demo/DefinitionMeans_PathRaw.R

In OpenMx: Extended Structural Equation Modelling

#
#   Copyright 2007-2018 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.

# -----------------------------------------------------------------------------
# Program: DefinitionMeans_PathRaw.R  
# Author: Mike Neale
# Date: 2009.08.01 
#
# ModelType: Means
# DataType: Continuous
# Field: None
#
# Purpose: 
#      Definition Means model to estimate moderation effect 
#      of measured variable 
#      Path style model input - Raw data input
#
# RevisionHistory:
#      Hermine Maes -- 2009.10.08 updated & reformatted
#      Ross Gore -- 2011.06.15 added Model, Data & Field metadata
#      Hermine Maes -- 2014.11.02 piecewise specification
# -----------------------------------------------------------------------------

#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 used to define a mean deviation of the group
# with definition value 1.

require(OpenMx)
library(MASS)
# Load Libraries
# -----------------------------------------------------------------------------

set.seed(200)
N=500
Sigma          <- matrix(c(1,.5,.5,1),2,2)
group1         <- mvtnorm::rmvnorm(N, c(1,2), Sigma) # Use mvrnorm from MASS package
group2         <- mvtnorm::rmvnorm(N, c(0,0), Sigma)

xy             <- rbind(group1,group2)      # Bind groups together by rows
dimnames(xy)[2]<- list(c("x","y"))          # Add names
def            <- rep(c(1,0),each=N);       # Add def var [2n] for group status
selVars        <- c("x","y")                # Make selection variables object
# Simulate data
# -----------------------------------------------------------------------------

# variances
variances    <- mxPath( from=c("x","y"), arrows=2, 
                        free=TRUE, values=1, labels=c("Varx","Vary") )
# covariances
covariances  <- mxPath( from="x", to="y", arrows=2, 
                        free=TRUE, values=.1, labels=c("Covxy") )
# means
means        <- mxPath( from="one", to=c("x","y"), arrows=1, 
                        free=TRUE, values=1, labels=c("meanx","meany") )
# definition value
defValues    <- mxPath( from="one", to="DefDummy", arrows=1, 
                        free=FALSE, values=1, labels="data.def" )
# beta weights
betaWeights  <- mxPath( from="DefDummy", to=c("x","y"), arrows=1, 
                        free=TRUE, values=1, labels=c("beta_1","beta_2") )
# dataset
dataRaw      <- mxData( observed=data.frame(xy,def), type="raw" )
defMeansModel <- mxModel("Definition Means Path Specification", type="RAM",
                         manifestVars=selVars, latentVars="DefDummy",
                         dataRaw, variances, covariances, means, 
                         defValues, betaWeights)
# Define model
# -----------------------------------------------------------------------------

defMeansFit<-mxRun(defMeansModel)
# Run the model
# -----------------------------------------------------------------------------

defMeansFit$matrices
defMeansFit$algebras



# Remember 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 <- mxEval(S[1:2,1:2], defMeansFit)
Mu    <- mxEval(M[1:2], defMeansFit)
beta  <- mxEval(A[1:2,3], defMeansFit)

# 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)
# Compare OpenMx estimates to summary statistics from raw data, 
# -----------------------------------------------------------------------------