argument “at" matched by multiple actual arguments
Does anyone know how I might be able to specify the tick marks that I want for
these particular functions?
Best,
Jacob Berv
Ph.D. Student
Lovette Lab
Cornell Laboratory of Ornithology
___
R-sig-
t be
>> able
>> to help me with.
>>
>> When using either function, the spacing between ticks on the scale is too
>> large for the figure I’m trying to generate. I have tried passing variations
>> of at=c(1,2,3,4,5), or at=seq(0,10,1) etc, but for either functi
> On Mar 2, 2015, at 11:10 PM, Santiago Claramunt wrote:
>
> axis(1, at=max(branching.times(tree))-0:10, labels=0:10)
Jacob Berv
Ph.D. Student
Lovette Lab
Cornell Laboratory of Ornithology
[[alternative HTML version deleted]]
___
R-sig
> y1 <- y1 - tips.per.page
>>> y2 <- y2 - tips.per.page
>>> }
>>> }
>>>
>>
>
> [[alternative HTML version deleted]]
>
> ___
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y
> 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 Liam,
>>
>> Would there be a way to modify this so that annotations like n
h case you can fiddle with the split
> 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.
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/
Jacob Berv
Ph.D. Student
Lovette Lab
Cornell Laboratory of Ornithology
___
R-si
t;)
But this doesn’t seem to work when I try it on my larger trees. Not sure where
I’m going wrong…
Best,
Jacob Berv
Ph.D. Student
Lovette Lab
Cornell Laboratory of Ornithology
[[alternative HTML version deleted]]
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R-sig-phylo mailing
, 2015, at 10:57 AM, Emmanuel Paradis wrote:
>
> Hi Jacob,
>
> Can you send an example of your output with rotateConstr()? Thanks.
>
> Best,
>
> Emmanuel
>
> Le 08/04/2015 06:41, Jacob Berv a écrit :
>> Hi all,
>>
>> Is there an easy way to get R t
mar = rep(0, 4))
> plot(A)
> plot(B)
> plot(C, d = "l")
>
> C and A appear identical on the plot.
>
> Best,
>
> Emmanuel
>
> Le 08/04/2015 18:15, Jacob Berv a écrit :
>> The rotateConstr() function does not give me any errors -
>>
>> He
m. Any thoughts would be appreciated!
Thanks,
Jacob Berv
Ph.D. Student
Lovette Lab
Cornell Laboratory of Ornithology
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https://stat.ethz.ch/mailman/list
://nimbios.org/postdocs/>
> Calendar: http://www.brianomeara.info/calendars/omeara
> <http://www.brianomeara.info/calendars/omeara>
> On Sat, Oct 17, 2015 at 10:12 PM, Jacob Berv <mailto:jakeberv.r.sig.ph...@gmail.com>> wrote:
> Dear R-sig-phylo,
>
> I have a somew
effective population size?
>
> All the best, Liam
>
> Liam J. Revell, Associate 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 10/17/2015 11:
, substitution rate
information). I emailed the developer of that tool and he indicated this was by
design (though he may be able to offer a solution).
Jake
> On Oct 18, 2015, at 12:04 PM, Jacob Berv
> wrote:
>
> Yes, this has come up in my reading…but there do seem to be situ
> Tel. 416-586-8025
> Website: https://sites.google.com/site/santiagosnchezrmirez/
>
> [[alternative HTML version deleted]]
>
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There appears to be some issues with ggtree plotting BEAST output - I just
tried to run through the example and got the following errors:
source("https://bioconductor.org/biocLite.R";)
biocLite("ggtree")
require("ggtree")
> file <- system.file("extdata/BEAST", "beast_mcc.tree", package="ggtree
Whoops! nevermind. It appears read.beast was being masked from read.beast in
phyloch. Working now.
Jake
> On Dec 11, 2015, at 12:56 PM, Jacob Berv
> wrote:
>
> There appears to be some issues with ggtree plotting BEAST output - I just
> tried to run through the example and go
Hi everyone,
Given an annotated tree file with continuously varying ancestral states, is
there an easy way to plot the median or mean value of the trait from the root
to the tip, using a user defined sliding window? Does anyone know if there is a
package or function that exists to do this? I kno
You could do a bayes factor test using MrBayes or BEAST, by applying
topological constraints. This is an elegant solution for conducting explicit
topological hypothesis tests. But you aren’t likely to get BEAST or MrBayes to
run with 200kb. I’ve been thinking about doing this myself with data pa
Also see BayesTraits for the bayesian version.
Jake
> On May 3, 2016, at 8:11 PM, Liam J. Revell wrote:
>
> Hi Michael.
>
> This is essentially the method of Pagel (1994). Though often interpreted as a
> test for correlated evolution of two binary characters, the model that is
> actually bei
Hi all,
Does anyone know if there is an easy way to suppress the axes in phytools
phenogram() without altering the code (which is easy to do, but inconvenient
when using the function in multiple different contexts)? yaxt=’n’ and xaxt=’n’
have no effect.
Best,
Jacob Berv
Cool - that works - but now I can’t use axis() to add custom axes…
Jake
> On Jul 7, 2016, at 5:03 PM, Liam J. Revell wrote:
>
> par(xaxt="n",yaxt="n")
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My ugly solution is to comment out lines 195 and 196 in the phenogram code.
Jake
> On Jul 7, 2016, at 5:06 PM, Jacob Berv wrote:
>
> Cool - that works - but now I can’t use axis() to add custom axes…
> Jake
>
>> On Jul 7, 2016, at 5:03 PM, Liam J. Revell > <mailto:
edu>
> www.fourdimensionalbiology.com <http://www.fourdimensionalbiology.com/>
> On Thu, Jul 7, 2016 at 4:10 PM, Jacob Berv <mailto:jakeberv.r.sig.ph...@gmail.com>> wrote:
> My ugly solution is to comment out lines 195 and 196 in the phenogram code.
> Jake
>
>
Personally, I don’t think I’d have a problem with this approach (especially
given the paper Liam cited) given that you are using a phylogeny (a model) to
test a hypothesis, which is, after all, all we can ever do. You can always do
more, so any threshold of phylogenetic tree “quality” is going t
To clarify - the idea here is that you are asking which clades appear in
’subordinate’ trees relative to clades that exist in a consensus tree, and then
interrogating the support values of the shared clades which exist in the
’subordinate’ trees? So for example, clade A appears in consensus tree
Dear R-sig-phylo,
When analyzing comparative data in a PCM framework, is it be appropriate to use
an AIC score to advocate for log transforming input data? ie model(data) vs
model(log(data))
I’m running a few OUwie models and it’s not entirely clear from the biology
whether or not the ‘standar
ave one or more
> independent variables), then you CAN look at residuals to see if they are
> better/worse behaved (e.g., approximately normal, no nasty outliers,
> homoscedasticity).
>
> Cheers,
> Ted
>
>
> On Thu, Jan 26, 2017 at 2:25 PM, Jacob Berv <mailto:jakeberv.
Can you do this in MEGA?
Jake
> On Feb 1, 2017, at 5:52 PM, kolte...@rub.de
> wrote:
>
> Dear Phylothusiasts,
> I need to compare multiple substitution models side-by-side (species
> clustering stuff by distances only). Unfortunately, I am not aware of an
> implementation of HKY and GTR dista
Not sure if a function for that already exists. You could plot posterior
distributions at each node (or perhaps, nodes of interest) if that is workable
graphically…Alternatively you could print the numerical 95% ci or HPD interval
at each node, along with mean or median value (for a bayesian rec
Hi all,
I’m trying to compute size corrected phylogenetic residuals on data where the
independent variable (size) is complete but the dependent variables have
varying amounts of missing data. phyl.resid() in phytools doesn’t appear to be
able to handle pairwise dropping (to only consider rows wh
I noticed today that the compression ratio for an interleaved phylip file (zip
compressed) was about 84:1, (390MB uncompressed —> 4.6MB compressed) whereas
the compression ratio for the same data non-interleaved was a much worse 3.4:1
(390 MB uncompressed —> 113.9 MB). Not knowing much about how
Indeed - this is a population genomic dataset with very few site patterns
relative to the size of the full dataset. Cool!
Jake
> On Apr 18, 2017, at 2:18 PM, Joe Felsenstein wrote:
>
> I would guess that the compressibility of interleaved sequences would
> be highest when the sequences are clos
Very interested in this too!
Jake
> On Apr 25, 2017, at 1:20 PM, Vojtěch Zeisek wrote:
>
> Hello,
> for comparison of two trees I can use very nice function cophyloplot plotting
> two trees (left and right) and connecting respective nodes by lines. Very
> nice
> and convenient to read. But on
Dear R-sig-phylo,
I was wondering - is anyone aware of methods or models that can deal with
traits that are have evolved seasonal discrete plasticity in some lineages,
whereas in other lineages such seasonality has not evolved (and so traits
evolve as a discrete character?). I’m helping a colle
see root() in the R package ape or reroot() in phytools
J
> On May 23, 2017, at 1:22 PM, Valentine Usongo
> wrote:
>
> Dear members
>
> My name is Valentine Usongo and I am a postdoctoral trainee at the INSPQ
> Montreal-Quebec. I am working on the use of whole genome sequenced based
> metho
Hi all,
Does anyone know of a function to plot a geologic time scale as a series of
concentric circles on a circularly plotted tree?
As far as I can tell there are three available functions that can do this on a
regular cladogram:
axisGeo (phyloch)
geoscale.Phylo (strap)
geo.legend (phytools)
Even if those models may fit the data better, they may not necessarily help
Rafael determine whether or not the parameter estimates of interest are
different across regimes (though perhaps BMS might be informative).
Rafael, maybe you could try fixing the ancestral regimes to match most likely
s
This is cool — so this looks like it will work on a set of posterior trees even
if they don’t all share the same topology?
Jake
> On Apr 10, 2018, at 3:37 AM, jschenk wrote:
>
> Thank you Graham, Liam, and Emmanuel for your suggestions. Applying the
> .uncompressTipLabel did the trick for my
What about situations in which fossil calibrations are used as priors to inform
reconstructions for uncalibrated important/interesting nodes? Sure, there is
great uncertainty, but that doesn’t necessarily imply we should entirely
abandon hypothesis testing using this approach, does it? I like th
This is so cool. Thanks Liam!
J
> On Jun 21, 2018, at 8:22 PM, Liam J. Revell wrote:
>
> Dear Theo.
>
> This can be done with the function rerootingMethod as described here
> http://blog.phytools.org/2013/04/estimating-ancestral-states-when.html,
> although it is *very* important to note that
Dear R-sig-phylo,
Does there exist a function to plot heatmaps at internal nodes of a tree? For
example, to illustrate support values from different phylogenetic analyses — ie
given a set of 3x3 matricies of support values for particular nodes.
It seems like there may be a partial (and definite
rs-to-contmap.html)
>
> All the best, Liam
>
> Liam J. Revell
> Associate Professor, University of Massachusetts Boston
> Profesor Asistente, Universidad Católica de la Ssma Concepción
> web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org
>
> On 8/29/2018
Dear R-sig-phylo,
I was wondering if anyone on here might be able to help me understand the
difference between phytool’s implementation of phylogenetic ANOVA and geiger’s
implementation. From the respective documentation, it seems that both
approaches rely on and cite the same reference:
Garlan
end along the data that has generated this incongruency if you are
> unable to figure it out.
>
> All the best, Liam
>
> Liam J. Revell
> Associate Professor, University of Massachusetts Boston
> Profesor Asistente, Universidad Católica de la Ssma Concepción
> web: http://f
Sorry— I meant aov.phylo (geiger function), not phly.aov.
J
> On Nov 15, 2018, at 3:00 PM, Jacob Berv
> wrote:
>
> Hi everyone —
> It seems like the solution is that I was looking at the wrong p-value, as is
> often the case!
>
> From Liam:
> "The issue may
Dear R-sig phylo
I’ve been running a few discrete character Mk type models using phytool's
SIMMAP — and I had the idea that it might be useful to try model averaging
across posterior probabilities for node states.
Might this make sense to do, to avoid problems associated with model ranking
via
de la Ssma Concepción
> web: http://faculty.umb.edu/liam.revell/
> <http://faculty.umb.edu/liam.revell/>, http://www.phytools.org
> <http://www.phytools.org/>
>
> Academic Director UMass Boston Chile Abroad (starting 2019):
> https://www.umb.edu/academics/caps/internationa
Accidentally replied directly to Marguerite, instead of to the list:
> On Aug 9, 2019, at 10:01 AM, Jacob Berv
> wrote:
>
> Great points Marguerite. I agree that the idea of using ‘all possible’ models
> is probably a bit too overzealous— and as Brian pointed out, s
Dear R-sig-phylo,
Over the weekend, I asked Liam Revell if he had a solution to use matchNodes
for a particular problem I’m trying to solve—finding all phylogenetically
equivalent nodes when comparing trees that have uneven taxon samples and
different topologies. Liam was kind enough to take so
Hi Diego,
If your tree has polytomies and the branches have no length information, I am
not sure if likelihood model-based reconstruction is right.
The ace function (and all other similar functions based on likelihood) will
assume that your branch lengths represent some kind biological informat
Interesting thought. I am not familiar with these analyses, but it would not
surprise me if your intuition is correct.
J
> On Sep 19, 2021, at 1:00 PM, Ferenc Tibor Kagan wrote:
>
> Dear r-sig-phylo community
>
> I am writing to you in hopes of you giving me your inputs on a specific topic.
>
One way to do it with pGLS and root to tip path length may be to include
the number of nodes along a root to tip path as a control for node density
effects (maybe with some transformation). I don't know how well that will
work, but I am also experimenting with similar questions.
Another way is to
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