Hi Rafael,
Rafael Rubio de Casas wrote on 02/02/2012 06:24:
Hi Nicolai,
Thanks for your message. I guess I wasn't completely clear in my
previous message.
tiplabels() does do a similar thing to what I want. In fact, it is what
I ahve been using. The problem is that I think that with tiplabels
Greetings!
I'm new to the list, thanks to Emanuel for bringing it to my attention.
I have a general question for the group. Several years ago I used r8s
for estimating mrca dates for a tree using an internal node date as a
prior. I believe BEAST also does this. But is there an R package for
Ape can do this, function chronopl. In general, one good way to find out
which package can do something is by looking at the task view for
phylogenetics: http://cran.r-project.org/web/views/Phylogenetics.html .
This will also allow you to install all the phylogenetics packages (at
least those on
Hi,
Thanks, Emmanuel. I did try to play around with tip.labels (by the by, I
did not know it called points, although I guess it makes a lot of sense).
The problem I run into is that, for some reason, label.offset does not
seem to work with the graphical labels. For instance, I would expect two
Hi Brian-
It has been awhile since I played with chronopl(), but at the time, I convinced
myself that results were substantially different from penalized likelihood as
implemented in r8s. I haven't explored this exhaustively, but at the time, I
was very much convinced that the results of
I'm not sure if this is the best place to make a bug report, but I thought
others might be interested.
I was trying to replicate, with geiger, a demonstration of estimating lambda
with measurement error from Liam's blog:
http://phytools.blogspot.com/2011/11/including-measurement-error-in.html
Hi all.
If you don't want to apply the fix, you can circumvent the problem by
first assuring that meserr is in the same order as the tree tip labels,
and then removing the names from the input vector of standard errors.
So, for instance:
se-se[tree$tip.label]
names(se)-NULL
Hi Dan,
This is indeed an issue. I had the opportunity a few months ago to get
the outputs from r8s and chronopl on the same data: this showed some
difficulties with r8s, namely the starting and final values of the PL
were identical.
I'm currently working on chronopl because it fails to
Rafael Rubio de Casas wrote on 02/02/2012 22:02:
Hi,
Thanks, Emmanuel. I did try to play around with tip.labels (by the by, I
did not know it called points, although I guess it makes a lot of sense).
The problem I run into is that, for some reason, label.offset does not
seem to work with the
