Re: [R-sig-phylo] Consensus frequencies

[Emmanuel Paradis]

Hi Sam,

Have a look at the function prop.part: it is the working function of  
consensus and other similar functions.


EP

Sam Brown s_d_j_br...@hotmail.com a écrit :


Hello one and all

I'm wondering if there is any way of obtaining the consensus   
frequencies of nodes in majority-rule consensus trees where p=0.5.


i.e. given:


t1 - ((t4,t8),((t10,((t2,t5),t3)),((t6,t9),(t1,t7;
t2 - ((t4,t8),((t10,((t2,t5),t3)),((t6,t9),(t1,t7;
t3 - ((t4,t8),((t10,((t2,t5),t3)),((t6,t9),(t1,t7;
t4 - ((t2,t10),((t5,((t4,t3),t8)),((t6,t9),(t1,t7;
t5 - ((t10,t5),((t8,((t2,t4),t3)),((t6,t9),(t1,t7;
t6 - ((t4,t10),((t8,((t3,t5),t2)),((t6,t9),(t1,t7;
t7 - ((t4,t3),((t5,((t2,t10),t8)),((t6,t9),(t1,t7;
t8 - ((t4,t2),((t10,((t8,t5),t3)),((t6,t9),(t1,t7;
t9 - ((t4,t3),((t8,((t10,t5),t2)),((t6,t9),(t1,t7;
t10 - ((t10,t8),((t4,((t2,t3),t5)),((t6,t9),(t1,t7;

tr-read.tree(text=c(t1,t2,t3,t4,t5,t6,t7,t8,t9,t10))

conTR-consensus(tr, p=0.5)
plot(conTR)



The node (t3,t2,t5) will have a consensus frequency of 0.5 (50%) and  
  the three nodes ((t6,t9),(t1,t7)) will each have a frequency of 1   
(100%).


Are there any quick ways of getting this information?

Thanks for any help/pointers

Sam



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[R-sig-phylo] Trait simulations

[jeremy . beaulieu]

Hi all~

I was just wondering if there is a package or function in R that can simulate
two continuous traits with a user-specified correlation coefficient using a
known tree topology, branch lengths, and a model of Brownian motion (or even
OU, if possible)?

All the best,

Jeremy Beaulieu

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