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library(OpenMx)
library(testthat)
context("definition variables")

#Definition Variable Test 1
#Author: Ryne Estabrook
#Date: 12 May 2009
#Modified: Mike Neale
#Date: July 28 2009


#This script is used to test the definition variable functionality in OpenMx
#The definition variable in this example is dichotomous, and describes two different groups
#These two groups are measured on two variables, x and y
#The group with a definition value of 1 has a covariance of 1 between x and y
#The group with a definition value of 0 has no relationship between x and y (beyond chance)
#The definition variable is then used to define the covariance between x and y

#make some data!
set.seed(200)
x1<-rnorm(500)
y1<-x1+rnorm(500, sd=1)

x2<-rnorm(500)
y2<-rnorm(500)+rnorm(500, sd=1)
n = 500

#put them both together, add a definition variable, and make an MxData object
x<-c(x1,x2)
y<-c(y1,y2)
def<-rep(c(1,0),each=500)
selvars<-c("x","y")


# Three covariance model matrices: 
#  "cov" for the zero relationship group
#  "def" for the definition variable, 
#   and "beta" for estimating difference between groups' covariances
# One common mean vector, "M"

#define the model, including a FIML objective function, which will optimize the matrix S
model<-mxModel("model", mxFitFunctionML(),mxExpectationNormal("S", "M"), 
				mxData((data.frame(x,y,def)), type="raw"),
				mxMatrix("Symm", nrow=2, ncol=2, free=FALSE, values=c(0, 0, 0), labels=c(NA, "data.def", NA),
					dimnames=list(selvars,selvars), name="def"),
				mxMatrix("Symm", nrow=2, ncol=2, free=c(FALSE,TRUE,TRUE,FALSE), values=c(0, 0.0001, .0001, 0),
					dimnames=list(selvars,selvars), name="beta"),
				mxMatrix("Symm", nrow=2, ncol=2, free=TRUE, values=c(1, 0, 1),
					lbound=c(0.001, NA, 0.001), dimnames=list(selvars,selvars), name="cov"),
				mxMatrix("Full", nrow = 1, ncol = 2, free=TRUE, dimnames=list(NULL, selvars), name = "M"),
				mxAlgebra(cov+beta*def, name="S", dimnames=list(selvars,selvars))
			)

#run the model
run<-mxRun(model)


#Compare OpenMx results to hard-coded Mx 1.0 results 

omxCheckCloseEnough(1.011952, mxEval(beta[1,2], run), .001)
omxCheckCloseEnough(as.vector(c(0.982984089,0.004713885,0.004713885,2.052462084)),
	as.vector(mxEval(cov, run)),.001)
omxCheckCloseEnough(0.02570572, mxEval(M[1,1], run), .001)
omxCheckCloseEnough(0.01611651, mxEval(M[1,2], run), .001)

