.
All the best, Liam
Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/liam.revell/
Book: Phylogenetic Comparative Methods in R
<https://press.princeton.edu/books/phylogenetic-comparative-methods-in-r>
(/Princeton University Press/, 2022)
O
ons are encouraged
to apply.
--
Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/liam.revell/
Book: Phylogenetic Comparative Methods in R
<https://press.princeton.edu/books/phylogenetic-comparative-methods-in-r>
(/Princeton University Press/,
ractices on the reliability of findings, & 'meta-science' (the science
of science) to help ask if ecology & evolutionary biology are on the
cusp of their own replication crisis & what can be done about it.
--
Liam J. Revell
Professor of Biology, University of Massachus
al-on-evolutionary.html.
I hope this helps you figure out what you need to do!
All the best, Liam
Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/liam.revell/
Book: Phylogenetic Comparative Methods in R
<https://press.princeton.edu/books/phylogenetic-com
tools.org/2023/10/visualizing-lineage-accumulation-on.html.
All the best, Liam
Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/liam.revell/
Book: Phylogenetic Comparative Methods in R
<https://press.princeton.edu/books/phylogenetic-comparative-
urie Postdoctoral Fellow.
--
Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/liam.revell/
Book: Phylogenetic Comparative Methods in R
<https://press.princeton.edu/books/phylogenetic-comparative-methods-in-r>
(/Princeton University Press/,
Dear Felipe.
Assuming your "multiSimmap" object is called /maps/, you can try
something like /summary(maps)$ace/. That should be a matrix with the
posterior probabilities from stochastic mapping at all the nodes and
tips of the tree.
All the best, Liam
Liam J. Revell
Professor
at you might find useful on my blog:
http://blog.phytools.org/2023/08/coloring-nodes-by-bootstrap-or-bayesian.html.
All the best, Liam
Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/liam.revell/
Book: Phylogenetic Comparative Methods in R
ce-of-fitted-m.html>)
-- but if you'd like help, please send me your tree & data (or, even
better, a saved .RData workspace) and I will take a look at your problem.
All the best, Liam
Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.ed
Dear Felipe.
It's possible that .eps doesn't support transparency. Have you tried
plotting to a different device, e.g., .pdf or .png? Alternatively, you
could undo the transparency by changing /make.transparent("blue",0.1)/
for just /"blue"/.
All the best, Lia
probably indicative of unexplained variance in the tip taxa, rather than
a genuine temporal rate shift. This could be due, for example, to
measurement error / uncertainty in the species means for the trait we're
studying.
I hope this is helpful.
All the best, Liam
Liam J. Revell
Profess
this /phytools/ function
/likeSurface.rateshift/. See more information here:
http://blog.phytools.org/2016/08/function-to-plot-likelihood-surface-for.html.
Unfortunately, it is also bound to be pretty slow for larger
phylogenetic trees.
Let us know if this is of help.
Sincerely, Liam
Liam J. Revell
Professor o
e multiple optimization iterations
using /foreach/.
When I get both of these fixes working I'll push the update to the
/phytools/ GitHub and you can install the package from there.
All the best, Liam
Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://
ke a subsequent follow-up post
covering that.
Let us know if this works!
All the best, Liam
Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/liam.revell/
Book: Phylogenetic Comparative Methods in R
<https://press.princeton.edu/books/phylo
Dear Sishuo.
Yes, I think this would be a good way to do this.
All the best, Liam
Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/liam.revell/
Book: Phylogenetic Comparative Methods in R
<https://press.princeton.edu/books/phylogene
5-1)/ to *Depends:* in your
DESCRIPTION file and /importFrom(phytools, rescale)/ to NAMESPACE. (This
should work immediately because currently on CRAN /rescale/ is defined &
exported by both /phytools/ and /geiger/.)
Please let me know if that works.
All the best, Liam
Liam J. Revell
Professo
I'm not sure how it scales to a large tree, though! For an example
phylogeny of 1,000 tips and a clade of 116 species it ran in the blink
of an idea, so I suppose it's probably OK.
Obviously, I meant to write "blink of an eye." It's been a long day.
Liam J. Re
gh! For an example
phylogeny of 1,000 tips and a clade of 116 species it ran in the blink
of an idea, so I suppose it's probably OK.
Let me know if it works for you.
All the best, Liam
Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/li
correctly together.
Please let me know if you run into any problems with this while
Emmanuel, Klaus, & I try to get both ape & phytools updated on CRAN.
That is all. Sincerely, Liam
--
Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/l
veryone! All the best, Liam
--
Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/liam.revell/
Book: Phylogenetic Comparative Methods in R
<https://press.princeton.edu/books/phylogenetic-comparative-methods-in-r>
(/Princeton University Press/, 2
)
All the best, Liam
Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/liam.revell/
On 1/11/2023 7:58 AM, Lindsey Dehaan wrote:
> CAUTION: EXTERNAL SENDER
> Hey Liam,
>
> Thanks alot! I really appreciate it! I installed the new vers
from a fresh R session):
remotes::install_github("liamrevell/phytools")
Let us know if this fixes everything!
All the best, Liam
Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/liam.revell/
On 1/10/2023 4:42 PM, Lindsey Dehaan wr
best, Liam
Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/liam.revell/
On 1/10/2023 4:20 PM, Lindsey Dehaan wrote:
> CAUTION: EXTERNAL SENDER
>
> Hi all,
>
> I have a question regarding the phytools function locate.fossil().
>
oot of each node with two descendants (cherry).
If your tree is ultrametric, to get the /depth/ you would just subtract
this value from the total height of the tree.
Let me know if it works!!
All the best, Liam
Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://fa
d with speciation events -- something that a simple Mk model
ignores).
All the best, Liam
Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/liam.revell/
On 12/14/2022 9:18 AM, William Brown wrote:
CAUTION: EXTERNAL SENDER
I am using fitContinuous to m
easily be modified to just show abundances.
All the best, Liam
Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/liam.revell/
On 12/9/2022 4:51 PM, Saleh Rahimlou wrote:
CAUTION: EXTERNAL SENDER
Hello,
I require to make a phylogenetic bubble plot
http://blog.phytools.org/2019/07/stochastic-character-mapping-with.html.
All the best, Liam
Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/liam.revell/
On 11/8/2022 2:35 PM, Krzysztof Kozak wrote:
CAUTION: EXTERNAL SENDER
Hello,
Is there a method for ance
arguments
dec="," and sep=";".)
Hopefully this solves your problem.
All the best, Liam
Liam J. Revell
University of Massachusetts Boston [Assoc. Prof.]
Universidad Católica de la Ssma Concepción [Adj. Res.]
Web & phytools:
http://faculty.umb.edu/liam.r
on)
## simulate the ancestral states for each subtree in tipward under
## pure Brownian motion
aa<-fastBM(rootward)
## create a vector of values
xx<-vector()
## simulate on each subtree to populate it. a is the ancestral state
## for each simulation
for(i in 1:length(tipward))
xx&l
ty of 0 at a
node. This can be done using phytools::mergeMappedStates and then
running the "simmap" summary methods as normal.
I hope this is of some help in getting you started Felipe.
All the best, Liam
Liam J. Revell
University of Massachusetts Boston [Assoc. Prof.]
Universidad Católi
want to show the amount of evolution that's
expected to occur on each edge, that would be equivalent to the product
of the edge length and it's edge-specific rate.
phy.sig2<-phy
phy.sig2$edge.length<-phy$edge.length*sig2
phytools::plotTree(phy.sig2)
I hope I'm understanding the
ity, you need to update phytools from GitHub using
devtools -- e.g.,
devtools::install_github("liamrevell/phytools")
All the best, Liam
Liam J. Revell
University of Massachusetts Boston [Assoc. Prof.]
Universidad Católica de la Ssma Concepción [Adj. Res.]
Web & phytools:
htt
lso compare to:
as.Qmatrix(fitMk(tree,x,model="ARD"))
where the labeling is better.
All the best, Liam
Liam J. Revell
University of Massachusetts Boston [Assoc. Prof.]
Universidad Católica de la Ssma Concepción [Adj. Res.]
Web & phytools:
http://faculty.umb.edu/liam.revell/, ht
Dear Rafa.
Try this to get the transition matrix, Q:
k<-nrow(ace$index.matrix)
Q<-matrix(ace$rates[ace$index.matrix],k,k)
diag(Q)<--rowSums(Q,na.rm=TRUE)
This should match what you get running:
as.Qmatrix(fitMk(tree,x,model="ARD"))
with phytools.
All the best, L
fastMRCA instead of getMRCA.
newtree<-mapply(bind.tip,tree=tree,where=lapply(tree,fastMRCA,
sp1="Cercopithecus_mitis",sp2="Cercopithecus_mitis"),
MoreArgs=list(tip.label="Cercopithecus_albogularis",
position=0.59,edge.length=0.59),SIMPLIFY=FA
you're computing an N x N matrix in each iteration of
your function call just to get one node index.
Good luck! All the best, Liam
--
Liam J. Revell
University of Massachusetts Boston
Universidad Católica de la Ssma Concepción
Web & phytools:
http://faculty.umb.edu/liam.revell/, htt
uot;
(Code is not guaranteed! I don't have the data file, so I didn't
actually test it -- but something like this ought to work.)
Regardless, I recommend using ape::getMRCA (or phytools::fastMRCA)
because otherwise you're computing an N x N matrix in each iteration of
you
gth=0.59),SIMPLIFY=FALSE)
class(newtree)<-"multiPhylo"
(Code is not guaranteed! I don't have the data file, so I didn't
actually test it -- but something like this ought to work.)
Regardless, I recommend using ape::getMRCA (or phytools::fastMRCA)
because otherwise you
phylo(tree))
spp<-names(w)
corLambda<-corPagel(1,phy=tree,form=~spp)
fit<-gls(...,correlation=corLambda,weights=varFixed(~w))
(I'm not sure the exact code, but it should be something like that.)
All the best, Liam
Liam J. Revell
University of Massachusetts Boston [Assoc. Prof.]
U
t works, if not I can see about adding the option you
need to the function.
All the best, Liam
Liam J. Revell
University of Massachusetts Boston [Assoc. Prof.]
Universidad Católica de la Ssma Concepción [Adj. Res.]
Web & phytools:
http://faculty.umb.edu/liam.revell/, http://www.phytools.o
Dear Nick.
When you encounter a bug or issue in ape have you tried emailing
Emmanuel (emmanuel.para...@ird.fr) or this list? Usually he is pretty
responsive.
All the best, Liam
Liam J. Revell
University of Massachusetts Boston
Universidad Católica de la Ssma Concepción
Web & phytools:
problem as this will tend to give the observations for those
tips very high weight in your analysis. Instead, you might consider
pruning one or the other species from your analysis.
All the best, Liam
Liam J. Revell
University of Massachusetts Boston
Universidad Católica de la Ssma Concepción
Web
. The point of this
article, like Anscombe 1973, was about graphing - but it may also apply
to your problem.)
All the best, Liam
Liam J. Revell
University of Massachusetts Boston
Universidad Católica de la Ssma Concepción
web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org
Acad
servations for x - but it may
not mean a whole lot about how x & y genuinely co-vary.)
All the best, Liam
Liam J. Revell
University of Massachusetts Boston
Universidad Católica de la Ssma Concepción
web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org
Academic Director UMass Bo
cause for low measured
values of phylogenetic signal.
Hope this is of some help Karla.
All the best, Liam
Liam J. Revell
University of Massachusetts Boston
Universidad Católica de la Ssma Concepción
web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org
Academic Director UMass
n the bootstrapping analysis estimates an unrooted tree, you
should set prop.clades(rooted=FALSE). *Most* phylogeny inference methods
(ML, MP, NJ, ME, LS) estimate *unrooted* trees; only UPGMA and molecular
clock methods estimate rooted trees.
All the best, Liam
Liam J. Revell
University of Massachu
g/blog/Elvira-tree.png
so it's kind of hard to tell which taxa are extinct
Sorry I can't be of more help! All the best, Liam
Liam J. Revell
University of Massachusetts Boston
Universidad Católica de la Ssma Concepción
web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org
ry:
par(mfrow=c(1,1),mar=c(5.1,4.1,2.1,2.1),bty="n")
ltt(tree,lty="dashed",log.lineages=FALSE,log="y")
ltt(pruned,lty="solid",add=TRUE,log.lineages=FALSE,
log="y")
legend("topleft",c("observed","reconstructe
se the phytools version not the posted
code).
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
Academic Director UMass Bost
s has even
been discussed on this list); and "The statistical hypothesis testing is
based on Clarke (1980; reviewed in McArdle 1988), which differs from
some other implementations of non-phylogenetic major axis regression in R."
All the best, Liam
Liam J. Revell
Associate Profes
discrete
character with states: 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,
41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55" is
surprising. Does your discrete character really have 27 states?
All the best, Liam
Liam J. Revell
Associate Professor, University of Massachusetts Bo
s) <- "DNAbin"
for(...) { ## your for loop
seqs <- c(seqs,
read.dna(file = ..., format="fasta", as.matrix=FALSE))
}
(In which you substitute ... for your original code.)
In theory, I believe that this (or something like this) should do what
you want.
.summary,ftype="off",lwd=1,cex=c(0.7,0.4))
map.summary$ace ## probabilities at nodes
All the best, Liam
Liam J. Revell
Associate Professor, University of Massachusetts Boston
Profesor Asistente, Universidad Católica de la Ssma Concepción
web: http://faculty.umb.edu/liam.revell/, http:/
you can also set them all to be 1.
The likelihood changes, but ancestral states are the same.)
I hope this is helpful. All the best, Liam
Liam J. Revell
Associate Professor, University of Massachusetts Boston
Profesor Asistente, Universidad Católica de la Ssma Concepción
web: http://faculty.umb.edu
if
you give either method data vectors without taxon names both work, but
only phylANOVA gives a warning.
Please send along the data that has generated this incongruency if you
are unable to figure it out.
All the best, Liam
Liam J. Revell
Associate Professor, University of Massachusetts
blog.
I hope that this helps you find your error. If it does not, please free
to send me your saved workspace & I will try to figure it out.
All the best, Liam
Liam J. Revell
Associate Professor, University of Massachusetts Boston
Profesor Asistente, Universidad Católica de la Ssma Concepció
eetree$tip.label,"_sp.",sep="")
for(i in 1:length(species$Genus_species)){
beetree<-add.species.to.genus(beetree,species$Genus_species[i],
where="root")
}
## prune out these same taxa
ii<-grep("sp.",beetree$tip.label)
beetree<-drop.tip(b
the posterior probability of
being in the alphanumerically first state, rather than the second.
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:
Hi Kimberly.
What version of phytools are you using? Neither make.simmap nor
describe.simmap call MatrixExp.
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
d",fg="transparent")
plotTree(sim_tree,type="fan",lwd=1,add=TRUE)
par(fg="black")
For a more general solution you might offset your taxon labels by a
constant amount, or you can use the function strwidth and some basic
trigonometry to find the position outs
es, as this can give very high weight to the associated tips. It
might be by pruning one tip or the other from the analysis, or by using
some reasonable criterion to modify the terminal edge lengths.
All the best,
Liam J. Revell
Associate Professor, University of Massachusetts Boston
Profesor Asi
Dear Iara.
In fact, it is now possible to conduct a null hypothesis test with this
method in phytools. I posted about it in my blog in 2017:
http://blog.phytools.org/2017/11/bivariate-phylogenetic-regression-with.html.
All the best, Liam
Liam J. Revell, Associate Professor of Biology
6. Compute t3=h-(t1+t2). Simulate a birth-death tree for t3 with birth &
death rates b & d. Attach the b/d tree to the current tip. Advance to
the next tip & go back to step 2.
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
is of only whales or only mice it will make relatively
little difference whether you use log-scaled data or the original values.
I hope this is of some help. All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu
ll converge on the marginal
ancestral states under the defaults for make.simmap, so long as a flat
prior is used on internal nodes. This is also on my blog here:
http://blog.phytools.org/2013/03/estimating-ancestral-states-when-tips.html.
All the best, Liam
Liam J. Revell, Associate Professor
No idea. Are they running different R or package versions?
phytools::midpoint.root has not been updated recently, but other
internally used functions may have been.
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor Asoc
,PfH24:0.00242401):0.002458328,(PfH15:0.003791243,PfH17:0.001056495):0.001058053):0.003886796,PfH23:0.004767665):0.1242874):0.1359654):0.7442934008);
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor Asociado, Programa de Biología
Universidad del Ros
-midpoint.root(tree)
t2<-midpoint(tree)
all.equal.phylo(t1,t2)
I get TRUE.
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor Asociado, Programa de Biología
Universidad del Rosario
web: http://faculty.umb.edu/liam.revell/
On 5/1
is helps.
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor Asociado, Programa de Biología
Universidad del Rosario
web: http://faculty.umb.edu/liam.revell/
On 5/14/2018 10:41 AM, Graham Slater wrote:
Hi Pedro,
multi2di on this newi
velopment-in.html.
All the best, Liam
--
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor Asociado, Programa de Biología
Universidad del Rosario
web: http://faculty.umb.edu/liam.revell/
___
R-sig-phylo mai
Just to clarify, force.ultrametric is not a formal rate-smoothing method
or anything like that. It is intended only for use to resolve numerical
precision issues such as the one raised in this thread.
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Prof
I haven't been closing following this thread, so I'm not sure that this
is relevant - but phytools has a function called 'force.ultrametric' (I
believe) that does precisely what its name suggests it might.
Liam J. Revell, Associate Professor of Biology
University of
ather than the estimation of phylogeny -
but please contact me if you'd like clarification.
The deadline to apply is May 11. More information along with a link to
apply is available on my blog:
http://blog.phytools.org/2018/04/postdoc-to-work-on-pcm-development-in.html.
All the best, Liam
$edge.length[which(backbone$edge[,2]==tip)]-h
backbone<-bind.tree(backbone,subtrees[[i]],where=tip)
}
plotTree(backbone)
Something like that.
(Of course you could also modify this so that you just manually identify
the tips to bind to. Given the small size of your problem this is
probably
Dear John.
You could try running .uncompressTipLabel on the "multiPhylo" object.
Let us know if that works.
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor Asociado, Programa de Biología
Universidad del Ros
data.
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor Asociado, Programa de Biología
Universidad del Rosario
web: http://faculty.umb.edu/liam.revell/
On 4/4/2018 2:30 PM, Rafael S Marcondes wrote:
Dear all,
I'm writing
Try ftype="off".
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor Asociado, Programa de Biología
Universidad del Rosario
web: http://faculty.umb.edu/liam.revell/
On 3/13/2018 11:27 AM, Juan Antonio Balbuena wrote:
Hi,
Yes!! It worked
ng to the latest version on GitHub using devtools
as follows:
library(devtools)
install_github("liamrevell/phytools")
Let us know if the problem persists.
Saludos, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor Asociado, Programa de B
uncertainty in the values of species means has been ignored.
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor Asociado, Programa de Biología
Universidad del Rosario
web: http://faculty.umb.edu/liam.revell/
On 3/12/2018 11:29
D as a factor,
you could compute means and variances for each component by species.
I hope this is some help. All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor Asociado, Programa de Biología
Universidad del Rosario
web: http://facul
run:
install_github("liamrevell/phytools")
I hope this is of some help. All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor Asociado, Programa de Biología
Universidad del Rosario
web: http://faculty.umb.edu/liam.revell/
On
Hi Felipe.
What version of phytools are you using? A very old phytools version did
not default to interactive mode if no translation table (trans) was
supplied.
Otherwise, I do not know - but it should not be because the tree is not
ultrametric.
All the best, Liam
Liam J. Revell
-paste(strsplit(obj$colors[i],"")[[1]][1:7],collapse="")
draw.circle(0,0,radius=r[i],col=color,border="transparent")
}
par(fg="transparent")
plotTree(tree,type="fan",add=TRUE,fsize=0.6,lwd=1)
par(fg="black")
I will also post to my bl
strsplit(obj$colors[i],"")[[1]][1:7],collapse="")
draw.circle(0,0,radius=obj$leg[i,1],col=color,border="transparent")
}
par(fg="transparent")
plotTree(tree,type="fan",add=TRUE,lwd=1)
par(fg="black")
Otherwise you need to plot
x=dat, lwd=1, type='fan', scale=0.05,
width=0.35, col='red')
dev.off()
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 11/11/2017 1
Hi Rafael.
It seems to just be that some of the values in your data vector are NAs.
Try:
dat<-dat[!is.na(dat)]
tr<-drop.tip(tr,setdiff(tr$tip.label,names(dat)))
plotTree.wBars(tr,dat,type="fan",scale=0.1)
and you should obtain something that makes sense.
All the best, Liam
s) which is in some ways more
flexible & robust.
Failing any of these options you are welcome to send me your saved
workspace so I can investigate (& if there is a bug in phytools - fix it).
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachu
make it symmetric) is leptokurtic which is why
var.test is significant due to idiosyncratic differences in the variance
of lambda, even though the values were obtained by the same process.
(Invariably lamb_sub and lamb fail a normality test, so this seems like
a distinct possibility.)
All the best
t the postdoc is for *one year* with only a modest possibility
of extension to multiple years contingent on external funding.
Please circulate to interested parties. Any questions about the position
should be directed to this email address (liam.rev...@umb.edu).
Thanks!
--
Liam J. Revell, Asso
here:
http://blog.phytools.org/2017/09/possible-solution-for-functions-that.html
I'm not sure if this means I won't run into difficulty with this
solution, but I'm eager to hear why.
- Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
Hi George. Mario is correct that phytools can read a tree with singleton
nodes (if that is indeed your problem), but the name of the function is
read.newick. Good luck! - Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu
Hi Alejandro.
If the discrete character is mapped on the tree in a "simmap" style,
then the student could use the phytools function sim.rates. Let me know
if you need more information.
Sincerely, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts
ttps://goo.gl/Mbx4hn
I hope this is of some help. Sincerely, 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 8/11/2017 12:50 PM, Marko Djurakic wrote:
Hi Felipe.
I can't figure out your code or why tip labels might be being stripped.
Can you post a fully reproducible example of this problem?
All the best,
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
All the best,
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 7/22/2017 8:51 PM, Karla Shikev wrote:
Thanks, Liam!
Just a quick follow-up question: in the exa
unction you can search for
'ratebytree' on my blog, blog.phytools.org.
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 7/22/2017 3:
n you can test as follows:
library(phytools)
tree<-read.newick(text='((a))A),(((b),(b1)))B)))C;')
tree$edge.length<-rep(1,nrow(tree$edge))
plotTree.singletons(tree)
nodelabels(tree$node.label)
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of
Hi Laura.
I think multi2di also performs random resolutions, so if you wanted to
generate, say, 100 random resolutions could you not do:
trees<-replicate(100,multi2di(tree),simplify=FALSE)
class(trees)<-"multiPhylo"
All the best, Liam
Liam J. Revell, Associate Prof
Dear Laura.
I also just posted a possible solution to my blog here:
http://blog.phytools.org/2017/06/generating-set-of-random-resolutions-of.html.
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell
er can be high), you could start with one multifurcating node in the
tree, resolve it in all ways using resolveNode, pick one of those
resolutions, then move to the next node & so on. I will try to post a
formal solution & then share it to the list.
All the best, Liam
Liam J. Revell, As
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