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pbastide / PhylogeneticEM

Implementation of the EM algorithm for the detection of shifts in a phylogeny.
https://pbastide.github.io/PhylogeneticEM/
GNU General Public License v2.0
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standard error #24

Open jakeberv opened 10 months ago

jakeberv commented 10 months ago

Is it possible to provide estimates of standard error for traits going into PhylogeneticEM? What is the recommended procedure for accounting for within-species variation?

pbastide commented 10 months ago

Hi,

Indeed, accounting for within species variation is important in many analyses.

Unfortunately, there is currently no way of estimating standard errors, or taking it into account in PhyloEM. It is theoretically possible, but not implemented.

If you already have an idea of what the standard errors should be, one thing you could do is re-sample the data using this standard error, and for each new dataset re-run an analysis of PhyloEM, to see if the results change, and get an idea of the variation of the estimated parameters with the variation of the input data.

An other approach could be, once you estimated a model with PhyloEM, to use it in mvMORPH (as done in answer to #23), including individual variations (with the error argument).

Sorry these two answers are not ideal. Let me know if you come up with an other solution !

Kind regards, Paul