Please ignore my last message, it was sent by mistake. Sorry!
Happy new year to all.
E.
On 2 January 2014 11:41, Eduardo Ascarrunz <ear...@gmail.com> wrote:
> > alloreg2<-c(1:48)
> > dim(alloreg2)<-c(nrow=24,ncol=2)
> > for (i in 2:25) {
> +
> alloreg2[i-1,]<-c(summary((lm(datasetln[,i]~datasetln[,1])))$r.squared,anova((lm(datasetln[,i]~datasetln[,1])))$"Pr(>F)"[1])
> + }
> > alloreg2
> [,1] [,2]
> [1,] 2.480627e-01 4.692452e-06
> [2,] 1.583641e-02 2.787183e-01
> [3,] 1.332119e-04 9.211746e-01
> [4,] 6.954092e-04 8.211058e-01
> [5,] 2.449341e-02 1.769866e-01
> [6,] 3.009983e-02 1.339250e-01
> [7,] 4.976260e-02 5.274791e-02
> [8,] 1.146599e-02 3.572196e-01
> [9,] 7.008708e-03 4.721380e-01
> [10,] 4.136657e-05 9.560258e-01
> [11,] 1.142588e-02 3.580668e-01
> [12,] 4.828307e-02 5.649079e-02
> [13,] 5.808281e-03 5.128909e-01
> [14,] 1.738474e-02 2.562216e-01
> [15,] 2.213051e-03 6.865520e-01
> [16,] 5.806873e-03 5.129422e-01
> [17,] 1.488570e-02 2.937490e-01
> [18,] 9.790540e-05 9.323945e-01
> [19,] 1.908742e-06 9.905496e-01
> [20,] 4.690994e-03 5.566098e-01
> [21,] 4.412028e-02 6.857869e-02
> [22,] 1.726578e-02 2.578693e-01
> [23,] 5.252169e-03 5.338479e-01
> [24,] 6.538443e-05 9.447305e-01
> >
> > alloreg3<-c(1:48)
> > dim(alloreg3)<-c(nrow=24,ncol=2)
> > for (i in 2:25) {
> +
> alloreg3[i-1,]<-c(summary((lm(jmpthomas[,i]~jmpthomas[,1])))$r.squared,anova((lm(jmpthomas[,i]~jmpthomas[,1])))$"Pr(>F)"[1])
> + }
> > alloreg3
> [,1] [,2]
> [1,] 2.460384e-01 5.202590e-06
> [2,] 1.468026e-02 2.971299e-01
> [3,] 2.672849e-05 9.646462e-01
> [4,] 5.245843e-04 8.443070e-01
> [5,] 2.637115e-02 1.610467e-01
> [6,] 2.856208e-02 1.444444e-01
> [7,] 4.933823e-02 5.379439e-02
> [8,] 1.032559e-02 3.824230e-01
> [9,] 6.695454e-03 4.822442e-01
> [10,] 1.157413e-04 9.265097e-01
> [11,] 7.565447e-03 4.549905e-01
> [12,] 4.681145e-02 6.048797e-02
> [13,] 6.447833e-03 4.904846e-01
> [14,] 1.841212e-02 2.425089e-01
> [15,] 2.238318e-03 6.848614e-01
> [16,] 5.937185e-03 5.082370e-01
> [17,] 1.569970e-02 2.808195e-01
> [18,] 7.665993e-05 9.401625e-01
> [19,] 3.878511e-05 9.574187e-01
> [20,] 5.438222e-03 5.266709e-01
> [21,] 4.386239e-02 6.941131e-02
> [22,] 1.732606e-02 2.570328e-01
> [23,] 5.629804e-03 5.194573e-01
> [24,] 1.634704e-04 9.127115e-01
> >
> > alloreg2 - alloreg3
> [,1] [,2]
> [1,] 2.024287e-03 -5.101376e-07
> [2,] 1.156150e-03 -1.841153e-02
> [3,] 1.064834e-04 -4.347159e-02
> [4,] 1.708249e-04 -2.320121e-02
> [5,] -1.877741e-03 1.593991e-02
> [6,] 1.537743e-03 -1.051939e-02
> [7,] 4.243667e-04 -1.046481e-03
> [8,] 1.140399e-03 -2.520332e-02
> [9,] 3.132538e-04 -1.010615e-02
> [10,] -7.437470e-05 2.951609e-02
> [11,] 3.860437e-03 -9.692373e-02
> [12,] 1.471617e-03 -3.997175e-03
> [13,] -6.395521e-04 2.240629e-02
> [14,] -1.027378e-03 1.371264e-02
> [15,] -2.526664e-05 1.690596e-03
> [16,] -1.303119e-04 4.705225e-03
> [17,] -8.139970e-04 1.292944e-02
> [18,] 2.124547e-05 -7.767984e-03
> [19,] -3.687637e-05 3.313087e-02
> [20,] -7.472282e-04 2.993891e-02
> [21,] 2.578922e-04 -8.326114e-04
> [22,] -6.027869e-05 8.365089e-04
> [23,] -3.776347e-04 1.439056e-02
> [24,] -9.808602e-05 3.201904e-02
>
>
> On 25 December 2013 18:21, Eduardo Ascarrunz <ear...@gmail.com> wrote:
>
>> Thanks Joe!
>>
>>
>> On 24 December 2013 17:31, Joe Felsenstein <felse...@uw.edu> wrote:
>>
>>> Eduardo Ascarrunz <ear...@gmail.com> wrote:
>>>
>>> > Also, I figured out I could work with unrooted trees. I suspect the
>>> procedure would be similar to your rooted method, wouldn't it?
>>>
>>> There is a 1-1 correspondence between n-species rooted tree topologies
>>> and (n+1)-species unrooted tree topologies (this is discussed in
>>> Chapter 3 of my book). So you can simply generate a bifurcating
>>> rooted tree, or a multifurcating rooted tree, of n-1 tips, and then
>>> unroot it, making the previous root now be species n. Then you get
>>> a randomly sampled unrooted tree.
>>>
>>> This works for tree topologies but not, I think, for labeled histories.
>>>
>>> Joe
>>> ----
>>> Joe Felsenstein j...@gs.washington.edu
>>> Department of Genome Sciences and Department of Biology,
>>> University of Washington, Box 355065, Seattle, WA 98195-5065 USA
>>>
>>
>>
>
[[alternative HTML version deleted]]
_______________________________________________
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
