#
# Copyright 2007-2014 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
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# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
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# See the License for the specific language governing permissions and
# limitations under the License.
require(OpenMx)
library(MASS)
#Definition Variable Test 3
#Author: Mike Neale
#Date: July 29 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 means of 1 and 2 for x and y
#The group with a definition value of 0 has means af zero for x and y
#The definition variable is then used to define a mean deviation of the group with definition value 1
#make some data!
set.seed(200)
n = 500
Sigma <- matrix(c(1,.5,.5,1),2,2)
group1<-mvrnorm(n=n, c(1,2), Sigma)
group2<-mvrnorm(n=n, c(0,0), Sigma)
#put them both together, add a definition variable, and make an selection variables object
y<-rbind(group1,group2)
dimnames(y)[2]<-list(c("x","y"))
def<-rep(c(1,0),each=n)
selvars<-c("x","y")
if (0) {
#write data to a file for the mx script to read (not necessary for running in R)
write.table(cbind(y,def),file="temp-files/xydefmeans.rec",col.names=F,row.names=F)
}
#define the model with path commands, triggered by type="RAM"
defmeansmodel<-mxModel("Definition Means via Paths",
type="RAM",
mxData(data.frame(y,def), type="raw"),
manifestVars=c("x","y"),
latentVars="DefDummy",
mxPath(from=c("x","y"),
arrows=2,
free=TRUE,
values=c(1,1),
labels=c("Varx","Vary")
), # variances
mxPath(from="x", to="y",
arrows=2,
free=TRUE,
values=c(.1),
labels=c("Covxy")
), # covariances
mxPath(from="one",
to=c("x","y","DefDummy"),
arrows=1,
free=c(TRUE,TRUE,FALSE),
values=c(1,1,1),
labels =c("meanx","meany","data.def")),
mxPath(from="DefDummy",
to=c("x","y"),
arrows=1,
free=c(TRUE,TRUE),
values=c(1,1),
labels =c("beta_1","beta_2"))
)
#run the model
defmeansresult<-mxRun(defmeansmodel)
defmeansresult$matrices
defmeansresult$algebras
#Compare OpenMx estimates to summary statistics from raw data, remembering to knock off 1 and 2 from group 1's
# data, so as to estimate variance of combined sample without the mean correction.
# First we compute some summary statistics from the data
ObsCovs <- cov(rbind(group1 - rep(c(1,2), each=n), group2))
ObsMeansGroup1 <- c(mean(group1[,1]), mean(group1[,2]))
ObsMeansGroup2 <- c(mean(group2[,1]), mean(group2[,2]))
# Second we extract the parameter estimates and matrix algebra results from the model
Sigma<-defmeansresult$matrices$S$values[1:2,1:2]
Mu<-defmeansresult$matrices$M$values[1:2]
beta<-defmeansresult$matrices$A$values[1:2,3]
# Third, we check to see if things are more or less equal
omxCheckCloseEnough(ObsCovs,Sigma,.01)
omxCheckCloseEnough(ObsMeansGroup1,as.vector(Mu+beta),.001)
omxCheckCloseEnough(ObsMeansGroup2,as.vector(Mu),.001)