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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.
require(OpenMx)
set.seed(1234)
dat <- cbind(rnorm(5),rep(1,5))
colnames(dat) <- c("y","x")
dat[5,1] <- NA
ge <- mxExpectationGREML(V="V",yvars="y", Xvars="x", addOnes=FALSE)
gff <- mxFitFunctionGREML(dV=c(ve="I"))
plan <- mxComputeSequence(steps=list(
mxComputeNewtonRaphson(fitfunction="fitfunction"),
mxComputeOnce('fitfunction', c('fit','gradient','hessian','ihessian')),
mxComputeStandardError(),
mxComputeReportDeriv(),
mxComputeReportExpectation()
))
testmod <- mxModel(
"GREMLtest",
mxData(observed = dat, type="raw", sort=FALSE),
mxMatrix(type = "Full", nrow = 1, ncol=1, free=T, values = 2, labels = "ve", lbound = 0.0001, name = "Ve"),
mxMatrix(type="Unit", nrow=5,ncol=1,name="Uni"),
mxAlgebra(vec2diag(Uni), name="I"),
mxAlgebra( vec2diag(Uni%x%Ve), name="V"),
ge,
gff,
plan
)
testrun <- mxRun(testmod)
summary(testrun)
omxCheckEquals(mxEval(nrow(I),testrun,T), 5)
omxCheckEquals(mxEval(ncol(I),testrun,T), 5)
#mxGetExpected() knows how to drop rows and columns of the covariance matrix due to missing data; mxEvalByName() does not:
omxCheckEquals(nrow(mxEvalByName("V", testrun, compute=T)), 5)
omxCheckEquals(nrow(mxGetExpected(testrun, "covariance")), 4)
omxCheckTrue( all(abs(mxGetExpected(testrun,"means") - mean(dat[,1],na.rm=T)) < 1e-8) )
omxCheckTrue(is.na(mxGetExpected(testrun,"thresholds")))
testmod2 <- mxModel(
"GREMLtest",
mxData(observed = dat, type="raw", sort=FALSE),
mxMatrix(type = "Full", nrow = 1, ncol=1, free=T, values = 2, labels = "ve", lbound = 0.0001, name = "Ve"),
mxMatrix(type="Unit", nrow=5,ncol=1,name="Uni"),
mxAlgebra(vec2diag(Uni), name="I"),
mxAlgebra( I%x%Ve, name="V"),
ge,
gff,
plan
)
testrun2 <- mxRun(testmod2)
summary(testrun2)
omxCheckEquals(mxEval(nrow(I),testrun2,T), 5)
omxCheckEquals(mxEval(ncol(I),testrun2,T), 5)
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