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#
# 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: TwoFactorModel_PathCov.R
# Author: Ryne Estabrook
# Date: 08 01 2009
#
# Two Factor model to estimate factor loadings, residual variances and means
# Path style model input - Covariance matrix data input
#
# Revision History
# Hermine Maes -- 10 08 2009 updated & reformatted
# -----------------------------------------------------------------------
require(OpenMx)
#Prepare Data
# -----------------------------------------------------------------------
myFADataCov <- matrix(
c(0.997, 0.642, 0.611, 0.672, 0.637, 0.677, 0.342, 0.299, 0.337,
0.642, 1.025, 0.608, 0.668, 0.643, 0.676, 0.273, 0.282, 0.287,
0.611, 0.608, 0.984, 0.633, 0.657, 0.626, 0.286, 0.287, 0.264,
0.672, 0.668, 0.633, 1.003, 0.676, 0.665, 0.330, 0.290, 0.274,
0.637, 0.643, 0.657, 0.676, 1.028, 0.654, 0.328, 0.317, 0.331,
0.677, 0.676, 0.626, 0.665, 0.654, 1.020, 0.323, 0.341, 0.349,
0.342, 0.273, 0.286, 0.330, 0.328, 0.323, 0.993, 0.472, 0.467,
0.299, 0.282, 0.287, 0.290, 0.317, 0.341, 0.472, 0.978, 0.507,
0.337, 0.287, 0.264, 0.274, 0.331, 0.349, 0.467, 0.507, 1.059),
nrow=9,
dimnames=list(
c("x1", "x2", "x3", "x4", "x5", "x6", "y1", "y2", "y3"),
c("x1", "x2", "x3", "x4", "x5", "x6", "y1", "y2", "y3")),
)
twoFactorCov <- myFADataCov[c("x1","x2","x3","y1","y2","y3"),c("x1","x2","x3","y1","y2","y3")]
myFADataMeans <- c(2.988, 3.011, 2.986, 3.053, 3.016, 3.010, 2.955, 2.956, 2.967)
names(myFADataMeans) <- c("x1", "x2", "x3", "x4", "x5", "x6", "y1", "y2", "y3")
twoFactorMeans <- myFADataMeans[c(1:3,7:9)]
#Create an MxModel object
# -----------------------------------------------------------------------
twoFactorModel <- mxModel("Two Factor Model Path", type="RAM",
mxData(
observed=twoFactorCov,
type="cov",
numObs=500,
means=twoFactorMeans
),
manifestVars=c("x1", "x2", "x3", "y1", "y2", "y3"),
latentVars=c("F1","F2"),
# residual variances
mxPath(
from=c("x1", "x2", "x3", "y1", "y2", "y3"),
arrows=2,
free=TRUE,
values=1,
labels=c("e1","e2","e3","e4","e5","e6")
),
# latent variances and covaraince
mxPath(
from=c("F1","F2"),
arrows=2,
# all=TRUE,
connect="unique.pairs",
free=TRUE,
values=c(1, .5, 1),
labels=c("varF1", "cov", "varF2")
),
# factor loadings for x variables
mxPath(
from="F1",
to=c("x1","x2","x3"),
arrows=1,
free=c(FALSE,TRUE,TRUE),
values=c(1,1,1),
labels=c("l1","l2","l3")
),
# factor loadings for y variables
mxPath(
from="F2",
to=c("y1","y2","y3"),
arrows=1,
free=c(FALSE,TRUE,TRUE),
values=c(1,1,1),
labels=c("l4","l5","l6")
),
# means
mxPath(
from="one",
to=c("x1","x2","x3","y1","y2","y3","F1","F2"),
arrows=1,
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","meany1","meany2","meany3",NA,NA)
)
) # close model
omxCheckError(twoFactorModel$intervals <- NULL,
"I'm very sorry, but direct modification of objects inside an mxModel is not supported. The recommended approach to modifying an mxMatrix, mxAlgebra or other object within a model is to rebuild the mxModel. So, for example, 'model <- mxModel(model, Something)' can be used to replace Something inside the model, instead of 'model$Something <- Something' which does not work")
elimination <- twoFactorModel
elimination <- mxModel(elimination, remove = TRUE,
mxPath(
from=c("x1", "x2", "x3", "y1", "y2", "y3"),
arrows=2
),
mxPath(
from=c("F1","F2"),
arrows=2,
# all=TRUE
connect="unique.pairs"
),
mxPath(
from="F1",
to=c("x1","x2","x3"),
arrows=1
),
mxPath(
from="F2",
to=c("y1","y2","y3"),
arrows=1
),
# means
mxPath(
from="one",
to=c("x1","x2","x3","y1","y2","y3","F1","F2")
)
)
omxCheckIdentical(c(elimination$A$values), rep(0, 8*8))
omxCheckIdentical(c(elimination$A$free), rep(FALSE, 8*8))
omxCheckIdentical(c(elimination$A$labels), rep(as.character(NA), 8* 8))
omxCheckIdentical(c(elimination$S$values), rep(0, 8 * 8))
omxCheckIdentical(c(elimination$S$free), rep(FALSE, 8 * 8))
omxCheckIdentical(c(elimination$S$labels), rep(as.character(NA), 8 * 8))
omxCheckIdentical(c(elimination$M$values), rep(0, 8))
omxCheckIdentical(c(elimination$M$free), rep(FALSE, 8))
omxCheckIdentical(c(elimination$M$labels), rep(as.character(NA), 8))
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