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macroevolution / bamm

A program for multimodel inference on speciation and trait evolution
GNU General Public License v2.0
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finish R functions for trait evolution #10

Closed drabosky closed 10 years ago

drabosky commented 10 years ago

R functions for summarizing rates etc for speciationextinction model but I don't think they are yet finished for trait evolution.

huatengh commented 10 years ago

The function getEventData is modified so that when the event data file is from a trait-BAMM run, it will set all the extinction rates (mu) to zero, and all the rest calculations/functions should be the same?

ptitle commented 10 years ago

That is how we've been setting it up, but I don't think we've gone through all of the functions yet to make sure that that makes conceptual sense.

blueraleigh commented 10 years ago

All current summary functions require the output from getEventData. getEventData returns a 'bamm-data' class object with an attribute named 'type' that currently is either 'diversification' or 'traits'. If type equals 'traits' then the mu vectors are all set to 0 because there are no columns in the trait-bamm eventdata outfile for these rates. This means that all other functions and calculations can operate as normal without duplication. The only changes that have been made to the other functions are name changes, e.g. getBySpeciesDiversificationRateMatrix changed to getBySpeciesRateMatrix to indicate that it can handle rates of speciation, extinction, and phenotypic evolution. I will leave the issue open because there are probably other useful summary functions that can be introduced.

redcurry commented 10 years ago

Is this still an issue?

ptitle commented 10 years ago

No, everything is now bamm-trait compatible.