fixed some global variables in PEcAn.MA package

[nanu1605]

No description provided.

[infotroph]

It looks like this branch contains a lot of changes (everything up to commit 8ad821e) that are already present in #2956 -- this will cause issues when trying to merge them all into develop. @nanu1605 can you please cherry-pick the last three commits (95880de, 49905f5, 57c8786) into a new branch that starts from the current tip of the develop branch, open a new PR from that branch, and close this one?

I'm sorry that this will be some hassle, but it's better to resolve it now than to wait -- Git branch divergences only get more painful the longer they continue.

Edit: I take it back. Since this branch contains ALL the changes from #2956 and #2963, we can resolve this cleanly by merging this PR (once it passes CI) and closing the other two.

[dlebauer]

looks great!

• most important thing would be to add a comment about how and why new.env is being used
• consider not exporting the p.point.in.prior function

[dlebauer]

Suggested change

##' @export p.point.in.prior

I think this will at least make it an unexported function, which is appropriate since it isn't particularly useful outside of the one place in run.meta.analysis where it is used:

pecan/modules/meta.analysis/R/run.meta.analysis.R

Line 78 in ee38544

p.data <- p.point.in.prior(point = data.median, prior = prior)

FYI if you replaced this line in run.meta.analysis with

  p.data <- do.call(paste0("p", prior[['distn']]), 
                              list(point, prior[['parama']], prior[['paramb']]))

and deleted the test of this function I think that would be fine. This isn't necessary, but something to keep an eye out for useless functions that are my legacy from PEcAn v 0.1, and that could make everyone's life easier by not exporting, and perhaps deprecating and merging with existing code.

[nanu1605]

Sure I will do the changes and commit ASAP.

[mdietze]

@dlebauer just wanted to check if @nanu1605 addressed your requested changes, as otherwise I think this is ready to pull in.