Meta-Analysis using Structural Equation Modeling

A collection of functions for conducting meta-analysis using a structural equation modeling (SEM) approach via the 'OpenMx' and 'lavaan' packages. It also implements various procedures to perform meta-analytic structural equation modeling on the correlation and covariance matrices.


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The metaSEM package conducts univariate and multivariate meta-analyses using a structural equation modeling (SEM) approach via the OpenMx package. It also implements the two-stage SEM approach to conduct meta-analytic structural equation modeling on correlation/covariance matrices.

The stable version can be installed from CRAN by:

install.packages("metaSEM")

The developmental version can be installed from GitHub by:

# install.packages("devtools")

devtools::install_github("mikewlcheung/metasem")

News

Release 1.2.0 (Oct 18, 2018)

  • Added .onLoad()
  • Added osmasem() and its related functions.
  • Added the argument type=c("tssem", "osmasem") in pattern.na().
  • Added datasets Gnambs18 and vanderPol17.

Release 1.1.0 (May 09, 2018)

  • Released to CRAN.
  • Added checkRAM().
  • Added list.output argument in smdMTS() and smdMES().
  • Added dataset Gleser94.
  • Added dataset Scalco17.
  • Modified plotting methods for lavaan models and wls objects.
  • Fixed a bug in list2matrix() for 2x2 matrices when the diag=FALSE.
  • Fixed a minor bug in asyCov() with acov="weighted" or "unweighted" when the cor.analysis=TRUE with covariance matrices as the input.

Release 1.0.0 (January 12, 2018)

  • Released to CRAN.
  • Added lavaan in import.
  • Changed the defaults of tssem1(): From method="FEM" to method="REM", From RE.type="Symm" to RE.type="Diag", and From acov="individual" to acov="weighted."
  • Added tssemParaVar() to estimate heterogeneity of parameter estimates in tssem approach.
  • Added basic tests.
  • Added fixed.x=FALSE automatically in uniR2lavaan().
  • Fixed coef.wls() so that it always follows the order of the parameter estimates in vcov.wls()
  • Rename bootMASEM functions to bootuniR functions.
  • Changed the variable names in the output of asyCov().

Release 0.9.16 (September 29, 2017)

  • Released to CRAN.
  • Added bootMASEM functions.
  • Renamed the argument my.df to Cov in the tssem1 family.
  • Renamed the argument my.df to Cor in uniR1().
  • Renamed the argument asyCov to aCov in the wls() and tssem2().
  • Renamed the argument check.asyCov to check.aCov in is.pd().
  • Revised meta2semPlot() so that it generates nicer variable labels.
  • Changed the variable names in Becker94 so that they work better with lavaan2RAM().
  • Revised lavaan2RAM() to work with mean structure.
  • Revised as.mxMatrix() to work with definition variables.

Release 0.9.14 (May 18, 2017)

  • Released to CRAN.
  • Fixed a minor bug reported by GerardCY in meta() when lm() fails to get the starting values for coef.constraints.
  • Added rCor(), rCorPop(), rCorSam(), summary.CorPop(), and print.summary.CorPop.
  • Fixed a minor bug reported by John Ma when there are more than 120 variables in tssem1FEM().
  • Revised the formula in calculating the standard error in uniR1() by using the second improved approximation of Schmidt and Hunter (2015, p. 101)
  • Added smdMTS() and smdMES() to calculate standardized mean differences for multiple treatment studies and for multiple end-point studies.

Release 0.9.12 (January 23, 2017)

  • Released to CRAN.
  • Explicitly stated "SLSQP" as the optimizer in metaSEM as "CSOLNP" is the default optimizer in OpenMx 2.7.4.
  • Revised and renamed impliedSigma() to impliedR().
  • Fixed a bug in uniR2mx() that does not work for models with latent variables.
  • Added dataset Cooke16.
  • Changed solve() to chol2inv(chol()) and ginv() for matrix inversion.
  • Added dataset Boer16.
  • Added uniR1(), uniR2mx(), and uniR2lavaan().
  • Modified a variable name in Becker09.
  • Minor changes on how errors are handled in the main functions.
  • Added datasets Nohe15A1 and Nohe15A2
  • Modified some variable names in Hunter83

Release 0.9.10 (August 18, 2016)

  • Released to CRAN.
  • Added impliedSigma() to calculate the model implied correlation or covariance matrix based on the RAM model
  • Added VarCorr() to extract variance component matrix for the class meta objects.
  • Fixed a minor bug in summary.tssem1FEM that throws an error when tT is NA.
  • Added a check on the lengths of df and n in tssem1FEM() and tssem1REM().
  • Changed mxFitFunctionAlgebra() to mxFitFunctionMultigroup() in tssem1FEM().
  • Fixed a minor bug in lavaan2RAM() that does not honor the std.lv argument.
  • Modified the vignette and added examples.
  • Changed the definition of is.pd() from Matrix::nearPD to MASS::mvrnorm().

Release 0.9.8 (April 16, 2016)

  • Released to CRAN
  • Returned NA rather than error in calculating 95% CI of RMSEA when there are errors in summary.wls().
  • Fixed a minor bug in meta() that does not give a starting value on the last preditcor with intercept.constraints=0
  • Added lavaan2RAM() to convert lavaan models to RAM models
  • Added RMSEA 95% CI for wls and tssem1FEM classes

Release 0.9.6 (October 31, 2015)

  • Released to CRAN
  • Added several packages in NAMESPACE to satisfy R developmental version's (3.3.0) requirements
  • Added ellipse package in imports
  • Fixed a bug reported by S.-F. Cheung in rerun() for tssem1FEM objects
  • Added acov argument in asyCov() and tssem1()
  • Modified wls(diag.constraints=FALSE) so that "mediators" are properly handled
  • Added datasets Norton13 and Roorda11
  • Changed default model.name in tssem1REM(), tssem1FEM() and wls() to avoid potential error code with OpenMx 2.2.6
  • Added RE.constraints argument and "User" option in RE.type argument in tssem1() and tssem1REM()

Release 0.9.4 (June 7, 2015)

  • Modified to fit the CRAN policies
  • Removed deltaMethod()
  • Reverted the RE.lbound from NA to 1e10 in meta() and meta3()
  • Changed the default "Optimality tolerance" to "6.3e-14" in OpenMx
  • Changed the default "Gradient iterations" to "2" in OpenMx
  • Changed the default arguments in rerun()

Release 0.9.3-2 (May 25, 2015)

  • Changed the RE.lbound from 1e10 to NA in meta() and meta3()
  • Added trunction (0 and 1) in calculating R2 in summary.meta()
  • Changed the default optimizer from "NPSOL" to "SLSQP" (default in OpenMx)
  • Changed the default "Gradient algorithm" to "central" in OpenMx
  • Added metaSEM.Rnw in vignettes

Release 0.9.3-1 (May 12, 2015)

  • Corrected a typo in the example of Aloe14 (reported by Fred Li)
  • Modified to fit R-3.2.0

Release 0.9-2 (Jan 23, 2015)

  • Added dataset Cheung00
  • Added check.asyCov and cor.analysis arguments in is.pd()

Release 0.9-1 (Dec 22, 2014)

  • Added citation in "Frontiers in Psychology"
  • Released after the official release of OpenMx 2.0
  • Removed dataset Craft03 which is duplicated of Becker09

Release 0.9-0 (Nov 16, 2014)

  • Added semPlot package in Suggests and meta2semPlot() to convert wls objects to semPlotModel objects
  • Fixed a bug in tssem1REM() that may throw away correlation coefficients when there are missing correlations (not missing variables)
  • Added byrow argument in vec2symMat()
  • Added datasets Aloe14 and Becker09
  • Removed ellipse package in the dependence
  • Added silent=TRUE and run=TRUE arguments in most functions
  • Fixed the package to work in OpenMx 2.0
  • Used labels rather than Amatrix and Smatrix in wls() and tssem2()
  • Fixed a bug in create.mxMatrix() to respect byrow=TRUE for "Symm" and "Stand" types

Release 0.8-5 (Jun 6, 2014)

  • Change "." to "_" in datasets Jaramillo05 and wvs94a, and indirectEffect.R
  • Added pattern.n() to display the accumulative sample sizes of the matrices
  • Added a function deltaMethod() to calculate approximate sampling variance or covariance matrix
  • Added methods for coef.MxRAMModel and vcov.MxRAMModel
  • Modified the formula to calculate SRMR in summary.tssem1FEM()
  • Added xlim and ylim arguments in plot.meta()
  • Added datasets wvs94b and BCG
  • Renamed the dataset wvs94 to wvs94a
  • Revised is.pd() so that it returns NA rather than throws an error when there are NA in the input matrices
  • Added byrow argument in create.mxMatrix()
  • Added pattern.na() to display the pattern of missing data in TSSEM
  • Fixed a bug in asyCov() returning an error in diffferent dimensions when the input is a list of 2x2 matrices
  • Fixed a bug reported by Andre Plamondon that tssem1FEM() returns an error when acovS is a scalar

Release 0.8-4 (May 1, 2013)

  • Fixed an issue in diag() that breaks the metaSEM in R-3.0.0
  • Added Diag() that preserves the same functions as diag() prior to R-3.0.0
  • Added dataset Craft03

Release 0.8-2 (Dec 28, 2012)

  • Finalized features for release

Release 0.8-1 (Nov 28, 2012)

  • Added automatic constraint on the diagonals when diag.constraints=FALSE argument in wls() for cor.analysis=TRUE. It is usually not necessary to set diag.constraints=TRUE unless there are mediators.
  • Added meta3X() to handle missing covariates with FIML for 3-level meta-analysis
  • Fixed the issue that there are missing levels in "cluster" in meta3() (and reml3()) reported by David Stanley
  • Modified meta(), reml(), meta3() and reml3() functions so that intercept.constraints, coef.constraints, RE.constraints, RE2.constraints and RE3.constraints may accept a scalar or vector as inputs
  • Added mx.algebras argument in wls() and tssem2()
  • Added datasets Hunter83 and Jaramillo05
  • Changed the default in as.mxMatrix. If 'x' is not a matrix, as.matrix(x) is applied on 'x' instead of throwing an error.

Release 0.8-0 (Aug 30, 2012)

  • Finalized features for release

Release 0.7-1 (Aug 20, 2012)

  • Removed argument RE_diag and added RE.type in tssem1() and tssem1REM()
  • Removed standard error, z value and p values from summary() when intervals.type="LB"
  • Added rerun() to refit models
  • Renamed all mx fitted objects to mx.fit
  • Fixed a bug in .minus2LL(), tssem1FEM() and summary.tssem1FEM in calculating the df of the independence model when cor.analysis=FALSE
  • Fixed a bug in tssem1REM() that my.df is a list of covariance matrices when cor.analysis=TRUE
  • Fixed a bug in calculating acov (solve()) in asyCov(), indirectEffect, tssem1.FE()
  • Added indirectEffect() to calculate the asymptotic covariance matrix of indirect and direct effects
  • Added create.Fmatrix() and create.mxMatrix() to create mxMatrix objects
  • Added df.adjustment argument in summary.wls()
  • Rewrote wls() using RAM specification (A, S and F matrices)
  • Added diag.constraints argument in wls() to constrain diagonals as 1
  • Improved efficiency by removing the call on installed.packages() and summary() from OpenMx
  • Fixed a bug in vec2symMat() reported by Yonghao Lim
  • Added meta3() and reml3() for 3-level meta-analysis
  • Added datasets Becker92, Becker94, Cooper03, Mak09, issp05 and Bornmann07
  • Added I2 and R2 arguments to calculate heterogeneity and explained variance in meta()
  • Rewrote meta() so that the predictors are treated as design matrix rather than as variables
  • Revised meta() to replace NA with 1e5 in v object
  • Renamed coeff.constraints argument to coef.constraints in meta()
  • Added homoStat argument in summary.meta()
  • Renamed tssem1FE() and tssem1RE() to tssem1FEM() and tssem1REM()

Release 0.7-0 (Nov 6, 2011)

  • Fixed a bug in meta() that does not include RE.lbound in Tau matrix when RE.lbound is a matrix
  • Revised tssemFE() to handle incomplete data in the first group
  • Added tssem1RE() for random-effects TSSEM
  • Renamed tssem1() to tssem1FE() for fixed-effects TSSEM
  • Modified tssem1() to be a wrapper for tssem1FE() and tssem1RE()
  • Modified tssem2() to fit both fixed- and random-effects structural models from tssem1()
  • Added "cluster" argument in tssem1.FE() and some methods for it
  • Added "select" argument in coef.meta() and vcov.meta()
  • Fixed a bug by removing the characters in matrix column when OpenMx 1.1 is used
  • Fixed a bug in asyCov() that uses only the first sample size

Release 0.6-0 (May 24, 2011)

  • Added a dataset WVS94
  • Changed dropNA argument from TRUE to FALSE in asyCov()
  • Added data argument in meta() and reml()
  • Fixed a bug by addinng dimnames in M matrix in meta() when OpenMx 1.1 is used
  • Fixed a bug in summary.meta(), summary.reml() and summary.wls() when OpenMx 1.1 is used
  • Added plot() method for multivariate meta-analysis
  • Added the ellipse package on "Imports" in the DESCRIPTION
  • Added the metafor package on "Suggests" in the DESCRIPTION

Release 0.5-4 (March 19, 2011)

  • Fixed a bug in tssem1() when OpenMx 1.0.6 is used
  • Fixed a bug in tssem1() which ignores start.values argument

Release 0.5-3 (February 20, 2011)

  • Added model.name argument in tssem1(), tssem2(), wls(), meta() and reml()
  • Added anova() method for wls, meta and reml objects
  • Added no. of studies and no. of observed statistics in reml object (Ad-hoc)
  • Used Tau2 to represent variance component in both meta() and reml()
  • Fixed a bug in meta() that exists when no. of predictors is larger than 1

Release 0.5-2 (December 11, 2010)

  • Added name argument in as.mxMatrix()
  • Added reml() to estimate variance components with REML

Release 0.5-1 (October 10, 2010)

  • Added bdiagMat() and bdiagRep() functions to create block diagonal matrix
  • Fixed a bug in meta() that ignored RE.lbound when RE.constraints was used
  • Fixed a bug in readFullMat() that converts data into data.frames rather than matrices

Release 0.5-0 (October 2, 2010)

  • Added vcov() methods for tssem1, wls objects
  • Added coef() methods for tssem1, wls and meta objects

Release 0.3-9 (September 24, 2010)

  • Added a vignette

Release 0.3-8 (September 20, 2010)

  • Added suppressWarnings = TRUE in meta(), tssem1(), tssem2(), and wls()
  • Added OpenMx.status[[1]] into summary method

Release 0.3-7 (September 19, 2010)

  • Added vec2symMat(), matrix2bdiag() and homoStat() functions
  • Moved startValues(), minus2LL() and indepwlsChisq() to hidden functions
  • Updated datasets on Cheung09 and Digman97

Release 0.3-6 (September 16, 2010)

  • Renamed the package to "Meta-Analysis using Structural Equation Modeling"
  • Added vcov() method for meta object

Release 0.3-5 (September 14, 2010)

  • Fixed a few bugs

Release 0.3-4 (September 12, 2010)

  • Added summary.meta() for meta objects

Release 0.3-3 (September 8, 2010)

  • Added new arguments in asyCov()
  • Added meta() for univariate and multivariate meta-analysis
  • Added as.mxMatrix() to convert matrices to mxMatrices

Release 0.3-2 (August 29, 2010)

  • Added indepWLSChisq() to calculate the chi-square statistic for an independent model based on WLS
  • Added minus2LL() to calculate the chi-square statistic for independent and saturated models based on ML
  • Added summary.wls() and print.summary.wls() for wls objects
  • Added summary.tssem1() and print.summary.tssem1() for tssem1 objects

Release 0.3-1 (August 09, 2010)

  • First alpha release to R-forge
  • Added basic functions for TSSEM

Reference manual

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install.packages("metaSEM")

1.2.0 by Mike W.-L. Cheung, 6 months ago


https://github.com/mikewlcheung/metasem


Browse source code at https://github.com/cran/metaSEM


Authors: Mike W.-L. Cheung <[email protected]>


Documentation:   PDF Manual  


Task views: Meta-Analysis, Psychometric Models and Methods


GPL (>= 2) license


Imports Matrix, MASS, ellipse, graphics, stats, utils, mvtnorm, numDeriv, lavaan

Depends on OpenMx

Suggests metafor, semPlot, R.rsp, testthat


See at CRAN