I want to run a correlation matrix analysis between multiple response variables. The data was obtained from the operation of a continuous bioreactor over a 330 days period, but the operating conditions were changed every three months. I am not sure if I have to run a correlation test for each operational strategy (i.e. the condition that was changed every three months - in this case was the concentration of a contaminant) or if I can run a single test for the whole operation of the reactor.
The results make more sense if I run a single test, but I am not sure if I can do that assuming the conditions were changed. But I know that, for environmental analyses as whole, it is quite common to run correlation analysis even when there are other factors changing over time.