inst/models/passing/GREML_intercept_check.R

In OpenMx: Extended Structural Equation Modelling

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#   Copyright 2007-2019 by the individuals mentioned in the source code history
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#        http://www.apache.org/licenses/LICENSE-2.0
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require(OpenMx)
require(mvtnorm)

set.seed(21204)
Sigma <- matrix(0.5,4,4)
diag(Sigma) <- 1
Dat <- rmvnorm(n=26,mean=rep(0,4),sigma=Sigma)
Dat <- matrix(t(Dat))
colnames(Dat) <- "y"
famid <- sort(rep(LETTERS,4))
CRM <- outer(famid,famid,"==") + 0
ge <- mxExpectationGREML(V="V", yvars="y")

for(pds in 1:3){
	Cmod <- mxModel(
		"GREMLtest",
		mxData(observed = Dat, type="raw", sort=FALSE),
		ge,
		mxFitFunctionGREML(),
		mxMatrix(type = "Diag", nrow = 104, ncol=104, free=T, values = 0.5, labels = "ve", 
						 lbound = 0.0001, name = "Ve"),
		mxMatrix(type="Full",nrow=1,ncol=1,free=T,values=0.5,labels="vc",name="Vc"),
		mxMatrix(type="Full",nrow=104,ncol=104,free=F,values=CRM,name="C",condenseSlots = T),
		mxAlgebra( (Vc%x%C) + Ve, name="V")
	)
	Cmod$fitfunction@.parallelDerivScheme <- pds
	Crun <- mxRun(Cmod)
	Csumm <- summary(Crun)
	
	#Compare to lme4 REML results:
	omxCheckCloseEnough(Csumm$GREMLfixeff$coeff[1],-0.01313328,1e-5)
	omxCheckCloseEnough(Csumm$GREMLfixeff$se[1],0.1533185,1e-4)
	omxCheckCloseEnough(Crun$output$estimate,c(0.3797,0.5162),1e-3)
	
	#Intercept should equal grand mean:
	omxCheckCloseEnough(Csumm$GREMLfixeff$coeff[1],mean(Dat),1e-12)
}