How to reduce the number of constraints

blackrim / treePL

Phylogenetic penalized likelihood

https://github.com/blackrim/treePL/wiki

GNU General Public License v3.0

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How to reduce the number of constraints #31

Closed LuaBgd closed 4 years ago

LuaBgd commented 6 years ago

Hi everyone,

I am also using treePL with constraints and I got the error message: "Failed setting feasible start rates/dates after 10 attempts. Aborting." I obtained ages for the nodes to constrain from a tree, previsouly dated using treePL so they shouldn't be conflicting constraints as you present them : one node close to the tips older than one closer to the root. Is there other cases where constraints can be conflicting that I could check for ? I am dating a tree with 2340 species and using around 200 constraints, is it too much ? how can I choose the best ones ?

Thank you very much for your answers !

Have a nice day !

Luana phD student Toulouse, FRANCE

josephwb commented 6 years ago

@LuaBgd Are you certain there are no conflicting constraints? Even just 1 will make make an analysis impossible. For example, if there are any topological differences between your tree and the tree you referenced, then some constraints can be redundant or conflicting. I have (R) code that can check constraint consistency. If you post your tree & config file I can test things for you. If it proves useful I can clean it up a bit and put it in the treePL repo.

LuaBgd commented 6 years ago

Hi !

Thank you very much for your answer! I am definitely not certain there are no conflicting constraints but I extracted them as follow:

I extracted all node ages of a dated tree
- kept ages for nodes leading to a monophyletic group
- check in the phylogeny I want to date, if this node exists (is the same taxonomic group also monophyletic there?)
- removed contraints pointing the same node

So, I thought everything should be already consistent... But yes I can post the tree and the constraints, that would be lovely of you to look at it!

Thank you very much, Luana

Belinda333 commented 2 years ago

Hi everyone,

would it possible to share that R code to check constraint consistency? I have a similar issue and a lot of large trees to date where manually checking would take forever.... Thanks a lot!

Best wishes, Belinda