Re: [R-sig-phylo] Add terminal branches to tree

2017-06-28 Thread David Bapst
No problem. Glad someone other than me could make use of my function!

Cheers,
-Dave

On Tue, Jun 27, 2017 at 4:42 AM, Sergio Ferreira Cardoso
<sergio.ferreira-card...@umontpellier.fr> wrote:
> Hi Dave,
>
> Thanks a lot. It was exactly this I was trying to do.
> Thank you all for your advice.
>
> Cheers,
> Sérgio.
>
> - Mensagem original -
>> De: "David Bapst" <dwba...@gmail.com>
>> Para: "Sergio Ferreira Cardoso" <sergio.ferreira-card...@umontpellier.fr>
>> Cc: "Eliot Miller" <et...@cornell.edu>, "r-sig-phylo" 
>> <r-sig-phylo@r-project.org>
>> Enviadas: Terça-feira, 20 De Junho de 2017 0:11:02
>> Assunto: Re: [R-sig-phylo] Add terminal branches to tree
>
>> Hi Sergio,
>>
>> Sorry for being late to the party, but maybe expandTaxonTree in
>> paleotree does what you're looking for? I wrote it for turning trees
>> of genera into trees of species, with the resulting generic polytomies
>> collapsed or not (in case we know that the genera is paraphyletic).
>>
>> Cheers,
>> -Dave
>>
>> On Mon, Jun 19, 2017 at 9:36 AM, Sergio Ferreira Cardoso
>> <sergio.ferreira-card...@umontpellier.fr> wrote:
>>> Thank you all for your suggestions. I guess the more direct way is to use
>>> Megaptera. I tried and it worked (I added Man cra1, Man cra2, etc.).
>>> However, I wanted it to create a new node that would basically include all
>>> these taxa. I sthere any way to merge all the added species in a new node?
>>> Thank you all, once again.
>>>
>>> 
>>>
>>> De: "Eliot Miller" <et...@cornell.edu>
>>> Para: "Christoph Heibl" <christoph.he...@gmx.net>
>>> Cc: "Liam Revell" <liam.rev...@umb.edu>, "r-sig-phylo"
>>> <r-sig-phylo@r-project.org>, "Sergio Ferreira Cardoso"
>>> <sergio.ferreira-card...@umontpellier.fr>
>>> Enviadas: Segunda-feira, 19 De Junho de 2017 14:40:15
>>> Assunto: Re: [R-sig-phylo] Add terminal branches to tree
>>>
>>> Just to add to the slew of other good options, I have a small package up on
>>> GitHub (https://github.com/eliotmiller/addTaxa/tree/master/R) that is
>>> basically a big loop around Liam's bind.tip. There are examples included
>>> with the package. The main function you'd be interested in is
>>> randomlyAddTaxa(). It works fairly well last I checked, but there are some
>>> limitations and the package is in need of an overhaul. The main limitation
>>> is when two clades (A and B) are sister to one another and you intend to add
>>> a taxon into the clade (A+B); it's currently impossible to generate the
>>> topology (C,(A,B)), even though that's monophyletic and shouldn't be
>>> prohibited. I aim to fix this at some point within the next month or two if
>>> anyone's interested.
>>> Eliot
>>>
>>> On Mon, Jun 19, 2017 at 8:30 AM, Christoph Heibl <christoph.he...@gmx.net>
>>> wrote:
>>>>
>>>> Another possibility would be addSingleTip() and addTips() from the
>>>> megaptera package (https://github.com/heibl/megaptera). The latter function
>>>> can add any number of tips; the loop that Liam mentioned is already build
>>>> into that function. This is potentially very slow, but for your tree size 
>>>> it
>>>> should work. Note that you have to specify the 'tax' argument; it allows 
>>>> you
>>>> to add tips also to internal nodes of higher rank than genera. In your case
>>>> where you have only genera you can create 'tax' easily like this:
>>>>
>>>> ## 'species' is a vector of tip labels that you want to add
>>>> ## will work only if your tip labels are of the form
>>>> "Genus_epithet-or-any-other-string"
>>>> library(megaptera)
>>>> tax <- data.frame(genus = strip.spec(species),
>>>> species = species,
>>>> stringsAsFactors = FALSE)
>>>>
>>>>
>>>>
>>>> Christoph Heibl
>>>> An der Weiherleite 3
>>>> 86633 Neuburg an der Donau
>>>> 08431-53 96 534 (Festnetz)
>>>> 0176-23 86 57 92 (Mobil)
>>>> christoph.he...@gmx.net
>>>>
>>>>
>>>> Am 19.06.2017 um 14:06 schrieb Liam Revell:
>>>>
>>>> > The function add.species.to.genus may do what you want. It adds a single
>>>> > species t

Re: [R-sig-phylo] Add terminal branches to tree

2017-06-27 Thread Sergio Ferreira Cardoso
Hi Dave,

Thanks a lot. It was exactly this I was trying to do.
Thank you all for your advice.

Cheers,
Sérgio.

- Mensagem original -
> De: "David Bapst" <dwba...@gmail.com>
> Para: "Sergio Ferreira Cardoso" <sergio.ferreira-card...@umontpellier.fr>
> Cc: "Eliot Miller" <et...@cornell.edu>, "r-sig-phylo" 
> <r-sig-phylo@r-project.org>
> Enviadas: Terça-feira, 20 De Junho de 2017 0:11:02
> Assunto: Re: [R-sig-phylo] Add terminal branches to tree

> Hi Sergio,
> 
> Sorry for being late to the party, but maybe expandTaxonTree in
> paleotree does what you're looking for? I wrote it for turning trees
> of genera into trees of species, with the resulting generic polytomies
> collapsed or not (in case we know that the genera is paraphyletic).
> 
> Cheers,
> -Dave
> 
> On Mon, Jun 19, 2017 at 9:36 AM, Sergio Ferreira Cardoso
> <sergio.ferreira-card...@umontpellier.fr> wrote:
>> Thank you all for your suggestions. I guess the more direct way is to use
>> Megaptera. I tried and it worked (I added Man cra1, Man cra2, etc.).
>> However, I wanted it to create a new node that would basically include all
>> these taxa. I sthere any way to merge all the added species in a new node?
>> Thank you all, once again.
>>
>> 
>>
>> De: "Eliot Miller" <et...@cornell.edu>
>> Para: "Christoph Heibl" <christoph.he...@gmx.net>
>> Cc: "Liam Revell" <liam.rev...@umb.edu>, "r-sig-phylo"
>> <r-sig-phylo@r-project.org>, "Sergio Ferreira Cardoso"
>> <sergio.ferreira-card...@umontpellier.fr>
>> Enviadas: Segunda-feira, 19 De Junho de 2017 14:40:15
>> Assunto: Re: [R-sig-phylo] Add terminal branches to tree
>>
>> Just to add to the slew of other good options, I have a small package up on
>> GitHub (https://github.com/eliotmiller/addTaxa/tree/master/R) that is
>> basically a big loop around Liam's bind.tip. There are examples included
>> with the package. The main function you'd be interested in is
>> randomlyAddTaxa(). It works fairly well last I checked, but there are some
>> limitations and the package is in need of an overhaul. The main limitation
>> is when two clades (A and B) are sister to one another and you intend to add
>> a taxon into the clade (A+B); it's currently impossible to generate the
>> topology (C,(A,B)), even though that's monophyletic and shouldn't be
>> prohibited. I aim to fix this at some point within the next month or two if
>> anyone's interested.
>> Eliot
>>
>> On Mon, Jun 19, 2017 at 8:30 AM, Christoph Heibl <christoph.he...@gmx.net>
>> wrote:
>>>
>>> Another possibility would be addSingleTip() and addTips() from the
>>> megaptera package (https://github.com/heibl/megaptera). The latter function
>>> can add any number of tips; the loop that Liam mentioned is already build
>>> into that function. This is potentially very slow, but for your tree size it
>>> should work. Note that you have to specify the 'tax' argument; it allows you
>>> to add tips also to internal nodes of higher rank than genera. In your case
>>> where you have only genera you can create 'tax' easily like this:
>>>
>>> ## 'species' is a vector of tip labels that you want to add
>>> ## will work only if your tip labels are of the form
>>> "Genus_epithet-or-any-other-string"
>>> library(megaptera)
>>> tax <- data.frame(genus = strip.spec(species),
>>> species = species,
>>> stringsAsFactors = FALSE)
>>>
>>>
>>>
>>> Christoph Heibl
>>> An der Weiherleite 3
>>> 86633 Neuburg an der Donau
>>> 08431-53 96 534 (Festnetz)
>>> 0176-23 86 57 92 (Mobil)
>>> christoph.he...@gmx.net
>>>
>>>
>>> Am 19.06.2017 um 14:06 schrieb Liam Revell:
>>>
>>> > The function add.species.to.genus may do what you want. It adds a single
>>> > species to the group defined by the MRCA of members of a genus, according 
>>> > to
>>> > multiple criteria (randomly and so on). It can add only one species at a
>>> > time, so you will need to write a for loop or something to iterate over 
>>> > the
>>> > species that you‚d like to add.
>>> >
>>> > --
>>> > Liam J. Revell, Associate Professor of Biology
>>> > University of Massachusetts Boston
>>> > web: http://faculty.umb.edu/liam.revell
>>> > email: liam.rev...@umb.ed

Re: [R-sig-phylo] Add terminal branches to tree

2017-06-19 Thread David Bapst
Hi Sergio,

Sorry for being late to the party, but maybe expandTaxonTree in
paleotree does what you're looking for? I wrote it for turning trees
of genera into trees of species, with the resulting generic polytomies
collapsed or not (in case we know that the genera is paraphyletic).

Cheers,
-Dave

On Mon, Jun 19, 2017 at 9:36 AM, Sergio Ferreira Cardoso
<sergio.ferreira-card...@umontpellier.fr> wrote:
> Thank you all for your suggestions. I guess the more direct way is to use
> Megaptera. I tried and it worked (I added Man cra1, Man cra2, etc.).
> However, I wanted it to create a new node that would basically include all
> these taxa. I sthere any way to merge all the added species in a new node?
> Thank you all, once again.
>
> 
>
> De: "Eliot Miller" <et...@cornell.edu>
> Para: "Christoph Heibl" <christoph.he...@gmx.net>
> Cc: "Liam Revell" <liam.rev...@umb.edu>, "r-sig-phylo"
> <r-sig-phylo@r-project.org>, "Sergio Ferreira Cardoso"
> <sergio.ferreira-card...@umontpellier.fr>
> Enviadas: Segunda-feira, 19 De Junho de 2017 14:40:15
> Assunto: Re: [R-sig-phylo] Add terminal branches to tree
>
> Just to add to the slew of other good options, I have a small package up on
> GitHub (https://github.com/eliotmiller/addTaxa/tree/master/R) that is
> basically a big loop around Liam's bind.tip. There are examples included
> with the package. The main function you'd be interested in is
> randomlyAddTaxa(). It works fairly well last I checked, but there are some
> limitations and the package is in need of an overhaul. The main limitation
> is when two clades (A and B) are sister to one another and you intend to add
> a taxon into the clade (A+B); it's currently impossible to generate the
> topology (C,(A,B)), even though that's monophyletic and shouldn't be
> prohibited. I aim to fix this at some point within the next month or two if
> anyone's interested.
> Eliot
>
> On Mon, Jun 19, 2017 at 8:30 AM, Christoph Heibl <christoph.he...@gmx.net>
> wrote:
>>
>> Another possibility would be addSingleTip() and addTips() from the
>> megaptera package (https://github.com/heibl/megaptera). The latter function
>> can add any number of tips; the loop that Liam mentioned is already build
>> into that function. This is potentially very slow, but for your tree size it
>> should work. Note that you have to specify the 'tax' argument; it allows you
>> to add tips also to internal nodes of higher rank than genera. In your case
>> where you have only genera you can create 'tax' easily like this:
>>
>> ## 'species' is a vector of tip labels that you want to add
>> ## will work only if your tip labels are of the form
>> "Genus_epithet-or-any-other-string"
>> library(megaptera)
>> tax <- data.frame(genus = strip.spec(species),
>> species = species,
>> stringsAsFactors = FALSE)
>>
>>
>>
>> Christoph Heibl
>> An der Weiherleite 3
>> 86633 Neuburg an der Donau
>> 08431-53 96 534 (Festnetz)
>> 0176-23 86 57 92 (Mobil)
>> christoph.he...@gmx.net
>>
>>
>> Am 19.06.2017 um 14:06 schrieb Liam Revell:
>>
>> > The function add.species.to.genus may do what you want. It adds a single
>> > species to the group defined by the MRCA of members of a genus, according 
>> > to
>> > multiple criteria (randomly and so on). It can add only one species at a
>> > time, so you will need to write a for loop or something to iterate over the
>> > species that you‚d like to add.
>> >
>> > --
>> > Liam J. Revell, Associate Professor of Biology
>> > University of Massachusetts Boston
>> > web: http://faculty.umb.edu/liam.revell
>> > email: liam.rev...@umb.edu
>> >
>> > Sent from my Windows 10 phone
>> >
>> > From: Sergio Ferreira
>> > Cardoso<mailto:sergio.ferreira-card...@umontpellier.fr>
>> > Sent: Monday, June 19, 2017 6:58 AM
>> > To: r-sig-phylo<mailto:r-sig-phylo@r-project.org>
>> > Subject: [R-sig-phylo] Add terminal branches to tree
>> >
>> > Hello all,
>> >
>> > I'm using the package 'phytools' to try to add terminal branches to a
>> > tree (attached). I tried to use add.everywhere function to add terminal
>> > branches. I have 167 terminal taxa inside each of the 7 genera on my tree.
>> > Basically, I just wanted to add some dozens of specimens to the end of each
>> > branch, but I don't find a way to do it. Is there any tool that would allow
>> > me to do this? Like adding 30 

Re: [R-sig-phylo] Add terminal branches to tree

2017-06-19 Thread Sergio Ferreira Cardoso
Thank you all for your suggestions. I guess the more direct way is to use 
Megaptera. I tried and it worked (I added Man cra1, Man cra2, etc.). However, I 
wanted it to create a new node that would basically include all these taxa. I 
sthere any way to merge all the added species in a new node? 
Thank you all, once again. 

> De: "Eliot Miller" <et...@cornell.edu>
> Para: "Christoph Heibl" <christoph.he...@gmx.net>
> Cc: "Liam Revell" <liam.rev...@umb.edu>, "r-sig-phylo"
> <r-sig-phylo@r-project.org>, "Sergio Ferreira Cardoso"
> <sergio.ferreira-card...@umontpellier.fr>
> Enviadas: Segunda-feira, 19 De Junho de 2017 14:40:15
> Assunto: Re: [R-sig-phylo] Add terminal branches to tree

> Just to add to the slew of other good options, I have a small package up on
> GitHub ( https://github.com/eliotmiller/addTaxa/tree/master/R ) that is
> basically a big loop around Liam's bind.tip. There are examples included with
> the package. The main function you'd be interested in is randomlyAddTaxa(). It
> works fairly well last I checked, but there are some limitations and the
> package is in need of an overhaul. The main limitation is when two clades (A
> and B) are sister to one another and you intend to add a taxon into the clade
> (A+B); it's currently impossible to generate the topology (C,(A,B)), even
> though that's monophyletic and shouldn't be prohibited. I aim to fix this at
> some point within the next month or two if anyone's interested.
> Eliot

> On Mon, Jun 19, 2017 at 8:30 AM, Christoph Heibl < christoph.he...@gmx.net >
> wrote:

>> Another possibility would be addSingleTip() and addTips() from the megaptera
>> package ( https://github.com/heibl/megaptera ). The latter function can add 
>> any
>> number of tips; the loop that Liam mentioned is already build into that
>> function. This is potentially very slow, but for your tree size it should 
>> work.
>> Note that you have to specify the 'tax' argument; it allows you to add tips
>> also to internal nodes of higher rank than genera. In your case where you 
>> have
>> only genera you can create 'tax' easily like this:

>> ## 'species' is a vector of tip labels that you want to add
>> ## will work only if your tip labels are of the form
>> "Genus_epithet-or-any-other-string"
>> library(megaptera)
>> tax <- data.frame(genus = strip.spec(species),
>> species = species,
>> stringsAsFactors = FALSE)

>> Christoph Heibl
>> An der Weiherleite 3
>> 86633 Neuburg an der Donau
>> 08431-53 96 534 (Festnetz)
>> 0176-23 86 57 92 (Mobil)
>> christoph.he...@gmx.net

>> Am 19.06.2017 um 14:06 schrieb Liam Revell:

>>> The function add.species.to.genus may do what you want. It adds a single 
>>> species
>>> to the group defined by the MRCA of members of a genus, according to 
>>> multiple
>>> criteria (randomly and so on). It can add only one species at a time, so you
>>> will need to write a for loop or something to iterate over the species that
>> > you‚d like to add.

>> > --
>> > Liam J. Revell, Associate Professor of Biology
>> > University of Massachusetts Boston
>> > web: http://faculty.umb.edu/liam.revell
>> > email: liam.rev...@umb.edu

>> > Sent from my Windows 10 phone

>> > From: Sergio Ferreira Cardoso> > sergio.ferreira-card...@umontpellier.fr >
>> > Sent: Monday, June 19, 2017 6:58 AM
>> > To: r-sig-phylo
>> > Subject: [R-sig-phylo] Add terminal branches to tree

>> > Hello all,

>>> I'm using the package 'phytools' to try to add terminal branches to a tree
>>> (attached). I tried to use add.everywhere function to add terminal 
>>> branches. I
>>> have 167 terminal taxa inside each of the 7 genera on my tree. Basically, I
>>> just wanted to add some dozens of specimens to the end of each branch, but I
>>> don't find a way to do it. Is there any tool that would allow me to do this?
>> > Like adding 30 branches to 'Phal', adding 25 to 'Phat', etc.

>> > Thanks in advance.



>> > --
>> > Institut des Sciences de l'Evolution
>> > UMR5554, CNRS, IRD, EPHE
>> > Université de Montpellier
>> > Place Eugène Bataillon
>> > 34095 Montpellier Cedex 05
>> > France
>> > Email: sergio.ferreira-card...@umontpellier.fr
>> > Tel: +33 (4 ) 67 14 46 52

>> > [[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/

>> [[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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Re: [R-sig-phylo] Add terminal branches to tree

2017-06-19 Thread Eliot Miller
Just to add to the slew of other good options, I have a small package up on
GitHub (https://github.com/eliotmiller/addTaxa/tree/master/R) that is
basically a big loop around Liam's bind.tip. There are examples included
with the package. The main function you'd be interested in is
randomlyAddTaxa(). It works fairly well last I checked, but there are some
limitations and the package is in need of an overhaul. The main limitation
is when two clades (A and B) are sister to one another and you intend to
add a taxon into the clade (A+B); it's currently impossible to generate the
topology (C,(A,B)), even though that's monophyletic and shouldn't be
prohibited. I aim to fix this at some point within the next month or two if
anyone's interested.

Eliot

On Mon, Jun 19, 2017 at 8:30 AM, Christoph Heibl <christoph.he...@gmx.net>
wrote:

> Another possibility would be addSingleTip() and addTips() from the
> megaptera package (https://github.com/heibl/megaptera). The latter
> function can add any number of tips; the loop that Liam mentioned is
> already build into that function. This is potentially very slow, but for
> your tree size it should work. Note that you have to specify the 'tax'
> argument; it allows you to add tips also to internal nodes of higher rank
> than genera. In your case where you have only genera you can create 'tax'
> easily like this:
>
> ## 'species' is a vector of tip labels that you want to add
> ## will work only if your tip labels are of the form
> "Genus_epithet-or-any-other-string"
> library(megaptera)
> tax <- data.frame(genus = strip.spec(species),
> species = species,
> stringsAsFactors = FALSE)
>
>
>
> Christoph Heibl
> An der Weiherleite 3
> 86633 Neuburg an der Donau
> 08431-53 96 534 (Festnetz)
> 0176-23 86 57 92 (Mobil)
> christoph.he...@gmx.net
>
>
> Am 19.06.2017 um 14:06 schrieb Liam Revell:
>
> > The function add.species.to.genus may do what you want. It adds a single
> species to the group defined by the MRCA of members of a genus, according
> to multiple criteria (randomly and so on). It can add only one species at a
> time, so you will need to write a for loop or something to iterate over the
> species that you‚d like to add.
> >
> > --
> > Liam J. Revell, Associate Professor of Biology
> > University of Massachusetts Boston
> > web: http://faculty.umb.edu/liam.revell
> > email: liam.rev...@umb.edu
> >
> > Sent from my Windows 10 phone
> >
> > From: Sergio Ferreira Cardoso<mailto:sergio.
> ferreira-card...@umontpellier.fr>
> > Sent: Monday, June 19, 2017 6:58 AM
> > To: r-sig-phylo<mailto:r-sig-phylo@r-project.org>
> > Subject: [R-sig-phylo] Add terminal branches to tree
> >
> > Hello all,
> >
> > I'm using the package 'phytools' to try to add terminal branches to a
> tree (attached). I tried to use add.everywhere function to add terminal
> branches. I have 167 terminal taxa inside each of the 7 genera on my tree.
> Basically, I just wanted to add some dozens of specimens to the end of each
> branch, but I don't find a way to do it. Is there any tool that would allow
> me to do this? Like adding 30 branches to 'Phal', adding 25 to 'Phat', etc.
> >
> > Thanks in advance.
> >
> >
> >
> > --
> > Institut des Sciences de l'Evolution
> > UMR5554, CNRS, IRD, EPHE
> > Université de Montpellier
> > Place Eugène Bataillon
> > 34095 Montpellier Cedex 05
> > France
> > Email: sergio.ferreira-card...@umontpellier.fr
> > Tel: +33 (4 ) 67 14 46 52
> >
> >   [[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]]
>
>
> ___
> 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]]

___
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Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/

Re: [R-sig-phylo] Add terminal branches to tree

2017-06-19 Thread Christoph Heibl
Another possibility would be addSingleTip() and addTips() from the megaptera 
package (https://github.com/heibl/megaptera). The latter function can add any 
number of tips; the loop that Liam mentioned is already build into that 
function. This is potentially very slow, but for your tree size it should work. 
Note that you have to specify the 'tax' argument; it allows you to add tips 
also to internal nodes of higher rank than genera. In your case where you have 
only genera you can create 'tax' easily like this:

## 'species' is a vector of tip labels that you want to add
## will work only if your tip labels are of the form 
"Genus_epithet-or-any-other-string"
library(megaptera)
tax <- data.frame(genus = strip.spec(species),
species = species,
stringsAsFactors = FALSE)



Christoph Heibl
An der Weiherleite 3
86633 Neuburg an der Donau  
08431-53 96 534 (Festnetz)
0176-23 86 57 92 (Mobil)
christoph.he...@gmx.net


Am 19.06.2017 um 14:06 schrieb Liam Revell:

> The function add.species.to.genus may do what you want. It adds a single 
> species to the group defined by the MRCA of members of a genus, according to 
> multiple criteria (randomly and so on). It can add only one species at a 
> time, so you will need to write a for loop or something to iterate over the 
> species that you�d like to add.
> 
> --
> Liam J. Revell, Associate Professor of Biology
> University of Massachusetts Boston
> web: http://faculty.umb.edu/liam.revell
> email: liam.rev...@umb.edu
> 
> Sent from my Windows 10 phone
> 
> From: Sergio Ferreira Cardoso<mailto:sergio.ferreira-card...@umontpellier.fr>
> Sent: Monday, June 19, 2017 6:58 AM
> To: r-sig-phylo<mailto:r-sig-phylo@r-project.org>
> Subject: [R-sig-phylo] Add terminal branches to tree
> 
> Hello all,
> 
> I'm using the package 'phytools' to try to add terminal branches to a tree 
> (attached). I tried to use add.everywhere function to add terminal branches. 
> I have 167 terminal taxa inside each of the 7 genera on my tree. Basically, I 
> just wanted to add some dozens of specimens to the end of each branch, but I 
> don't find a way to do it. Is there any tool that would allow me to do this? 
> Like adding 30 branches to 'Phal', adding 25 to 'Phat', etc.
> 
> Thanks in advance.
> 
> 
> 
> --
> Institut des Sciences de l'Evolution
> UMR5554, CNRS, IRD, EPHE
> Universit� de Montpellier
> Place Eug�ne Bataillon
> 34095 Montpellier Cedex 05
> France
> Email: sergio.ferreira-card...@umontpellier.fr
> Tel: +33 (4 ) 67 14 46 52
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Re: [R-sig-phylo] Add terminal branches to tree

2017-06-19 Thread Liam Revell
The function add.species.to.genus may do what you want. It adds a single 
species to the group defined by the MRCA of members of a genus, according to 
multiple criteria (randomly and so on). It can add only one species at a time, 
so you will need to write a for loop or something to iterate over the species 
that you�d like to add.

--
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell
email: liam.rev...@umb.edu

Sent from my Windows 10 phone

From: Sergio Ferreira Cardoso<mailto:sergio.ferreira-card...@umontpellier.fr>
Sent: Monday, June 19, 2017 6:58 AM
To: r-sig-phylo<mailto:r-sig-phylo@r-project.org>
Subject: [R-sig-phylo] Add terminal branches to tree

Hello all,

I'm using the package 'phytools' to try to add terminal branches to a tree 
(attached). I tried to use add.everywhere function to add terminal branches. I 
have 167 terminal taxa inside each of the 7 genera on my tree. Basically, I 
just wanted to add some dozens of specimens to the end of each branch, but I 
don't find a way to do it. Is there any tool that would allow me to do this? 
Like adding 30 branches to 'Phal', adding 25 to 'Phat', etc.

Thanks in advance.



--
Institut des Sciences de l'Evolution
UMR5554, CNRS, IRD, EPHE
Universit� de Montpellier
Place Eug�ne Bataillon
34095 Montpellier Cedex 05
France
Email: sergio.ferreira-card...@umontpellier.fr
Tel: +33 (4 ) 67 14 46 52

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Re: [R-sig-phylo] Add terminal branches to tree

2017-06-19 Thread f.k...@mailbox.org
Hi Sergio, 

try ‘bind.tip' and just make a loop to add more. Or ‘bind.tree’ if you want to 
add a clade.

Cheers, 
Franz

> On 19 Jun 2017, at 13:58, Sergio Ferreira Cardoso 
>  wrote:
> 
> Hello all,
> 
> I'm using the package 'phytools' to try to add terminal branches to a tree 
> (attached). I tried to use add.everywhere function to add terminal branches. 
> I have 167 terminal taxa inside each of the 7 genera on my tree. Basically, I 
> just wanted to add some dozens of specimens to the end of each branch, but I 
> don't find a way to do it. Is there any tool that would allow me to do this? 
> Like adding 30 branches to 'Phal', adding 25 to 'Phat', etc.
> 
> Thanks in advance.
> 
> 
> 
> -- 
> Institut des Sciences de l'Evolution
> UMR5554, CNRS, IRD, EPHE
> Université de Montpellier
> Place Eugène Bataillon
> 34095 Montpellier Cedex 05
> France
> Email: sergio.ferreira-card...@umontpellier.fr
> Tel: +33 (4 ) 67 14 46 52 
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[R-sig-phylo] Add terminal branches to tree

2017-06-19 Thread Sergio Ferreira Cardoso
Hello all, 

I'm using the package 'phytools' to try to add terminal branches to a tree 
(attached). I tried to use add.everywhere function to add terminal branches. I 
have 167 terminal taxa inside each of the 7 genera on my tree. Basically, I 
just wanted to add some dozens of specimens to the end of each branch, but I 
don't find a way to do it. Is there any tool that would allow me to do this? 
Like adding 30 branches to 'Phal', adding 25 to 'Phat', etc. 

Thanks in advance. 



-- 
Institut des Sciences de l'Evolution 
UMR5554, CNRS, IRD, EPHE 
Université de Montpellier 
Place Eugène Bataillon 
34095 Montpellier Cedex 05 
France 
Email: sergio.ferreira-card...@umontpellier.fr 
Tel: +33 (4 ) 67 14 46 52 
#NEXUS

BEGIN TREES;
Title 'Pango_dist_1';
ID 015c8c71a66c9;
LINK Taxa = Untitled_Block_of_Taxa;
TRANSLATE
[0] 1 Manc,
[1] 2 Smug,
[2] 3 Smut,
[3] 4 Phat,
[4] 5 Phal,
[5] 6 Manj,
[6] 7 Manp;
TREE 'Tree_pangos_dist1' = 
((1:2,(6:1,7:1):1):1,((2:1,3:1):1,(4:1,5:1):1):1):1[% ] [% ] [%  setBetweenBits 
= selected ];
END;



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