Great! Thanks for all the help!
Lindsey
On Wed, Jan 11, 2023 at 9:33 AM Liam J. Revell wrote:
> Dear Lindsey.
>
> You should not adjust tol at all -- use the default. Sorry I wasn't clear
> on that. It is just an (arbitrarily) small value that helps us avoid
> evaluating solutions that are not
Dear Lindsey.
You should not adjust tol at all -- use the default. Sorry I wasn't
clear on that. It is just an (arbitrarily) small value that helps us
avoid evaluating solutions that are not "legal." (E.g., in your case,
trying to attach a tip to an edge /below/ its parent node.)
All the
Hey Liam,
Thanks alot! I really appreciate it! I installed the new version and I saw
your edits to the locate.fossil function on github.
I just have one more question, I am new to the tol argument and I am not
sure what the default should be set to. I've set it to a couple numbers
(ex, 0.5, 0.1
Dear Lindsey.
Thanks for sharing the code & data. It made the problem pretty easy to
resolve.
Turns out it is a simple numerical precision issue.
I have resolved it by adding an optional argument tolwith a sensible
default value which most users can probably ignore (but can set to tol=0
if
Dear Lindsey.
Thanks for posting your code, but would you mind sending me (it can be
off-list) an example in which I can also pull your data & tree and
re-run it with the real data that is generating the error? This might be
helpful in getting to the bottom of your issue. Thanks!
All the
Hi all,
I have a question regarding the phytools function locate.fossil().
I have had a lot of success with this function but there are two fossils of
mine that the function does not like. I give the function my phylogeny, a
max and min age for the fossil, and the edge for the fossil to be
