#
#   Copyright 2007-2017 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,
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# -----------------------------------------------------------------------------
# Program: OneFactorModel_PathCov.R  
# Author: Ryne Estabrook
# Date: 2009.08.01 
#
# ModelType: Factor
# DataType: Continuous
# Field: None
#
# Purpose:
#      One Factor model to estimate factor loadings, 
#      residual variances and means
#      Path style model input - Covariance matrix data input
#
# RevisionHistory:
#      Hermine Maes -- 2009.10.08 updated & reformatted
#      Ross Gore -- 2011.06.06 added Model, Data & Field metadata
# -----------------------------------------------------------------------------

require(OpenMx)
# Load Library
# -----------------------------------------------------------------------------

myFADataCov<-matrix(
	c(0.997, 0.642, 0.611, 0.672, 0.637, 0.677,
	  0.642, 1.025, 0.608, 0.668, 0.643, 0.676,
	  0.611, 0.608, 0.984, 0.633, 0.657, 0.626,
	  0.672, 0.668, 0.633, 1.003, 0.676, 0.665,
	  0.637, 0.643, 0.657, 0.676, 1.028, 0.654,
	  0.677, 0.676, 0.626, 0.665, 0.654, 1.020),
	nrow=6,
	dimnames=list(
		c("x1","x2","x3","x4","x5","x6"),
		c("x1","x2","x3","x4","x5","x6"))
)

myFADataMeans <- c(2.988, 3.011, 2.986, 3.053, 3.016, 3.010)
names(myFADataMeans) <- c("x1","x2","x3","x4","x5","x6")
# Prepare Data
# -----------------------------------------------------------------------------

oneFactorModel <- mxModel("Common Factor Model Path Specification", 
	type="RAM",
	mxData(
		observed=myFADataCov, 
		type="cov", 
		numObs=500,
		mean=myFADataMeans
	),
	manifestVars=rev(c("x1","x2","x3","x4","x5","x6")),
	latentVars="F1",
	mxPath(
		from=c("x1","x2","x3","x4","x5","x6"),
		arrows=2,
		free=TRUE,
		values=c(1,1,1,1,1,1),
		labels=c("e1","e2","e3","e4","e5","e6")
	),
	# residual variances
	# -------------------------------------
	mxPath(from="F1",
		arrows=2,
		free=TRUE,
		values=1,
		labels ="varF1"
	),
	# -------------------------------------
	# latent variance
	mxPath(from="F1",
		to=c("x1","x2","x3","x4","x5","x6"),
		arrows=1,
		free=c(FALSE,TRUE,TRUE,TRUE,TRUE,TRUE),
		values=c(1,1,1,1,1,1),
		labels =c("l1","l2","l3","l4","l5","l6")
	),
	# factor loadings
	# --------------------------------------
	mxPath(from="one",
		to=c("x1","x2","x3","x4","x5","x6","F1"),
		arrows=1,
		free=c(TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE),
		values=c(1,1,1,1,1,1,0),
		labels =c("meanx1","meanx2","meanx3","meanx4","meanx5","meanx6",NA)
	)
	# means
	# ------------------------------------- 
) # close model
# Create an MxModel object
# -----------------------------------------------------------------------------

oneFactorFit <- mxRun(oneFactorModel)

summary(oneFactorFit)
oneFactorFit$output$estimate

omxCheckCloseEnough(oneFactorFit$output$estimate[["l2"]], 0.999, 0.01)
omxCheckCloseEnough(oneFactorFit$output$estimate[["l3"]], 0.959, 0.01)
omxCheckCloseEnough(oneFactorFit$output$estimate[["l4"]], 1.028, 0.01)
omxCheckCloseEnough(oneFactorFit$output$estimate[["l5"]], 1.008, 0.01)
omxCheckCloseEnough(oneFactorFit$output$estimate[["l6"]], 1.021, 0.01)
omxCheckCloseEnough(oneFactorFit$output$estimate[["varF1"]], 0.645, 0.01)
omxCheckCloseEnough(oneFactorFit$output$estimate[["e1"]], 0.350, 0.01)
omxCheckCloseEnough(oneFactorFit$output$estimate[["e2"]], 0.379, 0.01)
omxCheckCloseEnough(oneFactorFit$output$estimate[["e3"]], 0.389, 0.01)
omxCheckCloseEnough(oneFactorFit$output$estimate[["e4"]], 0.320, 0.01)
omxCheckCloseEnough(oneFactorFit$output$estimate[["e5"]], 0.370, 0.01)
omxCheckCloseEnough(oneFactorFit$output$estimate[["e6"]], 0.346, 0.01)
omxCheckCloseEnough(oneFactorFit$output$estimate[["meanx1"]], 2.988, 0.01)
omxCheckCloseEnough(oneFactorFit$output$estimate[["meanx2"]], 3.011, 0.01)
omxCheckCloseEnough(oneFactorFit$output$estimate[["meanx3"]], 2.986, 0.01)
omxCheckCloseEnough(oneFactorFit$output$estimate[["meanx4"]], 3.053, 0.01)
omxCheckCloseEnough(oneFactorFit$output$estimate[["meanx5"]], 3.016, 0.01)
omxCheckCloseEnough(oneFactorFit$output$estimate[["meanx6"]], 3.010, 0.01)
# Compare OpenMx results to Mx results 
# -----------------------------------------------------------------------------
