One thing you have to keep in mind is that, in matrix operation sigma=C'*C, C is not simply the element-wise square root of sigma.
Say sigma is the covariance matrix of X. You need to guarantee the simulated data X satisfying cov(X)=sigma.
If you use sigma directly in your simulation, the covariance matrix of X cov(X) =sigma'*I*sigma=sigma'*sigma, where I is the covariance matrix of random normal and has to be identity matrix. Then this is not what your want for X.
Using the root matrix C, you get the right X ( cov(X)=C'*I *C=C'*C=sigma ).


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