Hi Franz,
Look at this paper :
http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2745.2010.01717.x/abstract
Em 28/07/2017 07:03, <r-sig-phylo-requ...@r-project.org> escreveu:
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Today's Topics:
1. phylogenetic circular linear regression (f.k...@mailbox.org)
2. Re: phylogenetic circular linear regression (Florian Boucher)
3. Re: phylogenetic circular linear regression (Florian Boucher)
4. Re: selecting a set of incongruent trees from a posterior
distribution (Jesse Delia)
5. Re: phylogenetic circular linear regression (Peter Smits)
----------------------------------------------------------------------
Message: 1
Date: Thu, 27 Jul 2017 13:06:49 +0200
From: "f.k...@mailbox.org" <f.k...@mailbox.org>
To: r-sig-phylo <r-sig-phylo@r-project.org>
Subject: [R-sig-phylo] phylogenetic circular linear regression
Message-ID: <c23123aa-eea7-489c-b731-445ad31a6...@mailbox.org>
Content-Type: text/plain; charset=utf-8
Hi all,
it there something like a phylogenetic circular linear regression or such?
I want to test if the hue (circular 360?) of species differs between two
lifestyles?
Hope someone can help?
If this is not there please also let me know.
Cheers,
Franz
------------------------------
Message: 2
Date: Thu, 27 Jul 2017 14:09:27 +0200
From: Florian Boucher <floflobouc...@gmail.com>
To: "f.k...@mailbox.org" <f.k...@mailbox.org>
Cc: r-sig-phylo <r-sig-phylo@r-project.org>
Subject: Re: [R-sig-phylo] phylogenetic circular linear regression
Message-ID:
<cakfou5gelcj9vapds+a6rbmhmfi4fpjwtyh5kf+tgldnbx5...@mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hi Franz,
I don't know about anything like what you propose but maybe you could
sine-transform your trait and then use phylogenetic linear or logistic
regression?
Florian
2017-07-27 13:06 GMT+02:00 f.k...@mailbox.org <f.k...@mailbox.org>:
> Hi all,
>
> it there something like a phylogenetic circular linear regression or such?
>
> I want to test if the hue (circular 360?) of species differs between two
> lifestyles?
>
> Hope someone can help?
>
> If this is not there please also let me know.
>
> Cheers,
> Franz
>
> _______________________________________________
> 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-ph...@r-project.org/
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------------------------------
Message: 3
Date: Thu, 27 Jul 2017 16:55:06 +0200
From: Florian Boucher <floflobouc...@gmail.com>
To: "f.k...@mailbox.org" <f.k...@mailbox.org>
Cc: r-sig-phylo <r-sig-phylo@r-project.org>
Subject: Re: [R-sig-phylo] phylogenetic circular linear regression
Message-ID:
<cakfou5fexkzr4dcdb85fpjelbqj4nvxjyqsdezug4fqp7vx...@mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hi again Frank,
I just realized that a sine or cosine transformation would leave you with
opposite colors on the hue having the same value... probably not so handy.
Sorry, that was a poor suggestion...
Florian
2017-07-27 14:09 GMT+02:00 Florian Boucher <floflobouc...@gmail.com>:
> Hi Franz,
>
> I don't know about anything like what you propose but maybe you could
> sine-transform your trait and then use phylogenetic linear or logistic
> regression?
>
> Florian
>
> 2017-07-27 13:06 GMT+02:00 f.k...@mailbox.org <f.k...@mailbox.org>:
>
>> Hi all,
>>
>> it there something like a phylogenetic circular linear regression or
such?
>>
>> I want to test if the hue (circular 360?) of species differs between two
>> lifestyles?
>>
>> Hope someone can help?
>>
>> If this is not there please also let me know.
>>
>> Cheers,
>> Franz
>>
>> _______________________________________________
>> 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-ph...@r-project.org/
>
>
>
[[alternative HTML version deleted]]
------------------------------
Message: 4
Date: Thu, 27 Jul 2017 15:11:54 -0400
From: Jesse Delia <jdeli...@gmail.com>
To: Jarrod Hadfield <j.hadfi...@ed.ac.uk>
Cc: Santiago S?nchez <santiago.snc...@gmail.com>,
r-sig-phylo@r-project.org, "ear...@gmail.com" <ear...@gmail.com>
Subject: Re: [R-sig-phylo] selecting a set of incongruent trees from a
posterior distribution
Message-ID:
<ca+lom6ghu2vg36wsrd7hku0nxhnuc5mh+ke3i1ptanou6i7...@mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Thank you everyone for your help, I really appreciate it!
On Wed, Jul 26, 2017 at 11:55 AM, Jarrod Hadfield <j.hadfi...@ed.ac.uk>
wrote:
> Hi Jesse,
>
> In order to account for phylogenetic uncertainty you are better just
> pulling trees from their posterior rather than choosing trees that are
> incongruent. The latter will give estimates biased toward those associated
> with extreme trees.
>
> If the analysis is the binomial model you posted on R-sig-mixed you can
> speed up the analysis by passing the latent variables from one model as
the
> starting values in the next model without a long burn-in. If the data are
> Gaussian you just need to pass the (co)varinaces as starting values.
>
> Code is below. It is untested, and clearly you need to replace ... with
> the exact specifications of the model.
>
> Note that this type of approach is still biased towards a lambda/h2 of 0.
> To fix that you would need to simultaneously estimate the phylogeny and
the
> parameters of the comparative analysis. The bias is probably small if the
> tree is well estimated, and doing it 'properly' would be difficult -
> perhaps BEAST can do it.
>
> Cheers,
>
> Jarrod
>
> ntree<-100 # number of trees
>
> nsample<-100 # number of samples per tree
>
> thin<-10 # thinning interval
>
> model_all<-MCMCglmm(...., pl=TRUE) # initial model object to which
> results will be written
>
> model_i<-model_all
>
> model_all$Sol<-matrix(NA, nsample*ntree, ncol(model_all$Sol))
>
> model_all$VCV<-matrix(NA, nsample*ntree, ncol(model_all$VCV))
>
> # create empty matrices for writing results from each tree
>
> for(i in 1:ntree){
>
> # iterate over trees
>
> model_i<-MCMCglmm(...., pl=TRUE, start=list(liab=model_i$Liab[nsample,]),
> pedigree=tree[[i]], burnin=thin, thin=thin, nitt=thin*(nsample+1))
>
> # fit model to tree i using starting values from previous model
>
> model_all$Sol[(i-1)*nsample+1:nsample]<-model_i$Sol
>
> model_all$VCV[(i-1)*nsample+1:nsample]<-model_i$VCV
>
> }
>
> model_all$Sol<-mcmc(model_all$Sol, thin=thin)
>
> model_all$VCV<-mcmc(model_all$VCV, thin=thin)
>
>
>
> On 26/07/2017 16:06, Santiago S?nchez wrote:
>
>> Hi Jesse,
>>
>> As Eduardo says, if in fact you want to see how different trees are from
a
>> "consensus", something that you could try is find the
>> maximum-clade-credibility (MCC) tree (you can do this with treeAnnotator
>> from BEAST). This will be a fully bifurcating tree and is essentially the
>> tree in the posterior distribution that maximizes the overall clade
>> posterior probabilities (e.g. sum(posterior)). Once you have the MCC
tree,
>> you can use the Robinson-Foulds distance metric (there is a function in
>> phytools) to compare all the topologies in your posterior distribution.
>> The
>> trees with the lowest values will be the most incongruent with respect to
>> the MCC tree. Just remember to exclude the burnin.
>>
>> Cheers,
>> Santiago
>>
>> On Wed, Jul 26, 2017 at 6:01 AM <r-sig-phylo-requ...@r-project.org>
>> wrote:
>>
>> Send R-sig-phylo mailing list submissions to
>>> r-sig-phylo@r-project.org
>>>
>>> To subscribe or unsubscribe via the World Wide Web, visit
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>>> or, via email, send a message with subject or body 'help' to
>>> r-sig-phylo-requ...@r-project.org
>>>
>>> You can reach the person managing the list at
>>> r-sig-phylo-ow...@r-project.org
>>>
>>> When replying, please edit your Subject line so it is more specific
>>> than "Re: Contents of R-sig-phylo digest..."
>>>
>>>
>>> Today's Topics:
>>>
>>> 1. selecting a set of incongruent trees from a posterior
>>> distribution (Jesse Delia)
>>> 2. Re: selecting a set of incongruent trees from a posterior
>>> distribution (Eduardo Ascarrunz)
>>>
>>>
>>> ----------------------------------------------------------------------
>>>
>>> Message: 1
>>> Date: Tue, 25 Jul 2017 16:16:30 -0400
>>> From: Jesse Delia <jdeli...@gmail.com>
>>> To: R-sig-phylo@r-project.org
>>> Subject: [R-sig-phylo] selecting a set of incongruent trees from a
>>> posterior distribution
>>> Message-ID:
>>> <
>>> ca+lom6ehmv6c2v_lso8b2sdqqvoqwfcrl56-4jhcmicvjyv...@mail.gmail.com>
>>> Content-Type: text/plain; charset="UTF-8"
>>>
>>> Dear list,
>>>
>>> Does anyone know of a function or script that could select a set of the
>>> most incongruent trees from a list of trees? Maybe I missed a post, but
>>> haven't found anything.
>>>
>>> I running mixed models, which take a lot of computational space on my
lap
>>> top. In effort to account for phylogenetic uncertainty, without having
to
>>> run 100s of chains, I figured maybe i could run models across a (much)
>>> shorter list that accounts for more diversity in tree shape observed
>>> within
>>> the posterior distribution. Not sure if this makes sense, and/or is
>>> extremely complicated?
>>>
>>> Thanks for you time!
>>>
>>> Jesse
>>>
>>> [[alternative HTML version deleted]]
>>>
>>>
>>>
>>> ------------------------------
>>>
>>> Message: 2
>>> Date: Wed, 26 Jul 2017 11:33:12 +0200
>>> From: Eduardo Ascarrunz <ear...@gmail.com>
>>> To: Jesse Delia <jdeli...@gmail.com>
>>> Cc: R Sig Phylo Listserv <R-sig-phylo@r-project.org>
>>> Subject: Re: [R-sig-phylo] selecting a set of incongruent trees from a
>>> posterior distribution
>>> Message-ID:
>>> <
>>> cakxhxpxj_8ucosjt-bzpzvsn+5quet9vxnd4ssd4bqaq-fp...@mail.gmail.com>
>>> Content-Type: text/plain; charset="UTF-8"
>>>
>>> Hi Jesse,
>>>
>>> Do you want to select the trees that are most incongruent with some sort
>>> of
>>> average of the tree distribution? The `treespace`and `phytools` packages
>>> have functions that compute average trees with different metrics, and
>>> they
>>> also allow you to measure the distance between each tree and the average
>>> tree.
>>>
>>> Cheers,
>>>
>>> Eduardo
>>>
>>> 2017-07-25 22:16 GMT+02:00 Jesse Delia <jdeli...@gmail.com>:
>>>
>>> Dear list,
>>>>
>>>> Does anyone know of a function or script that could select a set of the
>>>> most incongruent trees from a list of trees? Maybe I missed a post, but
>>>> haven't found anything.
>>>>
>>>> I running mixed models, which take a lot of computational space on my
>>>> lap
>>>> top. In effort to account for phylogenetic uncertainty, without having
>>>> to
>>>> run 100s of chains, I figured maybe i could run models across a (much)
>>>> shorter list that accounts for more diversity in tree shape observed
>>>>
>>> within
>>>
>>>> the posterior distribution. Not sure if this makes sense, and/or is
>>>> extremely complicated?
>>>>
>>>> Thanks for you time!
>>>>
>>>> Jesse
>>>>
>>>> [[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-ph...@r-project.org/
>>>>
>>>> [[alternative HTML version deleted]]
>>>
>>>
>>>
>>> ------------------------------
>>>
>>> Subject: Digest Footer
>>>
>>> _______________________________________________
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>>> R-sig-phylo@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>>>
>>> ------------------------------
>>>
>>> End of R-sig-phylo Digest, Vol 114, Issue 10
>>> ********************************************
>>>
>>>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
[[alternative HTML version deleted]]
------------------------------
Message: 5
Date: Thu, 27 Jul 2017 18:33:13 +0000
From: Peter Smits <peterdavidsm...@gmail.com>
To: "f.k...@mailbox.org" <f.k...@mailbox.org>, r-sig-phylo
<r-sig-phylo@r-project.org>
Subject: Re: [R-sig-phylo] phylogenetic circular linear regression
Message-ID:
<cahm0ea4o93omxa7jjf_sp5mu5ovo3fmgtlymuzhz1s51cp7...@mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hi,
If your adventurous you could probably write your own model in R or Stan
or similar. The wrapped Normal or the Von Mise distribution are circular
and map from 0 to 2pi. My suggestion would be to include a species level
phylogenetic "random effect" for the mean parameter to account for the
autocorrelation. This is how the MCMCglmm package includes phylogeny.
If you write it as sampling statements it might look like
y ~ MV(mu, k)
mu = a + bx + h
h ~ MVN (Mu, Sigma)
Hope that helps lead you on the right track.
Cheers,
Peter
On Thu, Jul 27, 2017, 4:07 AM f.k...@mailbox.org <f.k...@mailbox.org> wrote:
> Hi all,
>
> it there something like a phylogenetic circular linear regression or such?
>
> I want to test if the hue (circular 360?) of species differs between two
> lifestyles?
>
> Hope someone can help?
>
> If this is not there please also let me know.
>
> Cheers,
> Franz
>
> _______________________________________________
> 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/
--
Peter D Smits
Postdoctoral Researcher (Finnegan lab)
Integrative Biology
University of California Berkeley
https://psmits.github.io/
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