tree_Discrete improvements

[caterinap]

Hey guys, I've been testing tree_Discrete. It works nicely! Just some thoughts for small improvements:

• when transformis different from "none" it prints a bunch of stuff, we could silent it
• when optparis NA, don't show it in summary and plot
• L.105 of the tree_Discrete function you had N.obs=n, I assumed it was n.tree - please change it if it's not the case. I changed this and some very minor typos in 2649a3b

[gijsbertwerner]

Cool thanks Caterina! I have now done all of these things, and pushed back on Github. Great suggestions! I have also changed substantially so that now prints in the same style as tree_physig, for unity of style across!

[gijsbertwerner]

The way I have currently set up tree_Discrete (and will set up the other xxx_Discretes) is that there is no match_dataphy call. The reason for this is the different way in which Geiger/fitDiscrete wants the data compared to phylolm (i.e. as a named vector, rather than a data frame). We could either update match_dataphy to also process this, or write a new specific function for this purpose, but let's not for now. Would be nicer and more consistent if we did so here too, but if people wrongly feed the data, the fitDiscrete call will throw its standard error anyway, so not doing this is sufficient for now, I think.

[paternogbc]

Very nice Gijsbert! I agree with this approach. Also people might find it easier if the data input follows the same style of the original function on Geiger.

On Tue, 21 Nov 2017 at 22:25 Gijsbert Werner notifications@github.com wrote:

The way I have currently set up tree_Discrete (and will set up the other xxx_Discretes) is that there is no match_dataphy call. The reason for this is the different way in which Geiger/fitDiscrete wants the data compared to phylolm (i.e. as a named vector, rather than a data frame). We could either update match_dataphy to also process this, or write a new specific function for this purpose, but let's not for now. Would be nicer and more consistent if we did so here too, but if people wrongly feed the data, the fitDiscrete call will throw its standard error anyway, so not doing this is sufficient for now, I think.

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Gustavo Brant Paterno Doutorando em Ecologia Departamento de Ecologia Universidade Federal do Rio Grande do Norte

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[gijsbertwerner]

This is now all done, plotting works nicely and I think the tree_discrete/continuous functions are pretty much done :-)