Re: [R-sig-phylo] convergence issues with hansen model
Speaking of OUwie, the paper just came out today:
Jeremy M. Beaulieu, Dwueng-Chwuan Jhwueng, Carl Boettiger Brian C. OMeara.
MODELING STABILIZING SELECTION: EXPANDING THE ORNSTEIN-UHLENBECK MODEL OF
ADAPTIVE EVOLUTION. Evolution, Accepted Article, DOI:
10./j.1558-5646.2012.01619.x (link:
http://onlinelibrary.wiley.com/doi/10./j.1558-5646.2012.01619.x/abstract )
Has anyone tried it out yet? Is there a way of converting SIMMAP trees to the
format to be used with the OUwie function?
Thanks!
Abraços,
Rafael Maia
---
webpage: http://gozips.uakron.edu/~rm72
A little learning is a dangerous thing; drink deep, or taste not the Pierian
spring. (A. Pope)
Graduate Student - Integrated Bioscience
University of Akron
http://gozips.uakron.edu/~shawkey/
On Mar 12, 2012, at 2:39 PM, Liam J. Revell wrote:
You might want to try the OUWie package by Beaulieu O'Meara
(http://cran.r-project.org/web/packages/OUwie/index.html). I have not tried
it yet, but it promises to do multi-optimum OU model fitting as well.
All the best, 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 3/12/2012 2:31 PM, Pascal Title wrote:
Hi all
I have a dataset of 5 PC axes for a phylogeny with 52 tips and I would like
to get the variance-covariance matrix under a global OU model of
evolution. I find that OU is strongly favored over BM, based on
fitContinuous in GEIGER.
However, I am having issues with convergence when trying to fit a hansen
model to my data. What can I do to get around this problem? Alternatively,
is there another way to get at the multivariate VCV matrix other than with
the OUCH package?
The error is:
*unsuccessful convergence, code 1, see documentation for `optim'*
*Warning message:*
*In hansen(tree = ot, data = otd[varnames], regimes = otd[regimes], :*
* unsuccessful convergence*
I have posted a small file that contains the following R script along with
the data herehttp://dl.dropbox.com/u/34644229/OUhansen.zip.
Any advice would be greatly appreciated! Thanks!
require(ouch)
require(ape)
tree-read.nexus('tree.nex')
data-read.csv('data.csv')
rownames(data)-data$X
data$X-NULL
tree
head(data)
colnames(data)-varnames #for hansen()
ot-ape2ouch(tree)
otd-as(ot,data.frame)
data$labels-rownames(data)
otd-merge(otd,data,by=labels,all=TRUE)
rownames(otd)-otd$nodes
ot-with(otd,ouchtree(nodes=nodes,ancestors=ancestors,times=times,labels=labels))
otd$regimes-as.factor(global)
h1-hansen(tree=ot,data=otd[varnames],regimes=otd[regimes],sqrt.alpha=c(1,0,0,0,0,1,0,0,0,1,0,0,1,0,1),sigma=c(1,0,0,0,0,1,0,0,0,1,0,0,1,0,1))
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Re: [R-sig-phylo] convergence issues with hansen model
Hi Rafael.
I don't want to speak on behalf of the authors who are also on this
list, but OUwie can read in modified phylo objects created by the
phytools functions read.simmap make.simmap.
All the best, 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 3/13/2012 4:35 PM, Rafael Maia wrote:
Speaking of OUwie, the paper just came out today:
Jeremy M. Beaulieu, Dwueng-Chwuan Jhwueng, Carl Boettiger Brian C.
O’Meara. MODELING STABILIZING SELECTION: EXPANDING THE
ORNSTEIN-UHLENBECK MODEL OF ADAPTIVE EVOLUTION. Evolution, Accepted
Article, DOI: 10./j.1558-5646.2012.01619.x (link:
http://onlinelibrary.wiley.com/doi/10./j.1558-5646.2012.01619.x/abstract
)
Has anyone tried it out yet? Is there a way of converting SIMMAP trees
to the format to be used with the OUwie function?
Thanks!
Abraços,
Rafael Maia
---
webpage: http://gozips.uakron.edu/~rm72
A little learning is a dangerous thing; drink deep, or taste not the
Pierian spring. (A. Pope)
Graduate Student - Integrated Bioscience
University of Akron
http://gozips.uakron.edu/~shawkey/
On Mar 12, 2012, at 2:39 PM, Liam J. Revell wrote:
You might want to try the OUWie package by Beaulieu O'Meara
(http://cran.r-project.org/web/packages/OUwie/index.html). I have not
tried it yet, but it promises to do multi-optimum OU model fitting as
well.
All the best, Liam
--
Liam J. Revell
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu mailto:liam.rev...@umb.edu
blog: http://phytools.blogspot.com
On 3/12/2012 2:31 PM, Pascal Title wrote:
Hi all
I have a dataset of 5 PC axes for a phylogeny with 52 tips and I
would like
to get the variance-covariance matrix under a global OU model of
evolution. I find that OU is strongly favored over BM, based on
fitContinuous in GEIGER.
However, I am having issues with convergence when trying to fit a hansen
model to my data. What can I do to get around this problem?
Alternatively,
is there another way to get at the multivariate VCV matrix other than
with
the OUCH package?
The error is:
*unsuccessful convergence, code 1, see documentation for `optim'*
*Warning message:*
*In hansen(tree = ot, data = otd[varnames], regimes = otd[regimes], :*
* unsuccessful convergence*
I have posted a small file that contains the following R script along
with
the data herehttp://dl.dropbox.com/u/34644229/OUhansen.zip.
Any advice would be greatly appreciated! Thanks!
require(ouch)
require(ape)
tree-read.nexus('tree.nex')
data-read.csv('data.csv')
rownames(data)-data$X
data$X-NULL
tree
head(data)
colnames(data)-varnames #for hansen()
ot-ape2ouch(tree)
otd-as(ot,data.frame)
data$labels-rownames(data)
otd-merge(otd,data,by=labels,all=TRUE)
rownames(otd)-otd$nodes
ot-with(otd,ouchtree(nodes=nodes,ancestors=ancestors,times=times,labels=labels))
otd$regimes-as.factor(global)
h1-hansen(tree=ot,data=otd[varnames],regimes=otd[regimes],sqrt.alpha=c(1,0,0,0,0,1,0,0,0,1,0,0,1,0,1),sigma=c(1,0,0,0,0,1,0,0,0,1,0,0,1,0,1))
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Re: [R-sig-phylo] convergence issues with hansen model
ah, I see. Thanks! Indeed, if I simulate trees with make.simmap or sim.history,
they work fine. But the trees I read in with read.simmap I still get the error:
OUwie(arv,randdat,model='BM1',simmap.tree=T)
Begin subplex optimization routine -- Starting value: 1
Error in which(edges[i, 5:(k + 4)] == 1) : subscript out of bounds
Which is why I thought they wouldn't work together. Looking at the trees using
print.default(), the only difference I can spot is that my imported trees don't
have a $node.states or a $states elements. Could this have something to do with
it?
Many thanks!
Code I used for simulations:
require(OUwie)
require(phytools)
require(geiger)
tree-drop.tip(birthdeath.tree(b=1,d=0,taxa.stop=101),101)
Q-matrix(c(0.8,0.2,0.2,0.8),2,2, dimnames=list(c(A,B),c(A,B)))
simtree - sim.history(tree,Q)
simtrait-data.frame(spp=names(simtree$states),state=simtree$states,trait=rnorm(100))
OUwie(simtree,simtrait,model='BMS',simmap.tree=T)
Q-matrix(c(-1,0.8,0.2,0.8,-1.2,0.4,0.2,0.4,-0.6),3,3,
dimnames=list(c(A,B,C),c(A,B,C)))
simtree - sim.history(tree,Q)
simtrait-data.frame(spp=names(simtree$states),state=simtree$states,trait=rnorm(100))
OUwie(simtree,simtrait,model='BMS',simmap.tree=T)
Abraços,
Rafael Maia
---
webpage: http://gozips.uakron.edu/~rm72
A little learning is a dangerous thing; drink deep, or taste not the Pierian
spring. (A. Pope)
Graduate Student - Integrated Bioscience
University of Akron
http://gozips.uakron.edu/~shawkey/
On Mar 13, 2012, at 5:05 PM, Liam J. Revell wrote:
Hi Rafael.
I don't want to speak on behalf of the authors who are also on this list, but
OUwie can read in modified phylo objects created by the phytools functions
read.simmap make.simmap.
All the best, 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 3/13/2012 4:35 PM, Rafael Maia wrote:
Speaking of OUwie, the paper just came out today:
Jeremy M. Beaulieu, Dwueng-Chwuan Jhwueng, Carl Boettiger Brian C.
OMeara. MODELING STABILIZING SELECTION: EXPANDING THE
ORNSTEIN-UHLENBECK MODEL OF ADAPTIVE EVOLUTION. Evolution, Accepted
Article, DOI: 10./j.1558-5646.2012.01619.x (link:
http://onlinelibrary.wiley.com/doi/10./j.1558-5646.2012.01619.x/abstract
)
Has anyone tried it out yet? Is there a way of converting SIMMAP trees
to the format to be used with the OUwie function?
Thanks!
Abraços,
Rafael Maia
---
webpage: http://gozips.uakron.edu/~rm72
A little learning is a dangerous thing; drink deep, or taste not the
Pierian spring. (A. Pope)
Graduate Student - Integrated Bioscience
University of Akron
http://gozips.uakron.edu/~shawkey/
On Mar 12, 2012, at 2:39 PM, Liam J. Revell wrote:
You might want to try the OUWie package by Beaulieu O'Meara
(http://cran.r-project.org/web/packages/OUwie/index.html). I have not
tried it yet, but it promises to do multi-optimum OU model fitting as
well.
All the best, Liam
--
Liam J. Revell
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu mailto:liam.rev...@umb.edu
blog: http://phytools.blogspot.com
On 3/12/2012 2:31 PM, Pascal Title wrote:
Hi all
I have a dataset of 5 PC axes for a phylogeny with 52 tips and I
would like
to get the variance-covariance matrix under a global OU model of
evolution. I find that OU is strongly favored over BM, based on
fitContinuous in GEIGER.
However, I am having issues with convergence when trying to fit a hansen
model to my data. What can I do to get around this problem?
Alternatively,
is there another way to get at the multivariate VCV matrix other than
with
the OUCH package?
The error is:
*unsuccessful convergence, code 1, see documentation for `optim'*
*Warning message:*
*In hansen(tree = ot, data = otd[varnames], regimes = otd[regimes], :*
* unsuccessful convergence*
I have posted a small file that contains the following R script along
with
the data herehttp://dl.dropbox.com/u/34644229/OUhansen.zip.
Any advice would be greatly appreciated! Thanks!
require(ouch)
require(ape)
tree-read.nexus('tree.nex')
data-read.csv('data.csv')
rownames(data)-data$X
data$X-NULL
tree
head(data)
colnames(data)-varnames #for hansen()
ot-ape2ouch(tree)
otd-as(ot,data.frame)
data$labels-rownames(data)
otd-merge(otd,data,by=labels,all=TRUE)
rownames(otd)-otd$nodes
ot-with(otd,ouchtree(nodes=nodes,ancestors=ancestors,times=times,labels=labels))
otd$regimes-as.factor(global)
h1-hansen(tree=ot,data=otd[varnames],regimes=otd[regimes],sqrt.alpha=c(1,0,0,0,0,1,0,0,0,1,0,0,1,0,1),sigma=c(1,0,0,0,0,1,0,0,0,1,0,0,1,0,1))
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Re: [R-sig-phylo] convergence issues with hansen model
Hi Rafael, Hi Liam~ Just wanted to quickly chime in by saying that yes, OUwie can read in SIMMAP objects. This feature should be available in the current version posted on CRAN. If not there you can definitely download it off R-Forge. Rafael -- let me know if you have any issues, and don't hesitate to contact me off-thread if you need further assistance. All the best, Jeremy ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] convergence issues with hansen model
Thanks for the response, Liam. I just tried out OUwie and it works.
However, it appears to only fit 1 variable at a time (I only get one sigma
squared value).
When running some tests with OUCH, I found that sigma squared is different
when one variable is fit to an OU model, versus when multiple variables are
fit together. Is that expected?
-Pascal
On Mon, Mar 12, 2012 at 11:39 AM, Liam J. Revell liam.rev...@umb.eduwrote:
You might want to try the OUWie package by Beaulieu O'Meara (
http://cran.r-project.org/**web/packages/OUwie/index.htmlhttp://cran.r-project.org/web/packages/OUwie/index.html
)**. I have not tried it yet, but it promises to do multi-optimum OU
model fitting as well.
All the best, 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 3/12/2012 2:31 PM, Pascal Title wrote:
Hi all
I have a dataset of 5 PC axes for a phylogeny with 52 tips and I would
like
to get the variance-covariance matrix under a global OU model of
evolution. I find that OU is strongly favored over BM, based on
fitContinuous in GEIGER.
However, I am having issues with convergence when trying to fit a hansen
model to my data. What can I do to get around this problem? Alternatively,
is there another way to get at the multivariate VCV matrix other than with
the OUCH package?
The error is:
*unsuccessful convergence, code 1, see documentation for `optim'*
*Warning message:*
*In hansen(tree = ot, data = otd[varnames], regimes = otd[regimes], :*
* unsuccessful convergence*
I have posted a small file that contains the following R script along with
the data
herehttp://dl.dropbox.com/u/**34644229/OUhansen.ziphttp://dl.dropbox.com/u/34644229/OUhansen.zip
.
Any advice would be greatly appreciated! Thanks!
require(ouch)
require(ape)
tree-read.nexus('tree.nex')
data-read.csv('data.csv')
rownames(data)-data$X
data$X-NULL
tree
head(data)
colnames(data)-varnames #for hansen()
ot-ape2ouch(tree)
otd-as(ot,data.frame)
data$labels-rownames(data)
otd-merge(otd,data,by=**labels,all=TRUE)
rownames(otd)-otd$nodes
ot-with(otd,ouchtree(nodes=**nodes,ancestors=ancestors,**
times=times,labels=labels))
otd$regimes-as.factor(**global)
h1-hansen(tree=ot,data=otd[**varnames],regimes=otd[**
regimes],sqrt.alpha=c(1,0,0,**0,0,1,0,0,0,1,0,0,1,0,1),**
sigma=c(1,0,0,0,0,1,0,0,0,1,0,**0,1,0,1))
--
Pascal Title
Graduate Student
Burns Lab
http://kevinburnslab.com/
Department of Evolutionary Biology
San Diego State University
5500 Campanile Drive
San Diego, CA 92182-4614
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Re: [R-sig-phylo] convergence issues with hansen model
Just wanted to note that there's a fundamental difference between the
way OUCH is handling the multivariate traits and the way geiger and
similar packages are handling it. If you're giving geiger a data
frame with multiple traits, it is fitting each independently, just
saving you the trouble from passing them in one at a time.
OUCH is actually fitting the multivariate trait model, which is the
reason that you get different results fitting a single trait or
fitting multiple traits simultaneously.
In the OUCH model, dX = alpha ( theta - X) dt + sigma dB_t,
X is a vector, alpha is a matrix, theta is a vector, sigma is a
matrix, and dB_t is a vector of Brownian walks.
Only if the off-diagonal terms of alpha and sigma matrices are zero
will the results be the same.
hope that helps,
-Carl
On Mon, Mar 12, 2012 at 4:56 PM, Pascal Title pascalti...@gmail.com wrote:
Thanks for the response, Liam. I just tried out OUwie and it works.
However, it appears to only fit 1 variable at a time (I only get one sigma
squared value).
When running some tests with OUCH, I found that sigma squared is different
when one variable is fit to an OU model, versus when multiple variables are
fit together. Is that expected?
-Pascal
On Mon, Mar 12, 2012 at 11:39 AM, Liam J. Revell liam.rev...@umb.eduwrote:
You might want to try the OUWie package by Beaulieu O'Meara (
http://cran.r-project.org/**web/packages/OUwie/index.htmlhttp://cran.r-project.org/web/packages/OUwie/index.html
)**. I have not tried it yet, but it promises to do multi-optimum OU
model fitting as well.
All the best, 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 3/12/2012 2:31 PM, Pascal Title wrote:
Hi all
I have a dataset of 5 PC axes for a phylogeny with 52 tips and I would
like
to get the variance-covariance matrix under a global OU model of
evolution. I find that OU is strongly favored over BM, based on
fitContinuous in GEIGER.
However, I am having issues with convergence when trying to fit a hansen
model to my data. What can I do to get around this problem? Alternatively,
is there another way to get at the multivariate VCV matrix other than with
the OUCH package?
The error is:
*unsuccessful convergence, code 1, see documentation for `optim'*
*Warning message:*
*In hansen(tree = ot, data = otd[varnames], regimes = otd[regimes], :*
* unsuccessful convergence*
I have posted a small file that contains the following R script along with
the data
herehttp://dl.dropbox.com/u/**34644229/OUhansen.ziphttp://dl.dropbox.com/u/34644229/OUhansen.zip
.
Any advice would be greatly appreciated! Thanks!
require(ouch)
require(ape)
tree-read.nexus('tree.nex')
data-read.csv('data.csv')
rownames(data)-data$X
data$X-NULL
tree
head(data)
colnames(data)-varnames #for hansen()
ot-ape2ouch(tree)
otd-as(ot,data.frame)
data$labels-rownames(data)
otd-merge(otd,data,by=**labels,all=TRUE)
rownames(otd)-otd$nodes
ot-with(otd,ouchtree(nodes=**nodes,ancestors=ancestors,**
times=times,labels=labels))
otd$regimes-as.factor(**global)
h1-hansen(tree=ot,data=otd[**varnames],regimes=otd[**
regimes],sqrt.alpha=c(1,0,0,**0,0,1,0,0,0,1,0,0,1,0,1),**
sigma=c(1,0,0,0,0,1,0,0,0,1,0,**0,1,0,1))
--
Pascal Title
Graduate Student
Burns Lab
http://kevinburnslab.com/
Department of Evolutionary Biology
San Diego State University
5500 Campanile Drive
San Diego, CA 92182-4614
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UC Davis
http://www.carlboettiger.info/
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Re: [R-sig-phylo] convergence issues with hansen model
That helps alot, Carl, thank you. So to bring this back to my original
question, it sounds like the only way to get sigma squared values from a
multivariate OU model is with OUCH. I'm currently not able to get results
because of convergence issues. Does that mean that I simply won't be able
to get such data? Is this the end of the line? Or are there parameters that
I can tweak to get convergence? I know you can increase the number of
iterations, and you can choose different optimization methods, but I don't
know enough about these methods to know whether or not it is appropriate to
change these, or if this could somehow affect the output.
I really appreciate the help!
-Pascal
On Mon, Mar 12, 2012 at 3:01 PM, Carl Boettiger cboet...@gmail.com wrote:
Just wanted to note that there's a fundamental difference between the
way OUCH is handling the multivariate traits and the way geiger and
similar packages are handling it. If you're giving geiger a data
frame with multiple traits, it is fitting each independently, just
saving you the trouble from passing them in one at a time.
OUCH is actually fitting the multivariate trait model, which is the
reason that you get different results fitting a single trait or
fitting multiple traits simultaneously.
In the OUCH model, dX = alpha ( theta - X) dt + sigma dB_t,
X is a vector, alpha is a matrix, theta is a vector, sigma is a
matrix, and dB_t is a vector of Brownian walks.
Only if the off-diagonal terms of alpha and sigma matrices are zero
will the results be the same.
hope that helps,
-Carl
On Mon, Mar 12, 2012 at 4:56 PM, Pascal Title pascalti...@gmail.com
wrote:
Thanks for the response, Liam. I just tried out OUwie and it works.
However, it appears to only fit 1 variable at a time (I only get one
sigma
squared value).
When running some tests with OUCH, I found that sigma squared is
different
when one variable is fit to an OU model, versus when multiple variables
are
fit together. Is that expected?
-Pascal
On Mon, Mar 12, 2012 at 11:39 AM, Liam J. Revell liam.rev...@umb.edu
wrote:
You might want to try the OUWie package by Beaulieu O'Meara (
http://cran.r-project.org/**web/packages/OUwie/index.html
http://cran.r-project.org/web/packages/OUwie/index.html
)**. I have not tried it yet, but it promises to do multi-optimum OU
model fitting as well.
All the best, 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 3/12/2012 2:31 PM, Pascal Title wrote:
Hi all
I have a dataset of 5 PC axes for a phylogeny with 52 tips and I would
like
to get the variance-covariance matrix under a global OU model of
evolution. I find that OU is strongly favored over BM, based on
fitContinuous in GEIGER.
However, I am having issues with convergence when trying to fit a
hansen
model to my data. What can I do to get around this problem?
Alternatively,
is there another way to get at the multivariate VCV matrix other than
with
the OUCH package?
The error is:
*unsuccessful convergence, code 1, see documentation for `optim'*
*Warning message:*
*In hansen(tree = ot, data = otd[varnames], regimes = otd[regimes],
:*
* unsuccessful convergence*
I have posted a small file that contains the following R script along
with
the data herehttp://dl.dropbox.com/u/**34644229/OUhansen.zip
http://dl.dropbox.com/u/34644229/OUhansen.zip
.
Any advice would be greatly appreciated! Thanks!
require(ouch)
require(ape)
tree-read.nexus('tree.nex')
data-read.csv('data.csv')
rownames(data)-data$X
data$X-NULL
tree
head(data)
colnames(data)-varnames #for hansen()
ot-ape2ouch(tree)
otd-as(ot,data.frame)
data$labels-rownames(data)
otd-merge(otd,data,by=**labels,all=TRUE)
rownames(otd)-otd$nodes
ot-with(otd,ouchtree(nodes=**nodes,ancestors=ancestors,**
times=times,labels=labels))
otd$regimes-as.factor(**global)
h1-hansen(tree=ot,data=otd[**varnames],regimes=otd[**
regimes],sqrt.alpha=c(1,0,0,**0,0,1,0,0,0,1,0,0,1,0,1),**
sigma=c(1,0,0,0,0,1,0,0,0,1,0,**0,1,0,1))
--
Pascal Title
Graduate Student
Burns Lab
http://kevinburnslab.com/
Department of Evolutionary Biology
San Diego State University
5500 Campanile Drive
San Diego, CA 92182-4614
[[alternative HTML version deleted]]
___
R-sig-phylo mailing list
R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
--
Carl Boettiger
UC Davis
http://www.carlboettiger.info/
--
Pascal Title
Graduate Student
Burns Lab
http://kevinburnslab.com/
Department of Evolutionary Biology
San Diego State University
5500 Campanile Drive
San Diego, CA 92182-4614
[[alternative HTML version deleted]]
