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_&d=DwIGaQ&c=
> imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_
> 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu-
> 6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=5CdlhUFqJAcw9qGduCmWrGXPwhWFUh
> ZMcOss0uysZ34&e= ). nexml is supported by
> > rOpenSci (https://urldefense.proofpoint.com/v2/url?u=https-
> 3A__github.com_ropensci_RNeXML&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6Y
> HLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_
> Y&m=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=E2KdcumsPG-
> JacTs6EbDx9PNds1g15J0lpbZVFgcnLs&e= ), 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_&d=DwIGaQ&c=
> imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_
> 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu-
> 6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=qCOKU5kc59kVmuDmY13hm0h_F0-
> 5VtB-8YC5dp3Nc_I&e= , 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&d=DwIGaQ&c=
> imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_
> 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu-
> 6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=GH2YmJwH3j59FpvbwH0pJu3-
> LJHbo4BTkG73yMtknFw&e=
> >
> > 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&d=DwIGaQ&c=
> imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_
> 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu-
> 6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=ZI73M-7QB4r4wS6k6y4ZjA4nQsF0MMbpxv-
> IATJ8VuI&e=
> >> 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&d=DwIGaQ&c=
> imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_
> 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu-
> 6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=GH2YmJwH3j59FpvbwH0pJu3-
> LJHbo4BTkG73yMtknFw&e=
> >>
> >> 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&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6Y
> HLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_
> Y&m=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=Xaz1EafJxnCZMDhwVbMq39-
> DSlGClnlW10wmp8307EA&e=
> >>>
> >>>
> >>>
> >>>
> >>> 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>
> >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__ggvy.cl&;
> d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_
> 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu-
> 6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=GH2YmJwH3j59FpvbwH0pJu3-
> LJHbo4BTkG73yMtknFw&e=
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
> >>> R-sig-phylo mailing list - R-sig-phylo@r-project.org
> >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.
> ethz.ch_mailman_listinfo_r-2Dsig-2Dphylo&d=DwIGaQ&c=
> imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_
> 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu-
> 6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=F6nfY69ENJtHqcPhA_
> so8xyQlwQpn3HwI63r5ov4Xf8&e=
> >>> Searchable archive at https://urldefense.proofpoint.
> com/v2/url?u=http-3A__www.mail-2Darchive.com_r-2D&d=DwIGaQ&c=
> imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_
> 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu-
> 6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=ysaFlE8Zm70teQET_
> RVPd9xB5EvNFPojxC-Pt7Ekpuk&e=
> >>> sig-ph...@r-project.org/
> >>>
> >>>
> >>
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-sig-phylo mailing list - R-sig-phylo@r-project.org
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.
> ethz.ch_mailman_listinfo_r-2Dsig-2Dphylo&d=DwIGaQ&c=
> imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_
> 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu-
> 6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=F6nfY69ENJtHqcPhA_
> so8xyQlwQpn3HwI63r5ov4Xf8&e=
> > Searchable archive at https://urldefense.proofpoint.
> com/v2/url?u=http-3A__www.mail-2Darchive.com_r-2Dsig-
> 2Dphylo-40r-2Dproject.org_&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6Y
> HLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_
> Y&m=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=JBS4-
> wowjXN2N2zGbTKrOkxo5314bZIjY40wPxcc9cY&e=
>
> --
> Hilmar Lapp -:- genome.duke.edu -:- lappland.io
>
>

        [[alternative HTML version deleted]]

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