documenting predict/plot/etc. methods

[bbolker]

This is a long-standing issue of mine with S4 methods: it's pretty hard for a user (or at least me) to guess where we should be looking for documentation for, say, the predict() or plot() method for fitode objects. In fact the answers are help("predict,fitode-method)") and help("plot,fitode,missing-method") (the latter means "the method for plot when the function signature is {fitode,missing} - ugh).

I would suggest adding an alias to each of these so that predict.fitode and plot.fitode will find the relevant help pages, even thought these aren't S3 methods ...

[davidearn]

I'm glad it's not just me that finds this issue annoying. I like the idea of S3-style aliases. In fact, I tried ?plot.fitode the other day, knowing this is an S4 pkg but thinking maybe you'd have done that :)

[parksw3]

Will work on adding aliases and better documentation

[parksw3]

OK so I added aliases to most (all?) methods. I also added methods documentation to class objects, which seemed more appropriate (and consistent with mle2).

So if you do ?fitode it'll take you to fitode-class and ?fitode-class now has a new section called methods. The same goes for fitodeMCMC. Can close this issue if either/both of you are happy with the documentation in ?fitode-class.