Alanna-
It's because when multi2di() resolves the polytomies, it puts in zero-length
edges. This causes the phylogenetic variance-covariance matrix calculated
from your tree to be singular.
One solution would be to add a small arbitrary constant to your zero-length
edges, although I would caution
a") at URL:
>>http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/
>><http://anolis.oeb.harvard.edu/%7Eliam/R-phylogenetics/> which
>>
>>does not have this issue.
>>
>>Good luck.
>>
>>- Liam
>>
>
a given time interval bin?
>
> Thanks in advance for any suggestion
> best
> paolo
>
> ___
> R-sig-phylo mailing list
> R-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>
--
David Bapst
Dept of Geophysical Sciences
University
ngs/2011/)
Please let me or Emily know if you have any questions.
-Dave Bapst, UChicago
--
David Bapst
Dept of Geophysical Sciences
University of Chicago
5734 S. Ellis
Chicago, IL 60637
http://home.uchicago.edu/~dwbapst/
[[alternative HTML version deleted]]
ength(y)){z[[i]]<-y[[i]]}
...but that's kind of inelegant. I feel like there must be a simpler
solution.Is there any simple way to convert a list of trees into a
multiPhylo object?
-Dave
--
David Bapst
Dept of Geophysical Sciences
University of Chicago
5734 S. Ellis
Chicago, IL 60637
ht
can generate all of them.
>
> Thanks,
>
> Liutauras
> ___
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> R-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>
--
David Bapst
Dept of Geophysical Sciences
University of
Hello all,
Just wanted to send a final reminder that abstracts for our session at GSA
2011 is due today, June 26th. See my previous email below for more details.
Thanks,
-Dave Bapst and Emily King, UChicago
On Mon, Jul 18, 2011 at 11:39 AM, David Bapst wrote:
> Hello all,
> I just wan
t; in
> >>> >> > tree and ages list are the same. I still keep getting:
> >>> >> >
> >>> >> > ttree<-date.phylo(archotreeresolved, ages, rlen=1,
> method="equal")
> >>> >> > Error in ages[tre
an Motion process to change more in their vicinity,
> which may help some.
>
> Joe
>
> Joe Felsenstein j...@gs.washington.edu
> Dept of Genome Sciences and Dept of Biology, Univ. of Washington,
> Box 5065, Seattle Wa 98195-5065
>
>
> [[alternative
on the tree?
>
>
> Any help is greatly appreciated!
>
>
> Morgan Langille
> http://morganlangille.com
>
> ___
> R-sig-phylo mailing list
> R-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>
--
Geneticos
>> Campus Agrario de Vairao, 4485-661 Vairao
>> PORTUGAL
>> Department of Ecology, Evolution, and Organismal Biology
>> Iowa State University, Ames,
>> Iowa 50011, USA
>>
>> tel: +351 91 3086188
>> mail to: antig...@mail.icav.up.pt
>&g
how
to apply that explanation to the habitat degradation example.
So, what do people think? How should we test for correlation when
non-evolving quasi-traits are involved? I'm very interested to hear
people's thoughts on this matter.
-Dave Bapst, UChicago
--
David Bapst
Dept of Geophysical S
ld equally apply to extinction
selectivity cases.
-Dave
On 11/10/2011 3:36 PM, David Bapst wrote:
>
>> Hello all,
>> A recent discussion set my mind thinking on a particular issue and, once
>> again, I decided to ask for the general opinion of R-Sig-Phylo denizens.
>>
ese
species belong to? It may be easier to start by making a new list with
200 elements; a list of lists that records all the families found in
each plot. Than you will be able to easily count the number of plots
that contain each family.
I hope that helps,
-Dave, UChicago
--
David Bapst
Dept o
h arguments in rapply doesn't stop this behavior; indeed, it
seems nothing will stop rapply from ignoring the type 'list' of the phylo
objects themselves. Does anyone know of an alternative to rapply that
considers the class of the nested objects instead?
Thanks,
-Dave B.
--
Da
ove function won't be a good idea in all cases, and isn't much
> tested, etc, etc. This also doesn't preserve class attributes, of the
> component lists, but that could be done in the same way as names() is.
>
> Cheers,
> Rich
>
> On 2012-03-14, at 2:39 PM, David Bap
scent.org <mailto:r...@duke.edu>
> 919.668.9107
>
>[[alternative HTML version deleted]]
>
> ___
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> R-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>
--
David Bapst
Dept of Geophysic
l seems to generate this or a similar
error with compar.ou, so it doesn't seem to be an issue with me using a
non-ultrametric tree. Any ideas?
Thanks, all!
-Dave
--
David Bapst
Dept of Geophysical Sciences
University of Chicago
5734 S. Ellis
Chicago, IL 60637
http://home.uchicago.edu
_
> R-sig-phylo mailing list
> R-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>
--
David Bapst
Dept of Geophysical Sciences
University of Chicago
5734 S. Ellis
Chicago, IL 60637
http://home.uchicago.edu/~dwbapst/
http://cran.r-project.org/web/packag
cript
> where needed, and then simulate trees of the same size as the orginal (e.g.
> with TreeSim functions) to get the null distribution of gamma values. Is that
> feasible?
> thanks,
>
> Pas
>
> ___
> R-sig-phylo mailing l
there used to be an error (around version 2.5) where the
edges of as.phylo.hclust output were multiplied by 2. Maybe the
reverse bug has crept in?
-Dave
--
David Bapst
Dept of Geophysical Sciences
University of Chicago
5734 S. Ellis
Chicago, IL 60637
http://home.uchicago.edu/~dwbapst/
http
369
>
> Of course the cophenetic distances must be the same:
>
>> cophenetic(t)
> 1 2
> 1 0.00 2.562737
> 2 2.562737 0.00
>> cophenetic(h)
> 1
> 2 2.562737
>
>
> Cheers,
>
> Emmanuel
> --Original Message
t;
> Any help is much appreciated
>
> cheers
>
> Tom
> ___
> R-sig-phylo mailing list
> R-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
--
David Bapst
Dept of Geophysical Sciences
University of
f Toronto
> 25 Wilcocks St.
> Toronto, ON
> Canada M5S 3B2
>
> Royal Ontario Museum
> 100 Queen's Park
> Toronto, ON
> Canada M5S 2C6
> Office: 416-586-5591
> Email: nicolas.campi...@mail.utoronto.ca
>
> [[alternative HTML version deleted]]
>
>
", bounds=list(alpha=c(0,1)))
> Fitting EB model:
> $Trait1
> $Trait1$lnl
> [1] -264.4297
>
> $Trait1$beta
> [1] 0.8355526
>
> $Trait1$a
> [1] 0.001813503
>
> $Trait1$aic
> [1] 534.8593
>
> $Trait1$aicc
> [1] 535.1042
>
> $Trait1$k
>
> ___
> > R-sig-phylo mailing list
> > R-sig-phylo@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>
>
>
> --
> NEW EMAIL ADDRESS:
> frank.burbr...@csi.cuny.edu
> **
ore trying prop.clades?
-Dave
On Thu, Nov 8, 2012 at 2:04 PM, Jeremy Yoder wrote:
> All,
>
> I'm working on some analyses that require comparison of tree structures,
> and I've bumped into the problem David Bapst posted about back in March:
> http://www.mail-archive.com/r-si
ssigned time slots of 15
minutes and selected based on relevance for the symposium.
Sincerely,
Lee Hsiang Liow & Thomas F. Hansen
--
David Bapst
Dept of Geophysical Sciences
University of Chicago
5734 S. Ellis
Chicago, IL 60637
http://home.uchicago.edu/~dwbapst/
http://cran.r-project.org/
studies, using
character evolution as a focal point.
Sincerely,
Lee Hsiang Liow & Thomas F. Hansen
--
David Bapst
Dept of Geophysical Sciences
University of Chicago
5734 S. Ellis
Chicago, IL 60637
http://home.uchicago.edu/~dwbapst/
http://cran.r-project.org/web/packages/pa
chable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
--
David Bapst
Dept of Geophysical Sciences
University of Chicago
5734 S. Ellis
Chicago, IL 60637
http://home.uchicago.edu/~dwbapst/
http://cran.r-project.org/web/packages/paleotree/index.html
___
Hi John,
I'm not familiar with any such function either. However, a handy trick
for doing this sort of thing is changing the branch lengths of
descendant nodes to zero and using the ape function di2multi to
collapse those edges, creating a polytomy.
Now, it isn't clear to me from your email wheth
Tristan-
I found this to be the most important how-to reference, but I am a windows user.
http://robjhyndman.com/hyndsight/building-r-packages-for-windows/
For distributing on CRAN, making help files and examples is the most
critical step. package.skeleton() is helpful in setting up the
necessa
degradeTree() in paleotree sort of does this: it collapses some
proportion of internal edges, but then returns the tree with the
zero-length branches collapsed into polytomies, with the original
branch length completely removed.
However, it doesn't take too much to modify it to do a specific numbe
Hi Jurriaan-
I've been thinking about this after your email and my sense is that
such a simulation would be very difficult. Just dropping onto the tree
branching events on the extant tree that only produced one living
daughter might not be too difficult under a homogenous birth-death
model. Howev
Hi Emmanuel and the rest of the list,
In some code, I use the ape function is.binary.tree to test if a
phylogeny is fully dichotomous. However, some recent analyses have
made me wonder if this wasn't the right choice. I'm not sure if the
following is a bug report me or me not understand the reason
cendants, as the tree is unrooted) is just an artifact of the way the
> object is stored in memory & thus is.binary.tree is behaving correctly.
>
> All the best, Liam
>
> Liam J. Revell, Assistant Professor of Biology
> University of Massachusetts Boston
> web: http://faculty
descendant have no meaning until the tree is
>>> rooted. The fact that an unrooted tree stored as an object of class
>>> "phylo"
>>> has one node with three 'descendants' (these aren't actually all
>>> descendants, as the tree is unro
At the risk of inundating you with options, Henry, there is also
expandTaxonTree in the package paleotree (on CRAN) which is similar to the
above, but also lets you collapse higher taxa you list as paraphyletic,
which can be useful if the taxonomic work of your group has never been
concerned with m
Hi all,
I seem to have found a combination of topology and characters that causes
ancestral.pars in phangorn to hard crash, at least in Windows7 with R v3.03
and phangorn v1.99-7.
This issue seems to have been introduced recently; the code works fine in
phangorn v1.99-5 with R v3.02.
I have a re
Hi John,
A fully reproducible example of the error you have encountered would be this:
trees.pool<-rmtree(N=10,n=100)
trees.pool[[1]]<-NULL
Which returns the same error; the reason for this is that 'multiphylo'
is an S3 class so ape has a specific function that replaces the
generic replacement
Julien-
Does mvSHIFT account for the OU rescaling issue on non-ultrametric
trees that Graham mentions? If so, how?
Cheers,
-Dave
On Mon, Jun 2, 2014 at 5:26 PM, Julien Clavel wrote:
> Hi Jon,
>
> Take a look at the "mvSHIFT" function in mvMORPH. This is typically what you
> are looking for and
Hello all,
Recently, I wanted to display posterior probabilities on a 50%
compatibility tree from a MrBayes run, created with the 'sumt'
command. I looked around for ways to do this and found this email
thread from last year:
https://stat.ethz.ch/pipermail/r-sig-phylo/2013-June/002825.html
...wh
> Graham Slater
> Peter Buck Post-Doctoral Fellow
> Department of Paleobiology
> National Museum of Natural History
> The Smithsonian Institution [NHB, MRC 121]
> P.O. Box 37012
>
>
> (202) 633-1316
> slat...@si.edu
> www.fourdimensionalbiology.com
>
>
just plots it in a pdf, which isn't important at all but
I included it for the heck of it. The important stuff is the innards
of the first for loop, which reads in the 'simple' consensus tree
nexus file, reroots it and then rearranges the posterior probabilities
to match the same sp
Klaus and Everyone Else-
> here is a small function which it is very similar to David's 2nd script, but
> it is a bit more compact:
> library(phangorn) # requires the newest pangorn version >= 1.99-8
> addConfidences.phylo <- function(to, from){
> conf = attr(addConfidences(as.splits(to), from
Cecile, Peter, Joe and all-
As far as I understand, Peter's analysis involves paleontological data with
non-ultrametric trees, and based on my understanding of Slater (2014), the
Freckleton approach using PIC is invalid for that type of dataset, although
Fitzjohn's pruning algorithm might still ap
Off-topic, but I wanted to comment on Anthony's wariness about
commenting on R-sig lists...
Yes, it can certainly be very difficult to give advice that is
tailored specifically to the problem of a particular worker on R-sig
lists, particularly as one can't just tell the other person to open
their
William,
Yes, the different PCM models make very different statements about
what is happening biologically in your data. Additionally, the three
Pagel parameters are not always easy to interpret biologically. Carl
Boettiger has some particularly lucid thoughts on Pagel's lambda:
http://www.carlboe
Milton, Brian, etc,
Just wanted to add some background on Alroy's anc-desc change
analyses, and the recognition of these relationships in the fossil
record. This may be tangential; it isn't clear to me what sort of
dataset that Milton has. So, Brian said...
> In Paleo, you can (well, arguably) se
Aaron,
While contemplating Nate's question, I wondered, doesn't hansen
currently support NA codings for missing variables for tip taxa?
Unfortunately the donotrun{} example for hansen() using geiger data
isn't currently functioning, so I couldn't test this.
-Dave Bapst
On Thu, Jun 4, 2015 at 10:
Hello all,
As those of you who directly manipulate the guts of phylo objects in
your code (or construct new phylo objects whole cloth from
un-phylo-like data structures) have probably experienced, it is
sometimes easy to create $edge matrices that aren't accepted by ape
functions (I often use plot
b-ntips] = tmp
> }
> tree
> }
>
> library(phangorn)
> attr(tree1, "order") = NULL
> getRoot(tree1)
>
> tree2 = switch.nodes(tree1, 131, 151)
> plot(tree2) # now works for me
>
> Cheers and have a nice weekend,
> Klaus
>
>
>
>
>
>
>
misc/FormatTreeR_24Oct2012.pdf
>>
>> Recently, I put a function on github to help code writters:
>>
>> https://github.com/emmanuelparadis/checkValidPhylo
>>
>> This could help you to detect problems that would be tough to find
>> otherwise.
>>
>> C
Whoops, I meant a 'function in ape?'
-Dave
On Mon, Jun 15, 2015 at 10:26 AM, David Bapst wrote:
> Hi Brian,
>
> I was already aware of the read.tree(write.tree()) fix, however I've
> run into (corner?) cases where a particular sorting of edges or
> whatever can le
i David,
>
> collapse.singles() seems to work correctly if the "phylo" object is
> correctly conformed. Some features of this class may seem annoying (and
> Klaus and I alredy discussed about this), but these help for other things.
> As a reminder the class "phylo"
Hello all,
(I'm a troublemaker today.)
Sometimes, in ordered discrete data, there are states we know might
exist as intermediary between observed states but aren't observed
themselves. I suppose this is probably common for meristic data. At
least to me, it seems like it should be possible to reco
lly to do the
> calculations - so if ace does not permit this presently, it could easily be
> modified to allow it. phangorn too must allow this because for many
> nucleotide sites we want to reconstruct ancestral states - but we will have
> observed only a subset of the four nucleotides at
s.
>
> 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 6/17/2015 3:06 PM, David Bapst wrote:
>>
Hi all,
I was plotting some trees with obscenely long taxon names (long story)
and found an odd plotting artifact that leaves white-space when
show.tip.labels=FALSE, as if the plot was trying make room for the
extraordinarily long tip labels, even though they wouldn't be plotted.
I'm using R versi
Just to clarify for future users who stumble on Liam's solution for
Lilian, the second block of code attaches the new tips to
non-ultrametric trees at the same distance as the current tips at
maximum distance from the root.
If this is a time-scaled phylogeny and the tree's root depth is equal
to i
Hi Solomon,
Comparatives methods are routinely applied to non-ultrametric trees,
contrary to the text you quoted. See the last chapter of that book.
The phylogeny-based analyses that do generally require ultrametric
trees are those that fit some form of a lineage diversification model,
because the
Hello all,
Recently I noticed a complex function of mine that does some tree
transformations was randomly scrambling node.label elements.
In the course of doing so, I found this old email (below) from Rebecca
Best in 2012, which outlined an issue that occurred when a ladderized
tree had tips drop
<-
> < (n + 2):(n + phy$Nnode)
> ---
>> newNb[sort(phy$edge[sndcol, 2])] <- (n + 2):(n + phy$Nnode)
>> phy$edge[sndcol, 2] <- newNb[phy$edge[sndcol, 2]]
>
> Since this function is widely used, this requires more tests to validate
> this fix.
>
thing strange, just
>> tell me.
>>
>> I attach the new source file.
>>
>> Best,
>>
>> Emmanuel
>>
>> Le 25/07/2015 18:54, David Bapst a écrit :
>>>
>>> Hi Emmanuel,
>>>
>>> Thank you for the fix! And, yes, I r
Just thinking out loud here, but maybe one could use a rate matrix that
doesn't allow gains of 1, and instead reroot the tree at various points
with a fixed root state of 1? The only semi tricky bit would be searching
for the optimal position of this 'root', which is where the single gain of
1 occu
Hi Gustavo,
I'm paleotree's author and maintainer. Just to be clear that I
understand your problem, I believe you are saying that when you use
timeSliceTree, you are getting an error that the internal call to
dist.nodes is failing? Is that right?
The first thought I have is that maybe the solutio
gt;> Thanks again for the help so far!
>>
>> Best,
>>
>>
>> *Gustavo Burin Ferreira, **Msc.*
>> Instituto de Biociências
>> Universidade de São Paulo
>> Tel: (11) 98525-8948
>>
>> On Fri, Oct 16, 2015 at 5:06 PM, Nick Matzke wrote:
>>
>&
ed changing the highlighted part to something like
>>>> double(as.numeric(nm) * as.numeric(nm)), and when I try running it, I
>>>> get
>>>> the error I wrote on the first e-mail:
>>>>
>>>>
>>>> > *Error in dist.nod
-Dave
On Tue, Oct 20, 2015 at 1:39 PM, David Bapst wrote:
> Thanks, Klaus. I was unaware of node.depth.edgelength; I believe I use
> dist.nodes to calculate root-to-tip distances in a number of functions
> in paleotree, so this could mean improvement potentially to a large
> number
Hello Tristan,
Does the code below work for your purpose? I don't know of a function
off the top of my head that does this in a current package on CRAN
(and although I might have missed such, I try to keep myself aware of
time-scaling functions in R, given my interests). However, its not too
diffi
Tristan,
It's alright. To be honest, I am (and should be) quite embarrassed
that I overlooked an ape function... I was a nice warm-up exercise,
nonetheless, and I can see how to extend it to handle dates for
non-ultrametric fossil trees, which is a case not covered by
compute.brtimes, and would ma
Hi Roger,
I'm not aware of any existing solution. Could you send around a small
example of the data format of an output sampled ancestor tree from
BEAST or MrBayes? Are they just typical Newick/NEXUS format with
ancestors indicated tipis with zero-length branches or something more
complicated?
Re
se, Postdoctoral Research Associate
> Department of Earth Sciences, Oxford University
> South Parks Road
> Oxford OX1 3AN
> United Kingdom
>
> On 8 December 2015 at 18:56, David Bapst wrote:
>>
>> Hi Roger,
>>
>> I'm not aware of any existing soluti
line so it is more specific
>> than "Re: Contents of R-sig-phylo digest..."
>>
>>
>> Today's Topics:
>>
>>1. Re: Plotting sampled-ancestor trees in R (Roger Close)
>>2. Implementation of Mir et al.'s (2013) tree balance ind
Dear Lev and all,
First, to answer the actual question in your postscriptum, ape's
branching.times() is not for non-ultrametric trees, but it does
silently accept them as input, unfortunately. The branching.times it
returns assume that some tip (the first tip?) is at time=0, which
means that often
Lev,
This is easy, if the newick strings are structured the same so that
the resulting edge matrix and tip labels are identical. Here's a
worked example:
```
library(ape)
# with edge lengths
newick1<-"(Homo:30,(Echinus:18,(Cephalodiscus:12,(Rhabdopleura:8,(Dictyonema:1,(Rhabdinopora:1,Dicellogra
FYI, in case one wants to install the testing version of ape to
R-devel (in my case, also a Windows machine), I found I needed:
install.packages("ape",contriburl="http://ape-package.ird.fr/bin/windows/contrib/3.2";)
Emmanuel, I've tested the testing version with paleotree and a few
other projects
Darrin, list-
I'm sure there's people on this list with better answers, so I'll
throw in first with what might be the wrong answer (but feels right to
me), and say you more or less need to report all of them: like, show a
full histogram of the p-values. At least, as a reviewer, that is what
would
Hello all,
We are pleased to announce a topical session that we believe is of
special interest to the R-Sig-Phylo list, scheduled for the 2016
annual Geological Society of America meeting held from September
25th-28th in Denver, Colorado, USA. Our oral topical session, “New
Approaches to Phylogene
Brian-
Is your tree non-ultrametric because it contains extinct taxa from the
fossil record, or is it simply an undated tree of extant taxa?
To my knowledge, there isn't yet a satisfactory solution to the first
(no BISSE for paleo-phylogenies) but if the second then, it seems the
best route would
Hi all,
Just a short reminder, that abstract submission for GSA (and thus for
our session) closes on July 12th, which is less than a week away.
Cheers!
-Dave
On Mon, Apr 4, 2016 at 10:25 AM, David Bapst wrote:
> Hello all,
>
> We are pleased to announce a topical session that we beli
John,
I had to double-check this with someone who knew better first, but
they confirmed for me that the answer is that MrBayes doesn't infer a
Q matrix. By default, the Q matrix for Mk in MrBayes is always held
fixed so the rates of transition are always equal and fully
reversible, i.e. a simple J
Hi Emmanuel (and list!),
These changes are appreciated, and will make dealing with multiPhylo
objects much easier. I know I certainly have blocks of code where I
need to 'carry' the multiPhylo class tag through every other line; it
always been a bit of a chore. However, two questions from the pean
Thanks, Emmanuel. That answers my questions.
Cheers,
-Dave
On Tue, Oct 4, 2016 at 4:03 AM, Emmanuel Paradis
wrote:
> Hi David,
>
> Le 03/10/2016 à 17:25, David Bapst a écrit :
>>
>> Hi Emmanuel (and list!),
>>
>> These changes are appreciated, and will make d
(cough) Well, I for one never saw your original email, Will. At least
from my perspective, it looks like it never made it to the list.
Um, well, what are you trying to obtain? A supertree analysis that
thinks about the stratigraphic order of taxa? This sounds like your
trying to create some strato
hing usable.
> Presumably I should use the strict consensus tree for the MrBayes
> constraint and then analyze a sample of the posterior?
> Does your createMrBayesConstraints function play nicely with polytomies?
>
> Thanks,
> Will
>
> On Wed, Oct 5, 2016 at 2:38 PM, David Bap
Manabu-
Can you give us a reproducible example? Is it as simple as plotting
any tree does it or is it only particular trees?
Cheers,
-Dave
On Fri, Oct 28, 2016 at 7:53 AM, Manabu Sakamoto
wrote:
> Dear List,
>
> I'm getting fatal errors when plotting phylo objects, which terminates the
> RStudi
A deep thought on this topic, from a mind run aground amidst grading papers.
While I am a big fan of using multiple trees, we should keep in mind
that phylogenetic uncertainty makes signal into a rather snaky
concept. By this, I mean that there could have only been one true
history (which may or m
That's really cool, Liam. Would it also be possible for one to do
multiple such error bars per node, for plotting ASRs for multiple
traits?
-Dave
On Mon, Feb 27, 2017 at 12:13 PM, Liam J. Revell wrote:
> Hi Kevin.
>
> This is not automatic - but it is indeed fairly easy to do using phytools.
> To
Ross,
An interesting question. I understand it as that you want to test if
the trait is overdispersed relative to phylogeny, which still makes me
think that measures of 'phylogenetic signal' might be still be useful,
even though the typical interpretation is 'signal' as 'heritability'.
I would try
I think the way to go is to treat it as separate characters: using the
zero-length branches assumes that the different seasonal morphs are
separate populations that evolved different phenotypes
instantaneously... the Markov model is going to consider that very
strange, and think transition rates ar
Hi,
It appears you are keeping track of the ancestor by its character
matrix. (So this is a speciational model of character evolution, I
guess?) I've coded simulations that produce similar data for
paleobiological comparison, but I just have a single column for the
ancestor ID. (My own functions u
Hello all,
Not entirely an R question, but the reconstructed phylogenies will end up in
R eventually and I would really appreciate hearing the opinions of those on
this list. I know there are at least a few people on here with experience in
morphology-based phylogenies.
I deal with morphological d
Hello all,
I have several genus-level trees that I want to convert to species-level
trees, with the underlying assumption that species within a genus form a
monophyletic polytomy. In other words, on my current tree there is a tip
taxon labeled "Dicellograptus" which I want to replace with a polytom
Hello,
Thank you all for the help on my previous question.
I'd like to draw some horizontal lines (of varying lengths, in the
same units as the branch lengths) at the tips of a phylo plot. Not all
the tips are coeval, though.
In other words, I have a tree that looks like:
Hello all,
I have been using ace() to reconstruct ancestral states for a number
of continuous morphological traits. I need confidence intervals for my
analysis. However, for some sets of traits, I get the following error:
Warning message:
In sqrt(diag(solve(out$hessian))) : NaNs produced
The only
Hello all,
I am having trouble with write.tree() in ape, when used on a tree
produced with stree() with type="left", at a certain number of tip
taxa.
You can reproduce the error with:
x<-stree(1000,type="left")
write.tree(x,file.choose())
produces the following:
Error: evaluation nested too d
for trees with 1700 taxa.
>
> Cheers,
> Klaus
>
>
> On 9/15/10, David Bapst wrote:
>> Hello all,
>>
>> I am having trouble with write.tree() in ape, when used on a tree
>> produced with stree() with type="left", at a certain number of tip
>
Ulrik-
Hello! What do you want the names for?
The following will give you a ranked vector that corresponds to the
internal nodes, as ordered by the phylo object. Uses the dist.nodes
function in ape to find the distance to root for internal nodes. This
assumes your tree is a phylo object.
tree<-
You mention read.tree(), but have you tried read.nexus()? I just tried it
now on your file and it was read into R by read.nexus() fine and plotted
with plot.phylo() without error.
-Dave
On Mon, Oct 25, 2010 at 4:13 PM, Joey Pakes wrote:
> Hello,
>
> I have made a tree with RAXML have viewed it i
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