Nothing
runBackShift <- function(X, environment, parentsOf, pointEst,
setOptions, verbose, ...){
# additional options for backShift
optionsList <- list("covariance"=TRUE, "ev"=0, "threshold"=0.75, "nsim"=100,
"sampleSettings"=1/sqrt(2), "sampleObservations"=1/sqrt(2),
"nodewise"=TRUE, "tolerance"=10^(-4), "baseSettingEnv"=1)
# adjust according to setOptions if necessary
optionsList <- adjustOptions(availableOptions = optionsList,
optionsToSet = setOptions)
p <- ncol(X)
if(nrow(X) < p)
stop("backShift not suitable if there are more variables
than observations")
dots <- list(...)
if(length(dots) > 0){
warning("options provided via '...' not taken")
}
res <- try(backShift::backShift(
X, environment, covariance=optionsList$covariance,
ev=optionsList$ev, threshold=optionsList$threshold,
nsim=optionsList$nsim,
sampleSettings=optionsList$sampleSettings,
sampleObservations=optionsList$sampleObservations,
nodewise=optionsList$nodewise,
tolerance=optionsList$tolerance,
baseSettingEnv = optionsList$baseSettingEnv,
verbose = verbose),
silent = FALSE)
if(inherits(res, "try-error")){
warning("backShift -- no stable model found. Possible model
mispecification. Returning the empty graph.\n")
res<- list(Ahat=0*diag(p), AhatAdjacency = 0*diag(p),
varianceEnv = matrix(0, nrow = length(unique(environment)),
ncol = p))
}
result <- vector("list", length = length(parentsOf))
for (k in 1:length(parentsOf)){
if(optionsList$ev == 0)
result[[k]] <- (wh <- which(res$Ahat[, k]!=0))
else
result[[k]] <- (wh <- which(res$AhatAdjacency[, k]!=0))
attr(result[[k]],"parentsOf") <- parentsOf[k]
if(pointEst) attr(result[[k]],"coefficients") <- res$Ahat[ wh,k ]
}
resMat <- if(optionsList$ev == 0) res$Ahat else res$AhatAdjacency
if(pointEst & optionsList$ev > 0){
resMat[resMat != 0] <- res$Ahat[resMat != 0]
}
if(length(parentsOf) < p){
resMat <- resMat[,parentsOf]
}
list(resList = result, resMat = resMat)
}
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