#
# Copyright 2007-2019 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: TwoFactorModel_MatrixRaw.R
# Author: Ryne Estabrook
# Date: 2009.08.01
#
# ModelType: Factor
# DataType: Continuous
# Field: None
#
# Purpose:
# Two Factor model to estimate factor loadings, residual variances and means
# Matrix style model input - Raw data input
#
# RevisionHistory:
# Hermine Maes -- 2009.10.08 updated & reformatted
# Ross Gore -- 2011.06.06 added Model, Data & Field metadata
# Hermine Maes -- 2014.11.02 piecewise specification
# -----------------------------------------------------------------------------
require(OpenMx)
# Load Library
# -----------------------------------------------------------------------------
data(myFADataRaw)
# Prepare Data
# -----------------------------------------------------------------------------
manifestVars <- c("x1","x2","x3","y1","y2","y3")
latentVars <- c("F1","F2")
twoFactorRaw <- myFADataRaw[,manifestVars]
dataRaw <- mxData( observed=myFADataRaw, type="raw" )
matrA <- mxMatrix( type="Full", nrow=8, ncol=8,
free= c(F,F,F,F,F,F,F,F,
F,F,F,F,F,F,T,F,
F,F,F,F,F,F,T,F,
F,F,F,F,F,F,F,F,
F,F,F,F,F,F,F,T,
F,F,F,F,F,F,F,T,
F,F,F,F,F,F,F,F,
F,F,F,F,F,F,F,F),
values=c(0,0,0,0,0,0,1,0,
0,0,0,0,0,0,1,0,
0,0,0,0,0,0,1,0,
0,0,0,0,0,0,0,1,
0,0,0,0,0,0,0,1,
0,0,0,0,0,0,0,1,
0,0,0,0,0,0,0,0,
0,0,0,0,0,0,0,0),
labels=c(NA,NA,NA,NA,NA,NA,"l1",NA,
NA,NA,NA,NA,NA,NA,"l2",NA,
NA,NA,NA,NA,NA,NA,"l3",NA,
NA,NA,NA,NA,NA,NA,NA,"l4",
NA,NA,NA,NA,NA,NA,NA,"l5",
NA,NA,NA,NA,NA,NA,NA,"l6",
NA,NA,NA,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA,NA),
byrow=TRUE, name="A" )
matrS <- mxMatrix( type="Symm", nrow=8, ncol=8,
free= c(T,F,F,F,F,F,F,F,
F,T,F,F,F,F,F,F,
F,F,T,F,F,F,F,F,
F,F,F,T,F,F,F,F,
F,F,F,F,T,F,F,F,
F,F,F,F,F,T,F,F,
F,F,F,F,F,F,T,T,
F,F,F,F,F,F,T,T),
values=c(1,0,0,0,0,0,0,0,
0,1,0,0,0,0,0,0,
0,0,1,0,0,0,0,0,
0,0,0,1,0,0,0,0,
0,0,0,0,1,0,0,0,
0,0,0,0,0,1,0,0,
0,0,0,0,0,0,1,.5,
0,0,0,0,0,0,.5,1),
labels=c("e1",NA, NA, NA, NA, NA, NA, NA,
NA, "e2", NA, NA, NA, NA, NA, NA,
NA, NA, "e3", NA, NA, NA, NA, NA,
NA, NA, NA, "e4", NA, NA, NA, NA,
NA, NA, NA, NA, "e5", NA, NA, NA,
NA, NA, NA, NA, NA, "e6", NA, NA,
NA, NA, NA, NA, NA, NA,"varF1","cov",
NA, NA, NA, NA, NA, NA,"cov","varF2"),
byrow=TRUE, name="S" )
matrF <- mxMatrix( type="Full", nrow=6, ncol=8,
free=FALSE,
values=c(1,0,0,0,0,0,0,0,
0,1,0,0,0,0,0,0,
0,0,1,0,0,0,0,0,
0,0,0,1,0,0,0,0,
0,0,0,0,1,0,0,0,
0,0,0,0,0,1,0,0),
byrow=TRUE, name="F" )
matrM <- mxMatrix( type="Full", nrow=1, ncol=8,
free=c(T,T,T,T,T,T,F,F),
values=c(1,1,1,1,1,1,0,0),
labels=c("meanx1","meanx2","meanx3",
"meanx4","meanx5","meanx6",NA,NA),
name="M" )
exp <- mxExpectationRAM("A","S","F","M",
dimnames=c(manifestVars, latentVars))
funML <- mxFitFunctionML()
twoFactorModel <- mxModel("Two Factor Model Matrix Specification",
dataRaw, matrA, matrS, matrF, matrM, exp, funML)
# Create an MxModel object
# -----------------------------------------------------------------------------
twoFactorFit <- mxRun(twoFactorModel)
summary(twoFactorFit)
coef(twoFactorFit)
omxCheckCloseEnough(coef(twoFactorFit)[["l2"]], 0.9723, 0.01)
omxCheckCloseEnough(coef(twoFactorFit)[["l3"]], 0.9313, 0.01)
omxCheckCloseEnough(coef(twoFactorFit)[["l5"]], 1.0498, 0.01)
omxCheckCloseEnough(coef(twoFactorFit)[["l6"]], 1.0531, 0.01)
omxCheckCloseEnough(coef(twoFactorFit)[["varF1"]], 0.6604, 0.01)
omxCheckCloseEnough(coef(twoFactorFit)[["varF2"]], 0.4505, 0.01)
omxCheckCloseEnough(coef(twoFactorFit)[["cov"]], 0.2952, 0.01)
omxCheckCloseEnough(coef(twoFactorFit)[["e1"]], 0.3349, 0.01)
omxCheckCloseEnough(coef(twoFactorFit)[["e2"]], 0.3985, 0.01)
omxCheckCloseEnough(coef(twoFactorFit)[["e3"]], 0.4091, 0.01)
omxCheckCloseEnough(coef(twoFactorFit)[["e4"]], 0.5404, 0.01)
omxCheckCloseEnough(coef(twoFactorFit)[["e5"]], 0.4809, 0.01)
omxCheckCloseEnough(coef(twoFactorFit)[["e6"]], 0.5571, 0.01)
omxCheckCloseEnough(coef(twoFactorFit)[["meanx1"]], 2.988, 0.01)
omxCheckCloseEnough(coef(twoFactorFit)[["meanx2"]], 3.0113, 0.01)
omxCheckCloseEnough(coef(twoFactorFit)[["meanx3"]], 2.9861, 0.01)
omxCheckCloseEnough(coef(twoFactorFit)[["meanx4"]], 2.9554, 0.01)
omxCheckCloseEnough(coef(twoFactorFit)[["meanx5"]], 2.9562, 0.01)
omxCheckCloseEnough(coef(twoFactorFit)[["meanx6"]], 2.9673, 0.01)
# Compare OpenMx results to Mx results
# -----------------------------------------------------------------------------
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