Re: [R-sig-phylo] dating cladograms in R

[Fábio Machado]

Dear Nicolai,

I don’t have branch lengths, just the topology. Is there a way to estimate a 
posteriori the branch-lengths using molecular data for most, but not all 
species? In any way, I was aware of chronos function but I haven’t seen it used 
in the literature and wondered if there was any particular reason for that. 

I will look into O’Meara’s package for the time being,

Thanks to you and to Joseph for the reply,

Fabio

> On May 17, 2017, at 10:26, Nürk, Nicolai  
> wrote:
> 
> Dear Fabio,
> 
> you might also use the chronos function in ape, which demands a data frame 
> with calibrations (if you have information from published trees that could be 
> use to calibrate your tree; cf. email from Joe), and which assumes that you 
> have a phylogenetic tree whose branch lengths are in number of substitution 
> per sites.
> 
> 
> library(ape)
> 
> #make calibration df (interactive: you can click on a node on the tree and 
> specify the min/max age)
> cal <- makeChronosCalib(your.phy, node = "root", age.min = 1, age.max = 
> age.min, interactive = TRUE, soft.bounds = FALSE)
> 
> #calculate the chronogram e.g. using a strict clock model (better check 
> ?chronos)
> phy.ultra <- chronos(your.phy, lambda = 1, model = "correlated", calibration 
> = cal)
> 
> 
> HTH,
> nmn
> ---
> Dr. Nicolai M. Nürk
> 
> Institute of Plant Systematics
> Department of Biology 
> University of Bayreuth
> Universitätsstraße 30
> 95447 Bayreuth
> 
> 
> On 17 May 2017, at 14:26, Joseph W. Brown wrote:
> 
>> Fabio you might have luck with Brian O'Meara's datelife: 
>> https://github.com/phylotastic/datelife 
>>  
>> > > Essentially it grabs dates from 
>> published trees and applies it to your own.
>> 
>> Brian can provide more details. (^_<)〜☆
>> 
>> HTH.
>> JWB
>> 
>> Joseph W. Brown
>> Post-doctoral Researcher, Smith Laboratory
>> University of Michigan
>> Department of Ecology & Evolutionary Biology
>> Room 2071, Kraus Natural Sciences Building
>> Ann Arbor MI 48109-1079
>> josep...@umich.edu 
>> 
>> 
>> 
>>> On 17 May, 2017, at 08:12, Fábio Machado  wrote:
>>> 
>>> Dear community,
>>> 
>>> I was wondering if there is any methodology implemented in R to date 
>>> cladograms, either using only the tree topology or using additional 
>>> molecular data. If not, what would be the best solution to obtain a dated 
>>> phylogeny, given that I have only a tree topology to work with.
>>> 
>>> Best regards,
>>> 
>>> Fabio Andrade Machado
>>> Becario Postdoctoral - CONICET
>>> Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”
>>> División de Mastozoología, 
>>> Buenos Aires, Av. Ángel Gallardo 470 (C1405DJR)
>>> Argentina
>>> f.mach...@usp.br  ; macfa...@gmail.com 
>>>  
>>> +55 11 982631029
>>> skype: fabio_a_machado
>>> 
>>> Lattes: http://lattes.cnpq.br/3673327633303737 
>>> 
>>> Google Scholar: http://scholar.google.com/citations?hl=en=2l6-VrQJ 
>>> 
>>> 
>>> [[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/
>> 
>> 
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>> 
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>> 
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>> 
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>> 

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Re: [R-sig-phylo] dating cladograms in R

[Nürk , Nicolai]

Dear Fabio,

you might also use the chronos function in ape, which demands a data frame with 
calibrations (if you have information from published trees that could be use to 
calibrate your tree; cf. email from Joe), and which assumes that you have a 
phylogenetic tree whose branch lengths are in number of substitution per sites.


library(ape)

#make calibration df (interactive: you can click on a node on the tree and 
specify the min/max age)
cal <- makeChronosCalib(your.phy, node = "root", age.min = 1, age.max = 
age.min, interactive = TRUE, soft.bounds = FALSE)

#calculate the chronogram e.g. using a strict clock model (better check 
?chronos)
phy.ultra <- chronos(your.phy, lambda = 1, model = "correlated", calibration = 
cal)


HTH,
nmn
---
Dr. Nicolai M. Nürk

Institute of Plant Systematics
Department of Biology
University of Bayreuth
Universitätsstraße 30
95447 Bayreuth


On 17 May 2017, at 14:26, Joseph W. Brown wrote:

Fabio you might have luck with Brian O'Meara's datelife: 
https://github.com/phylotastic/datelife 
 Essentially it grabs dates from 
published trees and applies it to your own.

Brian can provide more details. (^_<)〜☆

HTH.
JWB

Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
University of Michigan
Department of Ecology & Evolutionary Biology
Room 2071, Kraus Natural Sciences Building
Ann Arbor MI 48109-1079
josep...@umich.edu



On 17 May, 2017, at 08:12, Fábio Machado  wrote:

Dear community,

I was wondering if there is any methodology implemented in R to date 
cladograms, either using only the tree topology or using additional molecular 
data. If not, what would be the best solution to obtain a dated phylogeny, 
given that I have only a tree topology to work with.

Best regards,

Fabio Andrade Machado
Becario Postdoctoral - CONICET
Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”
División de Mastozoología,
Buenos Aires, Av. Ángel Gallardo 470 (C1405DJR)
Argentina
f.mach...@usp.br  ; macfa...@gmail.com 

+55 11 982631029
skype: fabio_a_machado

Lattes: http://lattes.cnpq.br/3673327633303737 

Google Scholar: http://scholar.google.com/citations?hl=en=2l6-VrQJ 


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Re: [R-sig-phylo] dating cladograms in R

[Joseph W. Brown]

Fabio you might have luck with Brian O'Meara's datelife: 
https://github.com/phylotastic/datelife 
 Essentially it grabs dates from 
published trees and applies it to your own.

Brian can provide more details. (^_<)〜☆

HTH.
JWB

Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
University of Michigan
Department of Ecology & Evolutionary Biology
Room 2071, Kraus Natural Sciences Building
Ann Arbor MI 48109-1079
josep...@umich.edu



> On 17 May, 2017, at 08:12, Fábio Machado  wrote:
> 
> Dear community,
> 
> I was wondering if there is any methodology implemented in R to date 
> cladograms, either using only the tree topology or using additional molecular 
> data. If not, what would be the best solution to obtain a dated phylogeny, 
> given that I have only a tree topology to work with.
> 
> Best regards,
> 
> Fabio Andrade Machado
> Becario Postdoctoral - CONICET
> Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”
> División de Mastozoología, 
> Buenos Aires, Av. Ángel Gallardo 470 (C1405DJR)
> Argentina
> f.mach...@usp.br  ; macfa...@gmail.com 
>  
> +55 11 982631029
> skype: fabio_a_machado
> 
> Lattes: http://lattes.cnpq.br/3673327633303737 
> 
> Google Scholar: http://scholar.google.com/citations?hl=en=2l6-VrQJ 
> 
> 
>   [[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/


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