#
#   Copyright 2007-2012 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
# 
#   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)
	
data(myFADataRaw)

oneFactorOrd <- myFADataRaw[,c("z1", "z2", "z3")]

oneFactorOrd$z1 <- mxFactor(oneFactorOrd$z1, levels=c(0, 1))
oneFactorOrd$z2 <- mxFactor(oneFactorOrd$z2, levels=c(0, 1))
oneFactorOrd$z3 <- mxFactor(oneFactorOrd$z3, levels=c(0, 1, 2))

	oneFactorModel <- mxModel("Common Factor Model Path Specification", 
	type="RAM",
	mxData(
		observed=oneFactorOrd,
		type="raw"
	),
	manifestVars=c("z1","z2","z3"),
	latentVars="F1",
	# residual variances
	mxPath(
		from=c("z1","z2","z3"),
		arrows=2,
		free=FALSE,
		values=c(1,1,1),
		labels=c("e1","e2","e3")
	),
	# latent variance
	mxPath(
		from="F1",
		arrows=2,
		free=TRUE,
		values=1,
		labels ="varF1"
	),
	# factor loadings
	mxPath(
		from="F1",
		to=c("z1","z2","z3"),
		arrows=1,
		free=c(FALSE,TRUE,TRUE),
		values=c(1,1,1),
		labels=c("l1","l2","l3")
	),
	# means
	mxPath(
		from="one",
		to=c("z1","z2","z3","F1"),
		arrows=1,
		free=FALSE,
		values=0,
		labels=c("meanz1","meanz2","meanz3","meanF")
	),
	# thresholds
	mxThreshold(vars=c("z1", "z2", "z3"),
		nThresh=c(1,1,2),
		free=TRUE,
		values=c(-1, 0, -.5, 1.2)
		)
) # close model

oneFactorResults <- mxRun(oneFactorModel)

# joint ordinal-continuous model

oneFactorJoint <- myFADataRaw[,c("x1", "x2", "x3", "z1", "z2", "z3")]
	
oneFactorJoint$z1 <- mxFactor(oneFactorOrd$z1, levels=c(0, 1))
oneFactorJoint$z2 <- mxFactor(oneFactorOrd$z2, levels=c(0, 1))
oneFactorJoint$z3 <- mxFactor(oneFactorOrd$z3, levels=c(0, 1, 2))

    oneFactorJointModel <- mxModel("Common Factor Model Path Specification", 
        type="RAM",
        mxData(
            observed=oneFactorJoint,
            type="raw"
        ),
        manifestVars=c("x1", "x2", "x3", "z1","z2","z3"),
        latentVars="F1",
        # residual variances
        mxPath(
            from=c("x1", "x2", "x3", "z1","z2","z3"),
            arrows=2,
            free=c(TRUE, TRUE, TRUE, FALSE, FALSE, FALSE),
            values=1,
            labels=c("e1","e2","e3","e4","e5","e6")
        ),
        # latent variance
        mxPath(
            from="F1",
            arrows=2,
            free=FALSE,
            values=1,
            labels ="varF1"
        ),
        # factor loadings
        mxPath(
            from="F1",
            to=c("x1", "x2", "x3", "z1","z2","z3"),
            arrows=1,
            free=TRUE,
            values=1,
            labels=c("l1","l2","l3","l4","l5","l6")
        ),
        # means
        mxPath(
            from="one",
            to=c("x1", "x2", "x3","z1","z2","z3","F1"),
            arrows=1,
            free=c(TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE),
            values=0,
            labels=c("meanx1","meanx2","meanx3","meanz1","meanz2","meanz3","meanF")
        ),
	# thresholds
	mxThreshold(vars=c("z1", "z2", "z3"),
		nThresh=c(1,1,2),
		free=TRUE,
		values=c(-1, 0, -.5, 1.2)
		)
) # close model

oneFactorJointResults <- mxRun(oneFactorJointModel)