Re: [R-sig-phylo] Will phyloXML in R be useful?
is 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=DwIGaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I=GH2YmJwH3j59FpvbwH0pJu3-LJHbo4BTkG73yMtknFw= >>> >>> >>> [[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=DwIGaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I=F6nfY69ENJtHqcPhA_so8xyQlwQpn3HwI63r5ov4Xf8= >>> >>> Searchable archive at >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_r-2D=DwIGaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I=ysaFlE8Zm70teQET_RVPd9xB5EvNFPojxC-Pt7Ekpuk= >>> >>> 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=DwIGaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I=F6nfY69ENJtHqcPhA_so8xyQlwQpn3HwI63r5ov4Xf8= > > Searchable archive at > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_r-2Dsig-2Dphylo-40r-2Dproject.org_=DwIGaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I=JBS4-wowjXN2N2zGbTKrOkxo5314bZIjY40wPxcc9cY= -- Hilmar Lapp -:- genome.duke.edu -:- lappland.io ___ 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] RMesquite package
Ayelet - If you provide the exact error that prevents you from loading RMesquite, I can try to see what the underlying cause might be. I can’t help you with using Mesquite itself , but others on the list may, which is why I’m copying the list. Jeannine - I don’t know right now which version(s) of R won’t work with RMesquite. But the rJava package that it’s dependent on has I believe undergone some changes recently, so I’m not surprised if recent versions of R don’t work. (Can you report the error you were getting?) I think if there’s some continued interest for this package what would be best is to migrate it to being hosted on Github. At the time that would have made integration with the R package management difficult, which is why we chose R-Forge, but I think now if anything it’s the opposite. And Github is what I (and probably most others here) use all the time, so would be vastly preferable for maintenance for that reason alone. I’ll look into that later this month (unless someone wants to beat me to it). -hilmar Sent from away On Sep 23, 2017, at 3:31 AM, Ayelet Salman <ayelet.sal...@gmail.com<mailto:ayelet.sal...@gmail.com>> wrote: Dear Hilmar, I wasn't able to load RMesquite, I will very much appreciate your help with the Mesquite software Could you please guide me how to us Mesquite tools on batch data? e.g. applying the pairwise comparison tool on trees and character data, for several different genera. Currently I am loading the tree and data for every genera separately, and appling the pairwise comparison test for every genera. How can I save time and apply these same steps on the different genera data? Thanks, Ayelet [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animated-no-repeat-v1.gif]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avast.com_sig-2Demail-3Futm-5Fmedium-3Demail-26utm-5Fsource-3Dlink-26utm-5Fcampaign-3Dsig-2Demail-26utm-5Fcontent-3Dwebmail=DwMFaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=XtWaA86jwYiS-E38jiKUh2-Wy8M5rAzczsBO5xyAJ8I=scG5V3F1V1aUsSumjdxEGkXJSzdFYTKIJK_9JZ4hzWU=> בלי וירוסים. www.avast.com<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avast.com_sig-2Demail-3Futm-5Fmedium-3Demail-26utm-5Fsource-3Dlink-26utm-5Fcampaign-3Dsig-2Demail-26utm-5Fcontent-3Dwebmail=DwMFaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=XtWaA86jwYiS-E38jiKUh2-Wy8M5rAzczsBO5xyAJ8I=scG5V3F1V1aUsSumjdxEGkXJSzdFYTKIJK_9JZ4hzWU=> On Wed, Sep 13, 2017 at 5:28 PM, Hilmar Lapp <hilmar.l...@duke.edu<mailto:hilmar.l...@duke.edu>> wrote: Hi Ayelet, Instructions for installing RMesquite are on the project’s homepage: http://rmesquite.r-forge.r-project.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__rmesquite.r-2Dforge.r-2Dproject.org=DwMFaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=XtWaA86jwYiS-E38jiKUh2-Wy8M5rAzczsBO5xyAJ8I=D2Hm5Yrj5iT0hEg8gG21JtHki93r-kOPIVgtUq7LA9g=> Let us know if the information there doesn’t answer your question. -hilmar > On Sep 11, 2017, at 6:10 AM, Ayelet Salman > <ayelet.sal...@gmail.com<mailto:ayelet.sal...@gmail.com>> wrote: > > Dear r-SIG-phylo members, > > I have tried to call the RMesquite package from R but got an error that it > is not available. > Do you know how to download and install RMesquite (on windows or server)? > > Any other idea how to use Mesquite or the pairwise comparison tool > (Maddison 2000) on a large scale data? > > Best, > Ayelet > > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list - > R-sig-phylo@r-project.org<mailto:R-sig-phylo@r-project.org> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dphylo=DwICAg=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=nLcvm2XyiPq2SigT7Kkz_OgewmzetB3W_iyAKw37Moc=DHck5zYgVyyIMKf18p3DZPx7bi7GjTzk9iVikg8hqN4= > Searchable archive at > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_r-2Dsig-2Dphylo-40r-2Dproject.org_=DwICAg=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=nLcvm2XyiPq2SigT7Kkz_OgewmzetB3W_iyAKw37Moc=EjBfROurcmBvQ9sM3pHs1y9fP9PgQG5bBoN54T4tUsY= -- Hilmar Lapp -:- genome.duke.edu<http://genome.duke.edu> -:- lappland.io<https://urldefense.proofpoint.com/v2/url?u=http-3A__lappland.io=DwMFaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=XtWaA86jwYiS-E38jiKUh2-Wy8M5rAzczsBO5xyAJ8I=Hwjyv97NuUHJ6GMSST-7Y8_couWaYOezJVh_eQrA8X0=> [[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] RMesquite package
Hi Ayelet, Instructions for installing RMesquite are on the project’s homepage: http://rmesquite.r-forge.r-project.org Let us know if the information there doesn’t answer your question. -hilmar > On Sep 11, 2017, at 6:10 AM, Ayelet Salman <ayelet.sal...@gmail.com> wrote: > > Dear r-SIG-phylo members, > > I have tried to call the RMesquite package from R but got an error that it > is not available. > Do you know how to download and install RMesquite (on windows or server)? > > Any other idea how to use Mesquite or the pairwise comparison tool > (Maddison 2000) on a large scale data? > > Best, > Ayelet > > [[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=DwICAg=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=nLcvm2XyiPq2SigT7Kkz_OgewmzetB3W_iyAKw37Moc=DHck5zYgVyyIMKf18p3DZPx7bi7GjTzk9iVikg8hqN4= > > Searchable archive at > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_r-2Dsig-2Dphylo-40r-2Dproject.org_=DwICAg=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=nLcvm2XyiPq2SigT7Kkz_OgewmzetB3W_iyAKw37Moc=EjBfROurcmBvQ9sM3pHs1y9fP9PgQG5bBoN54T4tUsY= > -- Hilmar Lapp -:- genome.duke.edu -:- lappland.io ___ 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] caretaker / user for the rphylo.org domain?
Hi all, I noted a few weeks ago that I had restored the http://r-phylo.org <http://r-phylo.org/> wiki, and for now I will keep renewing the r-phylo.org <http://r-phylo.org/> domain name. As some of you may be aware, I have also held the rphylo.org <http://rphylo.org/> domain, as a remnant from NESCent’s December 2007 Comparative Methods in R hackathon (because at the time of the hackathon the long-term name variant hadn’t been settled yet). (BTW not everyone may be aware anymore that this list is an outcome of that hackathon, too :-) The rphylo.org <http://rphylo.org/> domain is up for renewal by Dec 16, and I am not planning to renew it. If someone else in the community is interested in taking care of or using the domain name (for whatever purpose - no strings attached), let me know off-list in the next few days and I will transfer it to you. (If you have a commercial affiliation, I reserve to ask to be reimbursed for renewal costs since 2007. To academic affiliates I will donate it. Of course, anyone can pick it up after it comes out of the 30-day grace period post-renewal date.) -hilmar -- Hilmar Lapp -:- genome.duke.edu -:- lappland.io [[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] Collapse a clade by tip labels while maintaining phylogenetic position
Hi BranchLizard, > On Sep 12, 2016, at 3:46 PM, branchlizard . <branch.liz...@gmail.com> wrote: > > I have posted this question at Stack Overflow. I hope this doesn't violate > any community rules about double posting. It doesn’t, but why not include the URL so that people can avoid answering what may already have been answered? -hilmar -- Hilmar Lapp -:- genome.duke.edu -:- lappland.io ___ 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] continued maintenance of the R-Phylo wiki
Vogtěch and others, Apologies if the context was lost from the original thread, which is from about a year ago. Here it is for your reference: http://www.mail-archive.com/r-sig-phylo@r-project.org/msg03877.html -hilmar > On Jun 7, 2016, at 8:12 AM, Vojtěch Zeisek <vo...@trapa.cz> wrote: > > Hello, > does this discussion last since yesterday? If not, I missed it and I'm sorry. > Anyway, I'm able to offer hosting of the wiki on the server where I rent space > for some of my projects. I can provide all needed background to run MediaWiki, > although I'm not Wiki expert. Well, I do not like Wiki as piece of software, > but otherwise it is good tool. :-) I'd be able to host it, maintain it, > upgrade the system etc. But someone else would have to take care about the > content. I wouldn't be able to really work on the content (except needed > administration). If this would be acceptable, we can discuss more details. > Sincerely, > Vojtěch > > Dne úterý 7. června 2016 8:00:02 CEST, Hilmar Lapp napsal(a): >> As an FYI for this community, I have reconstituted the R-phylo wiki from its >> archive [1], and it is now live again at the same URL it used to be: >> http://www.r-phylo.org >> >> The complete history of the pages is preserved, but user accounts need to be >> created from scratch (through Google Login). Have away at it. >> >> That notwithstanding, I still think that Jonathan’s suggestion of moving >> material to Wikipedia or Wikibooks is a good one, though I’m not sure much >> has happened in that regard. >> >> -hilmar >> >> [1] http://dx.doi.org/10.5281/zenodo.19004 >> >>> On May 6, 2015, at 5:22 PM, Jonathan Chang <jonathan.ch...@ucla.edu> >>> wrote: >>> >>> Hi all, >>> >>> I think the best solution would be to transfer the how-to material to >>> Wikibooks, which is run by the same people that run Wikipedia. The >>> current Phylogenetics "book" is pretty sparse. I'd be willing to take >>> some time to organize and transfer the text. >>> >>> http://en.wikibooks.org/wiki/Phylogenetics >>> >>> Jonathan >>> >>> On Wed, May 6, 2015 at 2:11 PM, Hilmar Lapp <hl...@nescent.org> wrote: >>>> On 5/6/15, 4:56 PM, Hilmar Lapp wrote: >>>>> If we do not hear expressions of interest in transfer of hosting before >>>>> May 22 2015, then the wiki will have to be taken offline when NESCent >>>>> closes. An XML dump of the wiki contents will be placed in the NESCent >>>>> digital archive with Duke Libraries, but will not be publicly >>>>> accessible. >>>> >>>> Actually let me correct myself. The XML dump would be placed in a >>>> publicly accessible archive (because this is one of our public wikis), >>>> likely in a NESCent collection we are putting together on Zenodo (see >>>> https://zenodo.org/collection/user-nescent). The XML dump will allow >>>> re-instating the wiki from it, but accounts and edit history would be >>>> lost. >>>> >>>> -hilmar > -- > Vojtěch Zeisek > https://trapa.cz/en/ > > Department of Botany, Faculty of Science > Charles University in Prague > Benátská 433/2, Prague, 12801, CZ > https://www.natur.cuni.cz/biology/botany/ > https://erasmusclub.natur.cuni.cz/ > > Institute of Botany, Academy of Sciences > Zámek 1, Průhonice, 25243, CZ > http://www.ibot.cas.cz/en/ > > Czech Republic > ___ > 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/ -- Hilmar Lapp -:- genome.duke.edu -:- lappland.io signature.asc Description: Message signed with OpenPGP using GPGMail ___ 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] Accounting for phylogeny in binary predictor, binary response data
So, just to recap, no .xyz email address is subscribed, and they have been summarily banned from doing for 4 months. For close to a month, the archives have been private. The list archives remain publicly indexed at mail-archive.com, but they hide email addresses. It’s possible that we have moles subscribed to the list, but we have >1000 subscribers, so no way of checking every one. I’m all ears to suggestions what to do next to stop this. Right now I’m coming up short of next things to try that wouldn’t be rather drastic (such as rebuilding the list from scratch). -hilmar > On Feb 11, 2016, at 10:40 AM, Alejandro Gonzalez Voyer > <alejandro.gonza...@iecologia.unam.mx> wrote: > > Hi, > > I received the very same E-mail, also disguised as a reply to my message. > > Cheers > > Alejandro > ___ > Dr Alejandro Gonzalez Voyer > > Laboratorio de Conducta Animal > Instituto de Ecología > Circuito Exterior S/N > Ciudad Universitaria > Universidad Nacional Autónoma de México > México, D.F. > 04510 > México > > Tel: +52 55 5622 9044 > E-mail: alejandro.gonza...@iecologia.unam.mx > > Web Site: http://alejandrogonzalezvoyer.com > > >> On 11 Feb 2016, at 12:21 am, Joe Felsenstein <j...@gs.washington.edu> wrote: >> >> I have received phishing spam through the R-sig-phylo mailing list >> (pretending I had expressed interest in renting something from them) from >> >> anya_phill...@casetotours.xyz >> >> disguised as a reply to my comment. So that address should immediately be >> removed from the list. >> >> Joe >> - >> j...@gs.washington.edu >> Joe Felsenstein, Department of Genome Sciences and Department of Biology >> Box 355065, University of Washington, Seattle, WA 98195-5065 >> >> [[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/ -- Hilmar Lapp -:- genome.duke.edu -:- lappland.io ___ 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] Problem with bootstraping microstallite NJ tree
The irony is of course that I just received a spam response myself in response to the below, so it’s clearly some automated scheme :-) I will make the mailman archives private now. (For those worried that this stops the archives from being publicly indexed at mail-archive.com, this should not be the case, because mail-archive.com is subscribed for this purpose. We’ll monitor this nonetheless.) -hilmar > On Jan 22, 2016, at 12:05 PM, Hilmar Lapp <hilmar.l...@duke.edu> wrote: > > >> On Jan 22, 2016, at 3:16 AM, Vojtěch Zeisek <vo...@trapa.cz> wrote: >> >> PS: Later yesterday I have received spam answering my original post. Spammer >> is obviously subscribed and harvesting mails passing through the conference >> and then mailing users off-list. > > Just to clarify for everyone, the perpetrators of this kind of spam are *not* > subscribed, at least not with the address (or one similar to it) that they > are spamming from. I can say this because I’ve blocked the whole TLD (.xyz) > from subscribing, and no .xyz emails are subscribed. > > It is of course possible that the perpetrators *are* subscribed with a > legit-looking email, and then spam from throw-away addresses. This would be > very difficult to combat (there are currently > 1000 subscribers to this > list, making it futile to try to scrutinize every subscribed address). It is > also possible (and much more likely IMO) that the perpetrators feed off of a > public mailing list archive. I just noticed that the public mailman archive > apparently does not obfuscate the sender addresses (which apparently is > controlled by a setting not available to list administrators, but only to > sysadmins at the host). I am probably going to make the list archives > private, which would require people perusing an indexed public 3rd party mail > archive (such as that at > http://www.mail-archive.com/r-sig-phylo@r-project.org/). Those are much more > usable than the mailman archive anyway, so perhaps the impact of this step in > terms of accessibility may be small. > > -hilmar > -- > Hilmar Lapp -:- genome.duke.edu -:- lappland.io > > ___ > 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/ -- Hilmar Lapp -:- genome.duke.edu -:- lappland.io signature.asc Description: Message signed with OpenPGP using GPGMail ___ 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] Problem with bootstraping microstallite NJ tree
> On Jan 22, 2016, at 3:16 AM, Vojtěch Zeisek <vo...@trapa.cz> wrote: > > PS: Later yesterday I have received spam answering my original post. Spammer > is obviously subscribed and harvesting mails passing through the conference > and then mailing users off-list. Just to clarify for everyone, the perpetrators of this kind of spam are *not* subscribed, at least not with the address (or one similar to it) that they are spamming from. I can say this because I’ve blocked the whole TLD (.xyz) from subscribing, and no .xyz emails are subscribed. It is of course possible that the perpetrators *are* subscribed with a legit-looking email, and then spam from throw-away addresses. This would be very difficult to combat (there are currently > 1000 subscribers to this list, making it futile to try to scrutinize every subscribed address). It is also possible (and much more likely IMO) that the perpetrators feed off of a public mailing list archive. I just noticed that the public mailman archive apparently does not obfuscate the sender addresses (which apparently is controlled by a setting not available to list administrators, but only to sysadmins at the host). I am probably going to make the list archives private, which would require people perusing an indexed public 3rd party mail archive (such as that at http://www.mail-archive.com/r-sig-phylo@r-project.org/). Those are much more usable than the mailman archive anyway, so perhaps the impact of this step in terms of accessibility may be small. -hilmar -- Hilmar Lapp -:- genome.duke.edu -:- lappland.io signature.asc Description: Message signed with OpenPGP using GPGMail ___ 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] thread response spam
Evidence has been brought to my attention that meanwhile spam accounts do subscribe to the mailing list, and then send spam as on-thread responses to senders and/or non-list recipients of messages, possibly spoofing the list as the legitimate sender or recipient. If this has happened to you, please email me off-list with the offending email account(s). It seems that at this time this issue is rather minor, but if it starts to get out of hand, I’ll change list subscription to moderate new members for their first post. -hilmar -- Hilmar Lapp -:- genome.duke.edu<http://genome.duke.edu> -:- lappland.io<http://lappland.io> [[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] continued maintenance of the R-Phylo wiki
Dear comparative phylogeneticists community, The Phylogenetic Comparative Methods wiki at http://www.r-phylo.org/, which is an outcome of the same venerable hackathon in 2007 that resulted in the founding of this list, has been hosted by NESCent. As you may be aware, NESCent is closing this summer, and as a consequence won't be able to provide continued hosting and maintenance of the wiki. We are currently making plans for transfer, archival and deletion of digital resources that we host, including the the R-Phylo wiki. The wiki contains tutorials on many different comparative analyses, but has had only minimal edits in the last few years [1]. Is this resource still of value to the community? If so, we welcome proposals for transferring hosting the wiki and/or its contents. A proposal should include a plan for transfer of content, information on where the resulting site would be hosted and a statement about plans for future sustainability of the resource. If we do not hear expressions of interest in transfer of hosting before May 22 2015, then the wiki will have to be taken offline when NESCent closes. An XML dump of the wiki contents will be placed in the NESCent digital archive with Duke Libraries, but will not be publicly accessible. FYI, we have just recently upgraded the MediaWiki version running the R-Phylo wiki to the latest version, and we installed the Google Login plugin (because Google's OpenID support, which used to be used for federated authentication, was sunset as of April 20). If someone or an institution or organization is willing to take over hosting, we will have resources until June 30 to assist with the transfer. Later transfers could potentially be negotiated, but will have to complete by Sep 2015. P.S. #1 To head off one question some of you may be asking yourselves, this does not affect this mailing list. The mailing list is not hosted by NESCent. I *am* the moderator, and don't mind doing that for some time longer, though I wouldn't mind sharing this with one or two other people. The load from that is relatively light, typically only a few spam and a few legit emails to be dealt with in the moderation queue per week. P.S. #2 I should note that I also (personally) own the r-phylo.org domain name(and in fact rphylo.org too) . If the R-Phylo wiki isn't going to persist and someone has plans or ideas for how to use this domain name in other ways that benefit this community, let me know and I'd be happy to consider transferring it. -hilmar [1] http://www.r-phylo.org/wiki/Special:AncientPages -- Hilmar Lapp -:- informatics.nescent.org/wiki -:- lappland.io ___ 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] continued maintenance of the R-Phylo wiki
On 5/6/15, 4:56 PM, Hilmar Lapp wrote: If we do not hear expressions of interest in transfer of hosting before May 22 2015, then the wiki will have to be taken offline when NESCent closes. An XML dump of the wiki contents will be placed in the NESCent digital archive with Duke Libraries, but will not be publicly accessible. Actually let me correct myself. The XML dump would be placed in a publicly accessible archive (because this is one of our public wikis), likely in a NESCent collection we are putting together on Zenodo (see https://zenodo.org/collection/user-nescent). The XML dump will allow re-instating the wiki from it, but accounts and edit history would be lost. -hilmar -- Hilmar Lapp -:- informatics.nescent.org/wiki -:- lappland.io ___ 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] Population Genetics in R Hackathon - Open Call for Participation
# Population Genetics in R Hackathon - Open Call for Participation Do you develop population genetics methods or algorithms in R? Are you a researcher wrestling with analyzing population genetics data in R? Have you run into difficulties with passing data or metadata from one R package to another? Have you run into problems with large datasets? Have you found documentation on building workflows from packages for population genetics analysis difficult to come by? Do you have expertise and ideas to share and energy to spend on overcoming these challenges? Do you enjoy collaborating with like-minded others to do so? If you answered some (or all) of these questions with yes, then the following event may be for you. ## Synopsis NESCent is sponsoring a hackathon to be held at NESCent in Durham, North Carolina, on March 16-20, 2015, with the objective to help foster an interoperating ecosystem of scalable tools and resources for population genetics data analysis in the popular R platform. The event is designed to target interoperability, scalability, and workflow building challenges among the many population genetics R packages that already exist. The gathering provides an opportunity for a diverse group of population genetics researchers, method developers, and people with other relevant areas of expertise to collaborate on code, documentation, use-cases, and other resources that will aid their communities. Full details and additional background are available at the following website: http://informatics.nescent.org/wiki/R_PopGen_Hackathon ## How to participate Applications to participate in the hackathon are now being accepted. To apply, please fill out the following form: http://goo.gl/forms/siwNo1P3ti Deadline for receiving your application is December 11, 2014. Support for travel, food and lodging costs are available to successful applicants who indicate need. We particularly welcome applications from women and members of other groups underrepresented in science and in software engineering. Our plan is to begin sending out acceptance letters December 15, 2014, and if your application is successful, we will need you to confirm attendance within 2 days of receiving notice, so please ensure you can receive and send email during the week of December 15. Sincerely, The organizing team: Thibaut Jombart, Hilmar Lapp, St�phanie Manel, Emmanuel Paradis, Bastian Pfeifer, and Greg Warnes -- Hilmar Lapp -:- informatics.nescent.org/wiki -:- lappland.io [[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] Transition matrix for ace in ape
Great, Rosemary! If you encounter a problem with editing something on the wiki, do let me know. -hilmar On Fri, May 23, 2014 at 5:29 PM, Rosemary McCloskey rmcclosk.m...@gmail.com wrote: Thanks! I didn't see an edit button, which is why I asked, but I figured out that you have to be a user to edit the wiki and made the change. On 14-05-23 01:48 PM, Sam Price wrote: Hi Rosemary, You are correct the wiki has a typo, as it is a wiki so you should be able to correct yourself! Sam --- Samantha Price, Ph.D. Dept. Evolution Ecology 1 Shields Ave, UC Davis Davis, CA 95616 USA Tel: +1 530-752-4720 Website: www.evovert.com http://www.evovert.com --- On May 23, 2014, at 9:34 AM, Rosemary McCloskey rmcclosk.m...@gmail.commailto: rmcclosk.m...@gmail.com wrote: Hello, I'm trying to do ancestral reconstruction of a discrete character state using ace. I'm referencing the Ancestral State Reconstruction HowTo on the R phylo wiki (http://www.r-phylo.org/wiki/HowTo/Ancestral_State_ Reconstruction). It says how to use a custom model with ace: What if you want to use a transition model that isn't hardwired into ace? You can do so by defining a custom transition matrix. For example, let's create a custom four-parameter matrix for a three state character, in which the the probability of transitioning from state 1 to 2 equals the probability of state 2 to 1 (parameter 1), the probability of transitioning from 1 to 3 equals the probability of transitioning from state 3 to 1 (parameter 2), but the probability of transitioning from state 2 to 3 (parameter 3) does not necessarily equal the probability of transitioning from state 3 to 2 (parameter 4). Right below, on the page, it shows this matrix: [,1] [,2] [,3] [1,] 0 1 2 [2,] 1 0 4 [3,] 2 3 0 Isn't this the transpose of how model matrices normally work? I would expect the probability of transitioning from state 2 to 3 (parameter 3) to be in position [2,3], but it's in position [3,2] here. I realize that it doesn't make a difference in this case, but in my case I'm trying to define a non-reversible model so it does matter. So, sorry if this is a dumb question, but I just want to make sure: when passing a custom rate matrix to ace, does the transition from state i to state j go in position [i,j] of the matrix, or in position [j,i]? If this is just a typo in the wiki, who do I contact about correcting it? Thanks! Rosemary ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org mailto: 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/ ___ 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/ -- Hilmar Lapp -:- informatics.nescent.org/wiki -:- lappland.io [[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] ATTN Liam Revell: please contact me off-list
I responded to Gabe off-list. I have been highly impressed with the near universal quality and on-subjectness of the posts on this list. Let's keep it that way. -Your moderator. On Oct 3, 2013, at 9:57 AM, Gabriel Yedid wrote: This is a shout-out to Liam Revell: I've been trying to contact you off-list but I'm not sure if my messages have been getting through. Please contact me at gyedi...@gmail.com. We now return you to your regularly scheduled programming... cheers, Gabe [[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/ -- === : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : === signature.asc Description: Message signed with OpenPGP using GPGMail ___ 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] phylogenetic regression and pPCA with intraspecific variability
FYI, I responded to Tanja. Her original email posted yesterday. -hilmar On Aug 20, 2013, at 7:13 AM, Tanja Vukov wrote: Dear mailing list moderator, I sent mail before more that 24 hours (you can see e-mail below) and I am still waiting to see it on mailing list. Did I do something wrong with mail format or my email is not legitimate from some other reason? I answered to some other posts on this list and you posted my answers almost immediately. Kind regards, Tanja -- Forwarded message -- From: Tanja Vukov tvu...@gmail.com Date: Mon, Aug 19, 2013 at 9:53 AM Subject: phylogenetic regression and pPCA with intraspecific variability To: r-sig-phylo@r-project.org Dear all, I am using pPCA with size corrected traits (obtained by phyl.resid) as a part of ecomorphology study of 20 salamander‚s species (whole process is done with mean values of traits per species). Few days ago I discovered a way to test for phylogenetic signal (Blomberg‚s K) with intraspecific variability. I wondering is there a way to do size correction (via phylogenetic regression) and pPCA taking intraspecific variability into account (by using multiple observations per species)? Thank you very in advance! Kind regards, Tanja Vukov. Institute for biological research Dept. of evolutionary biology Bulevar despota Stefana 142 11000 Belgrade Serbia [[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/ -- === : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : === ___ 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] Last reminder: Deadline for iEvoBio Challenge Competitions is approaching
The deadline for submissions to the yearly iEvoBio Challenge is June 25, 2012, and is rapidly approaching! This is our last reminder. This year’s theme is Synthesizing Phylogenies, and further information on criteria for challenge entries, how to submit them, and award amount can be found at http://ievobio.org/challenge.html. Also, Biomatters Ltd is running the Geneious Challenge alongside iEvoBio’s competition. The goal of this challenge is to develop a new and exciting visualization or analysis plugin to Geneious Pro, using the public API. See http://ievobio.org/geneious_challenge.html for more information. The deadline for this competition is also June 25. More details about the iEvoBio conference and program are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio and Google+ page, or subscribe to the low-traffic iEvoBio announcements mailing list at http://groups.google.com/group/ievobio-announce. iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Society of Systematic Biologists (SSB). The iEvoBio 2012 Organizing Committee: Hilmar Lapp, US National Evolutionary Synthesis Center (chair) Robert Beiko, Dalhousie University Nico Cellinese, University of Florida Robert Guralnick, University of Colorado at Boulder Rebecca Kao, Denver Botanic Gardens Ellinor Michel, Natural History Museum, London Nadia Talent, Royal Ontario Museum Andrea Thomer, University of Illinois at Urbana-Champaign ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Mentorship program the 2012 iEvoBio conference
The iEvoBio Mentorship Program pairs undergraduate and graduate students with faculty who have extensive experience in evolution, systematics, biodiversity, mathematics and/or software development to enhance their experience at iEvoBio 2012. Mentors will guide participants in collaborative and networking opportunities throughout the two-day conference. If you would like to gain the wisdom of your colleagues' experiences by participating in this program, please email the iEvoBio 2012 organizing committee at commit...@ievobio.org by June 1, indicating if you have any activities you would like to be included in the mentorship program, or a particular field of interest. You can find more information about the meeting and registration at http://ievobio.org/. iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Systematic Biologists (SSB). The iEvoBio 2012 Organizing Committee: Hilmar Lapp, US National Evolutionary Synthesis Center (chair) Robert Beiko, Dalhousie University Nico Cellinese, University of Florida Robert Guralnick, University of Colorado at Boulder Rebecca Kao, Denver Botanic Gardens Ellinor Michel, Natural History Museum, London Nadia Talent, Royal Ontario Museum Andrea Thomer, University of Illinois at Urbana-Champaign ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Call for Software Bazaar entries open for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
The Call for Software Bazaar entries is now open for the 2012 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), at http://ievobio.org/ocs2/index.php/ievobio/2012. See below for instructions. The Software Bazaar features presenters demonstrating their software live on a laptop. At iEvoBio, this session takes the place of a poster session, and will be approximately 2.0 hours in duration. Conference attendees will be able to walk from one demonstration to the next and talk with the presenters. Please also see our FAQ (http://ievobio.org/faq.html). Entries should be software aimed at advancing research in phylogenetics, evolution, and biodiversity, and can include interactive visualizations that have been pre-computed (such as SVGs, or Google Earth-compatible KML files). Note that commercial marketing activities are not permitted - presenters wishing to promote commercial or proprietary services or products should contact the Evolution conference about exhibitor space (http://www.confersense.ca/Evolution2012). Submissions consist of a title, which will typically be the name of the software (or visualization method) being presented, the URL of a website where more information can be obtained, and the license under which the source code is available. The website must contain a link to where the source code (and possibly binaries) can be downloaded. If it is not obvious from the website, the submission must describe what the software does. Reviewers will judge whether a submission is within scope of the conference (see above), and need to be able to verify whether the open-source requirement(*) is met. Presenters are expected to bring their own laptops for presentation, and any auxiliary devices necessary (such as a mouse). Power will be available at the presentation tables (110V/60Hz, US-style plugs; international presenters need to bring a suitable adaptor). Please let the organizing committee know as much in advance as possible if you expect to have unusually high demands for wireless network bandwidth, a large display, or other hardware. Review and acceptance of Software Bazaar submissions will be on a rolling basis. The deadline for submission is the morning of the first day of the conference (July 10), but, because space for Software Bazaar presentations is finite, we cannot guarantee the availability of slots for late submissions. We cannot accept submissions until the open-source requirements are met. Software Bazaar demonstrations are only 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Full talks (closed), 2) Lightning talks, 3) Challenge entries, and 4) Birds-of-a-Feather gatherings. The Calls for Challenge entries (http://ievobio.org/challenge.html) and Lightning Talks (same submission URL as above) remain open, and the Birds-of-a-Feather call is forthcoming. More details about the conference and program are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio and Google+ page, or subscribe to the low-traffic iEvoBio announcements mailing list at http://groups.google.com/group/ievobio-announce. iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Systematic Biologists (SSB). The iEvoBio 2012 Organizing Committee: Hilmar Lapp, US National Evolutionary Synthesis Center (chair) Robert Beiko, Dalhousie University Nico Cellinese, University of Florida and Florida Museum of Natural History Robert Guralnick, University of Colorado at Boulder Rebecca Kao, Denver Botanic Gardens Ellinor Michel, Natural History Museum, London Nadia Talent, Royal Ontario Museum Andrea Thomer, University of Illinois at Urbana-Champaign (*) iEvoBio and its sponsors are dedicated to promoting the practice and philosophy of Open Source software development (see http://www.opensource.org/docs/definition.php) and reuse within the research community. For this reason, software to be demonstrated to conference attendees must be licensed with a recognized Open Source License (see http://www.opensource.org/licenses/), and be available for download, including source code, by a tar/zip file accessed through ftp/http or through a widely used version control system like cvs, Subversion, git, Bazaar, or Mercurial. Authors are advised that non-compliant submissions must be revised to meet the requirement by July 8 at the latest, and in the event that presentation slots run out, precedence is established by the date they are first found in compliance, not the date of submission. ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Call for Challenge entries for conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
Many trees enter. Fresh analysis ensues. New insights emerge. The conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) is again holding a Challenge competition in 2012, on the theme Synthesizing Phylogenies. Somewhere, buried in large sets of trees, lies a stunning new revelation, a baffling discovery, the answer to a longstanding controversy, or simply something not obvious to the naked eye. The mission of the 2012 iEvoBio challenge is to find those revelations, discoveries and answers within your own data and/or within one of the datasets provided by the challenge. What new scientifically interesting results can you pull from these trees, using any combination of techniques at your disposal? Further information on the nature of challenge entries and how to submit them can be found on the iEvoBio website at http://ievobio.org/challenge.html. Submissions are due by June 25, 2012. Selected candidates will make short oral presentations to demonstrate their work in a Challenge session at the conference, and if suitable will automatically be entered into the Software Bazaar track of the conference. Cash prizes will be awarded for first place (USD 1,500) and runner-up entries. The winning entries will be selected by a vote of the iEvoBio meeting participants. Alongside the iEvoBio Challenge, 2012 iEvoBio sponsor Biomatters Ltd is running the Geneious Challenge. The goal of this challenge is to develop a new plugin to Geneious Pro, using the public API, that enables a new and exciting visualization or analysis. The winning entry will receive a $1000 cash prize, and all entrants who submit by the deadline will receive a 12-month subscription license. The Geneious Challenge has the same open and closing dates as the iEvoBio Challenge. See http://ievobio.org/geneious_challenge.html for more information. Separate from iEvoBio, the Encyclopedia of Life (EOL) is leading a Phylogenetic Tree challenge to encourage not only the development of large phylogenies, but their practical use. Together with the Global Names project they will choose two winning entries: one for the best large tree and one for the most promising but not necessarily large tree -- both in Darwin Core Archive format suitable for use in major biodiversity websites such as EOL. The two winners will receive paid trips to the 2012 iEvoBio conference. See http://eol.org/info/tree_challenge for more information. More details about the iEvoBio conference and program are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio and Google+ page, or subscribe to the low-traffic iEvoBio announcements mailing list at http://groups.google.com/group/ievobio-announce. iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Systematic Biologists (SSB). The iEvoBio 2012 Organizing Committee: Hilmar Lapp, US National Evolutionary Synthesis Center (chair) Robert Beiko, Dalhousie University Nico Cellinese, University of Florida Robert Guralnick, University of Colorado at Boulder Rebecca Kao, Denver Botanic Gardens Ellinor Michel, Natural History Museum, London Nadia Talent, Royal Ontario Museum Andrea Thomer, University of Illinois at Urbana-Champaign ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Call for Lightning Talks now open for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
The Call for Lightning Talks is now open for the 2012 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), at http://ievobio.org/ocs2/index.php/ievobio/2012. See below for instructions. Lightning talks are short presentations of 5 minutes. They are ideal for drawing the attention of the audience to new developments, tools, and resources, or to subsequent events where more in-depth information can be obtained. Please also see our FAQ for more information (http://ievobio.org/faq.html#lightning). Lightning talks will be part of the more interactive program elements on both conference days. Submitted talks should be in the area of informatics aimed at advancing research in phylogenetics, evolution, and biodiversity, including new tools, cyberinfrastructure development, large-scale data analysis, and visualization. Submissions should be 1 page long at most and include a title, a list of contributors, and an abstract. The abstract should provide an overview of the talk's subject. Reviewers will judge whether a submission is within scope of the conference (see above). If applicable, the abstract must also state the license and give the URL where the source code is available so reviewers can verify that the open-source requirement(*) is met. Review and acceptance of lightning talks will be on a rolling basis. The deadline for submission is the morning of the first day of the conference (July 10), but see below. Further instructions for submission are at the following URL: http://ievobio.org/ocs2/index.php/ievobio/2012/schedConf/cfp Please make sure to choose the Lightning Talks track for your submission. Note that the number of lightning talk slots is finite and that therefore the track may fill up early. We cannot accept lightning talks until the open-source requirements are met, and so waiting with that until the deadline risks that the track is full by that time. We ask all submitters of lightning talks to be willing to also serve as reviewers of such, as described above. Lightning talks are only 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Full talks (open until April 2), 2) Challenge entries, 3) Software bazaar demonstrations, and 4) Birds-of- a-Feather gatherings. The Call for Challenge entries remains open (see http://ievobio.org/challenge.html). The calls for contribution to the other two sessions will open later, and will remain open until shortly before the conference or until the respective track fills up. In addition, 2012 iEvoBio sponsor Biomatters Ltd will be running the Geneious Challenge alongside this year’s iEvoBio Challenge, see http://ievobio.org/geneious_challenge.html for more information. More details about the conference and program are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio and Google+ page, or subscribe to the low-traffic iEvoBio announcements mailing list at http://groups.google.com/group/ievobio-announce. iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Systematic Biologists (SSB). The iEvoBio 2012 Organizing Committee: Hilmar Lapp, US National Evolutionary Synthesis Center (chair) Robert Beiko, Dalhousie University Nico Cellinese, University of Florida and Florida Museum of Natural History Robert Guralnick, University of Colorado at Boulder Rebecca Kao, Denver Botanic Gardens Ellinor Michel, Natural History Museum, London Nadia Talent, Royal Ontario Museum Andrea Thomer, University of Illinois at Urbana-Champaign (*) iEvoBio and its sponsors are dedicated to promoting the practice and philosophy of Open Source software development (see http://www.opensource.org/docs/definition.php) and reuse within the research community. For this reason, if a submitted talk concerns a specific software system for use by the research community, that software must be licensed with a recognized Open Source License (see http://www.opensource.org/licenses/), and be available for download, including source code, by a tar/zip file accessed through ftp/http or through a widely used version control system like cvs, Subversion, git, Bazaar, or Mercurial. ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Call for Abstracts open for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
The Call for Abstracts for full talks is now open for the 2012 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), at http://ievobio.org/ocs2/index.php/ievobio/2012. See below for instructions. Accepted talks will be 15 minutes in length and will be presented during the full talk session of the conference. Because the number of program slots for full talks is limited, some talks may be moved to the Lightning Talk session (5 minutes in length). Submitted talks should be in the area of informatics aimed at advancing research in phylogenetics, evolution, and biodiversity, including new tools, cyberinfrastructure development, large-scale data analysis, and visualization. Submissions should be 1 page long at most and include a title, a list of contributors, and an abstract. The abstract should provide an overview of the talk's subject, and give enough detail to allow reviewers to decide whether the submission merits a full talk, or whether it should be moved to a Lightning Talk session. If the subject of the talk is a specific software component for use by the research community, the abstract must state the license and give the URL where the source code is available so reviewers can verify that the open-source requirement(*) is met. The deadline for submission is April 2, 2012. We intend to notify authors of accepted talks before early registration for iEvoBio (and Evolution) ends. Further instructions for submission are at the following URL: http://ievobio.org/ocs2/index.php/ievobio/2012/schedConf/cfp Full talks are one of the five kinds of contributed content that feature in iEvoBio. The other four are: 1) Lightning talks (5 mins long), 2) Challenge entries, 3) Software bazaar demonstrations, and 4) Birds-of-a-Feather gatherings. The Call for Challenge entries is already open (see http://ievobio.org/challenge.html). The calls for contribution to the other three sessions will open later, and will remain open until shortly before the conference or until the respective track fills up. In addition, 2012 iEvoBio sponsor Biomatters Ltd will be running the Geneious Challenge alongside this year’s iEvoBio Challenge, see http://ievobio.org/geneious_challenge.html for more information. More details about the conference and program are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio and Google+ page, or subscribe to the low-traffic iEvoBio announcements mailing list at http://groups.google.com/group/ievobio-announce. iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Systematic Biologists (SSB). The iEvoBio 2012 Organizing Committee: Hilmar Lapp, US National Evolutionary Synthesis Center (chair) Robert Beiko, Dalhousie University Nico Cellinese, University of Florida and Florida Museum of Natural History Robert Guralnick, University of Colorado at Boulder Rebecca Kao, Denver Botanic Gardens Ellinor Michel, Natural History Museum, London Nadia Talent, Royal Ontario Museum Andrea Thomer, University of Illinois at Urbana-Champaign (*) iEvoBio and its sponsors are dedicated to promoting the practice and philosophy of Open Source software development (see http://www.opensource.org/docs/definition.php) and reuse within the research community. For this reason, if a submitted talk concerns a specific software system for use by the research community, that software must be licensed with a recognized Open Source License (see http://www.opensource.org/licenses/), and be available for download, including source code, by a tar/zip file accessed through ftp/http or through a widely used version control system like cvs, Subversion, git, Bazaar, or Mercurial. Authors of full talks who cannot meet this requirement at the time of submission should state their intentions, and are advised that the requirement must be met by July 9, 2012, at the latest. ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] comar.gee
I don't know whether anyone's had a chance, so apologies if this is redundant. And, finally I can contribute something that's potentially useful :) On Nov 30, 2011, at 4:17 AM, Emmanuel Paradis wrote: Can you translate the error message from R? [...] stefan.abrahamc...@systbot.uzh.ch wrote on 24/11/2011 22:19: [...] Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 Fehler in model.frame.default(formula = Suc ~ Bestaeu, id = c(1, 1, 1, : Error in model.frame.default(...) Variablenlängen sind unterschiedlich (gefunden für '(id)') Length of variables differ (found for '(id)') -hilmar -- === : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : === ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Birds-of-a-Feather gatherings for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
In anticipation of the 2011 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), we solicit all attendees to propose and discuss Birds-of-a-Feather gatherings. See below for details. Birds-of-a-Feather gatherings (BoFs) are informal, ad-hoc, focused face-to-face discussion groups that form around a shared interest. BoFs can also take the form of a hands-on software tutorial on using a tool, or on programming an API. BoFs have a leader (usually, but not necessarily, the proposer) who initiates or moderates the discussion. The topics of BoFs can range widely, including general cultural or computational infrastructure issues, or narrower questions such as how to make the best use of a particular software tool or how to solve a particular computational challenge. Anyone willing to lead such a group can propose a BoF. iEvoBio will provide space that can accommodate up to 8-10 BoFs. Sign-up sheets will be provided on-site on the first day of the conference where attendees can propose a BoF or sign up for one proposed by someone else. BoFs will be about 1-1.5 hours in duration and take place in the afternoon of the second day of the conference. In line with their informal nature, there is no official prior call for or submission of BoFs. However, we encourage those intending to propose one to sound out or rally potential attendees ahead of time. We suggest to employ Twitter (http://twitter.com) for this, using the #ievobioBof tag to mark BoF proposals and comments. Similarly, users interested in seeing a hands-on tutorial BoF about their favorite tool are encouraged to use similar means to give tool developers a sense of the community interest in a tutorial BoF, and what common usage (or programming) questions are. Birds-of-a-Feather gatherings are only 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Full talks (closed), 2) Lightning talks, 3) Challenge entries, and 4) Software Bazaar entries. All Calls except for Full Talks remain open (see http://ievobio.org/ocs/index.php/ievobio/2011/) . More details about the program and guidelines for contributing content are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio. iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society for the Study of Evolution (SSE) and the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2011 Organizing Committee: Rob Guralnick (University of Colorado at Boulder) (Co-chair) Cynthia Parr (Encyclopedia of Life) (Co-chair) Dawn Field (UK National Environmental Research Center) Mark Holder (University of Kansas) Hilmar Lapp (NESCent) Rod Page (University of Glasgow) ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] PGLS (nlme?) problem, cont.
Hi Dan, this is easy accomplish using pastebins. Github has one meanwhile too, called gist, at gist.github.com, which has syntax highlighting and will turn snippets into cloneable etc git repos. Here's the one I created as an example from your code snippet: https://gist.github.com/999363 There are many pastebin services, such as http://pastebin.com, and many of them come with syntax highlighting too. -hilmar On May 30, 2011, at 3:20 PM, Dan Rabosky wrote: Howdy again- I suspect that the code chunk I just sent to illustrate the possible problem with gnls() is not going to work, due to line break and other issues (having just tried pasting and executing the text I just sent to everyone). If you are interested in the problem, I'll send you an attachment directly! Thanks! ~Dan ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- === : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Special Session on Metagenomics, Barcoding, and Biodiversity at iEvoBio (Informatics for Phyogenetics, Evolution, and Biodiversity)
This year, iEvoBio will have a special focus Session on Metagenomics, Barcoding, and Biodiversity and the challenges that these new approaches raise for evolutionary informatics. We now have over 6000 genomes and vast quantities of metagenomic sequences in the public domain, primarily from bacteria and archaea from many habitats. Various short sequences (e.g. barcodes) for quick identification of eukaryotes are emerging. The availability of this sequence data and ever-cheaper methods for producing it offer exciting opportunities forunderstanding molecular evolution and biodiversity. However, the data are growing faster than the infrastructure to support it. Moreover, the eukaryotic and microbial informatics communities have independent histories and approaches, so synergy is not easy. These challenges typify the intersection of fields that are the scope of iEvoBio. Invited speakers in this special session include Neil Davies (http://moorea.berkeley.edu/aboutus/people/ndavies ) from the Moorea Biocode project, Linda Amarral-Zettler (http://amarallab.mbl.edu/ ) from the Marine Biological Laboratory Wood's Hole, and Holly Bik, from the Hubbard Center for Genome Studies at the University of New Hampshire. After the talks, there will be an open panel with all the speakers, including keynote speaker Dawn Field (http://ceh.academia.edu/DawnField ) from the Center for Ecology and Hydrology at Oxford. More details about the program and guidelines for contributing content are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio. iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society for the Study of Ecolution (SSE) and the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2011 Organizing Committee: Rob Guralnick (University of Colorado at Boulder) (Co-chair) Cynthia Parr (Encyclopedia of Life) (Co-chair) Dawn Field (UK National Environmental Research Center) Mark Holder (University of Kansas) Hilmar Lapp (NESCent) Rod Page (University of Glasgow) ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] Running Mesquite.R
Hi Alanna,
I'm afraid I can't help you much on the Mesquite side, and that I
don't use Windows doesn't help either, but would you mind posting your
query to the Mesquite users list (which I know Wayne reads)? I could
do that for you, but then you might miss the answers.
-hilmar
On Apr 12, 2011, at 12:27 PM, Alanna Maltby wrote:
Dear all
I am having trouble installing Mesquite for R on both my computers.
On my laptop I am running Windows 7 32 bit and on my desktop I am
running Windows XP 64 bit. Both have the latest versions of Java
(the 64 bit version one on my desktop), R and Mesquite installed. I
have installed R packages ape and rJava as well.
On my desktop I have installed Mesquite for R and I can see the R
options on the menu when I 'Trace Character History', but clicking
on them results in the error R can't be started. It appears that
the JRI library file cannot be found. See log for more details. I
can see the jri.dll file in the folder 'lib', but apparently
Mesquite can't. Any ideas?
On my laptop I can't get Mesquite for R to install. When I try to
install it, I get the error: Installation was UNSUCCESSFUL;
Mesquite will attempt to restore any previous versions.
Uninstalling and reinstalling Mesquite makes no difference.
Any thoughts much appreciated - I only need it to work on one of my
computers!
Best wishes,
Alanna
-
Alanna Maltby
PhD Student - Evolution of Echolocation in Bats
University College London and Institute of Zoology
Tel: 020 7449 6322
Web: www.zsl.org/alannamaltby
The Zoological Society of London is incorporated by Royal Charter
Principal Office England. Company Number RC000749
Registered address:
Regent's Park, London, England NW1 4RY
Registered Charity in England and Wales no. 208728
_
This e-mail has been sent in confidence to the named a...{{dropped:15}}
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Re: [R-sig-phylo] chronopl
Hi Emmanuel: On Apr 11, 2011, at 12:55 AM, Emmanuel Paradis wrote: You should not used the transformation suggested on this wiki (it is a bit outdated, NPRS has been removed from ape). In most situations, you should just leave S=1. The wiki can be updated (by anyone, in fact). How would you suggest should this be corrected to be current? -hilmar -- === : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Phyloinformatics Summer of Code 2011 - Call for student applications
*** Please disseminate widely at your local institutions, ***
*** including posting to message and job boards, so that ***
*** we reach as many interested students as possible. ***
PHYLOINFORMATICS SUMMER OF CODE 2011
http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011
The Phyloinformatics Summer of Code program provides a unique
opportunity for undergraduate, masters, and PhD students to obtain
hands-on experience writing and extending open-source software for
evolutionary informatics under the mentorship of experienced
developers from around the world. The program is the participation of
the US National Evolutionary Synthesis Center (NESCent) as a mentoring
organization in the Google Summer of Code(tm) (http://code.google.com/soc/
).
Students in the program will receive a stipend from Google (and
possibly more importantly, a T-shirt solely available to successful
participants), and may work from their home, or home institution, for
the duration of the 3 month program. Each student will have at least
one dedicated mentor to show them the ropes and help them complete
their project.
NESCent is particularly targeting students interested in both
evolutionary biology and software development. Initial project ideas
are listed on the website. These range from visualizing viral
epidemics to 3D protein structure evolution, rich annotation for
TreeBASE content, exposing phenotype observations to the Encyclopedia
of Life, to enhancing R packages for phylogenetic analysis. All
project ideas are flexible and many can be adjusted in scope to match
the skills of the student. We also welcome novel project ideas that
dovetail with student interests.
TO APPLY: Apply online at the Google Summer of Code website (http://socghop.appspot.com/
), where you will also find GSoC program rules and eligibility
requirements. Each organization has a slightly different application
format, and ours is at http://bit.ly/PhyloSoC2011-apptemplate. The 12-
day application period for students opens on Monday, March 28th, and
runs through Friday, April 8th, 2011.
INQUIRIES: phylosoc {at} nescent {dot} org. We strongly encourage all
interested students to get in touch with us with their ideas as early
on as possible. Working closely with potential mentors to develop your
project proposal greatly increases your chance for acceptance. Do not
underestimate the amount of time it takes to develop a competitive
proposal.
2011 NESCent Phyloinformatics Summer of Code:
http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011
Google Summer of Code FAQ:
http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2011/faqs
-
Karen Cranston and Hilmar Lapp
National Evolutionary Synthesis Center
http://nescent.org
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Re: [R-sig-phylo] reading nexus file from treebase?
Thanks for tracking this down, Emmanuel. I'm forwarding this to the TreeBASE developers list for consideration. BTW the phylobase implementation uses NCL (NEXUS Class Library, in C+ +) for parsing NEXUS. Given the difference, probably ape does not? -hilmar On Mar 25, 2011, at 12:00 AM, Emmanuel Paradis wrote: Scott, readNexus (phylobase) can read your tree but not read.nexus (ape). The problem is the two lines inserted within the TREES block: BEGIN TREES; TITLE Tb10793; LINK TAXA = M4787; TREE Fig._3c = [R] If you delete them, it's OK. FigTree also cannot read this file. Cheers, Emmanuel François Michonneau wrote on 25/03/2011 00:35: Hi Scott, Which version of phylobase are you using and which architecture? I can read the file on my machine. Cheers, -- François On Thu, Mar 24, 2011 at 12:39, Scott Chamberlain myrmecocys...@gmail.com wrote: Hello, I can't get read.nexus (ape) or readNexus (phylobase) to read nexus files downloaded from treebase with URLs parsed from xml files. I can't manually edit each file as I want to read a lot of these files. Is there an easy fix? One of the files is copied below. Thanks! Scott Chamberlain Rice University, EEB Dept. #NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Downloaded on March 24, 2011; 16:32 GMT TreeBASE (cc) 1994-2008 Study reference: Brown R., Yang Z. 2010. Bayesian Dating of Shallow Phylogenies with a Relaxed Clock. Systematic Biology, 59(2): 119-131. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10165] BEGIN TAXA; TITLE M4787; DIMENSIONS NTAX=16; TAXLABELS Chalcides_coeruleopunctatus_E2806.20 Chalcides_coeruleopunctatus_E2806.22 Chalcides_manueli_E2506.1 Chalcides_mionecton_mionecton_E2506.10 Chalcides_mionecton_mionecton_E2506.12 Chalcides_mionecton_trifasciatus_E2506.18 Chalcides_polylepis_E14124.1 Chalcides_polylepis_E14124.2 Chalcides_polylepis_E2506.21 Chalcides_sexlineatus_bistriatus_E2806.6 Chalcides_sexlineatus_sexlineatus_E2806.8 Chalcides_simonyi_E3007.2 Chalcides_sphenopsiformis_E8121.26 Chalcides_sphenopsiformis_E8121.27 Chalcides_viridanus_E2806.10 Chalcides_viridanus_E2806.14 ; END; BEGIN TREES; TITLE Tb10793; LINK TAXA = M4787; TREE Fig._3c = [R] ((Chalcides_sphenopsiformis_E8121.26,Chalcides_sphenopsiformis_E8121.27),(((Chalcides_viridanus_E2806.10,Chalcides_viridanus_E2806.14),((Chalcides_sexlineatus_bistriatus_E2806.6,Chalcides_sexlineatus_sexlineatus_E2806.8),(Chalcides_coeruleopunctatus_E2806.22,Chalcides_coeruleopunctatus_E2806.20))),(Chalcides_simonyi_E3007.2,((Chalcides_mionecton_trifasciatus_E2506.18,(Chalcides_mionecton_mionecton_E2506.12,Chalcides_mionecton_mionecton_E2506.10)),(Chalcides_manueli_E2506.1,(Chalcides_polylepis_E14124.1,(Chalcides_polylepis_E14124.2,Chalcides_polylepis_E2506.21))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr6136] END; [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- === : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : === ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Reminder: Deadline for full talk abstracts for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
(Apologies if you receive multiple copies.) This is a reminder that the deadline for submitting abstracts for full talks to the 2011 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) is Friday, March 25, 2011, which is just two days away. Please see http://bit.ly/iEvoBio2011_CfA for the full Call for Abstracts and author instructions. As another reminder, full talks are only 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Lightning talks (5 mins long), 2) Challenge entries, 3) Software bazaar demonstrations, and 4) Birds-of-a-Feather gatherings. The Call for Challenge entries is also open (see http://ievobio.org/ challenge.html). Tentative submission deadlines are listed on the conference website (http://ievobio.org/program.html#dates). More details about the program and guidelines for contributing content are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/ iEvoBio, and there is an announcement-only Google group at http://groups.google.com/group/ievobio-announce . You can use the group's RSS feed (linked from its URL), or join the group to receive announcements by email. iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society for the Study of Ecolution (SSE) and the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2011 Organizing Committee: Rob Guralnick (University of Colorado at Boulder) (Co-chair) Cynthia Parr (Encyclopedia of Life) (Co-chair) Dawn Field (UK National Environmental Research Center) Mark Holder (University of Kansas) Hilmar Lapp (NESCent) Rod Page (University of Glasgow) ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Deadline extension for full talk abstracts for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
The deadline for submitting abstracts for full talks to the inaugural conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) has been extended by one week to Friday, March 25, 2011. We hope that this will give those interested in contributing sufficient time to do so. Please see http://bit.ly/iEvoBio2011_CfA for the full Call for Abstracts and author instructions. We still expect to be able to notify accepted talks in time for the early registration deadline of iEvoBio (and Evolution). More details about the program and guidelines for contributing content are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/ iEvoBio, and there is a Google group you can join at http://groups.google.com/group/ievobio-announce to receive announcements. iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society for the Study of Ecolution (SSE) and the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2011 Organizing Committee: Rob Guralnick (University of Colorado at Boulder) (Co-chair) Cynthia Parr (Encyclopedia of Life) (Co-chair) Dawn Field (UK National Environmental Research Center) Mark Holder (University of Kansas) Hilmar Lapp (NESCent) Rod Page (University of Glasgow) ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] Dealing with Bounded Trait Measures
actually are at that bound? I have several traits where the bound is zero, and some taxa are actually at zero for this trait. (A practical example is 'spine length', where some taxa have virtually no spine.) And if there is no transformation applicable, is it analytically appropriate to remove taxa that have 'zero units' for that trait? Must we convert these traits to discrete categories to deal with them at all? As always, I appreciate your advice. -Dave Bapst, UChicago -- Enrico L. Rezende Departament de Genètica i de Microbiologia Facultat de Biociències, Edifici Cn Universitat Autònoma de Barcelona 08193 Bellaterra (Barcelona) SPAIN Telephone: +34 93 581 4705 Fax: +34 93 581 2387 E-mail: enrico.reze...@uab.cat ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo __ Alejandro Gonzalez Voyer Post-doc NEW ADDRESS Estación Biológica de Doñana Consejo Superior de Investigaciones Científicas (CSIC) Av Américo Vespucio s/n 41092 Sevilla Spain Tel: + 34 - 954 466700, ext 1749 E-mail: alejandro.gonza...@ebd.csic.es Web page: https://docs.google.com/View?id=dfs328dh_14gwwqsxcg ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- === : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : === ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Phyloinformatics Summer of Code 2011: Call for Mentors
(Apologies if you receive multiple copies.) Over the next 3 weeks we will be pulling together NESCent's application to the 2011 Google Summer of Code as a mentoring organization. This is a call for all prospective mentors, primary and secondary, to step forward. Participating as an organization is competitive. Over the last years the acceptance rate for organizations has been around 30-35%. The most important component of organization applications is the Ideas page, and specifically the quality and suitability of the project ideas. These project ideas are contributed by you, our mentors. In the past we have had a strong, diverse and well-documented portfolio of ideas with different degrees of difficulty, from different participating open-source projects, using different programming languages. If you can fancy yourself serving as a mentor, or helping someone else mentoring a student as a secondary mentor, or would like to help out in other capacities, please contact us as soon as you can at phylosoc-ad...@nescent.org . If you have not been a mentor with us in previous years, we'll send you guidance on what doing so involves, and how you can contribute to our participation. We will also add everyone who is interested in serving to our (private) mentors mailing list (at least those who aren't already). If you are new to Summer of Code and wonder what it takes or what it is like to be a mentor for us, don't hesitate to ask questions or to contact previous mentors (see URLs below for projects that got selected). Being a mentor does require time (see http://bit.ly/soc2011-mentortime) , but our past mentors have pretty much unanimously found it a fun and rewarding experience. That's aside from the code a student could contribute to your project, and, possibly most important of all in the long run, the chance to gain a new developer. The initial skeleton of our 2011 Ideas page is now up here and ready for adding project ideas and mentors(*). http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 We will send further guidance on drafting project ideas, but for now you can see examples of the format and scope of project ideas on the Ideas pages from previous years (click on Ideas): http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2010 http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2009 http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2008 http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2007 Dates: == Submission of organization applications starts Feb 28 and closes on March 11. For project ideas to contribute to the strength of our application they must be in reasonable shape by the morning of March 11. *If* we are accepted, ideas can be refined (or added) between March 18-27. Students apply March 28-April 8, and selected students are announced April 25. The coding period runs from May 23 to August 22. See http://bit.ly/soc2011-timeline for a full timeline of the whole program. Cheers, and we look forward to hearing from you! Karen Cranston Hilmar Lapp (*) Editing content on the NESCent Informatics wiki (f.k.a. Hackathon wiki) requires you to login. We had to disable local account creation due to spam getting out of control. The wiki is still open, though - just login with your OpenID. If you don't have an OpenID, the Login with OpenID page has information on you can easily get one, and if you have a Google account, you're all set to go. ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Phyloinformatics Summer of Code 2010: Call for Student Applications
(Apologies if you have received similar notices before. Note that 3 of
the project ideas listed on the page below are directly about R
package development, specifically ideas# 5, 9, and 17. The 12-day
student application period starts today.)
PHYLOINFORMATICS SUMMER OF CODE 2010
http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2010
The Phyloinformatics Summer of Code program provides a unique
opportunity for undergraduate, masters, and PhD students to obtain
hands-on experience writing and extending open-source software for
evolutionary informatics under the mentorship of experienced
developers from around the world. The program is the participation of
the US National Evolutionary Synthesis Center (NESCent) as a mentoring
organization in the Google Summer of Code(tm) (http://code.google.com/soc/
).
Students in the program will receive a stipend from Google (and
possibly more importantly, a T-shirt solely available to successful
participants), and may work from their home, or home institution, for
the duration of the 3 month program. Each student will have at least
one dedicated mentor to show them the ropes and help them complete
their project.
NESCent is particularly targeting students interested in both
evolutionary biology and software development. Initial project ideas
are listed on the website, among which are 3 that pertain directly to
R package development: #9, fast and robust ancestral state
reconstruction in R; #17, port Brownie from C++ to R; and #5,
accessing R phylogenetics tools from Python. Others include
phylogenetics pipeline development, interactive animations of gene
tree evolution, and rendering phylogenies on Google Earth and iPad
devices. Several of our mentors are regulars on this list. All project
ideas are flexible and many can be adjusted in scope to match the
skills of the student. We also welcome novel project ideas that
dovetail with student interests.
TO APPLY: Apply online at the Google Summer of Code website (http://socghop.appspot.com/
), where you will also find GSoC program rules and eligibility
requirements. The 12-day application period for students opens on
Monday March 29th and runs through Friday, April 9th, 2010.
INQUIRIES: phylosoc {at} nescent {dot} org. We strongly encourage all
interested students to get in touch with us with their ideas as early
on as possible.
2010 NESCent Phyloinformatics Summer of Code:
http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2010
-
Todd Vision and Hilmar Lapp
National Evolutionary Synthesis Center
http://nescent.org
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[R-sig-phylo] Reminder: Student application deadline for Summer of Code 2009
*** Please disseminate widely to students at your institution. ***
*** Note: Among the ideas and mentors are Phylobase and phylogenetics
in R ***
PHYLOINFORMATICS SUMMER OF CODE 2009 - STUDENT APPLICATION DEADLINE IS
APRIL 3
http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2009
The Phyloinformatics Summer of Code program provides a unique
opportunity for undergraduate, masters, and PhD students to obtain
hands-on experience writing and extending open-source software for
evolutionary informatics under the mentorship of experienced
developers from around the world. The program is the participation of
the US National Evolutionary Synthesis Center (NESCent) as a mentoring
organization in the Google Summer of Code(tm) (http://code.google.com/soc/
).
Students in the program will receive a stipend from Google (and a T-
shirt solely available to successful participants), and may work from
their home, or home institution, for the duration of the 3 month
program. Each student will have at least one dedicated mentor to show
them the ropes and help them complete their project.
NESCent is particularly targeting students interested in both
evolutionary biology and software development. Project ideas are
listed on the website and range from hardware acceleration for
phylogenetic inference, to support for phyloinformatics standards
within the BioPerl and BioRuby toolkits, to alignment of next-gen
sequencing data, to ontology term markup for biocuration, to semantic
interoperability of web-services, to 3D-printing of phylogenies. All
project ideas are flexible and many can be adjusted in scope to match
the skills of the student. We also welcome novel project ideas that
dovetail with student interests.
TO APPLY: Instructions are at the website (see When you apply). You
can find GSoC program rules and eligibility requirements at http://socghop.appspot.com
. ***The 12-day application period for students ends on Friday, April
3rd, 2009, at 19:00 UTC (3pm EDT, 12pm PDT).***
INQUIRIES: phylosoc {at} nescent {dot} org. We strongly encourage all
interested students to get in touch with us with their ideas as early
as possible.
2009 NESCent Phyloinformatics Summer of Code:
http://hackathon.nescent.net/Phyloinformatics_Summer_of_Code_2009
Google Summer of Code FAQ:
http://socghop.appspot.com/document/show/program/google/gsoc2009/faqs
Cyberinfrastructure Traineeships (managed separately from GSoC;
postdocs also eligible):
http://hackathon.nescent.org/Cyberinfrastructure_Summer_Traineeships_2009
To sign up for quarterly NESCent newsletters:
http://www.nescent.org/about/contact.php
-
Todd Vision and Hilmar Lapp
National Evolutionary Synthesis Center
http://nescent.org
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