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It's probably easiest to think about it in terms of a covariance matrix and then convert it to a correlation matrix after. If instead of the first matrix you have some covariance matrix of the assets $\Sigma$, then you could get the portfolio variance, for one portfolio, as $w' \Sigma w$, where you could have $w\equiv\left(w_{1},w_{2},w_{3}\right)'$. ...

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If you look at changes of the points on the yield curve, then you probably find something stationary - right? Applying PCA on the covariance of these changes makes sense. E.g. you will find out that on PC describes a parallel shift (a change in the yield curve). Look at this question too: What do eigenvalues/eigenvectors of the yield/forward rates ...

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There is a vast literature on modelling time-series with periodcities. Rob Hyndman is one of the leading reseaerchers in this area. He has published the R package forecast and a free online text book on this subject (with another package and R code in the book). Your task is covered starting here.

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There is a wide knowledge on correlation estimation, see other questions and answers: principal component analysis (PCA) - Equity Risk Model Using PCA random matrix theory (RMT) - Cleansing covariance matrices via Random matrix theory or Random matrix theory (RMT) in finance shrinkage - Portfolio Optimization : Shrinkage of Covariance Matrix when data is ...

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You can use the either, as both necessarily are symmetric positive definite; covariance is a personal preference. It's really just a matter of scaling, as $\mathcal{N}(0,\Sigma)$ is distributionally $\sqrt{\Sigma} \mathcal{N}(0,1)$. Correlation would require additional scaling (i.e. multiplication of every $\mathcal{N}(0,\rho)$ element by its respective ...

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