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# Copyright 2007-2018 The OpenMx Project
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
library(OpenMx)
#This test script doesn't need to be run with all 3 optimizers, and it runs fine with CSOLNP:
if(mxOption(NULL,"Default optimizer")!="CSOLNP"){stop("SKIP")}
data(twinData)
# Select Variables for Analysis
vars <- 'bmi' # list of variables names
nv <- 1 # number of variables
ntv <- nv*2 # number of total variables
selVars <- paste(vars,c(rep(1,nv),rep(2,nv)),sep="")
# Select Covariates for Analysis
twinData[,'age'] <- twinData[,'age']/100
twinData <- twinData[-which(is.na(twinData$age)),]
covVars <- 'age'
# Select Data for Analysis
mzData <- subset(twinData, zyg==1, c(selVars, covVars))
dzData <- subset(twinData, zyg==3, c(selVars, covVars))
# Set Starting Values
svBe <- 0.01 # start value for regressions
svMe <- 20 # start value for means
svPa <- .2 # start value for path coefficient
svPe <- .5 # start value for path coefficient for e
# ----------------------------------------------------------------------------------------------------------------------
# PREPARE MODEL
# Create Matrices for Covariates and linear Regression Coefficients
defL <- mxMatrix( type="Full", nrow=1, ncol=1, free=FALSE, labels=c("data.age"), name="defL" )
pathBl <- mxMatrix( type="Full", nrow=1, ncol=1, free=TRUE, values=svBe, label="b11", name="bl" )
# Create Algebra for expected Mean Matrices
meanG <- mxMatrix( type="Full", nrow=1, ncol=ntv, free=TRUE, values=svMe, labels="b0", name="meanG" )
expMean <- mxAlgebra( expression= meanG + cbind(defL%*%bl,defL%*%bl), name="expMean" )
# Create Matrices for Variance Components
covA <- mxMatrix( type="Symm", nrow=nv, ncol=nv, free=TRUE, values=svPa, label="A11", name="A" )
covC <- mxMatrix( type="Symm", nrow=nv, ncol=nv, free=TRUE, values=svPa, label="C11", name="C" )
covE <- mxMatrix( type="Symm", nrow=nv, ncol=nv, free=TRUE, values=svPa, label="E11", name="E" )
# Create Algebra for expected Variance/Covariance Matrices in MZ & DZ twins
covP <- mxAlgebra( expression= A+C+E, name="V" )
covMZ <- mxAlgebra( expression= A+C, name="cMZ" )
covDZ <- mxAlgebra( expression= 0.5%x%A+ C, name="cDZ" )
expCovMZ <- mxAlgebra( expression= rbind( cbind(V, cMZ), cbind(t(cMZ), V)), name="expCovMZ" )
expCovDZ <- mxAlgebra( expression= rbind( cbind(V, cDZ), cbind(t(cDZ), V)), name="expCovDZ" )
# Create Data Objects for Multiple Groups
dataMZ <- mxData( observed=mzData, type="raw" )
dataDZ <- mxData( observed=dzData, type="raw" )
# Create Expectation Objects for Multiple Groups
expMZ <- mxExpectationNormal( covariance="expCovMZ", means="expMean", dimnames=selVars )
expDZ <- mxExpectationNormal( covariance="expCovDZ", means="expMean", dimnames=selVars )
funML <- mxFitFunctionML()
# Create Model Objects for Multiple Groups
pars <- list( pathBl, meanG, covA, covC, covE, covP )
defs <- list( defL )
modelMZ <- mxModel( pars, defs, expMean, covMZ, expCovMZ, dataMZ, expMZ, funML, name="MZ" )
modelDZ <- mxModel( pars, defs, expMean, covDZ, expCovDZ, dataDZ, expDZ, funML, name="DZ" )
multi <- mxFitFunctionMultigroup( c("MZ","DZ") )
# Create Algebra for Variance Components
rowVC <- rep('VC',nv)
colVC <- rep(c('A','C','E','SA','SC','SE'),each=nv)
estVC <- mxAlgebra( expression=cbind(A,C,E,A/V,C/V,E/V), name="VC", dimnames=list(rowVC,colVC) )
# Create Confidence Interval Objects
ciACE <- mxCI( "VC[1,1:3]" )
# Build Model with Confidence Intervals
modelACE <- mxModel( "oneACEvca", pars, modelMZ, modelDZ, multi, estVC, ciACE )
# Run ACE Model
fitACE <- mxRun( modelACE, intervals=F )
#AE
modelAE <- omxSetParameters( fitACE, labels="C11", free=FALSE, values=0, name="oneAEvca" )
fitAE <- mxRun( modelAE, intervals=F )
#CE
modelCE <- omxSetParameters( modelACE, labels="A11", free=FALSE, values=0, name="oneCEvca" )
fitCE <- mxRun( modelCE, intervals=F )
#E
modelE <- omxSetParameters( fitAE, labels="A11", free=FALSE, values=0, name="oneEvca" )
fitE <- mxRun(modelE)
#Test omxAkaikeWeights():
omxAkaikeWeights(models=list(fitACE,fitAE,fitCE,fitE))
#Test mxModelAverage():
mxModelAverage(reference="C11",models=list(fitACE,fitAE,fitCE,fitE))
#Test mxModelAverage(), with free parameters only (which is faster),
#for all permutations of arguments `include`, `SE`, `refAsBlock`, & `type`:
mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=NULL,refAsBlock=FALSE,type="AIC")
mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=NULL,refAsBlock=FALSE,type="AIC")
mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=FALSE,refAsBlock=FALSE,type="AIC")
mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=FALSE,refAsBlock=FALSE,type="AIC")
mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=TRUE,refAsBlock=FALSE,type="AIC")
mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=TRUE,refAsBlock=FALSE,type="AIC")
omxCheckError(mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=NULL,refAsBlock=TRUE,type="AIC"),
"when refAsBlock=TRUE and include='onlyFree', no references may be fixed in any model")
mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=NULL,refAsBlock=TRUE,type="AIC")
omxCheckError(mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=FALSE,refAsBlock=TRUE,type="AIC"),
"when refAsBlock=TRUE and include='onlyFree', no references may be fixed in any model")
mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=FALSE,refAsBlock=TRUE,type="AIC")
omxCheckError(mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=TRUE,refAsBlock=TRUE,type="AIC"),
"when refAsBlock=TRUE and include='onlyFree', no references may be fixed in any model")
mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=TRUE,refAsBlock=TRUE,type="AIC")
mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=NULL,refAsBlock=FALSE,type="AICc")
mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=NULL,refAsBlock=FALSE,type="AICc")
mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=FALSE,refAsBlock=FALSE,type="AICc")
mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=FALSE,refAsBlock=FALSE,type="AICc")
mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=TRUE,refAsBlock=FALSE,type="AICc")
mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=TRUE,refAsBlock=FALSE,type="AICc")
omxCheckError(mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=NULL,refAsBlock=TRUE,type="AICc"),
"when refAsBlock=TRUE and include='onlyFree', no references may be fixed in any model")
mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=NULL,refAsBlock=TRUE,type="AICc")
omxCheckError(mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=FALSE,refAsBlock=TRUE,type="AICc"),
"when refAsBlock=TRUE and include='onlyFree', no references may be fixed in any model")
mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=FALSE,refAsBlock=TRUE,type="AICc")
omxCheckError(mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=TRUE,refAsBlock=TRUE,type="AICc"),
"when refAsBlock=TRUE and include='onlyFree', no references may be fixed in any model")
mxModelAverage(
reference=c("b11","b0","A11","C11","E11"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=TRUE,refAsBlock=TRUE,type="AICc")
#Test with MxAlgebra elements:
mxModelAverage(reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=NULL,refAsBlock=FALSE,type="AIC")
mxModelAverage(reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=NULL,refAsBlock=FALSE,type="AIC")
mxModelAverage(reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=FALSE,refAsBlock=FALSE,type="AIC")
mxModelAverage(reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=FALSE,refAsBlock=FALSE,type="AIC")
mxModelAverage(reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=TRUE,refAsBlock=FALSE,type="AIC")
mxModelAverage(reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=TRUE,refAsBlock=FALSE,type="AIC")
omxCheckError(mxModelAverage(
reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=NULL,refAsBlock=TRUE,type="AIC"),
"when refAsBlock=TRUE and include='onlyFree', no references may be fixed in any model")
mxModelAverage(reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=NULL,refAsBlock=TRUE,type="AIC")
omxCheckError(mxModelAverage(
reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=FALSE,refAsBlock=TRUE,type="AIC"),
"when refAsBlock=TRUE and include='onlyFree', no references may be fixed in any model")
mxModelAverage(reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=FALSE,refAsBlock=TRUE,type="AIC")
omxCheckError(mxModelAverage(
reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=TRUE,refAsBlock=TRUE,type="AIC"),
"when refAsBlock=TRUE and include='onlyFree', no references may be fixed in any model")
mxModelAverage(reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=TRUE,refAsBlock=TRUE,type="AIC")
mxModelAverage(reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=NULL,refAsBlock=FALSE,type="AICc")
mxModelAverage(reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=NULL,refAsBlock=FALSE,type="AICc")
mxModelAverage(
reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=FALSE,refAsBlock=FALSE,type="AICc")
mxModelAverage(
reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=FALSE,refAsBlock=FALSE,type="AICc")
mxModelAverage(
reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=TRUE,refAsBlock=FALSE,type="AICc")
mxModelAverage(
reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=TRUE,refAsBlock=FALSE,type="AICc")
omxCheckError(mxModelAverage(
reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=NULL,refAsBlock=TRUE,type="AICc"),
"when refAsBlock=TRUE and include='onlyFree', no references may be fixed in any model")
mxModelAverage(
reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=NULL,refAsBlock=TRUE,type="AICc")
omxCheckError(mxModelAverage(
reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=FALSE,refAsBlock=TRUE,type="AICc"),
"when refAsBlock=TRUE and include='onlyFree', no references may be fixed in any model")
mxModelAverage(
reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=FALSE,refAsBlock=TRUE,type="AICc")
omxCheckError(mxModelAverage(
reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="onlyFree",SE=TRUE,refAsBlock=TRUE,type="AICc"),
"when refAsBlock=TRUE and include='onlyFree', no references may be fixed in any model")
mxModelAverage(
reference=c("V","MZ.expCovMZ[2,1]"),models=list(fitACE,fitAE,fitCE,fitE),include="all",SE=TRUE,refAsBlock=TRUE,type="AICc")
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