Greetings R-sig-phylo,
This is my first post but happy to join this community
I have been having some trouble with the axisChrono of the phyloch package and
axisPhylo functions of the ape package that I was hoping someone might be able
to help me with.
When using either function, the spacing
Thank you all very much for the comments! They are so helpful.
Yes, I do only have 8 species, and 3 replicates each. It is not ideal, but it's
what we have and we have a phylogeny, so I'd like to try some tests
incorporating phylogeny.
I probably should have added that I plan on running OLS to
Andrea, remember that you can and should also do the OLS models (i.e.,
assuming a star phylogeny) with measurement error considered. That's in the
programs that accompany Ives, Midford, and Garland (2007, Syst. Biol.
56:252–270), and were in the batch I just sent you.
Cheers,
Ted
Theodore
Thanks Franz,
I tried modifying the axisChrono function, but when I change the “at=“ argument
to equal something like “at= c(1,2,3,4,5)” I can get it to list out specific
tick marks but they are always in increasing order, not reverse order as you
want with a right facing cladogram. I’m not
Hi Everyone,
I agree with what has been said so far. Tony, don't take my comments to
heart. Your contribution is most welcome as your opinion is highly
respected (by me and hopefully by others). Same goes for all the other
authorities on the list e.g Liam, Joe, Ben, Jarrod, Ted, Marguerite
Hi Jacob,
What I do is to use the basic axis() function. The trick is to transform the
scale by subtracting the depth of your tree like this:
axis(1, at=max(branching.times(tree))-0:10, labels=0:10)
Best,
Santiago
On Mar 2, 2015, at 4:38 PM, Jacob Berv jakeberv.r.sig.ph...@gmail.com wrote:
Excellent! Thanks Santiago.
In case anyone is interested, I ended up using the following three lines to
generate an axis with labeled and thick tick marks every 10 and thin
(unlabeled) ticks every 2. There is probably a more elegant way to do this but
this works:
axis(3,
Simon and Ben,
Of course, sample size of 8 is going to be an issue in almost any analysis. But
sometimes that is all the data there are.
Incidentally, this exchange reminded me that I’m still wary of making comments
on r-sig. If somebody comes into my office, I have the time to discuss with
