Re: [R-sig-phylo] Will phyloXML in R be useful?

2017-12-14 Thread George Vega Yon
Hi Hilmar,

That sounds good. I've actually managed to build rphyloxml very quickly for
creating phyloXML files from phylo (ape) objects.
https://uscbiostats.github.io/rphyloxml/

Perhaps we should continue this discussion outside of the list to see how
can we integrate both packages (no need to have rphyloxml as a package
aside, happy to join RNeXML :))

Best,

George G. Vega Yon
+1 (626) 381 8171
http://ggvy.cl

On Thu, Dec 14, 2017 at 4:22 PM, Hilmar Lapp <hilmar.l...@duke.edu> wrote:

> Hi George,
>
> Yes, there’s RNeXML. Glad you found it on your own, I’ve been occupied
> with a workshop. Note that there’s a publication on RNeXML too, as you’ve
> probably seen in the README on Github.
>
> Personally, I think it’d be great to have phyloXML support as well in the
> R ecosystem. However, I’d argue that while the two exchange standards have
> different strengths (and NeXML is not without its own “warts”), for the
> benefit of the user (typically a biology scientist-developer) it would seem
> to be vastly preferable if these standards converge at the R API level. So
> maybe phyloXML support could be added on to RNeXML, or if its own package,
> at least the R API signature could be kept in synchrony?
>
>   -hilmar
>
> > On Dec 14, 2017, at 3:41 PM, George Vega Yon <g.vega...@gmail.com>
> wrote:
> >
> > Hey,
> >
> > Just for the record. I just found two alternatives that seem to be in
> > active development, nexml (www.nexml.org) and RecPhyloXML (
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__
> phylariane.univ-2Dlyon1.fr_recphyloxml_=DwIGaQ=
> imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_
> 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=izAgipXSIMSu-
> 6nAHEQLMuJAo1iol6odf6w4kB7xE4I=5CdlhUFqJAcw9qGduCmWrGXPwhWFUh
> ZMcOss0uysZ34= ). nexml is supported by
> > rOpenSci (https://urldefense.proofpoint.com/v2/url?u=https-
> 3A__github.com_ropensci_RNeXML=DwIGaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6Y
> HLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_
> Y=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I=E2KdcumsPG-
> JacTs6EbDx9PNds1g15J0lpbZVFgcnLs= ), and both have C++/phython
> > APIs that can be useful for R package development.
> >
> > I still may try to get something done on PhyloXML since jsPhyloSVG, which
> > I'm working on now https://urldefense.proofpoint.com/v2/url?u=https-3A__
> uscbiostats.github.io_jsPhyloSVG_=DwIGaQ=
> imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_
> 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=izAgipXSIMSu-
> 6nAHEQLMuJAo1iol6odf6w4kB7xE4I=qCOKU5kc59kVmuDmY13hm0h_F0-
> 5VtB-8YC5dp3Nc_I= , only supports
> > annotations in PhyloXML (it does support nexml trees, but I don't think
> it
> > support annotations).
> >
> > Best,
> >
> > George G. Vega Yon
> > +1 (626) 381 8171 <(626)%20381-8171>
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__ggvy.cl=DwIGaQ=
> imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_
> 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=izAgipXSIMSu-
> 6nAHEQLMuJAo1iol6odf6w4kB7xE4I=GH2YmJwH3j59FpvbwH0pJu3-
> LJHbo4BTkG73yMtknFw=
> >
> > On Wed, Dec 13, 2017 at 11:35 AM, George Vega Yon <g.vega...@gmail.com>
> > wrote:
> >
> >> That's a good suggestion. I'll reach out  the rOpenSci people/
> >>
> >> Still, I'm starting a repo here: https://urldefense.proofpoint.
> com/v2/url?u=https-3A__github.com_USCBiostats_rphyloxml=DwIGaQ=
> imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_
> 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=izAgipXSIMSu-
> 6nAHEQLMuJAo1iol6odf6w4kB7xE4I=ZI73M-7QB4r4wS6k6y4ZjA4nQsF0MMbpxv-
> IATJ8VuI=
> >> will start dropping stuff there.
> >>
> >> Best,
> >>
> >> George G. Vega Yon
> >> +1 (626) 381 8171 <(626)%20381-8171>
> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__ggvy.cl=DwIGaQ=
> imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_
> 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=izAgipXSIMSu-
> 6nAHEQLMuJAo1iol6odf6w4kB7xE4I=GH2YmJwH3j59FpvbwH0pJu3-
> LJHbo4BTkG73yMtknFw=
> >>
> >> On Tue, Dec 12, 2017 at 4:31 PM, Daniel Fulop <dfulop@gmail.com>
> >> wrote:
> >>
> >>> Sounds like a good idea. Not sure if you’re reinventing the wheel or
> not.
> >>> Sounds like something ROpenSci might support; see:
> >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> com_ropensci_onboarding=DwIGaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6Y
> HLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_
> Y=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I=Xaz1EafJxnCZMDhwVbMq39-
> DSlGClnlW10wmp8307EA=
> >>>
> >>>
> >>>
> >>>
> 

Re: [R-sig-phylo] Will phyloXML in R be useful?

2017-12-14 Thread George Vega Yon
Hey,

Just for the record. I just found two alternatives that seem to be in
active development, nexml (www.nexml.org) and RecPhyloXML (
http://phylariane.univ-lyon1.fr/recphyloxml/). nexml is supported by
rOpenSci (https://github.com/ropensci/RNeXML), and both have C++/phython
APIs that can be useful for R package development.

I still may try to get something done on PhyloXML since jsPhyloSVG, which
I'm working on now https://uscbiostats.github.io/jsPhyloSVG/, only supports
annotations in PhyloXML (it does support nexml trees, but I don't think it
support annotations).

Best,

George G. Vega Yon
+1 (626) 381 8171 <(626)%20381-8171>
http://ggvy.cl

On Wed, Dec 13, 2017 at 11:35 AM, George Vega Yon <g.vega...@gmail.com>
wrote:

> That's a good suggestion. I'll reach out  the rOpenSci people/
>
> Still, I'm starting a repo here: https://github.com/USCBiostats/rphyloxml
> will start dropping stuff there.
>
> Best,
>
> George G. Vega Yon
> +1 (626) 381 8171 <(626)%20381-8171>
> http://ggvy.cl
>
> On Tue, Dec 12, 2017 at 4:31 PM, Daniel Fulop <dfulop@gmail.com>
> wrote:
>
>> Sounds like a good idea. Not sure if you’re reinventing the wheel or not.
>> Sounds like something ROpenSci might support; see:
>> https://github.com/ropensci/onboarding
>>
>>
>>
>>
>> From: George Vega Yon <g.vega...@gmail.com> <g.vega...@gmail.com>
>> Reply: George Vega Yon <g.vega...@gmail.com> <g.vega...@gmail.com>
>> Date: December 12, 2017 at 4:13:59 PM
>> To: Group R-sig-phylo <r-sig-phylo@r-project.org>
>> <r-sig-phylo@r-project.org>
>> Subject:  [R-sig-phylo] Will phyloXML in R be useful?
>>
>> Hey,
>>
>> Right now, I'm working on a wrapper for jsPhyloSVG (a javascript library
>> for visualizing phylogenetic trees on the web browser) in R, and just got
>> to learn about the phyloXML format. Googling around and checking out this
>> email list archives it seems that there's no support for this format in
>> R.
>>
>> My question is: how useful do you think having this in R will be? I'm
>> willing to write an R package to read/write trees in this format (done
>> before with GEXF, which is for networks in general). But I just want to
>> make sure that (1) this will be useful for the community, and (2) I'm not
>> reinventing the wheel (is anybody working on this now?). What are your
>> thoughts?
>>
>> Best,
>>
>> George G. Vega Yon
>> +1 (626) 381 8171 <(626)%20381-8171>
>> http://ggvy.cl
>>
>> [[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/
>>
>>
>

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Re: [R-sig-phylo] Will phyloXML in R be useful?

2017-12-13 Thread George Vega Yon
That's a good suggestion. I'll reach out  the rOpenSci people/

Still, I'm starting a repo here: https://github.com/USCBiostats/rphyloxml
will start dropping stuff there.

Best,

George G. Vega Yon
+1 (626) 381 8171
http://ggvy.cl

On Tue, Dec 12, 2017 at 4:31 PM, Daniel Fulop <dfulop@gmail.com> wrote:

> Sounds like a good idea. Not sure if you’re reinventing the wheel or not.
> Sounds like something ROpenSci might support; see:
> https://github.com/ropensci/onboarding
>
>
>
>
> From: George Vega Yon <g.vega...@gmail.com> <g.vega...@gmail.com>
> Reply: George Vega Yon <g.vega...@gmail.com> <g.vega...@gmail.com>
> Date: December 12, 2017 at 4:13:59 PM
> To: Group R-sig-phylo <r-sig-phylo@r-project.org>
> <r-sig-phylo@r-project.org>
> Subject:  [R-sig-phylo] Will phyloXML in R be useful?
>
> Hey,
>
> Right now, I'm working on a wrapper for jsPhyloSVG (a javascript library
> for visualizing phylogenetic trees on the web browser) in R, and just got
> to learn about the phyloXML format. Googling around and checking out this
> email list archives it seems that there's no support for this format in R.
>
> My question is: how useful do you think having this in R will be? I'm
> willing to write an R package to read/write trees in this format (done
> before with GEXF, which is for networks in general). But I just want to
> make sure that (1) this will be useful for the community, and (2) I'm not
> reinventing the wheel (is anybody working on this now?). What are your
> thoughts?
>
> Best,
>
> George G. Vega Yon
> +1 (626) 381 8171 <(626)%20381-8171>
> http://ggvy.cl
>
> [[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/
>
>

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[R-sig-phylo] Will phyloXML in R be useful?

2017-12-12 Thread George Vega Yon
Hey,

Right now, I'm working on a wrapper for jsPhyloSVG (a javascript library
for visualizing phylogenetic trees on the web browser) in R, and just got
to learn about the phyloXML format. Googling around and checking out this
email list archives it seems that there's no support for this format in R.

My question is: how useful do you think having this in R will be? I'm
willing to write an R package to read/write trees in this format (done
before with GEXF, which is for networks in general). But I just want to
make sure that (1) this will be useful for the community, and (2) I'm not
reinventing the wheel (is anybody working on this now?). What are your
thoughts?

Best,

George G. Vega Yon
+1 (626) 381 8171
http://ggvy.cl

[[alternative HTML version deleted]]

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Re: [R-sig-phylo] Possible Bug in ape::read.tree

2017-09-07 Thread George Vega Yon
Hi Klaus,

Since I'm actually working with the complete PANTHER 11.1 database, I wrote
a short document in our project's website comparing both ape and
rncl reading ~13,000 trees. ape::read.tree does the job and identifies and
reads the singleton as expected. Overall, while I see that the new version
of the read.tree function is significantly faster, it does not seem to be
significantly faster than rncl (both perform pretty good).

You can find the document here:
https://github.com/USCbiostats/aphylo/blob/master/playground/ape_now_supports_singletons.md

Best,



George G. Vega Yon
+1 (626) 381 8171
http://cana.usc.edu/vegayon

On Tue, Sep 5, 2017 at 5:55 PM, Klaus Schliep <klaus.schl...@gmail.com>
wrote:

> Dear George & list,
> you can try install the development version of ape, which can handle
> singleton nodes:
> download.packages("ape", ".", repos = "http://ape-package.ird.fr/;)
> and than install the package from source. See
> http://ape-package.ird.fr/ape_installation.html for more details.
> For you tree the new version seems to import tree fine.
> Emmanuel and I are keen to get feedback on the new read.tree() function so
> please give it a try.
> Kind regards,
> Klaus
>
>
>
>
> On Tue, Sep 5, 2017 at 5:37 PM, Liam J. Revell <liam.rev...@umb.edu>
> wrote:
>
>> Hi George. Mario is correct that phytools can read a tree with singleton
>> nodes (if that is indeed your problem), but the name of the function is
>> read.newick. Good luck! - 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 9/5/2017 4:17 PM, George Vega Yon wrote:
>>
>>> Hi Mario,
>>>
>>> That sounds great!
>>>
>>> Thanks,
>>>
>>> George G. Vega Yon
>>> +1 (626) 381 8171
>>> http://cana.usc.edu/vegayon
>>>
>>> On Tue, Sep 5, 2017 at 2:08 PM, Mario José Marques-Azevedo <
>>> mariojm...@gmail.com> wrote:
>>>
>>> Hi, George,
>>>>
>>>> Ape package do not read tree with singletons, yet. New version will
>>>> read.
>>>> You can use readTree from phytools package for while.
>>>>
>>>> Best regards,
>>>>
>>>> Mario
>>>>
>>>>
>>>> On 5 Sep 2017 5:53 p.m., "George Vega Yon" <g.vega...@gmail.com> wrote:
>>>>
>>>> Hi,
>>>>
>>>> When trying to read this tree with the ape::read.tree function :
>>>>
>>>> ((AN14:0.000,AN15:0.000):0.000[&:Ev=0>1:S=
>>>> Homo-Pan:ID=AN13],(AN17:0.000,AN18:0.000):0.000[&:Ev=0>
>>>> 1:S=Murinae:ID=AN16]):0.000[&:Ev=0>1:S=Euarchontoglires:
>>>> ID=AN12],(AN20:0.000,AN21:0.000):0.000[&:Ev=0>1:S=
>>>> Laurasiatheria:ID=AN19]):0.000[&:Ev=0>1:S=Eutheria:
>>>> ID=AN11],AN22:0.004):0.003[&:Ev=0>1:S=Mammalia:ID=AN10]
>>>> ,AN23:0.000):0.014[&:Ev=0>1:S=Amniota:ID=AN9],AN24:0.
>>>> 017):0.021[&:Ev=0>1:S=Tetrapoda:ID=AN8],((AN27:0.
>>>> 066,AN28:0.052):0.010[&:Ev=1>0:ID=AN26],(AN30:0.031,
>>>> AN31:0.014):0.003[&:Ev=1>0:ID=AN29]):0.021[&:Ev=0>
>>>> 1:S=Teleostei:ID=AN25]):0.147[&:Ev=0>1:S=Osteichthyes:
>>>> ID=AN7],AN32:0.194):0.104[&:Ev=0>1:S=Deuterostomia:ID=
>>>> AN6],((AN35:0.020,AN36:0.038):0.416[&:Ev=0>1:S=
>>>> Caenorhabditis:ID=AN34],((AN39:0.119,AN40:0.131):0.154[&
>>>> :Ev=0>1:S=Insecta:ID=AN38],AN41:0.317):0.104[&:Ev=0>
>>>> 1:S=Arthropoda:ID=AN37]):0.118[&:Ev=0>1:S=Ecdysozoa:
>>>> ID=AN33],AN42:0.381):0.594[&:Ev=0>1:S=Bilateria:ID=AN5]
>>>> ,AN43:2.000):0.414[&:Ev=0>1
>>>>  :S=Eumetazoa:ID=AN4],AN52:0.484,AN53:0.427):0.418[&
>>>> :Ev=0>1:S=
>>>> Saccharomycetaceae:ID=AN51],AN54:0.733):0.320[&:Ev=0>
>>>> 1:S=Saccharomycetaceae-Candida:ID=AN50],AN55:0.808):0.290[&&
>>>> NHX:Ev=0>1:S=
>>>> Saccharomycetales:ID=AN49],(AN57:0.793,((AN60:0.206,AN61:
>>>> 0.186):0.143[&:Ev=0>1:S=Sordariomyceta:ID=AN59],AN62:
>>>> 0.331):0.332[&:Ev=0>1:S=Sordariomycetes-Leotiomycetes:
>>>> ID=AN58]):0.467[&:Ev=0>1:S=Pezizomycotina:ID=AN56]):0.
>>>> 432[&:Ev=0>1:S=Pezizomycotina-Saccharomycotina:ID=AN48],
>>>> AN63:0.864):0.223[&:Ev=0

Re: [R-sig-phylo] Possible Bug in ape::read.tree

2017-09-05 Thread George Vega Yon
Hi Mario,

That sounds great!

Thanks,

George G. Vega Yon
+1 (626) 381 8171
http://cana.usc.edu/vegayon

On Tue, Sep 5, 2017 at 2:08 PM, Mario José Marques-Azevedo <
mariojm...@gmail.com> wrote:

> Hi, George,
>
> Ape package do not read tree with singletons, yet. New version will read.
> You can use readTree from phytools package for while.
>
> Best regards,
>
> Mario
>
>
> On 5 Sep 2017 5:53 p.m., "George Vega Yon" <g.vega...@gmail.com> wrote:
>
> Hi,
>
> When trying to read this tree with the ape::read.tree function :
>
> ((AN14:0.000,AN15:0.000):0.000[&:Ev=0>1:S=
> Homo-Pan:ID=AN13],(AN17:0.000,AN18:0.000):0.000[&:Ev=0>
> 1:S=Murinae:ID=AN16]):0.000[&:Ev=0>1:S=Euarchontoglires:
> ID=AN12],(AN20:0.000,AN21:0.000):0.000[&:Ev=0>1:S=
> Laurasiatheria:ID=AN19]):0.000[&:Ev=0>1:S=Eutheria:
> ID=AN11],AN22:0.004):0.003[&:Ev=0>1:S=Mammalia:ID=AN10]
> ,AN23:0.000):0.014[&:Ev=0>1:S=Amniota:ID=AN9],AN24:0.
> 017):0.021[&:Ev=0>1:S=Tetrapoda:ID=AN8],((AN27:0.
> 066,AN28:0.052):0.010[&:Ev=1>0:ID=AN26],(AN30:0.031,
> AN31:0.014):0.003[&:Ev=1>0:ID=AN29]):0.021[&:Ev=0>
> 1:S=Teleostei:ID=AN25]):0.147[&:Ev=0>1:S=Osteichthyes:
> ID=AN7],AN32:0.194):0.104[&:Ev=0>1:S=Deuterostomia:ID=
> AN6],((AN35:0.020,AN36:0.038):0.416[&:Ev=0>1:S=
> Caenorhabditis:ID=AN34],((AN39:0.119,AN40:0.131):0.154[&
> :Ev=0>1:S=Insecta:ID=AN38],AN41:0.317):0.104[&:Ev=0>
> 1:S=Arthropoda:ID=AN37]):0.118[&:Ev=0>1:S=Ecdysozoa:
> ID=AN33],AN42:0.381):0.594[&:Ev=0>1:S=Bilateria:ID=AN5]
> ,AN43:2.000):0.414[&:Ev=0>1
>  :S=Eumetazoa:ID=AN4],AN52:0.484,AN53:0.427):0.418[&:Ev=0>1:S=
> Saccharomycetaceae:ID=AN51],AN54:0.733):0.320[&:Ev=0>
> 1:S=Saccharomycetaceae-Candida:ID=AN50],AN55:0.808):0.290[&:Ev=0>1:S=
> Saccharomycetales:ID=AN49],(AN57:0.793,((AN60:0.206,AN61:
> 0.186):0.143[&:Ev=0>1:S=Sordariomyceta:ID=AN59],AN62:
> 0.331):0.332[&:Ev=0>1:S=Sordariomycetes-Leotiomycetes:
> ID=AN58]):0.467[&:Ev=0>1:S=Pezizomycotina:ID=AN56]):0.
> 432[&:Ev=0>1:S=Pezizomycotina-Saccharomycotina:ID=AN48],
> AN63:0.864):0.223[&:Ev=0>1:S=Ascomycota:ID=AN47],(AN65:
> 0.613,AN66:0.930,AN67:0.755):0.332[&:Ev=0>1:S=
> Basidiomycota:ID=AN64]):0.618[&:Ev=0>1:S=Dikarya:ID=
> AN46],((AN74:0.337,AN75:0.406):0.298[&:Ev=0>1:S=
> Saccharomycetaceae:ID=AN73],AN76:0.578):0.338[&:Ev=0>
> 1:S=Saccharomycetaceae-Candida:ID=AN72],AN77:0.567):0.304[&:Ev=0>1:S=
> Saccharomycetales:ID=AN71],(AN79:0.379,((AN82:0.398,AN83:
> 0.403):0.191[&:Ev=0>1:S=Sordariomyceta:ID=AN81],AN84:
> 0.366):0.140[&:Ev=0>1:S=Sordariomyc
>  etes-Leotiomycetes:ID=AN80]):0.457[&:Ev=0>1:S=
> Pezizomycotina:ID=AN78]):0.331[&:Ev=0>1:S=Pezizomycotina-
> Saccharomycotina:ID=AN70],AN85:0.737):0.128[&:Ev=0>
> 1:S=Ascomycota:ID=AN69],(AN87:0.599,AN88:0.698):0.161[&:
> Ev=0>1:S=Basidiomycota:ID=AN86]):0.398[&:Ev=0>1:S=
> Dikarya:ID=AN68]):0.117[&:Ev=1>0:ID=AN45],(AN90:0.984,
> AN91:0.893):0.158[&:Ev=1>0:ID=AN89]):0.262[&:Ev=0>
> 1:S=Fungi:ID=AN44]):0.394[&:Ev=0>1:S=Opisthokonts:ID=
> AN3],(AN93:0.457,AN94:0.462):0.860[&:Ev=0>1:S=
> Dictyostelium:ID=AN92]):0.301[&:Ev=0>1:S=Unikonts:ID=
> AN2],AN95:1.440,AN96:2.000):2.000[&:Ev=0>1:S=Eukaryota:
> ID=AN1])[&:Ev=1>0:ID=AN0];
>
> I get the following error: "The tree has apparently singleton node(s):
> cannot read tree file.  Reading Newick file aborted at tree no. 1",
> which seems to be wrong since I can actually read this tree without problem
> using rncl::read_newick_phylo and this online tool
> http://etetoolkit.org/treeview/?treeid=6e192f20a3226cfdde219531cc533e
> 9f=ce443ed1e53858bf4e11d1e069c7a927
>
> I understand that this particular tree is a modified version of Newick's
> format, but this is the first time that I have problems reading this type
> of tree.
>
> Here my session info:
>
> > devtools::session_info()
> Session info
> 
> -
>  setting  value
>  version  R version 3.4.1 (2017-06-30)
>  system   x86_64, linux-gnu
>  ui   RStudio (1.0.143)
>  language (EN)
>  collate  en_US.UTF-8
>  tz   America/New_York
>  date 2017-09-05
>
> Packages
> 
> -
>  package * version date   source
>  ape   4.1 2017-02-14 CRAN (R 3.4.0)
>  assertt

[R-sig-phylo] Possible Bug in ape::read.tree

2017-09-05 Thread George Vega Yon
Hi,

When trying to read this tree with the ape::read.tree function :

((AN14:0.000,AN15:0.000):0.000[&:Ev=0>1:S=Homo-Pan:ID=AN13],(AN17:0.000,AN18:0.000):0.000[&:Ev=0>1:S=Murinae:ID=AN16]):0.000[&:Ev=0>1:S=Euarchontoglires:ID=AN12],(AN20:0.000,AN21:0.000):0.000[&:Ev=0>1:S=Laurasiatheria:ID=AN19]):0.000[&:Ev=0>1:S=Eutheria:ID=AN11],AN22:0.004):0.003[&:Ev=0>1:S=Mammalia:ID=AN10],AN23:0.000):0.014[&:Ev=0>1:S=Amniota:ID=AN9],AN24:0.017):0.021[&:Ev=0>1:S=Tetrapoda:ID=AN8],((AN27:0.066,AN28:0.052):0.010[&:Ev=1>0:ID=AN26],(AN30:0.031,AN31:0.014):0.003[&:Ev=1>0:ID=AN29]):0.021[&:Ev=0>1:S=Teleostei:ID=AN25]):0.147[&:Ev=0>1:S=Osteichthyes:ID=AN7],AN32:0.194):0.104[&:Ev=0>1:S=Deuterostomia:ID=AN6],((AN35:0.020,AN36:0.038):0.416[&:Ev=0>1:S=Caenorhabditis:ID=AN34],((AN39:0.119,AN40:0.131):0.154[&:Ev=0>1:S=Insecta:ID=AN38],AN41:0.317):0.104[&:Ev=0>1:S=Arthropoda:ID=AN37]):0.118[&:Ev=0>1:S=Ecdysozoa:ID=AN33],AN42:0.381):0.594[&:Ev=0>1:S=Bilateria:ID=AN5],AN43:2.000):0.414[&:Ev=0>1
 
:S=Eumetazoa:ID=AN4],AN52:0.484,AN53:0.427):0.418[&:Ev=0>1:S=Saccharomycetaceae:ID=AN51],AN54:0.733):0.320[&:Ev=0>1:S=Saccharomycetaceae-Candida:ID=AN50],AN55:0.808):0.290[&:Ev=0>1:S=Saccharomycetales:ID=AN49],(AN57:0.793,((AN60:0.206,AN61:0.186):0.143[&:Ev=0>1:S=Sordariomyceta:ID=AN59],AN62:0.331):0.332[&:Ev=0>1:S=Sordariomycetes-Leotiomycetes:ID=AN58]):0.467[&:Ev=0>1:S=Pezizomycotina:ID=AN56]):0.432[&:Ev=0>1:S=Pezizomycotina-Saccharomycotina:ID=AN48],AN63:0.864):0.223[&:Ev=0>1:S=Ascomycota:ID=AN47],(AN65:0.613,AN66:0.930,AN67:0.755):0.332[&:Ev=0>1:S=Basidiomycota:ID=AN64]):0.618[&:Ev=0>1:S=Dikarya:ID=AN46],((AN74:0.337,AN75:0.406):0.298[&:Ev=0>1:S=Saccharomycetaceae:ID=AN73],AN76:0.578):0.338[&:Ev=0>1:S=Saccharomycetaceae-Candida:ID=AN72],AN77:0.567):0.304[&:Ev=0>1:S=Saccharomycetales:ID=AN71],(AN79:0.379,((AN82:0.398,AN83:0.403):0.191[&:Ev=0>1:S=Sordariomyceta:ID=AN81],AN84:0.366):0.140[&:Ev=0>1:S=Sordariomyc
 
etes-Leotiomycetes:ID=AN80]):0.457[&:Ev=0>1:S=Pezizomycotina:ID=AN78]):0.331[&:Ev=0>1:S=Pezizomycotina-Saccharomycotina:ID=AN70],AN85:0.737):0.128[&:Ev=0>1:S=Ascomycota:ID=AN69],(AN87:0.599,AN88:0.698):0.161[&:Ev=0>1:S=Basidiomycota:ID=AN86]):0.398[&:Ev=0>1:S=Dikarya:ID=AN68]):0.117[&:Ev=1>0:ID=AN45],(AN90:0.984,AN91:0.893):0.158[&:Ev=1>0:ID=AN89]):0.262[&:Ev=0>1:S=Fungi:ID=AN44]):0.394[&:Ev=0>1:S=Opisthokonts:ID=AN3],(AN93:0.457,AN94:0.462):0.860[&:Ev=0>1:S=Dictyostelium:ID=AN92]):0.301[&:Ev=0>1:S=Unikonts:ID=AN2],AN95:1.440,AN96:2.000):2.000[&:Ev=0>1:S=Eukaryota:ID=AN1])[&:Ev=1>0:ID=AN0];

I get the following error: "The tree has apparently singleton node(s):
cannot read tree file.  Reading Newick file aborted at tree no. 1",
which seems to be wrong since I can actually read this tree without problem
using rncl::read_newick_phylo and this online tool
http://etetoolkit.org/treeview/?treeid=6e192f20a3226cfdde219531cc533e9f=ce443ed1e53858bf4e11d1e069c7a927

I understand that this particular tree is a modified version of Newick's
format, but this is the first time that I have problems reading this type
of tree.

Here my session info:

> devtools::session_info()
Session info
-
 setting  value
 version  R version 3.4.1 (2017-06-30)
 system   x86_64, linux-gnu
 ui   RStudio (1.0.143)
 language (EN)
 collate  en_US.UTF-8
 tz   America/New_York
 date 2017-09-05

Packages
-
 package * version date   source
 ape   4.1 2017-02-14 CRAN (R 3.4.0)
 assertthat0.2.0   2017-04-11 CRAN (R 3.4.0)
 base* 3.4.1   2017-06-30 local
 compiler  3.4.1   2017-06-30 local
 datasets* 3.4.1   2017-06-30 local
 devtools  1.13.3  2017-08-02 CRAN (R 3.4.0)
 digest0.6.12  2017-01-27 CRAN (R 3.4.0)
 graphics* 3.4.1   2017-06-30 local
 grDevices   * 3.4.1   2017-06-30 local
 grid  3.4.1   2017-06-30 local
 lattice   0.20-35 2017-03-25 CRAN (R 3.4.1)
 magrittr  1.5 2014-11-22 CRAN (R 3.4.0)
 memoise   1.1.0   2017-04-21 CRAN (R 3.4.0)
 methods * 3.4.1   2017-06-30 local
 nlme  3.1-131 2017-02-06 CRAN (R 3.4.1)
 parallel  3.4.1   2017-06-30 local
 prettyunits   1.0.2   2015-07-13 CRAN (R 3.4.1)
 progress  1.1.2   2016-12-14 CRAN (R 3.4.1)
 R62.2.2   2017-06-17 CRAN (R 3.4.0)
 Rcpp  0.12.12 2017-07-15 CRAN (R 3.4.0)
 rncl  0.8.2   2016-12-16 CRAN (R 3.4.1)
 stats   * 3.4.1   2017-06-30 local
 tools 3.4.1   2017-06-30 local
 utils   * 3.4.1   2017-06-30 local
 withr 2.0.0   2017-07-28 CRAN (R 3.4.0)


Any ideas?

Best,

George G. Vega Yon
+1 (626) 381 8171
http://cana.usc.edu/vegayon

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