lvnetRefit <- function(
lvnetObject, # lvnet object
data, # New covariance matrix
sampleSize # New sample size
){
# If lvnetLasso or lvnetSearch, extract:
if (is(lvnetObject,"lvnetLasso") | is(lvnetObject,"lvnetSearch")){
lvnetObject <- lvnetObject$best
}
# Check if proper:
if (!is(lvnetObject,"lvnet")){
stop("Input must be a 'lvnet' object.")
}
# If dataset, compute cov:
if (nrow(data) > ncol(data)){
if (missing(sampleSize)){
sampleSize <- nrow(data)
}
data <- cov(data, use = "pairwise.complete.obs")
}
# Check if samplesize is missing:
if (missing(sampleSize)){
stop("sampleSize may not be missing")
}
# Extract inverse var-cov:
sigmaInverse <- corpcor::pseudoinverse(lvnetObject$matrices$sigma_positive)
# Obtain fit measures:
Res <- ggmFit(covMat = data, # sample variance-covariance matrix
sampleSize = sampleSize, # Sample sample-size
invSigma = sigmaInverse, # inverse variance covariance matrix instead of pcor
refit = FALSE,ebicTuning = lvnetObject$fitMeasures$ebicTuning,
nPar = lvnetObject$fitMeasures$npar)
return(Res)
}
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