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NEWS
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Release 1.5.0 (Sep 26, 2024)
====================================
* Add dataset Chan17.
* Add lbound and ubound in sem() and as.mxAlgebra().
* Add a field of citations in the Jaramillo05 dataset.
* Rename create.mxModel() to sem().
* Add osmasem2() and friends.
* Add mean data in issp05.
* Support means in Cor2DataFrame().
* Fix the means of the latent variables at 0 in lavaan2RAM().
* Add "<~" operator in lavaan2RAM().
* Fix startvalues not assigned in create.mxModel().
Release 1.4.0 (May 15, 2024)
====================================
* Release to CRAN.
* Revise create.mxModel().
* Replace dontrun with donttest.
Release 1.3.1 (Aug 8, 2023)
====================================
* Release to CRAN.
* Lower the tolerance in testing asyCov(), which returns an error in latest R.
Release 1.3.0 (Jan 7, 2023)
====================================
* Fix a bug reported by Noel Card that meta() reported incorrect number of statistics and dfs.
* Rewrite asyCov() and rename the old one to asyCovOld().
* Add rCor3L() and its summary method.
* Add subset.variables argument in tssem2() and wls().
* Rename meta3() to meta3L() and meta3X() and meta3LFIML().
* Fix a critical bug in create.Tau2() that uses variances as SDs.
* Add a new argument 'level' in create.Tau2().
* Add a mxModel.Args in wls().
* Add A.lbound and A.ubound arguments in create.vechsR() and osmasem().
* Add data and group arguments in calEffSizes().
* Modify Nohe15A1 and Nohe15A2.
* Add a RAM argument in impliedR() and rimpliedR() and an SmatrixSD argument in rimpliedR().
* Add a starting value argument in as.mxAlgebra().
* Teach lavaan2RAM() to recognize functions of parameters and constraints in lavaan and convert them to mxAlgebra and mxConstraint in OpenMx.
* Experimental: teach create.mxModel() to recognize mxAlgrebra and mxConstraint converted from lavaan2RAM().
Release 1.2.5.1 (May 17, 2021)
====================================
* Release to CRAN.
* Fix a bug in an example in wls.Rd that triggers warning in R-Devel.
* Add Id, expCov, and expMean in create.mxModel().
Release 1.2.5 (Nov 29, 2020)
====================================
* Release to CRAN.
* Fix a bug in create.vechsR() with S0 argument to ensure that diagonals are 0.
* Fix a bug in create.Tau2() with the RE.type = "User" argument that incorrectly fixes all fixed parameters at 0.
* Add subset.rows argument in osmasem().
* Rename subset argument in osmasem() to subset.variables.
* Add an argument extraTries in rerun().
* Add dataset Mathieu15.
* Add calEffSizes().
* Add create.modMatrix().
* Rewrite Cor2DataFrame() to automatically append additional variables.
Release 1.2.4 (Jun 13, 2020)
====================================
* Release to CRAN.
* Add CFI and TLI in summary.osmasem().
* Rename the "Saturated" argument to "fitIndices" in summary.osmasem().
* Add "@" in the syntax of as.mxMatrix().
* Add as.mxAlgebra().
* Add as.symMatrix().
* Add an argument Jmatrix in osmasem().
* Add an argument ngroups in lavaan2RAM().
* Change the variable names in Becker92 and Becker94 so that they work better with lavaan2RAM().
Release 1.2.3.1 (Dec 8, 2019)
====================================
* Release to CRAN.
* Change class(x) == "foo" to inherits(x, "foo") to avoid errors in R 4.0.0.
Release 1.2.3 (Oct 10, 2019)
====================================
* Release to CRAN.
* Fix a minor bug in lavaan2RAM() that arranges variables according to x1, x10, x2, ...
* Improve tssem1FEM() in handling missing variables.
* Replace bootstrap vcov() with OpenMx's vcov() when there are constraints in wls().
* Add a subset argument in osmasem().
* Add a plotting method for osmasem object.
* Add metaFIML().
* Add an argument autofixtau2 for tssem1REM and osmasem objects in rerun().
* Add an argument RAM=NULL in wls(), tssem2(), and uniR2mx().
* Add dataset Kalaian96.
* Add robust argument in vcov.meta(), vcov.meta3X(), vcov.osmasem(), vcov.tssem1REM(), summary.meta(), summary.meta3X(), summary.osmasem(), and summary.tssem1REM().
Release 1.2.2 (May 29, 2019)
====================================
* Release to CRAN.
* Add dataset Stadler15.
* Add create.mxModel()
Release 1.2.0 (Oct 18, 2018)
====================================
* Release to CRAN.
* Add .onLoad()
* Add osmasem() and its related functions.
* Add an argument type=c("tssem", "osmasem") in pattern.na().
* Add datasets Gnambs18 and vanderPol17.
Release 1.1.0 (May 09, 2018)
====================================
* Release to CRAN.
* Add checkRAM().
* Add list.output argument in smdMTS() and smdMES().
* Add dataset Gleser94.
* Add dataset Scalco17.
* Modify plotting methods for lavaan models and wls objects.
* Fix a bug in list2matrix() for 2x2 matrices when the diag=FALSE.
* Fix 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)
====================================
* Release to CRAN.
* Add lavaan in import.
* Change 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."
* Add tssemParaVar() to estimate heterogeneity of parameter estimates in tssem approach.
* Add basic tests.
* Add fixed.x=FALSE automatically in uniR2lavaan().
* Fix coef.wls() so that it always follows the order of the parameter estimates in vcov.wls()
* Rename bootMASEM functions to bootuniR functions.
* Change the variable names in the output of asyCov().
Release 0.9.16 (September 29, 2017)
====================================
* Release to CRAN.
* Add bootMASEM functions.
* Rename the argument my.df to Cov in the tssem1 family.
* Rename the argument my.df to Cor in uniR1().
* Rename the argument asyCov to aCov in the wls() and tssem2().
* Rename the argument check.asyCov to check.aCov in is.pd().
* Revise meta2semPlot() so that it generates nicer variable labels.
* Change the variable names in Becker94 so that they work better with lavaan2RAM().
* Revise lavaan2RAM() to work with mean structure.
* Revise as.mxMatrix() to work with definition variables.
Release 0.9.14 (May 18, 2017)
====================================
* Release to CRAN.
* Fix a minor bug reported by GerardCY in meta() when lm() fails to get the starting values for coef.constraints.
* Add rCor(), rCorPop(), rCorSam(), summary.CorPop(), and print.summary.CorPop.
* Fix a minor bug reported by John Ma when there are more than 120 variables in tssem1FEM().
* Revise the formula in calculating the standard error in uniR1() by using the second improved approximation of Schmidt and Hunter (2015, p. 101)
* Add 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)
====================================
* Release to CRAN.
* Explicitly state "SLSQP" as the optimizer in metaSEM as "CSOLNP" is the default optimizer in OpenMx 2.7.4.
* Revise and rename impliedSigma() to impliedR().
* Fix a bug in uniR2mx() that does not work for models with latent variables.
* Add dataset Cooke16.
* Change solve() to chol2inv(chol()) and ginv() for matrix inversion.
* Add dataset Boer16.
* Add uniR1(), uniR2mx(), and uniR2lavaan().
* Modify a variable name in Becker09.
* Minor changes on how errors are handled in the main functions.
* Add datasets Nohe15A1 and Nohe15A2
* Modify some variable names in Hunter83
Release 0.9.10 (August 18, 2016)
====================================
* Release to CRAN.
* Add impliedSigma() to calculate the model implied correlation or covariance matrix based on the RAM model
* Add VarCorr() to extract variance component matrix for the class meta objects.
* Fix a minor bug in summary.tssem1FEM that throws an error when tT is NA.
* Add a check on the lengths of df and n in tssem1FEM() and tssem1REM().
* Change mxFitFunctionAlgebra() to mxFitFunctionMultigroup() in tssem1FEM().
* Fix a minor bug in lavaan2RAM() that does not honor the std.lv argument.
* Modify the vignette and added examples.
* Change the definition of is.pd() from Matrix::nearPD to MASS::mvrnorm().
Release 0.9.8 (April 16, 2016)
====================================
* Release to CRAN
* Return NA rather than error in calculating 95% CI of RMSEA when there are errors in summary.wls().
* Fix a minor bug in meta() that does not give a starting value on the last preditcor with intercept.constraints=0
* Add lavaan2RAM() to convert lavaan models to RAM models
* Add RMSEA 95% CI for wls and tssem1FEM classes
Release 0.9.6 (October 31, 2015)
====================================
* Release to CRAN
* Add several packages in NAMESPACE to satisfy R developmental version's (3.3.0) requirements
* Add ellipse package in imports
* Fix a bug reported by S.-F. Cheung in rerun() for tssem1FEM objects
* Add acov argument in asyCov() and tssem1()
* Modify wls(diag.constraints=FALSE) so that "mediators" are properly handled
* Add datasets Norton13 and Roorda11
* Change default model.name in tssem1REM(), tssem1FEM() and wls() to avoid potential error code with OpenMx 2.2.6
* Add RE.constraints argument and "User" option in RE.type argument in tssem1() and tssem1REM()
Release 0.9.4 (June 7, 2015)
====================================
* Modify to fit the CRAN policies
* Remove deltaMethod()
* Revert the RE.lbound from NA to 1e10 in meta() and meta3()
* Change the default "Optimality tolerance" to "6.3e-14" in OpenMx
* Change the default "Gradient iterations" to "2" in OpenMx
* Change the default arguments in rerun()
Release 0.9.3-2 (May 25, 2015)
====================================
* Change the RE.lbound from 1e10 to NA in meta() and meta3()
* Add trunction (0 and 1) in calculating R2 in summary.meta()
* Change the default optimizer from "NPSOL" to "SLSQP" (default in OpenMx)
* Change the default "Gradient algorithm" to "central" in OpenMx
* Add metaSEM.Rnw in vignettes
Release 0.9.3-1 (May 12, 2015)
====================================
* Correct a typo in the example of Aloe14 (reported by Fred Li)
* Modify to fit R-3.2.0
Release 0.9-2 (Jan 23, 2015)
====================================
* Add dataset Cheung00
* Add check.asyCov and cor.analysis arguments in is.pd()
Release 0.9-1 (Dec 22, 2014)
====================================
* Add citation in "Frontiers in Psychology"
* Release after the official release of OpenMx 2.0
* Remove dataset Craft03 which is duplicated of Becker09
Release 0.9-0 (Nov 16, 2014)
====================================
* Add semPlot package in Suggests and meta2semPlot() to convert wls objects to semPlotModel objects
* Fix a bug in tssem1REM() that may throw away correlation coefficients when there are missing correlations (not missing variables)
* Add byrow argument in vec2symMat()
* Add datasets Aloe14 and Becker09
* Remove ellipse package in the dependence
* Add silent=TRUE and run=TRUE arguments in most functions
* Fix the package to work in OpenMx 2.0
* Use labels rather than Amatrix and Smatrix in wls() and tssem2()
* Fix 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
* Add pattern.n() to display the accumulative sample sizes of the matrices
* Add a function deltaMethod() to calculate approximate sampling variance or covariance matrix
* Add methods for coef.MxRAMModel and vcov.MxRAMModel
* Modify the formula to calculate SRMR in summary.tssem1FEM()
* Add xlim and ylim arguments in plot.meta()
* Add datasets wvs94b and BCG
* Rename the dataset wvs94 to wvs94a
* Revise is.pd() so that it returns NA rather than throws an error when there are NA in the input matrices
* Add byrow argument in create.mxMatrix()
* Add pattern.na() to display the pattern of missing data in TSSEM
* Fix a bug in asyCov() returning an error in diffferent dimensions when the input is a list of 2x2 matrices
* Fix a bug reported by Andre Plamondon that tssem1FEM() returns an error when acovS is a scalar
Release 0.8-4 (May 1, 2013)
====================================
* Fix an issue in diag() that breaks the metaSEM in R-3.0.0
* Add Diag() that preserves the same functions as diag() prior to R-3.0.0
* Add dataset Craft03
Release 0.8-2 (Dec 28, 2012)
====================================
* Finalize features for release
Release 0.8-1 (Nov 28, 2012)
====================================
* Add 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.
* Add meta3X() to handle missing covariates with FIML for 3-level meta-analysis
* Fix the issue that there are missing levels in "cluster" in meta3() (and reml3()) reported by David Stanley
* Modify 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
* Add mx.algebras argument in wls() and tssem2()
* Add datasets Hunter83 and Jaramillo05
* Change 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)
====================================
* Finalize features for release
Release 0.7-1 (Aug 20, 2012)
====================================
* Remove argument RE_diag and added RE.type in tssem1() and tssem1REM()
* Remove standard error, z value and p values from summary() when intervals.type="LB"
* Add rerun() to refit models
* Rename all mx fitted objects to mx.fit
* Fix a bug in .minus2LL(), tssem1FEM() and summary.tssem1FEM in calculating the df of the independence model when cor.analysis=FALSE
* Fix a bug in tssem1REM() that my.df is a list of covariance matrices when cor.analysis=TRUE
* Fix a bug in calculating acov (solve()) in asyCov(), indirectEffect, tssem1.FE()
* Add indirectEffect() to calculate the asymptotic covariance matrix of indirect and direct effects
* Add create.Fmatrix() and create.mxMatrix() to create mxMatrix objects
* Add df.adjustment argument in summary.wls()
* Rewrite wls() using RAM specification (A, S and F matrices)
* Add diag.constraints argument in wls() to constrain diagonals as 1
* Improve efficiency by removing the call on installed.packages() and summary() from OpenMx
* Fix a bug in vec2symMat() reported by Yonghao Lim
* Add meta3() and reml3() for 3-level meta-analysis
* Add datasets Becker92, Becker94, Cooper03, Mak09, issp05 and Bornmann07
* Add I2 and R2 arguments to calculate heterogeneity and explained variance in meta()
* Rewrite meta() so that the predictors are treated as design matrix rather than as variables
* Revise meta() to replace NA with 1e5 in v object
* Rename coeff.constraints argument to coef.constraints in meta()
* Add homoStat argument in summary.meta()
* Rename tssem1FE() and tssem1RE() to tssem1FEM() and tssem1REM()
Release 0.7-0 (Nov 6, 2011)
====================================
* Fix a bug in meta() that does not include RE.lbound in Tau matrix when RE.lbound is a matrix
* Revise tssemFE() to handle incomplete data in the first group
* Add tssem1RE() for random-effects TSSEM
* Rename tssem1() to tssem1FE() for fixed-effects TSSEM
* Modify tssem1() to be a wrapper for tssem1FE() and tssem1RE()
* Modify tssem2() to fit both fixed- and random-effects structural models from tssem1()
* Add "cluster" argument in tssem1.FE() and some methods for it
* Add "select" argument in coef.meta() and vcov.meta()
* Fix a bug by removing the characters in matrix column when OpenMx 1.1 is used
* Fix a bug in asyCov() that uses only the first sample size
Release 0.6-0 (May 24, 2011)
====================================
* Add a dataset WVS94
* Change dropNA argument from TRUE to FALSE in asyCov()
* Add data argument in meta() and reml()
* Fix a bug by addinng dimnames in M matrix in meta() when OpenMx 1.1 is used
* Fix a bug in summary.meta(), summary.reml() and summary.wls() when OpenMx 1.1 is used
* Add plot() method for multivariate meta-analysis
* Add the ellipse package on "Imports" in the DESCRIPTION
* Add the metafor package on "Suggests" in the DESCRIPTION
Release 0.5-4 (March 19, 2011)
====================================
* Fix a bug in tssem1() when OpenMx 1.0.6 is used
* Fix a bug in tssem1() which ignores start.values argument
Release 0.5-3 (February 20, 2011)
====================================
* Add model.name argument in tssem1(), tssem2(), wls(), meta() and reml()
* Add anova() method for wls, meta and reml objects
* Add no. of studies and no. of observed statistics in reml object (Ad-hoc)
* Use Tau2 to represent variance component in both meta() and reml()
* Fix a bug in meta() that exists when no. of predictors is larger than 1
Release 0.5-2 (December 11, 2010)
====================================
* Add name argument in as.mxMatrix()
* Add reml() to estimate variance components with REML
Release 0.5-1 (October 10, 2010)
====================================
* Add bdiagMat() and bdiagRep() functions to create block diagonal matrix
* Fix a bug in meta() that ignored RE.lbound when RE.constraints was used
* Fix a bug in readFullMat() that converts data into data.frames rather than matrices
Release 0.5-0 (October 2, 2010)
====================================
* Add vcov() methods for tssem1, wls objects
* Add coef() methods for tssem1, wls and meta objects
Release 0.3-9 (September 24, 2010)
====================================
* Add a vignette
Release 0.3-8 (September 20, 2010)
====================================
* Add suppressWarnings = TRUE in meta(), tssem1(), tssem2(), and wls()
* Add OpenMx.status[[1]] into summary method
Release 0.3-7 (September 19, 2010)
====================================
* Add vec2symMat(), matrix2bdiag() and homoStat() functions
* Move startValues(), minus2LL() and indepwlsChisq() to hidden functions
* Update datasets on Cheung09 and Digman97
Release 0.3-6 (September 16, 2010)
====================================
* Rename the package to "Meta-Analysis using Structural Equation Modeling"
* Add vcov() method for meta object
Release 0.3-5 (September 14, 2010)
====================================
* Fix a few bugs
Release 0.3-4 (September 12, 2010)
====================================
* Add summary.meta() for meta objects
Release 0.3-3 (September 8, 2010)
====================================
* Add new arguments in asyCov()
* Add meta() for univariate and multivariate meta-analysis
* Add as.mxMatrix() to convert matrices to mxMatrices
Release 0.3-2 (August 29, 2010)
====================================
* Add indepWLSChisq() to calculate the chi-square statistic for an independent model based on WLS
* Add minus2LL() to calculate the chi-square statistic for independent and saturated models based on ML
* Add summary.wls() and print.summary.wls() for wls objects
* Add summary.tssem1() and print.summary.tssem1() for tssem1 objects
Release 0.3-1 (August 09, 2010)
====================================
* First alpha release to R-forge
* Add basic functions for TSSEM