Re: [R-sig-phylo] new testing version of ape

2016-02-26 Thread Emmanuel Paradis 

Hi Klaus,

Le 22/02/2016 21:17, Klaus Schliep a écrit :

Hi Emmanuel,
agree looks cool. When do you want to push the new version to CRAN?


Nothing's scheduled for the moment. I want to let colleagues test it.

Best,

Emmanuel


Newest phangorn development has now a as.AAbin.phyDat function and
dist.ml  has transition rate matrices for amino acids.
Does anybody know how to set .travis.yaml on github to install ape from
Emmanuel's repository instead of CRAN server?
Cheers,
Klaus

On Mon, Feb 22, 2016 at 5:37 AM, Thibaut Jombart
> wrote:

Hi Emmanuel,

this looks really cool - especially the new AAbin class. Looking
forward to playing with the new version!

Best
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology
Imperial College London
https://sites.google.com/site/thibautjombart/
https://github.com/thibautjombart
Twitter: @TeebzR 

On 22 February 2016 at 09:16, Emmanuel Paradis
>
wrote:

 > Dear all,
 >
 > A new testing version of ape (3.4-0.3) is available. It includes
 > three main new features:
 >
 > - A new data class, "AAbin", to store amino acid sequences; there are
 > eleven new functions to generate and manipulate them including
 > translation from DNA.
 >
 > - The function checkAlignment does some diagnostics on a DNA
alignment.
 >
 > - Some extra plotting functions built on ape's basic plotting
functions
 > (plot.phylo, nodelabels, phydataplot, ring) for a specific task.
For the
 > moment, there are two such functions: drawSupportOnEdges() and
 > plotBreakLongEdges().
 >
 > Information on the new functions can be found at:
 >
 > http://ape-package.ird.fr/NEWS
 >
 > And instructions on how to get and install the testing version here:
 >
 > http://ape-package.ird.fr/ape_installation.html#versions
 >
 > A Windows version is available.
 >
 > Best,
 >
 > Emmanuel
 >
 > ___
 > 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/




--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston



___
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/

Re: [R-sig-phylo] new testing version of ape

2016-02-22 Thread Klaus Schliep 
Hi Emmanuel,
agree looks cool. When do you want to push the new version to CRAN? Newest
phangorn development has now a as.AAbin.phyDat function and dist.ml has
transition rate matrices for amino acids.
Does anybody know how to set .travis.yaml on github to install ape from
Emmanuel's repository instead of CRAN server?
Cheers,
Klaus

On Mon, Feb 22, 2016 at 5:37 AM, Thibaut Jombart 
wrote:

> Hi Emmanuel,
>
> this looks really cool - especially the new AAbin class. Looking forward to
> playing with the new version!
>
> Best
> Thibaut
>
>
> --
> Dr Thibaut Jombart
> Lecturer, Department of Infectious Disease Epidemiology
> Imperial College London
> https://sites.google.com/site/thibautjombart/
> https://github.com/thibautjombart
> Twitter: @TeebzR 
>
> On 22 February 2016 at 09:16, Emmanuel Paradis 
> wrote:
>
> > Dear all,
> >
> > A new testing version of ape (3.4-0.3) is available. It includes three
> > main new features:
> >
> > - A new data class, "AAbin", to store amino acid sequences; there are
> > eleven new functions to generate and manipulate them including
> translation
> > from DNA.
> >
> > - The function checkAlignment does some diagnostics on a DNA alignment.
> >
> > - Some extra plotting functions built on ape's basic plotting functions
> > (plot.phylo, nodelabels, phydataplot, ring) for a specific task. For the
> > moment, there are two such functions: drawSupportOnEdges() and
> > plotBreakLongEdges().
> >
> > Information on the new functions can be found at:
> >
> > http://ape-package.ird.fr/NEWS
> >
> > And instructions on how to get and install the testing version here:
> >
> > http://ape-package.ird.fr/ape_installation.html#versions
> >
> > A Windows version is available.
> >
> > Best,
> >
> > Emmanuel
> >
> > ___
> > 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/
>



-- 
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston

[[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/

Re: [R-sig-phylo] new testing version of ape

2016-02-22 Thread David Bapst 
FYI, in case one wants to install the testing version of ape to
R-devel (in my case, also a Windows machine), I found I needed:

install.packages("ape",contriburl="http://ape-package.ird.fr/bin/windows/contrib/3.2;)

Emmanuel, I've tested the testing version with paleotree and a few
other projects I'm working on and I haven't found any issues.

Cheers,
-Dave

On Mon, Feb 22, 2016 at 2:16 AM, Emmanuel Paradis
 wrote:
> Dear all,
>
> A new testing version of ape (3.4-0.3) is available. It includes three main
> new features:
>
> - A new data class, "AAbin", to store amino acid sequences; there are eleven
> new functions to generate and manipulate them including translation from
> DNA.
>
> - The function checkAlignment does some diagnostics on a DNA alignment.
>
> - Some extra plotting functions built on ape's basic plotting functions
> (plot.phylo, nodelabels, phydataplot, ring) for a specific task. For the
> moment, there are two such functions: drawSupportOnEdges() and
> plotBreakLongEdges().
>
> Information on the new functions can be found at:
>
> http://ape-package.ird.fr/NEWS
>
> And instructions on how to get and install the testing version here:
>
> http://ape-package.ird.fr/ape_installation.html#versions
>
> A Windows version is available.
>
> Best,
>
> Emmanuel
>
> ___
> 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/



-- 
David W. Bapst, PhD
Adjunct Asst. Professor, Geology and Geol. Eng.
South Dakota School of Mines and Technology
501 E. St. Joseph
Rapid City, SD 57701

http://webpages.sdsmt.edu/~dbapst/
http://cran.r-project.org/web/packages/paleotree/index.html

___
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/

Re: [R-sig-phylo] new testing version of ape

2016-02-22 Thread Thibaut Jombart 
Hi Emmanuel,

this looks really cool - especially the new AAbin class. Looking forward to
playing with the new version!

Best
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology
Imperial College London
https://sites.google.com/site/thibautjombart/
https://github.com/thibautjombart
Twitter: @TeebzR 

On 22 February 2016 at 09:16, Emmanuel Paradis 
wrote:

> Dear all,
>
> A new testing version of ape (3.4-0.3) is available. It includes three
> main new features:
>
> - A new data class, "AAbin", to store amino acid sequences; there are
> eleven new functions to generate and manipulate them including translation
> from DNA.
>
> - The function checkAlignment does some diagnostics on a DNA alignment.
>
> - Some extra plotting functions built on ape's basic plotting functions
> (plot.phylo, nodelabels, phydataplot, ring) for a specific task. For the
> moment, there are two such functions: drawSupportOnEdges() and
> plotBreakLongEdges().
>
> Information on the new functions can be found at:
>
> http://ape-package.ird.fr/NEWS
>
> And instructions on how to get and install the testing version here:
>
> http://ape-package.ird.fr/ape_installation.html#versions
>
> A Windows version is available.
>
> Best,
>
> Emmanuel
>
> ___
> 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/

[R-sig-phylo] new testing version of ape

2016-02-22 Thread Emmanuel Paradis 

Dear all,

A new testing version of ape (3.4-0.3) is available. It includes three 
main new features:


- A new data class, "AAbin", to store amino acid sequences; there are 
eleven new functions to generate and manipulate them including 
translation from DNA.


- The function checkAlignment does some diagnostics on a DNA alignment.

- Some extra plotting functions built on ape's basic plotting functions 
(plot.phylo, nodelabels, phydataplot, ring) for a specific task. For the 
moment, there are two such functions: drawSupportOnEdges() and 
plotBreakLongEdges().


Information on the new functions can be found at:

http://ape-package.ird.fr/NEWS

And instructions on how to get and install the testing version here:

http://ape-package.ird.fr/ape_installation.html#versions

A Windows version is available.

Best,

Emmanuel

___
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/