geiger dependency removed

[mwpennell]

now just depends on 'ape' plus the three plotting packages: "ggplot2", "grid", "gridExtra". added geiger to test-helper

i have added geospiza.Rd to arbutus just temporarily so examples still work. will find replacement tomorrow.

also, you mentioned that we could use "suggests" instead of "imports" for the plotting pkgs. what is the advantage/disadvantages of this??

[richfitz]

I think if you only use things in the examples, or they're fairly optional then they go in Suggests. But I get confused.

If you use "Suggests" then every time that a function is used it needs to be loaded with require(). So if we use the ggplot/grid stuff in only one place then Suggests might be better. If we use them in a couple of places, then keep it in Imports.

[mwpennell]

hmmm....so ggplot2 is used throughout. plot.phy.ss(), contrasts.var.plot(), contrast.nh.plot() and contrast.asr.plot but gridExtra and grid only used in plot.phy.ss (and internal fxns within it).

thinking maybe use require(grid, gridExtra) in plot.phy.ss?? and just suggest them. not sure how many people will want to look at these plots anyways...thoughts?

[richfitz]

Sounds like a good plan to me. If it turns out that gridExtra is used elsewhere, we can easily make it required. But not making it required makes it simpler for people to install. ggplot is pretty common these days, and everyone using this package will have ape.

But I don't think it's the end of the world to leave it in Imports either.

[mwpennell]

done. tested the fxns and this works well.