Hi, I am trying to get a matrix of shared proportion distances from a
phylogeny, as can be exported in the PDAP module of Mesquite. However, for some
odd reason the newick files written from R don't quite seem to be read
correctly in Mesquite. Having had a look at exporting vcv matrices of various
kinds from trees in R, I'm not sure if any of them allow the required matrix of
shared proportion distances. Does anyone know if this is possible in R, and if
so how?
Kev
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Sent: 06 March 2013 11:00
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Subject: R-sig-phylo Digest, Vol 62, Issue 2
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Today's Topics:
1. truncated downwards plot.phylo and plot margin (Not To Miss)
2. Re: truncated downwards plot.phylo and plot margin
(Liam J. Revell)
3. Re: Question about model selection using compar.gee (Ben Bolker)
4. Re: Question about model selection using compar.gee (Rob Lanfear)
----------------------------------------------------------------------
Message: 1
Date: Tue, 5 Mar 2013 00:32:15 -0700
From: Not To Miss <not.to.m...@gmail.com>
To: r-sig-phylo@r-project.org
Subject: [R-sig-phylo] truncated downwards plot.phylo and plot margin
Message-ID:
<CAAp=d8oFZWMJLtA6NLhzUYsPuaBc=x5u1c17ykvwgv4ayxf...@mail.gmail.com>
Content-Type: text/plain
Hi,
When plotting the phylo tree downwards, the tip labels are truncated:
>library(ape)
>data(bird.orders)
>plot(bird.orders, direction='downwards')
I found the problem on the website:
http://www.mail-archive.com/r-sig-phylo@r-project.org/msg00298.html. It
seems still not solved? It's kind of annoying.
Another annoying thing is that, when setting the margins to zero, the
plot.phylo still plot some margins around the tree, which is totally
inconsistent to the general plotting convention. Is it possible to be
changed?
Thanks,
Zech
[[alternative HTML version deleted]]
------------------------------
Message: 2
Date: Tue, 5 Mar 2013 11:21:52 -0500
From: "Liam J. Revell" <liam.rev...@umb.edu>
To: Not To Miss <not.to.m...@gmail.com>
Cc: r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] truncated downwards plot.phylo and plot
margin
Message-ID: <51361ba0.1050...@umb.edu>
Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
Hi Zech.
Regarding point (1), this is indeed a bug in plot.phylo, however there
is a work-around. Try the following:
library(ape)
data(bird.orders)
plot(bird.orders,direction="downwards")
axis(2)
plot(bird.orders,direction="downwards",y.lim=c(-15,30))
Regarding point (2), plot.phylo(...,no.margin=TRUE) *does* plot without
margins; however there is some space within a plotted graph between the
(invisible) plot axes and plotted points and lines. If we want our edges
to butt right up against the plot window, we can also accomplish this
with the arguments y.lim and x.lim. For instance, I found via trial &
error that:
plot(bird.orders,x.lim=c(1.3,35.5),y.lim=c(1.5,22.4),no.margin=T)
got me pretty darn close.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 3/5/2013 2:32 AM, Not To Miss wrote:
> Hi,
>
> When plotting the phylo tree downwards, the tip labels are truncated:
>> library(ape)
>> data(bird.orders)
>> plot(bird.orders, direction='downwards')
>
> I found the problem on the website:
> http://www.mail-archive.com/r-sig-phylo@r-project.org/msg00298.html. It
> seems still not solved? It's kind of annoying.
>
> Another annoying thing is that, when setting the margins to zero, the
> plot.phylo still plot some margins around the tree, which is totally
> inconsistent to the general plotting convention. Is it possible to be
> changed?
>
> Thanks,
> Zech
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-phylo mailing list - R-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
>
------------------------------
Message: 3
Date: Tue, 05 Mar 2013 16:28:41 -0500
From: Ben Bolker <bbol...@gmail.com>
To: Javier Lenzi <javier.le...@gmail.com>
Cc: r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] Question about model selection using
compar.gee
Message-ID: <51366389.5010...@gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
[taking the liberty of cc'ing this to r-sig-phylo, which is a better
place for such questions because (1) other people can answer (2) the
answers are publicly viewable and get archived]
On 13-03-05 10:44 AM, Javier Lenzi wrote:
> Dear Dr. Bolker,
>
> My name is Javier Lenzi and I am trying to perform a comparative analysis
> with seabirds (gulls). I am trying to implement a model selection approach
> using compar.gee in ape package and I have some problems. I was wondering
> if I could ask for your advice to deal with them. In case you could help me
> there some questions below that I would like to ask. I am sorry for
> bothering you, my skills in statistics are basic and I have to be fully
> autodidact in matters related to the comparative method.
>
> Thank you very much in advance,
> Best regards,
> Javier Lenzi
> ____________________________
>
> I would like to ask if it is possible to perform a model selection approach
> using compar.gee, because the articles I have read that use compar.gee do
> not use this approach when they have multiple explanatory variables.
>
> Then, I have a set of candidate models for each life history trait and when
> I run compar.gee I get the QIC and the parameter estimates, but I can not
> find an index of goodness of fit for the model and the P-value. Is there
> any available? How should I proceed?
>
> I would also like to ask if there is any function similar to step() in
> order to perform model selection using GEEs?
>
> Other question I would like to ask you is how can I get the amount of
> variance that is explained by the phylogeny? I think it would be nice to
> analyze and present it as a result.
Unfortunately none of these are simple questions. Generalized
estimating equations are not really designed for model selection and
comparison approaches, as they don't operate in terms of likelihoods
(which are the standard currency of such selection and comparison).
Thus they don't have model-level p-values, just t-statistics and
p-values for the individual parameters. If you are comfortable with QIC
you can use them in a standard information-theoretic multi-model
inference approach (i.e. decide to take the model with the best QIC, or
compute QIC weights and get parameter weights or averaged predictions).
I strongly recommend against stepwise model selection: google
"stepwise regression problems". You can do it by hand if you need to ...
Let's see if anyone else on the list has suggestions.
good luck,
Ben Bolker
------------------------------
Message: 4
Date: Wed, 6 Mar 2013 15:16:32 +1100
From: Rob Lanfear <rob.lanf...@gmail.com>
To: Ben Bolker <bbol...@gmail.com>
Cc: r-sig-phylo <r-sig-phylo@r-project.org>, Javier Lenzi
<javier.le...@gmail.com>
Subject: Re: [R-sig-phylo] Question about model selection using
compar.gee
Message-ID:
<CAGr+NmryxwfhJikDst7onsWdKg99eKqM4jogiAcW1vV5cP86=q...@mail.gmail.com>
Content-Type: text/plain
This is not so much an answer as a pointer.
If you did decide to look at all models to do some sort of multi-model
inference (as Ben suggested) you might be able to use or hack some
functions from the glmulti package to help you produce the list of all
possible models.
Once you have that list, and have optimised all the models, finding the
best model or calculating QIC-weighted averages of model parameters
shouldn't be too hard.
I mention this because I just found out about glmulti, after spending a
long time coding my own version.
Rob
On 6 March 2013 08:28, Ben Bolker <bbol...@gmail.com> wrote:
> [taking the liberty of cc'ing this to r-sig-phylo, which is a better
> place for such questions because (1) other people can answer (2) the
> answers are publicly viewable and get archived]
>
> On 13-03-05 10:44 AM, Javier Lenzi wrote:
> > Dear Dr. Bolker,
> >
> > My name is Javier Lenzi and I am trying to perform a comparative analysis
> > with seabirds (gulls). I am trying to implement a model selection
> approach
> > using compar.gee in ape package and I have some problems. I was wondering
> > if I could ask for your advice to deal with them. In case you could help
> me
> > there some questions below that I would like to ask. I am sorry for
> > bothering you, my skills in statistics are basic and I have to be fully
> > autodidact in matters related to the comparative method.
> >
> > Thank you very much in advance,
> > Best regards,
> > Javier Lenzi
> > ____________________________
> >
> > I would like to ask if it is possible to perform a model selection
> approach
> > using compar.gee, because the articles I have read that use compar.gee do
> > not use this approach when they have multiple explanatory variables.
> >
> > Then, I have a set of candidate models for each life history trait and
> when
> > I run compar.gee I get the QIC and the parameter estimates, but I can not
> > find an index of goodness of fit for the model and the P-value. Is there
> > any available? How should I proceed?
> >
> > I would also like to ask if there is any function similar to step() in
> > order to perform model selection using GEEs?
> >
> > Other question I would like to ask you is how can I get the amount of
> > variance that is explained by the phylogeny? I think it would be nice to
> > analyze and present it as a result.
>
> Unfortunately none of these are simple questions. Generalized
> estimating equations are not really designed for model selection and
> comparison approaches, as they don't operate in terms of likelihoods
> (which are the standard currency of such selection and comparison).
> Thus they don't have model-level p-values, just t-statistics and
> p-values for the individual parameters. If you are comfortable with QIC
> you can use them in a standard information-theoretic multi-model
> inference approach (i.e. decide to take the model with the best QIC, or
> compute QIC weights and get parameter weights or averaged predictions).
>
> I strongly recommend against stepwise model selection: google
> "stepwise regression problems". You can do it by hand if you need to ...
>
> Let's see if anyone else on the list has suggestions.
>
> good luck,
> Ben Bolker
>
> _______________________________________________
> R-sig-phylo mailing list - R-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at
> http://www.mail-archive.com/r-sig-phylo@r-project.org/
>
--
Rob Lanfear
Research Fellow,
Ecology, Evolution, and Genetics,
Research School of Biology,
Australian National University
phone: +61 (0)2 6125 3611
www.robertlanfear.com
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