section_the_tree in RASP

[cge...@gmail.com]

Hello

I'm trying to run a model test using BioGeoBears in RASP, but the analysis is stopped, and the following message appears in the log: "You have not turned on fossils by setting 'cut_fossils=FALSE' in section_the_tree().
So, I run the script section_the_tree: Section a tree for stratified analysis by cmd, not return any error, but the analysis still stops, and the message in RASP is:
ERROR:

Try [Tools->Scaling Branch Length] if you meet errors.

Does anyone have any idea how to solve this?
Thanks in advance.

Caio Geroto

[Nick Matzke]

Hi - I don't know the details of how RASP works, but you'll need to somehow internally change the script RASP is using, or just run the BioGeoBEARS script by itself.

The message means: BioGeoBEARS thinks you have a tree with fossils in it, which means a tree where not all the tips come up to the present.  If this is what you meant to do, then you need the cut_fossils=FALSE setting.

If you didn't mean to have fossils in the tree, then you have a tree that is not ultrametric for some other reason, e.g. you are using a molecular-branchlengths tree instead of a time-scaled tree.  For this, the best approach is a BEAST dating analysis, or barring that, some kind of relative timescaling with e.g. the r8s program, perhaps some R function, or maybe the RASP Tools->Scaling Branch Length option.

Cheers!

Nick

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[Caio Geroto]

Thanks for the answer, Nick.  I actually have fossils in the tree... almost every taxa... But now I have some idea of where to look.
Best regards
Caio Geroto

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Amor pelo efeito deificador da organização, ó materialistas!... Por que o pensamento, sendo uma secreção do cérebro, é mais maravilhoso que a gravidade, uma propriedade da matéria? Por nossa arrogância, por nossa auto-admiração. - Charles Darwin