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#
# Copyright 2007-2021 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.
##############################################################################
# Stable Trait, Autoregressive Trait, State Model with Multiple Indicators ##
# ##
# There are three indicators of the construct at each of 10 waves. However ##
# two of the waves (waves 5 and 7) are missing, so phantom variables are ##
# used in these years. A latent occasion factor is modeled in each year ##
# from the three indicators. This occasion factor is decomposed into a ##
# stable trait factor, an autoregressive trait factor, and an occasion- ##
# specific state factor. Stationarity is assumed, so the stabilities and ##
# variances are constrained to be equal across waves. ##
# ##
# The script was designed to handle different numbers of waves and different##
# missing waves, so it has a lot of extra stuff to make it flexible. But ##
# there are probably more efficient ways of doing this. ##
##############################################################################
data <- suppressWarnings(try(read.csv("data/fakeSTARTSMissing.csv",header=TRUE))) #With Missing Data
if (is(data, "try-error")) data <- read.csv("models/nightly/data/fakeSTARTSMissing.csv",header=TRUE)
waves <- 10 #Total number including phantom waves
indicators <- 3
phantom <- c(5,7) #List of waves that are missing
stabilitySV <- .85 #Starting value for stability
require(OpenMx)
library(testthat)
mxOption(key="feasibility tolerance", value = .0001)
#mxOption(key='Number of Threads', value=parallel::detectCores())
#mxOption(key="Parallel diagnostics", value = "Yes")
#SETUP FOR PHANTOM VARIABLES
indicatorPrefix <- c(paste("ind",1:indicators,sep=""))
allOccasions <- c(paste("occ",1:waves,sep=""))
if(phantom[1]=="0") obsOccasions <- allOccasions else
obsOccasions <- allOccasions[-phantom]
nActualWaves <- length(obsOccasions)
x <- matrix(obsOccasions,nrow=indicators,ncol=nActualWaves,byrow=T)
indicatorNames <- c(paste(x,indicatorPrefix,sep=""))
occNamesForPaths <- as.vector(x)
allStates <- c(paste("state",1:waves,sep=""))
if(phantom[1]=="0") obsStates <- allStates else
obsStates <- allStates[-phantom]
residualNames <- paste(indicatorNames,"res",sep="")
residualLabels <- paste(indicatorNames,"residVar",sep="")
#DEFINE MANIFEST AND LATENT VARIABLES
#Rename variables
names(data) <- indicatorNames
manifests <- names(data)
stableTraits <- c("ST")
arTraits <- c(paste("AR",1:waves,sep=""))
if(phantom[1]=="0") obsArTraits <- arTraits else
obsArTraits <- arTraits[-phantom]
#DATA STATEMENT
startsData <- mxData(observed=data, type="raw")
#CALCULATE START VALUES
##Start value for stability is set by user (.85 as default)
##Start values for the ST and first AR variances are set to be 1/3 of average variance of the indicators
##Start values for the S and residual variances are set to be 1/9 and 2/9 of the average variance
##Start value for the AR residual is set to AR1-AR1*stability^2.
#Calculate average variance for indicators
sumVar=0
for (i in 1:(nActualWaves*indicators)) {
sumVar <- sumVar+var(data, use="pairwise.complete.obs")[i,i]
}
avgVar <- sumVar/(nActualWaves*indicators)
##Set starting values
residSV <- 2*avgVar/9
stateSV <- avgVar/9
stSV <- avgVar/3
ar1SV <- avgVar/3
arSV <- ar1SV-ar1SV*stabilitySV*stabilitySV
##Set starting values for means to the average item mean
meanSV <- mean(colMeans(data, na.rm=TRUE))
#PATH STATEMENTS
##Variances
residVar <- mxPath(from=residualNames,
arrows=2,
#labels=residualLabels, #use if equality constraints aren't wanted
labels=c("resid1Var","resid2Var","resid3Var"), #constrain to be equal
free=TRUE,
values=residSV,
lbound=0)
stVar <- mxPath(from=stableTraits,
arrows=2,
labels="stableTrait",
free=TRUE,
values=stSV,
lbound=0)
ar1Var <- mxPath(from=arTraits[1],
arrows=2,
labels="ar1Trait",
free=TRUE,
values=ar1SV)
arVar <- mxPath(from=arTraits[2:waves],
arrows=2,
labels="arTrait",
free=TRUE,
values=arSV)
occasionVar <- mxPath(from=obsOccasions,
arrows=2,
labels="occTrait",
free=FALSE,
values=0) #All occasion variance is ST, AR, or S
stateVar <- mxPath(from=obsStates,
arrows=2,
labels="States",
free=TRUE,
values=stateSV,
lbound=0)
##Factor Loadings
stLoadings <- mxPath(from=stableTraits,
to=obsOccasions,
arrows=1,
free=FALSE,
values=1)
arLoadings <- mxPath(from=obsArTraits,
to=obsOccasions,
arrows=1,
free=FALSE,
values=1)
stateLoadings <- mxPath(from=obsStates,
to=obsOccasions,
arrows=1,
free=FALSE,
values=1)
residualLoadings <- mxPath(from=residualNames,
to=indicatorNames,
arrows=1,
free=FALSE,
values=1)
first <- (3*(c(1:nActualWaves))-2) #Indicator loadings to set to "1"
indicatorLoadings1 <- mxPath(from=occNamesForPaths[first],
to=indicatorNames[first],
arrows=1,
free=FALSE,
values=1)
indicatorLoadings <- mxPath(from=occNamesForPaths[-first],
to=indicatorNames[-first],
arrows=1,
labels=c("indLoading1","indLoading2"),
free=TRUE,
values=1)
##Stabilities
stabilityPath <- mxPath(from=arTraits[1:(waves-1)],
to=arTraits[2:waves],
arrows=1,
free=T,
values=stabilitySV,
labels="stability")
#Means
manifestMeans <- mxPath(from="one",
to=manifests,
arrows=1,
free=TRUE,
values=meanSV,
#labels=paste("mean",1:(nActualWaves*indicators),sep="")
labels=c("indicator1Mean","indicator2Mean","indicator3Mean")
)
stMeans <- mxPath(from="one", to=stableTraits, arrows=1, free=FALSE, values=0)
arMeans <- mxPath(from="one", to=arTraits, arrows=1, free=FALSE, values=0)
occMeans <- mxPath(from="one", to=obsOccasions, arrows=1, free=FALSE, values=0)
stateMeans <- mxPath(from="one", to=obsStates, arrows=1, free=FALSE, values=0)
residualMeans <- mxPath(from="one",to=residualNames,arrows=1,free=FALSE,values=0)
#Constraints: Stationarity Constraint for Autoregressive Component
matrixAr <- mxMatrix("Full",
nrow=1,
ncol=1,
free=T,
values=arSV,
labels="arTrait",
name="cMatAr")
matrixAr1 <- mxMatrix("Full",
nrow=1,
ncol=1,
free=T,
values=ar1SV,
labels="ar1Trait",
name="cMatAr1")
matrixStability <- mxMatrix("Full",
nrow=1,
ncol=1,
free=T,
values=stabilitySV,
labels="stability",
name="cMatStab")
algebraSTARTS <- mxAlgebra(cMatAr1-cMatAr1*cMatStab*cMatStab, name="AR2Variance")
stationarityConstraint <- mxConstraint(cMatAr == AR2Variance ,name="Stationarity")
#CREATE PATTERN OF CORRELATED RESIDUALS FOR SAME INDICATOR AT DIFFERENT WAVE
#FIRST COLUMN IS FIRST RESIDUAL; SECOND COLUMN IS SECOND RESIDUAL
residCorrMatrix <- matrix(NA,1,2)
tempMatrix <- matrix(NA,1,2)
for (i in 1:indicators) {
for (j in 1:(nActualWaves-1)) {
for (k in (j+1):nActualWaves) {
if(is.na(residCorrMatrix[1,1])) {
residCorrMatrix[1,1] <- (i+(j-1)*indicators)
residCorrMatrix[1,2] <- (i+(j-1)*indicators)+(k-j)*indicators
} else {
tempMatrix[1,1] <- (i+(j-1)*indicators)
tempMatrix[1,2] <- (i+(j-1)*indicators)+(k-j)*indicators
residCorrMatrix <- rbind(residCorrMatrix,tempMatrix)
}
}
}
}
#PATH STATEMENTS FOR CORRELATED RESIDUALS
correlatedResiduals <- mxPath(from=residualNames[residCorrMatrix[,1]],
to=residualNames[residCorrMatrix[,2]],
arrows=2,
free=TRUE,
values=.05)
#MODEL
STARTSM <- mxModel("STARTS",
type="RAM",
startsData,
manifestVars=manifests,
latentVars=c(stableTraits,arTraits,obsOccasions,obsStates,residualNames),
residVar,
stVar,
ar1Var,
arVar,
occasionVar,
stateVar,
stLoadings,
arLoadings,
stateLoadings,
indicatorLoadings1,
indicatorLoadings,
residualLoadings,
stabilityPath,
manifestMeans,
stMeans,
arMeans,
occMeans,
stateMeans,
residualMeans,
matrixAr,
matrixAr1,
matrixStability,
algebraSTARTS,
stationarityConstraint,
correlatedResiduals,
mxFitFunctionML(rowwiseParallel=FALSE))
startsModel <- mxRun(STARTSM)
omxCheckCloseEnough(startsModel$output$fit, 2718.410, .15)
if (.Platform$OS.type != 'windows' && parallel::detectCores() > 1) {
omxCheckTrue(startsModel$compute$steps[['GD']]$output$maxThreads > 1)
}
if (mxOption(key="default optimizer") == 'SLSQP') {
startsCI <- mxModel(startsModel, mxCI('stability'))
startsCI <- mxOption(startsCI, "Standard Errors", "No")
startsCI <- mxOption(startsCI, "Calculate Hessian", "No")
startsCI <- mxRun(startsCI, intervals = TRUE)
expect_equal(as.character(startsCI$compute$steps$CI$output$detail[,'diagnostic']),
c('success', 'active box constraint'))
expect_equal(startsCI$compute$steps$CI$output$detail[,'value'],
c(0.8907887, 0.9795628), 1e-3)
}
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