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I have calculated a hedge ratio that generates a mean reverting spread (stationary, without trends) 60-70% of the time. But the remaining 30% of the time, it seems like there is a trend in the spread. How do I handle such a case? Is there a way to account for that or make the spread stationary without trends?

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When you say "make the spread stationary", do you mean construct a feasible spread trade; or do you mean post-process the spread data to eliminate the trend component? –  pteetor Nov 15 '13 at 16:23
Can you answer both the cases you have mentioned? –  aajkal Dec 11 '13 at 22:15
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