of methods, including: The presence of publication bias (or more accurately, funnel plot asymmetry or "small-study effects") and its potential impact on the results can be examined via a variety of methods, including:
  
-  * the rank correlation test (''ranktest()'' function), +  * the rank correlation test (''[[https://wviechtb.github.io/metafor/reference/ranktest.html|ranktest()]]'' function), 
-  * Egger's regression test (''regtest()'' function), +  * Egger's regression test (''[[https://wviechtb.github.io/metafor/reference/regtest.html|regtest()]]'' function), 
-  * the trim and fill method (''trimfill()'' function), +  * the trim and fill method (''[[https://wviechtb.github.io/metafor/reference/trimfill.html|trimfill()]]'' function), 
-  * the Henmi and Copas approach (''hc()'' function), +  * the Henmi and Copas approach (''[[https://wviechtb.github.io/metafor/reference/hc.html|hc()]]'' function), 
-  * a file drawer analysis (fail-safe N computation) using the Rosenthal, Orwin, and Rosenberg methods (''fsn()'' function), +  * file drawer analysis / fail-safe N computation (''[[https://wviechtb.github.io/metafor/reference/fsn.html|fsn()]]'' function), 
-  * the test of excess significance (''tes()'' function), +  * the test of excess significance (''[[https://wviechtb.github.io/metafor/reference/tes.html|tes()]]'' function), 
-  * selection models (''selmodel()'' function).+  * selection models (''[[https://wviechtb.github.io/metafor/reference/selmodel.html|selmodel()]]'' function).
  
 ==== Inference Methods ==== ==== Inference Methods ====
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 The package provides standard and advanced methods for drawing inferences based on meta-analytic data and for assessing the model fit, including: The package provides standard and advanced methods for drawing inferences based on meta-analytic data and for assessing the model fit, including:
  
-  * likelihood ratio and Wald-type tests (''anova()'' function), +  * likelihood ratio and Wald-type tests (''[[https://wviechtb.github.io/metafor/reference/anova.rma.html|anova()]]'' function),
-  * confidence intervals for heterogeneity statistics (''confint()'' function), +
-  * permutation tests (''permutest()'' function), +
-  * (cluster) robust tests and confidence intervals (''robust()'' function), +
-  * cumulative meta-analysis (''cumul()'' function), +
-  * fitted and predicted outcomes (''fitted()'' and ''predict()'' functions), +
-  * best linear unbiased predictions (''ranef()'' and ''blup()'' functions),+
   * improved tests/confidence intervals using the Knapp and Hartung method,   * improved tests/confidence intervals using the Knapp and Hartung method,
-  * model fit criteria (''logLik()'' and ''deviance()'' functions), +  * confidence intervals for heterogeneity statistics (''[[https://wviechtb.github.io/metafor/reference/confint.rma.html|confint()]]'' function), 
-  * information criteria (''AIC()'', ''BIC()'', and ''fitstats()'' functions), +  * cluster-robust inference methods / robust variance estimation (''[[https://wviechtb.github.io/metafor/reference/robust.html|robust()]]'' function), 
-  * simulation of data from a fitted model (''simulate()'' function).+  * permutation tests (''[[https://wviechtb.github.io/metafor/reference/permutest.html|permutest()]]'' function), 
 +  * cumulative meta-analysis (''[[https://wviechtb.github.io/metafor/reference/cumul.html|cumul()]]'' function), 
 +  * fitted and predicted outcomes (''[[https://wviechtb.github.io/metafor/reference/fitted.rma.html|fitted()]]'' and ''[[https://wviechtb.github.io/metafor/reference/predict.rma.html|predict()]]'' functions), 
 +  * best linear unbiased predictions (''[[https://wviechtb.github.io/metafor/reference/ranef.html|ranef()]]'' and ''[[https://wviechtb.github.io/metafor/reference/blup.html|blup()]]'' functions), 
 +  * model fit criteria (''[[https://wviechtb.github.io/metafor/reference/fitstats.html|logLik()]]'' and ''[[https://wviechtb.github.io/metafor/reference/fitstats.html|deviance()]]'' functions), 
 +  * information criteria (''[[https://wviechtb.github.io/metafor/reference/fitstats.html|AIC()]]'', ''[[https://wviechtb.github.io/metafor/reference/fitstats.html|BIC()]]'', and ''[[https://wviechtb.github.io/metafor/reference/fitstats.html|fitstats()]]'' functions), 
 +  * simulation of data from a fitted model (''[[https://wviechtb.github.io/metafor/reference/simulate.rma.html|simulate()]]'' function).
  
-The package is also compatible with the [[https://cran.r-project.org/package=glmulti|glmulti]] and [[https://cran.r-project.org/package=MuMIn|MuMIn]] packages for model selection and (multi)model inference (see [[tips:model_selection_with_glmulti|here]] for an illustration), the [[https://cran.r-project.org/package=boot|boot]] package for bootstrapping (see [[tips:bootstrapping_with_ma|here]] for an illustration), and the [[https://cran.r-project.org/package=mice|mice]] and [[https://cran.r-project.org/package=Amelia|Amelia]] packages for multiple imputation (see [[tips:multiple_imputation_with_mice_and_metafor|here]] for an illustration).+The package is also compatible with the [[https://cran.r-project.org/package=glmulti|glmulti]] and [[https://cran.r-project.org/package=MuMIn|MuMIn]] packages for model selection and multimodel inference (see [[tips:model_selection_with_glmulti_and_mumin|here]] for an illustration), the [[https://cran.r-project.org/package=boot|boot]] package for bootstrapping (see [[tips:bootstrapping_with_ma|here]] and [[tips:ci_for_r2|here]] for illustrations), and the [[https://cran.r-project.org/package=mice|mice]] and [[https://cran.r-project.org/package=Amelia|Amelia]] packages for multiple imputation (see [[tips:multiple_imputation_with_mice_and_metafor|here]] for an illustration).
  
 ==== Outlier/Influence Diagnostics ==== ==== Outlier/Influence Diagnostics ====
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 Various methods are available to identify outliers and/or influential studies, and for conducting sensitivity analyses, including: Various methods are available to identify outliers and/or influential studies, and for conducting sensitivity analyses, including:
  
-  * raw/standardized/studentized residuals (''residuals()'', ''rstandard()'', and ''rstudent()'' functions), +  * raw/standardized/studentized residuals (''[[https://wviechtb.github.io/metafor/reference/residuals.rma.html|residuals()]]'', ''[[https://wviechtb.github.io/metafor/reference/residuals.rma.html|rstandard()]]'', and ''[[https://wviechtb.github.io/metafor/reference/residuals.rma.html|rstudent()]]'' functions), 
-  * DFFITS values, Cook's distances, covariance ratios, and DFBETAS values (''influence()'' function), +  * DFFITS values, Cook's distances, covariance ratios, and DFBETAS values (''[[https://wviechtb.github.io/metafor/reference/influence.rma.uni.html|influence()]]'' function), 
-  * model weights and hat values (''weights()'' and ''hatvalues()'' functions), +  * model weights and hat values (''[[https://wviechtb.github.io/metafor/reference/weights.rma.html|weights()]]'' and ''[[https://wviechtb.github.io/metafor/reference/influence.rma.uni.html|hatvalues()]]'' functions), 
-  * leave-one-out analyses (''leave1out()'' and ''influence()'' functions).+  * leave-one-out analyses (''[[https://wviechtb.github.io/metafor/reference/leave1out.html|leave1out()]]'' and ''[[https://wviechtb.github.io/metafor/reference/influence.rma.uni.html|influence()]]'' functions).
  
 ==== Datasets ==== ==== Datasets ====
  
-The package also includes over 50 datasets from published meta-analyses that can be used for teaching and illustration purposes.+The package also includes over 60 datasets from published meta-analyses that can be used for teaching and illustration purposes (now part of the [[https://wviechtb.github.io/metadat/|metadat]] package).
  
 ==== Notes ==== ==== Notes ====
features.1623249167.txt.gz · Last modified: 2021/06/09 14:32 by Wolfgang Viechtbauer