Hi, i have a new problem, when i try this :
> pglsModel3 <- gls(lnBRW ~ lnBW, correlation = corMartins(1,phy = DIV,
> fixed=FALSE),
+ data = classeur, method = "ML")
R send :
Error in recalc.corStruct(object[[i]], conLin) :
NA/NaN/Inf in foreign function call (arg 4)
How can i do to resol
Hye, This soltuion works well, but I cannot plot on the rooredt tree I
built just before searching bootstrap. I saw that in the option "type",
just "unrooted" was possible. The following code works,,but the tree is not
rooted byt the group I gave. (i have also pb with node rotation, but it is
anoth
Thanks a lot Klaus!
it works fine, I made a stupid mistake!
have a good day
2014-06-03 9:43 GMT+02:00 Klaus Schliep :
> Salut Catherine,
>
> try this:
>
> align1<-read.dna("datacr.fas", format="fasta") #class DNAbin
> align2<- as.phyDat(align1) #class phyDat
> treeMP <- pratchet(align2)
> tree
Salut Catherine,
try this:
align1<-read.dna("datacr.fas", format="fasta") #class DNAbin
align2<- as.phyDat(align1) #class phyDat
treeMP <- pratchet(align2)
treeMP <- acctran(treeMP, align2) # add some edge.length
bs<-bootstrap.phyDat(align2, pratchet, bs=100) # 100 bootstraped MP trees
plotBS(mid
Sorry I forgot the subject!
"Boostrap on mp tree"
2014-06-03 9:14 GMT+02:00 catherine reeb :
> Hello,
> I am trying to calcultae and plot bootstrap with pohangorn, but something
> does not work :
>
> align1<-read.dna("datacr.fas", format="fasta") #class DNAbin
> align2<- as.phyDat(align1) #cl
Hello,
I am trying to calcultae and plot bootstrap with pohangorn, but something
does not work :
align1<-read.dna("datacr.fas", format="fasta") #class DNAbin
align2<- as.phyDat(align1) #class phyDat
treeMP <- pratchet(align2)
bs<-bootstrap.phyDat(treeMP.new, bs=100)#just for test
but it gives
"Er
--
From: Julian WITTISCHE
Sender: r-sig-phylo-boun...@r-project.org
To: r-sig-phylo@r-project.org
Subject: [R-sig-phylo] (no subject)
Sent: 13 Dec 2011 07:22
Hello everybody,
does somebody know about the possibility of drawing hyperbolic trees with R
Hello everybody,
does somebody know about the possibility of drawing hyperbolic trees with R ?
Thanks a lot,
[[alternative HTML version deleted]]
___
R-sig-phylo mailing list
R-sig-phylo@r-project.org
Dear R users,
I am trying to fit different Ornstein-Uhlenbeck models in OUCH to my dataset. I
attached my data ("otd") in ouch format below, and code for Brownian, 1 optima
OU model, 3 optima OU model, and 4 optima OU model.
Does my code look right? I am particularly interested if I wrote th
Hi Anne,
You should build your model based on your scientific hypothesis - not on
which trait shows phylogenetic signal. However, GLS "corrects for"
non-independence in the residual error of y given X - non-independence
which may be due to (for instance) phylogenetic history. Incidentally,
ci.edu/
(A University of California Multicampus Research Project)
Original message
Date: Fri, 24 Sep 2010 16:54:58 +0200
From: Anne Kempel
Subject: [R-sig-phylo] (no subject)
To: r-sig-phylo@r-project.org
>Dear Phylo-people,
>
>I have a little q
Dear Phylo-people,
I have a little question. I am doing phylogenetically corrected
correlations of species traits (with GLS) and have been told, that this
method mainly corrects the variable on the y-axis for phylogeny.
Therefore, I decided to put the variable with the highest phylogenetic
si
Dear R users,
I noticed it is possible to simulate branching time under a
birth-death model using the package Geiger, but I have not found a
package that simulate trees under density-dependent cladogenesis.
Does any one know a package (or another program) that would offer
simulation of trees u
13 matches
Mail list logo
