Some more changes (sorry!)

[gijsbertwerner]

While going over the package one last time, I am running into a few minor things and have made changes. I know this means we'll have to rerun the manuals etc., @paternogbc . Sorry! Just thought I'd maintain a list of changes I have made for our records.

• clade_cont/clade_discrete had n.sim=1 for the first example for both. I think this is to limit the time for the CRAN checks. For the ones which are in the 'not-run' part which should not be tested anyway (right), but are shown to the end-user, I have again increased this to n=20, because otherwise looks weird.
• clade_cont/clade_discrete had an error in the output for full estimates (the optpar was printed twice).
• Minor typos in clade_cont/clade_discrete
• I discovered that summary calls for both clade_cont/clade_discrete give an error when the optpar is against the bounds. This makes sense, and should probably a warning for the user. We can write a better loop to catch and process this later.
• I rephrased some of the language describing the output to influe_cont/discrete, to be more accurate.
• The @return bit from Samp_continuous/discrete still contained some errors from being copied from other helps. Now solved.
• In the tree_continuous/discrete too there were examples visible to the end-user with n.tree = 1 or 2. I have changed these to 30, because I think these are not being run by CRAN anyway and otherwise they just look really weird to the user.

Ok, done now I think (with the exception of the bit below)!

[gijsbertwerner]

Stuff to do still:

• Include links to the sense_plots for the new traitevol methods (most are written already, but check them) into the general sensi_plot help page.

[paternogbc]

Hey @gijsbertwerner that is great! Thanks. Yep, the code with n.tree = 1 is to pass Cran tests. \dontshow are executed by CRAN but not shown to users. \dontrun are shown but not executed.

So we always want to run at least one test of the function (to be sure it is not broken), but this needs to be faster then 5 sec.

Regarding the other changes, excellent! And no worries about re-building stuff, it is great to know we cleared small typo/bugs =)

[gijsbertwerner]

Great, makes sense, Gustavo! I figured that that's what it would work like.

I can do the sensi_plot methods update tomorrow, but am afraid superbusy today.

[paternogbc]

@gijsbertwerner, I can do it no worries. I will try to submit the package tonight (Aussie time).

I have pushed this 91a5542c9faed1431e489ec906a63195faa779e9. Still missing the help for the sensi_plot.sensiSamp.TraitEvol.

Cheers!

[gijsbertwerner]

Cool, I have added the help for sensi_plot.sensiSamp.TraitEvol now in https://github.com/paternogbc/sensiPhy/commit/76e5f0ee031d5d83a9a03f7249223b05e5f5637e and in https://github.com/paternogbc/sensiPhy/commit/56a73775a019cb1bc14b15a19b1c9679064a943b

[paternogbc]

Perfect, all done then! Updates the documentation in b025bde69c918ba8671735785ac4dbfd2cfd5484