Re: [R-sig-phylo] Force read.nexus() to return a multiPhylo object, even if there is only one tree

2016-12-28 Thread Liam J. Revell 

Ahhh. I see. I missed the part in Yan's original email about the names.

All the best, Liam

Liam J. Revell, Associate 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 12/28/2016 6:45 AM, Emmanuel Paradis wrote:

Hi Liam,

Actually, this can be done with c():

R> tr <- rtree(10)
R> c(tr)
1 phylogenetic trees

With respect to Yan's initial query, this will not restore the tree name
from the NEXUS file which is (currently) lost if there is a single tree.

Best,

Emmanuel

Le 28/12/2016 à 03:11, Liam J. Revell a écrit :

Hi Yan.

In case it is useful I just pushed an update to phytools in which I have
added an as.multiPhylo method for objects of class "phylo". This will
also return an object of class "multiPhylo" if that is already the
object class. This means that:

obj<-as.multiPhylo(read.nexus(...))

in which ... are the arguments to read.nexus, will return an object of
class "multiPhylo" with length 1 if the file contains only one tree -
but will also return an object of class "multiPhylo" if the file has 2
or more trees.

To get this one needs to install phytools from GitHub using devtools:

library(devtools)
install_github("liamrevell/phytools")

All the best, Liam

Liam J. Revell, Associate 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 12/27/2016 5:11 PM, Yan Wong wrote:


On 27 Dec 2016, at 22:08, Emmanuel Paradis 
wrote:


Hi Yan,

Yes, you are right: this modification can be done. In the meantime,
you can fix the code with:

fix(read.nexus)

Find this line (#117):

   if (Ntree == 1) {

and change it to:

   if (FALSE) {

save and close. Tell me if you still have problem.


Yes, that works fine. Thanks a lot.

Yan
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Re: [R-sig-phylo] Force read.nexus() to return a multiPhylo object, even if there is only one tree

2016-12-28 Thread Emmanuel Paradis 

Hi Liam,

Actually, this can be done with c():

R> tr <- rtree(10)
R> c(tr)
1 phylogenetic trees

With respect to Yan's initial query, this will not restore the tree name 
from the NEXUS file which is (currently) lost if there is a single tree.


Best,

Emmanuel

Le 28/12/2016 à 03:11, Liam J. Revell a écrit :

Hi Yan.

In case it is useful I just pushed an update to phytools in which I have
added an as.multiPhylo method for objects of class "phylo". This will
also return an object of class "multiPhylo" if that is already the
object class. This means that:

obj<-as.multiPhylo(read.nexus(...))

in which ... are the arguments to read.nexus, will return an object of
class "multiPhylo" with length 1 if the file contains only one tree -
but will also return an object of class "multiPhylo" if the file has 2
or more trees.

To get this one needs to install phytools from GitHub using devtools:

library(devtools)
install_github("liamrevell/phytools")

All the best, Liam

Liam J. Revell, Associate 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 12/27/2016 5:11 PM, Yan Wong wrote:


On 27 Dec 2016, at 22:08, Emmanuel Paradis 
wrote:


Hi Yan,

Yes, you are right: this modification can be done. In the meantime,
you can fix the code with:

fix(read.nexus)

Find this line (#117):

   if (Ntree == 1) {

and change it to:

   if (FALSE) {

save and close. Tell me if you still have problem.


Yes, that works fine. Thanks a lot.

Yan
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Re: [R-sig-phylo] Force read.nexus() to return a multiPhylo object, even if there is only one tree

2016-12-27 Thread Liam J. Revell 

Hi Yan.

In case it is useful I just pushed an update to phytools in which I have 
added an as.multiPhylo method for objects of class "phylo". This will 
also return an object of class "multiPhylo" if that is already the 
object class. This means that:


obj<-as.multiPhylo(read.nexus(...))

in which ... are the arguments to read.nexus, will return an object of 
class "multiPhylo" with length 1 if the file contains only one tree - 
but will also return an object of class "multiPhylo" if the file has 2 
or more trees.


To get this one needs to install phytools from GitHub using devtools:

library(devtools)
install_github("liamrevell/phytools")

All the best, Liam

Liam J. Revell, Associate 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 12/27/2016 5:11 PM, Yan Wong wrote:


On 27 Dec 2016, at 22:08, Emmanuel Paradis  wrote:


Hi Yan,

Yes, you are right: this modification can be done. In the meantime, you can fix 
the code with:

fix(read.nexus)

Find this line (#117):

   if (Ntree == 1) {

and change it to:

   if (FALSE) {

save and close. Tell me if you still have problem.


Yes, that works fine. Thanks a lot.

Yan
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Re: [R-sig-phylo] Force read.nexus() to return a multiPhylo object, even if there is only one tree

2016-12-27 Thread Yan Wong 

On 27 Dec 2016, at 22:08, Emmanuel Paradis  wrote:

> Hi Yan,
> 
> Yes, you are right: this modification can be done. In the meantime, you can 
> fix the code with:
> 
> fix(read.nexus)
> 
> Find this line (#117):
> 
>if (Ntree == 1) {
> 
> and change it to:
> 
>if (FALSE) {
> 
> save and close. Tell me if you still have problem.

Yes, that works fine. Thanks a lot.

Yan
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Re: [R-sig-phylo] Force read.nexus() to return a multiPhylo object, even if there is only one tree

2016-12-27 Thread Emmanuel Paradis 

Hi Yan,

Yes, you are right: this modification can be done. In the meantime, you 
can fix the code with:


fix(read.nexus)

Find this line (#117):

if (Ntree == 1) {

and change it to:

if (FALSE) {

save and close. Tell me if you still have problem.

Best,

Emmanuel

Le 27/12/2016 à 21:15, Yan Wong a écrit :

Hi

I’m doing some analysis in which I produce a variable number of phylogenetic 
trees with the same tips in a nexus file, then import them into R for analysis 
(these are trees along a genome). The name of each tree is meaningful (it is a 
position along the genome). However, in a few simulations, the nexus file has 
only a single tree in it. In this case, read.nexus returns not a multiPhylo 
object, but a single tree, with the name of the tree lost. I wonder if it would 
be sensible to have a force.multi option to read.nexus(), by default set to 
FALSE (to retain compatibility), but which, if set to TRUE, returns a 
multiPhylo object even if there is only one tree in the file?

Yan
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Pour nous remonter une erreur de filtrage, veuillez vous rendre ici : 
http://f.security-mail.net/407pvJ9zSVE




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