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#
# Copyright 2007-2020 by the individuals mentioned in the source code history
#
# 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.
# This test is adapted from Hermine's oneACEo.R .
# It's a monophenotype ACE model with an ordinal trait, and uses an equality MxConstraint to identify the model.
# The script deliberately puts the MxConstraint into the container MxModel, the MZ submodel, and the DZ submodel,
# thereby making it redundant.
library(OpenMx)
library(testthat)
#library(polycor)
# ----------------------------------------------------------------------------------------------------------------------
# PREPARE DATA
# Load Data
data(twinData)
dim(twinData)
# Create Ordinal Variables
nth <- 3 # number of thresholds
ordData <- data.frame(obmi1= twinData[,'bmi1'],
obmi2= twinData[,'bmi2'], zyg= twinData[,'zyg'])
quant <- quantile(ordData[,c('obmi1','obmi2')],(0:(nth+1))/(nth+1),na.rm=TRUE)
for (i in c('obmi1','obmi2')) { ordData[,i] <- cut(ordData[,i], breaks=quant, labels=c(0:nth)) }
# Select Variables for Analysis
vars <- 'obmi' # 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 Data for Analysis
mzData <- subset(ordData, zyg==1, selVars)
dzData <- subset(ordData, zyg==3, selVars)
mzDataF <- mxFactor( x=mzData, levels=c(0:nth) )
dzDataF <- mxFactor( x=dzData, levels=c(0:nth) )
# Generate Descriptive Statistics
sapply(mzData,table)
sapply(dzData,table)
# Set Starting Values
svLTh <- -1.5 # start value for first threshold
svITh <- 1 # start value for increments
svTh <- matrix(rep(c(svLTh,(rep(svITh,nth-1)))),nrow=nth,ncol=nv) # start value for thresholds
lbTh <- matrix(rep(c(-3,(rep(0.001,nth-1))),nv),nrow=nth,ncol=nv) # lower bounds for thresholds
svPa <- .5 # start value for path coefficient
svPe <- .7 # start value for path coefficient for e
lbPa <- .0001 # lower bound for path coefficient
# ----------------------------------------------------------------------------------------------------------------------
# PREPARE MODEL
# Create Algebra for expected Mean & Threshold Matrices
meanG <- mxMatrix( type="Zero", nrow=1, ncol=ntv, name="meanG" )
thinG <- mxMatrix(
type="Full", nrow=nth, ncol=ntv, free=TRUE, values=svTh, lbound=lbTh,
labels=c("t11","t12","t13","t21","t22","t23"), name="thinG" )
inc <- mxMatrix( type="Lower", nrow=nth, ncol=nth, free=FALSE, values=1, name="inc" )
threG <- mxAlgebra( expression= inc %*% thinG, name="threG" )
# Create Matrices for Path Coefficients
pathA <- mxMatrix( type="Lower", nrow=nv, ncol=nv, free=TRUE, values=svPa, label="a11", lbound=lbPa, name="a" )
pathC <- mxMatrix( type="Lower", nrow=nv, ncol=nv, free=TRUE, values=svPa, label="c11", lbound=lbPa, name="c" )
pathE <- mxMatrix( type="Lower", nrow=nv, ncol=nv, free=TRUE, values=svPe, label="e11", lbound=lbPa, name="e" )
# Create Algebra for Variance Components
covA <- mxAlgebra( expression=a %*% t(a), name="A" )
covC <- mxAlgebra( expression=c %*% t(c), name="C" )
covE <- mxAlgebra( expression=e %*% t(e), 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" )
# Constrain Variance of Binary Variables
var1 <- mxConstraint( expression=diag2vec(V)==1, name="Var1" )
# Create Data Objects for Multiple Groups
dataMZ <- mxData( observed=mzDataF, type="raw" )
dataDZ <- mxData( observed=dzDataF, type="raw" )
# Create Expectation Objects for Multiple Groups
expMZ <- mxExpectationNormal( covariance="expCovMZ", means="meanG", dimnames=selVars, thresholds="threG" )
expDZ <- mxExpectationNormal( covariance="expCovDZ", means="meanG", dimnames=selVars, thresholds="threG" )
funML <- mxFitFunctionML()
# Create Model Objects for Multiple Groups
pars <- list( meanG, thinG, inc, threG, covA, pathA, pathC, pathE, covC, covE, covP )
modelMZ <- mxModel( pars, covMZ, expCovMZ, dataMZ, expMZ, funML, var1, name="MZ" )
modelDZ <- mxModel( pars, covDZ, expCovDZ, dataDZ, expDZ, funML, var1, 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( "oneACEo", pars, var1, modelMZ, modelDZ, multi, estVC, ciACE )
if(mxOption(NULL,"Default optimizer")!="CSOLNP"){
fitACE <- mxRun( modelACE, intervals=F )
summary(fitACE)
modelACE2 <- modelACE
modelACE2$MZ@constraints <- list()
modelACE2$DZ@constraints <- list()
fitACE2 <- mxRun(modelACE2,intervals=F)
summary(fitACE2)
omxCheckCloseEnough(coef(fitACE), coef(fitACE2), 1e-7)
omxCheckCloseEnough(fitACE$output$standardErrors, fitACE2$output$standardErrors, 1e-7)
omxCheckCloseEnough(fitACE$output$fit, fitACE2$output$fit, 1e-7)
} else{
plan <- omxDefaultComputePlan()
plan$steps <- list(GD=plan$steps$GD)
plan$steps$GD <- mxComputeNelderMead(eqConstraintMthd="GDsearch")
modelACE <- mxModel(modelACE, plan)
fitACE <- expect_warning(mxRun(modelACE),NA)
summary(fitACE)
}
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