Re: [R-sig-phylo] LTT plot non-ultrametric trees
Somewhere I wrote a function that samples at a series of user-set timepoints and counts the # of lineages crossing each timepoint -- this is pretty flexible, allows for increases/decreases in diversity etc., let me know if the other options aren't working for you I can dig it up... On 8/10/11 9:57 PM, Emmanuel Paradis wrote: Hi Liam Rob, You may try using dist.nodes() for this: x - dist.nodes(phy) n - Ntip(phy) ROOT - n + 1 x[ROOT, ] The last command returns the distance from the root to all nodes and tips which are ordered in the usual way. So you may create a vector with +1 for the nodes, -1 for the tips, and drop the tips not extinct. Then you sort on the values of x, and plot cumsum() of the vector of +/-1 against them. I can add this to ape if there's a general interest for it. Best, Emmanuel Liam J. Revell wrote on 11/08/2011 11:05: Hi Rob. I can reproduce your error, but I haven't figured out the problem yet. You can try an earlier version of this function, which seems to work: source(http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/ltt/v0.3/ltt.R;) p2 - ltt(t1, log.lineages=FALSE, drop.extinct=FALSE) Sorry about this. Also: max(p1$times)==max(p2$times) can be FALSE because if drop.extinct is set to TRUE, then the crown age of the pruned tree can be smaller than in the full tree if some lineages arising at the root of the tree do not leave any extant descendants. - Liam -- Nicholas J. Matzke Ph.D. Candidate, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Graduate Student Instructor, IB200B Principles of Phylogenetics: Ecology and Evolution http://ib.berkeley.edu/courses/ib200b/ http://phylo.wikidot.com/ Lab websites: http://ib.berkeley.edu/people/lab_detail.php?lab=54 http://fisher.berkeley.edu/cteg/hlab.html Dept. personal page: http://ib.berkeley.edu/people/students/person_detail.php?person=370 Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html Lab phone: 510-643-6299 Dept. fax: 510-643-6264 Cell phone: 510-301-0179 Email: mat...@berkeley.edu Mailing address: Department of Integrative Biology 3060 VLSB #3140 Berkeley, CA 94720-3140 - [W]hen people thought the earth was flat, they were wrong. When people thought the earth was spherical, they were wrong. But if you think that thinking the earth is spherical is just as wrong as thinking the earth is flat, then your view is wronger than both of them put together. Isaac Asimov (1989). The Relativity of Wrong. The Skeptical Inquirer, 14(1), 35-44. Fall 1989. http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] LTT plot non-ultrametric trees
Hi Rob. Thanks for identifying the bug. This should be fixed, I hope, in the newest version of phytools (v0.0-6; available: http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/). The way this function works is by first computing the heights above the root of all the nodes (including tip nodes) in the tree, and then at each event (that is, a speciation or extinction), it counts the number of edges that include that time point. This is slow. It seems likely that Emmanuel's suggestion (in a previous email) to use dist.nodes() would run much faster than this. - Liam -- Liam J. Revell University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://phytools.blogspot.com On 8/11/2011 12:42 AM, Rob Lanfear wrote: Hi Liam, Thanks for the help. Extremely useful. And thanks for clearing up my lack of understanding about the differences in maximum ages! Cheers, Rob On 11 August 2011 14:05, Liam J. Revell liam.rev...@umb.edu mailto:liam.rev...@umb.edu wrote: Hi Rob. I can reproduce your error, but I haven't figured out the problem yet. You can try an earlier version of this function, which seems to work: source(http://anolis.oeb.__harvard.edu/~liam/R-__phylogenetics/ltt/v0.3/ltt.R http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/ltt/v0.3/ltt.R) p2 - ltt(t1, log.lineages=FALSE, drop.extinct=FALSE) Sorry about this. Also: max(p1$times)==max(p2$times) can be FALSE because if drop.extinct is set to TRUE, then the crown age of the pruned tree can be smaller than in the full tree if some lineages arising at the root of the tree do not leave any extant descendants. - Liam -- Liam J. Revell University of Massachusetts Boston web: http://faculty.umb.edu/liam.__revell/ http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu mailto:liam.rev...@umb.edu blog: http://phytools.blogspot.com On 8/10/2011 9:50 PM, Rob Lanfear wrote: library(TreeSim) library(phytools) library(geiger) #simulate tree of 100 taxa with initial diversification followed by a period of B=D t1 - sim.rateshift.taxa(100, 1, c(0.2, 0.2), c(0.2, 0.05), c(1,1), c(0, 20))[[1]] t1 #confirm number of extant taxa is 100 n.extant- length(prune.extinct.taxa(t1)$__tip.label) n.extant #do ltt plot without extinct taxa (works fine) p1- ltt(t1, log.lineages=FALSE, drop.extinct=TRUE) #do ltt plot with extinct taxa (looks odd) p2- ltt(t1, log.lineages=FALSE, drop.extinct=FALSE) #max times don't seem to correspond between the two plots. max(p1$times)==max(p2$times) -- Rob Lanfear Postdoc, Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University Tel: +61 2 6125 7270 www.robertlanfear.com http://www.robertlanfear.com ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] LTT plot non-ultrametric trees
Hi Liam, Emmanuel, Nick, et al
Thanks for all the help.
Liam, I can confirm that your new function works fine on all the trees I've
tested (about 20). Thanks!
Some of my trees are pretty large (a few thousand taxa), so for interest's
sake I coded up Emmanuel's suggestion too.
The code is below (liberally borrowed from suggestion on this list, and from
Liam's code). For reasons I don't entirely understand, my code gives my an
ltt vector which is 2 shorter than Liam's. Part of the difference is that I
start with 2 taxa at the root node, so I count one less event than Liam at
the start of the vector. But I'm not sure where the other difference lies -
I've probably made a mistake somewhere.
Any clues gratefully received.
Rob
lttplot- function(phy, plot=TRUE, log.lineages=FALSE){
tol-1e-6
x - dist.nodes(phy)
n - Ntip(phy)
ROOT - n+1
#distances from root to all nodes and tips
events - x[ROOT,]
#tips are extinctions (we remove the extant tips later)
names(events)[1:n] - -1
#nodes are speciations
names(events)[-(1:n)] - +1
#but extant tips don't count
present - max(events)
events - events[-which(eventspresent-tol)]
#sort w.r.t. time
events - sort(events)
#the LTT plot is the cumsum of the names
ltt - cumsum(names(events))
#add 1 to LTT, because the root node actually represents the creation of 2
taxa
#and we don't know the timing of the creation of the first taxon (root
branch)
ltt - ltt+1
if(plot==TRUE){
if(log.lineages==TRUE)
plot(events,log(ltt),s,xlab=time,ylab=log(lineages))
else
plot(events,ltt,s,xlab=time,ylab=lineages)
}
return(list(ltt=ltt, times=events))
}
On 12 August 2011 07:44, Liam J. Revell liam.rev...@umb.edu wrote:
Hi Rob.
Thanks for identifying the bug. This should be fixed, I hope, in the
newest version of phytools (v0.0-6; available:
http://anolis.oeb.harvard.edu/**~liam/R-phylogenetics/http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/
).
The way this function works is by first computing the heights above the
root of all the nodes (including tip nodes) in the tree, and then at each
event (that is, a speciation or extinction), it counts the number of edges
that include that time point. This is slow. It seems likely that
Emmanuel's suggestion (in a previous email) to use dist.nodes() would run
much faster than this.
- Liam
--
Liam J. Revell
University of Massachusetts Boston
web:
http://faculty.umb.edu/liam.**revell/http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://phytools.blogspot.com
On 8/11/2011 12:42 AM, Rob Lanfear wrote:
Hi Liam,
Thanks for the help. Extremely useful.
And thanks for clearing up my lack of understanding about the
differences in maximum ages!
Cheers,
Rob
On 11 August 2011 14:05, Liam J. Revell liam.rev...@umb.edu
mailto:liam.rev...@umb.edu wrote:
Hi Rob.
I can reproduce your error, but I haven't figured out the problem yet.
You can try an earlier version of this function, which seems to work:
source(http://anolis.oeb.__ha**rvard.edu/~liam/R-__**
phylogenetics/ltt/v0.3/ltt.Rhttp://harvard.edu/~liam/R-__phylogenetics/ltt/v0.3/ltt.R
http://anolis.oeb.harvard.**edu/~liam/R-phylogenetics/ltt/**
v0.3/ltt.Rhttp://anolis.oeb.harvard.edu/~liam/R-phylogenetics/ltt/v0.3/ltt.R
)
p2 - ltt(t1, log.lineages=FALSE, drop.extinct=FALSE)
Sorry about this.
Also:
max(p1$times)==max(p2$times)
can be FALSE because if drop.extinct is set to TRUE, then the crown
age of the pruned tree can be smaller than in the full tree if some
lineages arising at the root of the tree do not leave any extant
descendants.
- Liam
--
Liam J. Revell
University of Massachusetts Boston
web:
http://faculty.umb.edu/liam.__**revell/http://faculty.umb.edu/liam.__revell/
http://faculty.umb.edu/liam.**revell/http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu mailto:liam.rev...@umb.edu
blog: http://phytools.blogspot.com
On 8/10/2011 9:50 PM, Rob Lanfear wrote:
library(TreeSim)
library(phytools)
library(geiger)
#simulate tree of 100 taxa with initial diversification followed
by a
period of B=D
t1 - sim.rateshift.taxa(100, 1, c(0.2, 0.2), c(0.2, 0.05),
c(1,1), c(0,
20))[[1]]
t1
#confirm number of extant taxa is 100
n.extant- length(prune.extinct.taxa(t1)$**__tip.label)
n.extant
#do ltt plot without extinct taxa (works fine)
p1- ltt(t1, log.lineages=FALSE, drop.extinct=TRUE)
#do ltt plot with extinct taxa (looks odd)
p2- ltt(t1, log.lineages=FALSE, drop.extinct=FALSE)
#max times don't seem to correspond between the two plots.
max(p1$times)==max(p2$times)
--
Rob Lanfear
Postdoc,
Centre for Macroevolution and Macroecology,
Research School of Biology,
Australian National University
Tel: +61 2 6125 7270
Re: [R-sig-phylo] LTT plot non-ultrametric trees
Hi all,
I'll make a new version of ltt.plot() that treats ultrametric and
non-ultrametric trees. After all, I don't see a logical reason why both
kinds of trees would be treated differently here. I'll add an option
backward (FALSE by default) so the time scale can start from the root,
and one tol as you did below. This will handle the root edge if present,
and also return the data invisibly. Any other suggestion?
Best,
Emmanuel
Rob Lanfear wrote on 12/08/2011 06:52:
Hi Liam, Emmanuel, Nick, et al
Thanks for all the help.
Liam, I can confirm that your new function works fine on all the trees I've
tested (about 20). Thanks!
Some of my trees are pretty large (a few thousand taxa), so for interest's
sake I coded up Emmanuel's suggestion too.
The code is below (liberally borrowed from suggestion on this list, and from
Liam's code). For reasons I don't entirely understand, my code gives my an
ltt vector which is 2 shorter than Liam's. Part of the difference is that I
start with 2 taxa at the root node, so I count one less event than Liam at
the start of the vector. But I'm not sure where the other difference lies -
I've probably made a mistake somewhere.
Any clues gratefully received.
Rob
lttplot- function(phy, plot=TRUE, log.lineages=FALSE){
tol-1e-6
x - dist.nodes(phy)
n - Ntip(phy)
ROOT - n+1
#distances from root to all nodes and tips
events - x[ROOT,]
#tips are extinctions (we remove the extant tips later)
names(events)[1:n] - -1
#nodes are speciations
names(events)[-(1:n)] - +1
#but extant tips don't count
present - max(events)
events - events[-which(eventspresent-tol)]
#sort w.r.t. time
events - sort(events)
#the LTT plot is the cumsum of the names
ltt - cumsum(names(events))
#add 1 to LTT, because the root node actually represents the creation of 2
taxa
#and we don't know the timing of the creation of the first taxon (root
branch)
ltt - ltt+1
if(plot==TRUE){
if(log.lineages==TRUE)
plot(events,log(ltt),s,xlab=time,ylab=log(lineages))
else
plot(events,ltt,s,xlab=time,ylab=lineages)
}
return(list(ltt=ltt, times=events))
}
On 12 August 2011 07:44, Liam J. Revell liam.rev...@umb.edu wrote:
Hi Rob.
Thanks for identifying the bug. This should be fixed, I hope, in the
newest version of phytools (v0.0-6; available:
http://anolis.oeb.harvard.edu/**~liam/R-phylogenetics/http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/
).
The way this function works is by first computing the heights above the
root of all the nodes (including tip nodes) in the tree, and then at each
event (that is, a speciation or extinction), it counts the number of edges
that include that time point. This is slow. It seems likely that
Emmanuel's suggestion (in a previous email) to use dist.nodes() would run
much faster than this.
- Liam
--
Liam J. Revell
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.**revell/http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://phytools.blogspot.com
On 8/11/2011 12:42 AM, Rob Lanfear wrote:
Hi Liam,
Thanks for the help. Extremely useful.
And thanks for clearing up my lack of understanding about the
differences in maximum ages!
Cheers,
Rob
On 11 August 2011 14:05, Liam J. Revell liam.rev...@umb.edu
mailto:liam.rev...@umb.edu wrote:
Hi Rob.
I can reproduce your error, but I haven't figured out the problem yet.
You can try an earlier version of this function, which seems to work:
source(http://anolis.oeb.__ha**rvard.edu/~liam/R-__**
phylogenetics/ltt/v0.3/ltt.Rhttp://harvard.edu/~liam/R-__phylogenetics/ltt/v0.3/ltt.R
http://anolis.oeb.harvard.**edu/~liam/R-phylogenetics/ltt/**
v0.3/ltt.Rhttp://anolis.oeb.harvard.edu/~liam/R-phylogenetics/ltt/v0.3/ltt.R
)
p2 - ltt(t1, log.lineages=FALSE, drop.extinct=FALSE)
Sorry about this.
Also:
max(p1$times)==max(p2$times)
can be FALSE because if drop.extinct is set to TRUE, then the crown
age of the pruned tree can be smaller than in the full tree if some
lineages arising at the root of the tree do not leave any extant
descendants.
- Liam
--
Liam J. Revell
University of Massachusetts Boston
web:
http://faculty.umb.edu/liam.__**revell/http://faculty.umb.edu/liam.__revell/
http://faculty.umb.edu/liam.**revell/http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu mailto:liam.rev...@umb.edu
blog: http://phytools.blogspot.com
On 8/10/2011 9:50 PM, Rob Lanfear wrote:
library(TreeSim)
library(phytools)
library(geiger)
#simulate tree of 100 taxa with initial diversification followed
by a
period of B=D
t1 - sim.rateshift.taxa(100, 1, c(0.2, 0.2), c(0.2, 0.05),
c(1,1), c(0,
20))[[1]]
t1
#confirm number of extant taxa is 100
n.extant- length(prune.extinct.taxa(t1)$**__tip.label)
n.extant
#do ltt plot without extinct taxa (works fine)
p1- ltt(t1,
Re: [R-sig-phylo] LTT plot non-ultrametric trees
This is implemented in my phytools package. This is not yet on CRAN, but can be downloaded from http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/. The function is ltt(). It is slow, but seems to work. Please let me know if you have success with this. - Liam -- Liam J. Revell University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://phytools.blogspot.com On 8/10/2011 8:51 PM, Rob Lanfear wrote: Hi All, I have a set of simulated birth-death trees, which include extinct and extant lineages. I'd like to see if my simulations are doing what I think they should be, by plotting out the number of lineages through time. Does anyone know of a method of doing this that incorporates extinct lineages, i.e. one where the number of lineages can decrease as well as increase through time. I can see how it could be done (I think...) by making an ordered data frame of node times (+1 lineage) and extinction events (-1 lineage), but it seems like somebody might already have done it. Cheers, Rob ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] LTT plot non-ultrametric trees
Hi Liam Rob, You may try using dist.nodes() for this: x - dist.nodes(phy) n - Ntip(phy) ROOT - n + 1 x[ROOT, ] The last command returns the distance from the root to all nodes and tips which are ordered in the usual way. So you may create a vector with +1 for the nodes, -1 for the tips, and drop the tips not extinct. Then you sort on the values of x, and plot cumsum() of the vector of +/-1 against them. I can add this to ape if there's a general interest for it. Best, Emmanuel Liam J. Revell wrote on 11/08/2011 11:05: Hi Rob. I can reproduce your error, but I haven't figured out the problem yet. You can try an earlier version of this function, which seems to work: source(http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/ltt/v0.3/ltt.R;) p2 - ltt(t1, log.lineages=FALSE, drop.extinct=FALSE) Sorry about this. Also: max(p1$times)==max(p2$times) can be FALSE because if drop.extinct is set to TRUE, then the crown age of the pruned tree can be smaller than in the full tree if some lineages arising at the root of the tree do not leave any extant descendants. - Liam -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
