,method=lambda)$lambda # obs. lambda
# lambda from randomized tips
ff-function(x){ x$tip.label-sample(x$tip.label); x }
ll-replicate(nn-1,phylosig(ff(tree),x,method=lambda)$lambda)
p-mean(c(lambda,ll)=lambda) # p.value from randomization
All the best, Liam
Liam J. Revell, Assistant Professor
to put priors on everything (or nothing, in which a pretty
uninformative prior is used). If you decide this is what you want to do
have difficulty figuring it out, please let me know.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http
does this - I posted it to my
blog here:
http://blog.phytools.org/2013/04/computing-strahler-numbers-for-nodes-on.html.
Check it out and let us know if this does what it is supposed to.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web
Glad to hear it Alastair.
I posted an answer to your second question (how to extract the set of
most inclusive clades with Strahler number i) here:
http://blog.phytools.org/2013/04/extracting-set-of-most-inclusive-clades.html.
All the best, Liam
Liam J. Revell, Assistant Professor
This is exactly what findMRCA in phytools does, but I wrote it a while
ago so I'm not sure how fast it is
- Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http
Glenn - if this function does what you were hoping for, then I have also
posted a version that works for non-binary trees. For more information,
check out my blog:
http://blog.phytools.org/2013/05/version-of-getcladesofsize-that-also.html.
All the best, Liam
Liam J. Revell, Assistant
-on-ancestral-state.html,
and
http://blog.phytools.org/2013/03/marginal-ancestral-state-reconstruction.html).
All the best,
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http
Hi Alejandro.
Do:
newmulti-lapply(unclass(trees),chronopl,lambda=0.5)
class(newmulti)-multiPhylo
Good luck.
- Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http
). Please make sure you have
the latest version of phytools (at least the latest CRAN version, if not
the most recent version here: http://www.phytools.org/nonstatic/) and
let me know if you have any questions.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University
I meant to say not being stored in tree$node.label - but what's the
difference. The instructions still work. All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http
(otherwise they are treated as additional trees to write). Let
us know if specifying the argument file by name fixes your problem.
- Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http
-tree$Nnode:1
To check, try:
library(phytools)
tree$node.label-tree$Nnode:1
plotTree(tree,setEnv=TRUE)
nodelabels(tree$node.label)
I think this is what you mean. - Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell
of the
SE. If you are using an arcsine transformation, as is common for
proportion data, you need to be aware that your standard errors are on
the original scale! (I don't know the formula for standard errors on the
transformed scale.)
- Liam
Liam J. Revell, Assistant Professor of Biology
number to real when it's
imaginary part disappears.
I'll try and fix this final issue, but I can't do much about (1) (2).
Thanks for the report!
- Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev
Hi Agus.
To follow up on (3), I just posted a version of new version of the
function that strips the imaginary part of the canonical correlations if
it is zero. (Details here:
http://blog.phytools.org/2013/07/complex-numbers-in-r-and-new-version-of.html).
All the best, Liam
Liam J. Revell
-of-residuals.html
for more information.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 7/23/2013 12:59 PM, Anna Rice wrote:
Hello,
I'm
data
coords-cbind(lat,lon)
rownames(coords)-species
phylo.to.map(tree,coords)
I've also attached a example plot with a simulated tree your lat/long
data as a .png.
My function does not use plot.phylo may need to be adjusted to allow
for longer tip labels.
Cool problem! Liam
Liam J. Revell
be.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 7/30/2013 9:47 AM, Juan Antonio Balbuena wrote:
Hello
I am using the function findMRCA
.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 7/30/2013 6:10 AM, Tom Wenseleers wrote:
Dear all,
Many thanks for all your advice so far. I
approach is best or if you have other options other
than collapsing or throwing out data.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 7
Joe is of course correct. However, if the tree is ultrametric than would
it not be the case that one zero length terminal edge implies that there
is zero branch length separating at least two terminal species? (I
believe this is right.)
All the best, Liam
Liam J. Revell, Assistant Professor
=outgroupname,resolve.root=TRUE)
Let us know if that does not work.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 8/6/2013 2:03 PM, SILVIA CALVO
nodes lead to only
one tip.
Feedback welcome.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 8/13/2013 10:43 AM, Nicholas Crouch wrote
' now has numbers as labels
write.tree(temp,file=filename)
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 8/19/2013 10:43 PM, Naxerova, Kamila
to zero. So any judgement on how good or bad it will be to
assume BM depends on the fitted parameter values for alpha.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http
as.phylo.formula
data(carnivora)
tree-as.phylo.formula(as.phylo(~SuperFamily/Family/Genus/Species,
data=carnivora)
plotTree(tree)
Let us know if this solves your problem.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu
Sorry - this is the correct source file. (I just neglected
as.phylo.formula- from the start of the source file.)
- Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http
to
install from source, then respond to the list I'm sure someone will
help out post a package binary for you.
- Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
phylogenetic signal using one or multiple
methods. For instance, you could use my function phylosig in the
phytools package.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
.
If you decide to use phytools, you should probably first install the
latest (non-CRAN) version (http://www.phytools.org/nonstatic or
http://www.phytools.org/nonstatic/bin for binaries).
Let us know if this helps you get started.
- Liam
Liam J. Revell, Assistant Professor of Biology
a
specific example, though, this is hard to assess.)
- Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 9/15/2013 10:21 PM, Ties Coomber wrote:
Hello,
I have
)
diag(Q)--rowSums(Q,na.rm=TRUE)
- Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 9/18/2013 1:08 PM, Rafael Rubio de Casas wrote:
Dear all
the lambda model in geiger =1.99 if you think this is a good idea - but
the argument/value has changed from treeTransform=lambda to
transform=lambda. Good luck. - Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email
messages (and I appreciate the irony of doing so
as I recommend that no one else should - my apologies to all for that).
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http
: http://www.phytools.org/mpma/phybase/. I also wrote a
tutorial (again, for my class) available here:
http://www.phytools.org/mpma/Exercise_8.1/. Perhaps this will be of some
help.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http
if
said problems did not exist in prior releases!).
All the best, Liam
--
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
to automate this if you have to iterate
across many samples. Let me know if you need help with that.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 11/8/2013 6:52 PM, Oscar Inostroza wrote:
Hi All
Currently ancestral state reconstruction for continuous
something
like this:
ii-sapply(B$edge[,2],function(x,y) which(y==x),y=A$edge[,2])
plot(B,no.margin=TRUE)
edgelabels(A$edge.length[ii])
If your node numbers *do not* match, then this gets a little more
complicated - but the same general logic can be used.
All the best, Liam
Liam J. Revell
(ee)
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 11/11/2013 7:06 PM, Jingchun Li wrote:
Thanks Liam. Unfortunately for now, the second
(and will definitely
be more conservative) than treating the tree as 'known', if that is the
alternative.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 12/6/2013 9:17 AM, Szymek Drobniak wrote:
Hello all,
I'm trying to reconstruct ancestral states in a 3-state trait
approaches should give the
same probabilities at internal nodes. However, a word of caution. With
such a very large tree, it's possible that different implementations of
the same method may give different results simply for having failed to
converge to the MLEs.
All the best, Liam
Liam J. Revell
) it
will even search for the path to the executable for you.
You can get Rphylip here: http://www.phytools.org/Rphylip/ it is also
on gitHub (http://github.com/liamrevell/Rphylip).
All the best, Liam
--
Liam J. Revell
web: http://faculty.umb.edu/liam.revell/
blog: http://blog.phytools.org
On 12/16/2013
the set of all bi- and
multifurcating topologies. It's not immediately obvious how you could do
that, but I'll think about it.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog
.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 1/15/2014 3:34 PM, David Bapst wrote:
Hi Emmanuel and the rest of the list,
In some code, I use
You might try investigating text to add labels to the plot and and
legend for a legend. Good luck! - Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 1/13
problem, you'll need to send me your
data code.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 1/28/2014 5:46 AM, Gabriel Yedid wrote:
Hi all
(I haven't tested
that). If it works, please let me know I will add to phytools.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 1/30/2014 1
in an ultrametric tree, just do:
H-max(H)-H
and then repeat the same.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 2/13/2014 12:16 AM, Simon Greenhill
Something similar to this is in phytools
(http://blog.phytools.org/2013/11/new-function-to-add-species-to-genus-in.html),
though not yet on CRAN. Let me know if this is what you're thinking of.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
, 2014. Las aplicaciones pueden ser escritas en inglés o
español; sin embargo todos los estudiantes deben tener un nivel básico
de inglés científico. Preguntas pueden ser dirigidas a liam.rev...@umb.edu.
--
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web
the opportunity to travel
all expenses paid to Bogotá with our group will be sufficient incentive
to consider applying for this position. I have never been, but I'm told
that Bogotá is a terrific city to visit, and I think the course will be
a lot of fun.
All the best, Liam
--
Liam J. Revell, Assistant
Oops. I forgot one step - collapsing singleton nodes using
collapse.singles in ape:
library(phytools)
## text is your tree string
tree-read.newick(text=text)
tree-collapse.singles(tree)
write.tree(phy=tree,file=Gudrun.tre)
write.nexus(tree,file=Gudrun.nex)
All the best, Liam
Liam J. Revell
a tree and vector (in which the vector names attribute corresponds to
the tip labels of the tree) as input.
- Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
) to see how to do that, or
you could refer to my very basic tutorial here:
http://www.phytools.org/mpma/Exercise_7.1/
Good luck.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
,
use stats function density with the column of interest from par as input.
Is that helpful? I hope a little bit.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http
be sent by May 29, 2014 for full
consideration.
UMass Boston provides equal employment opportunities (EEO) to all
employees and applicants for employment.
--
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email
will nearly
always be smaller than the rate on the original tree.
- Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 5/5/2014 6:15 AM, imran khaliq wrote:
Dear
be
straightforward to modify this so that tip labels are included, or so
that a stochastic map (instead of a standard tree) was plotted.
Let me know if this does what you want it to, or if you have any problems.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University
Dear Rosemary.
This appears to be a problem of older ape versions. If you update to the
latest version of ape (3-1.1) I believe that you will find this is fixed.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu
It looks like transform.phylo has been deprecated. Use rescale.phylo.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 5/16/2014 2:20 PM
(tree$tip.label))
For all nodes including tip nodes you can modify to:
library(phytools)
h-setNames(sapply(1:(tree$Nnode+length(tree$tip.label)),nodeheight,
tree=tree),c(tree$tip.label,1:tree$Nnode+
length(tree$tip.label)))
All the best, Liam
Liam J. Revell, Assistant Professor
Hi Gabriela.
You can use the function sim.corrs in the phytools package. For more
details see the help page here:
http://www.phytools.org/static.help/sim.corrs.html.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http
Hi Jonathan.
Can you share your R workspace R history so that we can replicate your error?
Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
--
Sent from
in islandRecon$marginal.anc should correspond to node
numbers in your original tree.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 6/4/2014 11:37
,] ## should be the edges tipward of the mrca of group
## visualize this:
plotSimmap(paintBranches(tree,tree$edge[ii,2],state=2),
colors=setNames(c(blue,red),1:2),lwd=3,node.numbers=T)
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http
Thanks Jonas.
I had just added this to phytools. Not yet on CRAN but more details
(including how to use it) can be seen here:
http://blog.phytools.org/2014/06/coloring-edges-in-phylomorphospace3d.html.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University
See comments below. I hope the instructions are helpful.
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 7/25/2014 1:27 PM, Eliot Miller wrote:
My first
know if this is what you had in mind.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 8/12/2014 9:23 AM, Ferguson-Gow, Henry wrote:
Dear list
-read.tree(text=x[length(x)])
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 8/15/2014 9:56 AM, Anna Bastian wrote:
Dear list members,
I am
(list(likelihood.ratio=LR,p=P))
}
## run likelihood-ratio test
lrtest(fitBM,fitLambda)
For small trees, we may want to generate a null distribution for the LR
using simulation under the null rather than the parametric distribution.
All the best, Liam
Liam J. Revell, Assistant Professor
(text=obj)
}
which is even simpler.
- Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 8/29/2014 5:25 PM, Liam J. Revell wrote:
Hi Daniel.
I think
the error.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 9/17/2014 10:46 PM, Nicholas Crouch wrote:
Hi,
I am having a problem
(i.e., Yule) process
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 9/26/2014 12:51 AM, Emmanuel Paradis wrote:
Hi,
compute.brtime() can
Hi Gabriel.
You could try the following, which worked for me with a simulated tree
containing 9898 tips, 7898 of which were extinct:
library(phytools)
obj-drop.tip(tree,getExtinct(tree))
obj
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
/pdfs/Revell_2014.MPCM-chapter.pdf)
as a guide.
All the best. - Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 10/17/2014 6:48 AM, Ondřej Mikula wrote
(specifically, descendants on either side of the node
will be all in state 0 or 1).
This should be straightforward to code, but I do not have time to
demonstrate right now. I will try to do it this evening. Let us know if
you first figure it out yourself.
- Liam
Liam J. Revell, Assistant Professor
instead change the code in minor ways and use
fitDiscrete, which is slower but should be more robust.
The demo is fairly explicit, but let us know if it works or if I have
made any errors.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
run fitTransform separately on each column of X and sum the
log-likelihoods. I don't know whether either of these things (or the
main exercise) are a good idea, but they are all certainly possible.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts
You could try something like the following:
tips-tree$tip.label
genera-unique(sapply(strsplit(tips,_),function(x) x[1]))
ii-sapply(genera,function(x,y) grep(x,y)[1],y=tips)
tree-drop.tip(tree,setdiff(tree$tip.label,tips[ii]))
Let us know if this works.
All the best, Liam
Liam J. Revell
,function(x,y) x[x=Ntip(y)][1],y=tree)]
tt-drop.tip(tree,setdiff(tree$tip.label,tips))
Let us know if this works. All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http
For a exercises in a class I teach, I previously posted source (with
NAMESPACE file), Windows Mac OS binaries here:
http://www.phytools.org/phybase. Maybe this will help.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http
if this works.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 11/5/2014 12:21 PM, Lara Budic wrote:
Hi Julien,
thank you for your
Sorry, that should have been: http://www.phytools.org/mpma/phybase
All the best,
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 11/6/2014 5:09 AM, Vojtěch
. There are
different views on whether or not this is a good idea; or if, perhaps,
fitting a model with a more explicit biological basis (such as an OU
model with two regimes) would be more sensible.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http
=LETTERS)
plot(tree,show.node.label=TRUE) ## no node labels plotted
tree$node.label-letters[1:25]
plot(tree,show.node.label=TRUE) ## labels exist so are plotted
Let us know if this clarifies your issue or if you still do not have
node labels.
All the best, Liam
Liam J. Revell, Assistant Professor
=filename.nex) ## does not work?
If so, I was able to get this to run on test datasets without a problem.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http
probability
density for q01 and q10 (in this case).
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 1/28/2015 8:42 AM, Maria Ghazali wrote:
Hi
, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 2/17/2015 3:19 PM, Yampolsky, Lev wrote:
Dear Colleagues,
I need to remove singleton nodes from a tree
for the transition matrix. This could tell you if the result you
have found is being influenced by the prior (although the mean of the
prior in make.simmap is 'hyper-parameterized' by the ML value of Q, so
this seems somewhat unlikely).
All the best, Liam
Liam J. Revell, Assistant Professor
(trees,aov.phylo,formula=y~x,nsim=100)
Then to pull out the 'phylogenetic p-values' only in a vector you could do:
Pr.phy-sapply(fits,function(x) attr(x,summary)$Pr(phy)[1])
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http
then the following highly
similar code does the same thing:
N-apply(as.matrix(X),2,function(x) length(unique(x)))
Let us know if you found another solution or if this does not work.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http
to root an unrooted tree at
the root node (i.e., the node with node number Ntip(tree)+1).
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 3/19
spots, I obtain an ultrametric tree from read.tree or read.newick.
This may be beside the point if the issue is that this text string when
read using read.tree crashes R rather than producing a more sensible
error. This I too experienced.
All the best, Liam
Liam J. Revell, Assistant Professor
check your
current package version using:
packageVersion(phytools)
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 3/10/2015 12:57 PM
positions replot the tree until it is the way you want it.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 3/5/2015 2:24 PM, Jacob Berv wrote:
Hi
Can I add the suggestion that you do:
ace.ER-ace(setNames(MCTree[,2],MCTree[,1]),phy=tree,
type=discrete,model=“ER”)
otherwise it will 'work', but ace will not notice if the row order of
MCTree is not the same as tree$tip.label.
All the best, Liam
Liam J. Revell, Assistant Professor
first pass through state AB, etc. This kind
of constraint is fairly straightforward to implement in ape's ace function.
Let us know I will see if I can give you any more concrete suggestions.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
simplified) example here:
http://blog.phytools.org/2015/03/converting-phylogeny-with-node-labels.html.
Let us know if this is more or less what you are looking for.
Good luck.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http
101 - 200 of 408 matches
Mail list logo
