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How does one use the Johansen cointegration test in a linear time series model?

Should I only use normalized coeffients for interpretation? Or, once I know that the variables are cointegrated, do I simply regress the variables and consider it the long-run relationship?

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no, you should use your original variables, no truncating, normalizing or whatever. And remember that you need Johansen only in case of more than one independent variable.

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