e of K.
Enrico's recommendation to check against picante::phylosignal is wise.
In my tests, the two functions produce values of K that are identical
and value of P that are highly similar. (The latter are from
permutation, so they are not expected to be precisely the same.)
- Liam
Liam J.
ot;ARD" & other
non-reversible models). Let us know if this helps.
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 12/5/2016 10
Hi John.
I believe this used to be possible using the package phybase.
Unfortunately, this package was not being maintained & was removed from
CRAN - however archived package versions can still be obtained (so it
may be possible to install from source).
All the best, Liam
Liam J. Re
install phytools from GitHub using devtools:
library(devtools)
install_github("liamrevell/phytools")
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://blo
Ahhh. I see. I missed the part in Yan's original email about the names.
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 12/28/2016 6:45 AM
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:
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 3:10 PM, Karla Shikev wrote
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
Hi Vojtech.
I just posted a handful of different possible solutions using phytools
on my blog:
http://blog.phytools.org/2017/04/showing-multiple-conflicting.html. Let
me know if any of them work for you.
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University
be installed from GitHub
using devtools.
- 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 4/26/2017 12:18 PM, Vojtěch Zeisek wrote:
Yes, it helps and makes
Hi Ting-Wen.
If you could (off-list) send me the simplest possible reproducible
example of the error (with your input data files or a saved R workspace)
I would be more than happy to look into it.
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts
to make an example & post it to my
blog.
- 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 4/25/2017 12:20 PM, Vojtěch Zeisek wrote:
Hello,
for compa
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/
email
Juan. findMRCA was written before getMRCA existed, but the latter was
faster so now it just calls getMRCA internally. 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
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
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 Massachuse
On the other hand, phytools does have a function - the somewhat
imprecisely named fastMRCA - which can find the MRCA of just a pair of
species much faster than getMRCA (however still slower than or only
about as fast as Joseph & Klaus's solutions).
Liam J. Revell, Associate Profe
<-"multiPhylo"
For some "multiPhylo" objects, for instance those read from a NEXUS
file, you may also want to first run:
trees<-.uncompressTipLabel(trees)
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http:
that 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, Associate
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
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
:
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
web: http://faculty
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 10:49 AM, Rafael S Ma
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
hich 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 Massachusetts Bost
est, 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 newick string returns
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
--
Liam J
ment-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 mailing
,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
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
-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
.length[which(backbone$edge[,2]==tip)]-h
backbone<-bind.tree(backbone,subtrees[[i]],where=tip)
}
plotTree(backbone)
Something like that.
(Of course you could also modify this so that you just manually identify
the tips to bind to. Given the small size of your problem this is
probably what
I haven't been closing following this thread, so I'm not sure that this
is relevant - but phytools has a function called 'force.ultrametric' (I
believe) that does precisely what its name suggests it might.
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
Just to clarify, force.ultrametric is not a formal rate-smoothing method
or anything like that. It is intended only for use to resolve numerical
precision issues such as the one raised in this thread.
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Prof
it symmetric) is leptokurtic which is why
var.test is significant due to idiosyncratic differences in the variance
of lambda, even though the values were obtained by the same process.
(Invariably lamb_sub and lamb fail a normality test, so this seems like
a distinct possibility.)
All the best,
run:
install_github("liamrevell/phytools")
I hope this is of some help. All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor Asociado, Programa de Biología
Universidad del Rosario
web: http://faculty.umb.edu/liam.revell/
On
Hi Felipe.
What version of phytools are you using? A very old phytools version did
not default to interactive mode if no translation table (trans) was
supplied.
Otherwise, I do not know - but it should not be because the tree is not
ultrametric.
All the best, Liam
Liam J. Revell
-paste(strsplit(obj$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
lit(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 'donuts'
ompute 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
web:
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
edges, 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
="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 outside the ta
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
ies ID 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
nty 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 AM, Graham
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
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
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 (again!) to ask for
ot;,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$tip.label)
beetree<-drop.tip(beetree,beetree$tip.label[ii])
elps 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 Concepción
web: http://faculty.umb.edu/
is that 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
ility 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://www.phytools.org
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
.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:/
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/liam.revell/, http://www.phytools.org
Academic Direct
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
frow=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","reconstructed"
ira-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
Academic Director UM
be a 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
ut 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 Boston Chile Abroad:
https:
in 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 Massachusetts
oint 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
Academic Director U
ven
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 Professor, Unive
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 Boston Chile Abroad
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:
the 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
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$edge.length*sig2
phytools::plotTree(phy.sig2)
I hope I'm understanding the problem correctly.
All
o compare to:
as.Qmatrix(fitMk(tree,x,model="ARD"))
where the labeling is better.
All the best, Liam
Liam J. Revell
University of Massachusetts Boston [Assoc. Prof.]
Universidad Católica de la Ssma Concepción [Adj. Res.]
Web & phytools:
http://faculty.umb.edu/liam.revell/, http://
ity, you need to update phytools from GitHub using
devtools -- e.g.,
devtools::install_github("liamrevell/phytools")
All the best, Liam
Liam J. Revell
University of Massachusetts Boston [Assoc. Prof.]
Universidad Católica de la Ssma Concepción [Adj. Res.]
Web & phytools:
htt
Dear Rafa.
Try this to get the transition matrix, Q:
k<-nrow(ace$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
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.]
Univer
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=FALSE)
class(newtree)<-"multiPhylo"
Please
n 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/, http://www.phytools.org,
http://blog.phyto
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're computing an N x N matrix in each i
ranteed! 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
your function call just to get one node ind
ks, 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.org,
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 Católica de la S
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
# 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<-c(
.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-metho
-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-comparat
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
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().
&
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
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
l 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 version a
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
ciation 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 model karyo
ne! 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)
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/liam.revell/
Book
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. Revell
Professor
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
://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 ancestral
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
Professor of
make 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
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
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