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khabbazian / l1ou

Detection of evolutionary shifts in Ornstein-Uhlenbeck models
GNU General Public License v2.0
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Fit Brownian motion #45

Closed oscarIM closed 4 years ago

oscarIM commented 4 years ago

Hello, I am writing to ask if it is possible to fit a Brownian model? I have tried setting the value of alpha.upper to 0 or a small value (eg. 0.001), as well as the parameters alpha.lower and alpha.starting. However, for any combination of these parameters, the program gives me the following error:

Error: $ operator is invalid for atomic vectors Error in fit_OU_model(tree, Y, shift.configuration, opt) : model score is NA in fit_OU_model function! This should not happen. Please set quietly to false to see the reason. Also: Warning message: In my_phylolm_interface(tr, y, s.c, opt) : phylolm returned error with a shift configuration of size 0. You may want to change alpha.upper/alpha.lower!

Greetings

cecileane commented 4 years ago

No, the BM is not an option in this package. Unfortunately, I am completely swamped with other projects to make any progress on this package, and @khabbazian has moved on...

cecileane commented 4 years ago

PhylogeneticEM has the option to use the BM, and shifts in the trait itself (instead of shifts in the optimal value).

oscarIM commented 4 years ago

Thank you very much Cécile for your prompt reply Best,