Documentation clash with network candidate 1.20.0

[CarterButts]

OK, we have folded in Pavel's proposed changes to network, which make a lot more things generic. revdepcheck suggests no major issues, except that networkDynamic shows the following:

 ```
 S3 methods shown with full name in Rd file 'network.extensions.Rd':
   ‘get.edgeIDs.active’ ‘get.edges.active’ ‘get.neighborhood.active’
   ‘is.adjacent.active’
 
 The \usage entries for S3 methods should use the \method markup and not
 their full name.
 See chapter ‘Writing R documentation files’ in the ‘Writing R
 Extensions’ manual.
 ```

This is because get.edgeIDs, get.edges, get.neighborhood, and is.adjacent are now S3 generics. Thus, R thinks that get.edges.active is a method, and is upset at the docs.

The fix I have used for the same kind of issue in the sna package has been to just write the command as if it is a method, e.g.

\method{as.edges}{active}(blah blah)

This seems to calm down the CRAN checks, at least for now.

I can try to implement a fix, or someone else can do so....

[skyebend]

This is because get.edgeIDs, get.edges, get.neighborhood, and is.adjacent are now S3 generics. Thus, R thinks that get.edges.active is a method, and is upset at the docs.

My (very vague) memory is that this collision is why we didn't implement the generics in network a long time ago. @CarterButts are you sure the issue is limited to documentation, won't it also cause dispatch issues looking for the active class? or will it still find the correct function as long as we don't have an active class?

[CarterButts]

I was indeed concerned about downstream problems, but I think we should be OK so long as the code explicitly calls the full function name. (Otherwise, various things in the sna package would have broken a long time ago.) I.e., if you call as.edges.active, then you should get that function per se, and will never call as.edges. But we should test before I commit! I created a branch, BTW, that has the doc change. The proposed version of network is now the master, so if you check it out, you'll have the changes.

FWIW, I just ran R CMD check --as-cran on networkDynamic with the changes made and the new network package installed, and I got no errors. But I will also experiment some more.

[CarterButts]

So far, so good - with the new network loaded, I am able to run the examples on the relevant methods without issues....

[CarterButts]

BTW, I also realized when making the change that we had already done this for some other functions in an earlier iteration (e.g., network.dyadcount). AFAIK, that has not caused problems, so hopefully we are also in the clear here.

[CarterButts]

(I also created a pull request for the proposed change.) @krivit, do you want to chime in on any of this? It is based on your proposed network change....