tree_bd: new function for diversification rate

[paternogbc]

Hey guys,

just pushed a new function tree_bd() to the branch https://github.com/paternogbc/sensiPhy/tree/new_div_rate

It implements tree_ method for net diversification rate (Magallon and Sanderson, 2000) and speciation rate (Kendall-Moran).

For sensi_plot() I tried to follow the same simple graphs for showing the distribution of estimates across different trees. Let me know what you think =)
As we discussed before, diversification rates dont vary much between trees.

[gijsbertwerner]

Looks great, Gustavo! Thanks :-)

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Dr. Gijsbert Werner Newton Fellow, Department of Zoology Junior Research Fellow, Balliol College University of Oxford

Balliol College Broad Street Oxford OX1 3BJ United Kingdom

On 26 Nov 2017, at 01:17, Gustavo Paterno notifications@github.com<mailto:notifications@github.com> wrote:

Hey guys,

just pushed a new function tree_bd() to the branch [https://github.com/paternogbc/sensiPhy/tree/new_div_rate].

It implements tree_ method for net diversification rate (Magallon and Sanderson, 2000) and speciation rate (Kendall-Moran).

For sensi_plot() I tried to follow the same simple graphs for showing the distribution of estimates across different trees. Let me know what you think =) As we discussed before, diversification rates dont vary much between trees. [image]https://user-images.githubusercontent.com/9639481/33236295-3110bae0-d2a3-11e7-8db7-8733762646e1.png

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[gijsbertwerner]

Sorry, but I have only had the chance to look into this a bit closer and check your implementations.

Seem to all work great to me, Gustavo :-)

Quite interesting that if you execute the examples the Kendall-Moran methods seems to be a bit more affect than Magallon. Might be nice to use that one in tutorial.

One small remarks For me the models only work if I use ‘phy = primates$phy’ rather than the example ‘pay = primates.phy’. Perhaps this has to do with the dataset issue from #167. I haven’t changed anything, because wanted to figure that out first, but thought I’d highlight.

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Dr. Gijsbert Werner Newton Fellow, Department of Zoology Junior Research Fellow, Balliol College University of Oxford

Balliol College Broad Street Oxford OX1 3BJ United Kingdom

On 26 Nov 2017, at 01:17, Gustavo Paterno notifications@github.com<mailto:notifications@github.com> wrote:

Hey guys,

just pushed a new function tree_bd() to the branch [https://github.com/paternogbc/sensiPhy/tree/new_div_rate].

It implements tree_ method for net diversification rate (Magallon and Sanderson, 2000) and speciation rate (Kendall-Moran).

For sensi_plot() I tried to follow the same simple graphs for showing the distribution of estimates across different trees. Let me know what you think =) As we discussed before, diversification rates dont vary much between trees. [image]https://user-images.githubusercontent.com/9639481/33236295-3110bae0-d2a3-11e7-8db7-8733762646e1.png

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/paternogbc/sensiPhy/issues/170, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AGauyIM1jkPj9fBOViG-aXAXOeRYrBmcks5s6LwZgaJpZM4Qqne9.

[paternogbc]

That is interesting, KM varies much more (I will update that for the example). Thanks!

@gijsbertwerner regarding the data problem I am also not sure how to deal with. In my computer phy = primates.phy" works fine... I will do some other tests and see if I have any idea about it. Thanks for spotting.