regularizeSimlr: Automatically produce regularization matrices for simlr
In stnava/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

regularizeSimlr

R Documentation

Automatically produce regularization matrices for simlr

Automatically produce regularization matrices for simlr

regularizeSimlr(x, knn, fraction = 0.1, sigma, kPackage = "FNN")

`x`	A list that contains the named matrices. Note: the optimization will likely perform much more smoothly if the input matrices are each scaled to zero mean unit variance e.g. by the `scale` function. Note: x may also contain a mixture of raw matrix data and masks which are binary antsImages. If a mask is passed, this function will assume the user wants spatial regularization for that entry.
`knn`	A vector of knn values (integers, same length as matrices)
`fraction`	optional single scalar value to determine knn
`sigma`	optional sigma vector for regularization (same length as matrices)
`kPackage`	name of package to use for knn. FNN is reproducbile but RcppHNSW is much faster (with nthreads controlled by enviornment variable ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS) for larger problems. For large problems, compute the regularization once and save to disk; load for repeatability.