I'm working on a project where I have collected data on dragonfly species across 12 sites, along with environmental parameters, over a two-year period. This gives me a total of 24 months of data, which I plan to use for PCA and CCA analyses. Given the size of the dataset, I'm looking for advice on the best approach for data aggregation. Would it be more appropriate to use yearly averages for each study site (one for each year), or should I calculate monthly averages instead?

Another thing is When I upload all the data in one frame, some species may be present at one site but not at another, which is causing errors in PAST and complicates the analysis. How should I proceed? Please advise.