----- Original Message ----- > From: "Dan Tenenbaum" <dtene...@fredhutch.org> > To: "Wolfgang Huber" <whu...@embl.de> > Cc: bioc-devel@r-project.org > Sent: Thursday, May 14, 2015 7:33:04 AM > Subject: Re: [Bioc-devel] Use and Usability metrics / shields > > > > ----- Original Message ----- > > From: "Wolfgang Huber" <whu...@embl.de> > > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > > Cc: bioc-devel@r-project.org > > Sent: Thursday, May 14, 2015 4:03:54 AM > > Subject: Re: [Bioc-devel] Use and Usability metrics / shields > > > > > > > > Can it be that the “in Bioc” shield is incorrect? > > For instance, it says “9.98 years” for vsn but the first commit was > > in Oct 2002 > > Curiously “9.98 years” is stated for many old packages - surely we > > can use R for more precise date arithmetic? > > > > It is not counting from the first commit (as it says in the tooltip > text) but from the day of the first release in which the package > appeared. > > So it does not count the time that the package is in devel only. >
Actually, it turns out that I don't have data for packages committed prior to BioC 1.6. I was using the release manifests (and associated release dates) to calculate "years in bioc"; I'll switch to using svn logs. Thanks, Dan > Dan > > > > > > Cheers > > Wolfgang > > > > > On May 13, 2015, at 21:36 GMT+2, Dan Tenenbaum > > > <dtene...@fredhutch.org> wrote: > > > > > > > > > > > > ----- Original Message ----- > > >> From: "Henrik Bengtsson" <henrik.bengts...@ucsf.edu> > > >> To: "COMMO Frederic" <frederic.co...@gustaveroussy.fr> > > >> Cc: bioc-devel@r-project.org > > >> Sent: Wednesday, May 13, 2015 12:28:54 PM > > >> Subject: Re: [Bioc-devel] Use and Usability metrics / shields > > >> > > >> Sweet; you went live with the badges/shields, e.g. > > >> > > >> http://bioconductor.org/packages/release/bioc/html/affxparser.html > > >> > > >> A positive side effect is that now there's a link from the > > >> package > > >> page to to the package's check results, which I always wanted :) > > >> > > > > > > That was there before (and still is, see the bottom of the > > > Details > > > section). But yes, it was not very visible. > > > > > > Dan > > > > > > > > >> Thanks for adding this > > >> > > >> /Henrik > > >> > > >> > > >> On Sun, May 10, 2015 at 11:39 AM, COMMO Frederic > > >> <frederic.co...@gustaveroussy.fr> wrote: > > >>> Dear Martin, > > >>> > > >>> All of these suggestions sound good. > > >>> > > >>> Wolfgang's suggestion regarding possible associated papers > > >>> might > > >>> be > > >>> also great. > > >>> > > >>> Another useful information would be to point to other > > >>> publications > > >>> where a given package was used, and cited. > > >>> I don't know if it's technically possible, but it would be > > >>> greatly > > >>> informative to know how frequently a package is used, and how > > >>> it > > >>> performs, in real contexts. > > >>> > > >>> Frederic Commo > > >>> Bioinformatics, U981 > > >>> Gustave Roussy > > >>> > > >>> ________________________________________ > > >>> De : Bioc-devel [bioc-devel-boun...@r-project.org] de la part > > >>> de > > >>> Wolfgang Huber [whu...@embl.de] > > >>> Date d'envoi : samedi 9 mai 2015 19:57 > > >>> À : Martin Morgan > > >>> Cc: bioc-devel@r-project.org > > >>> Objet : Re: [Bioc-devel] Use and Usability metrics / shields > > >>> > > >>> Dear Martin > > >>> > > >>> great idea. > > >>> "Current build status” could perhaps be wrapped with > > >>> "Cross-platform availability” into some sort of “Availability / > > >>> Accessibility”? > > >>> > > >>> I wonder how informative it would be to make metrics such as > > >>> (i) citations of the associated paper > > >>> (ii) full-text mentions e.g. in PubmedCentral > > >>> actually useful. (i) could be flawed if package and paper are > > >>> diverged; (ii) would require good disambiguation, e.g. like > > >>> bioNerDS http://www.biomedcentral.com/1471-2105/14/194 (or > > >>> other > > >>> tools? not my expertise). Do we have someone with capabilities > > >>> in > > >>> this area on this list? > > >>> > > >>> PS Martin you’ll like Fig. 2 of their paper. > > >>> > > >>> Wolfgang > > >>> > > >>> > > >>> > > >>> > > >>> > > >>>> On May 9, 2015, at 19:15 GMT+2, Martin Morgan > > >>>> <mtmor...@fredhutch.org> wrote: > > >>>> > > >>>> Bioc developers! > > >>>> > > >>>> It's important that our users be able to identify packages > > >>>> that > > >>>> are suitable for their research question. Obviously a first > > >>>> step > > >>>> is to identify packages in the appropriate research domain, > > >>>> for > > >>>> instance through biocViews. > > >>>> > > >>>> http://bioconductor.org/packages/release/ > > >>>> > > >>>> We'd like to help users further prioritize their efforts by > > >>>> summarizing use and usability. Metrics include: > > >>>> > > >>>> - Cross-platform availability -- biocLite()-able from all or > > >>>> only > > >>>> some platforms > > >>>> - Support forum activity -- questions and comments / > > >>>> responses, > > >>>> 6 > > >>>> month window > > >>>> - Download percentile -- top 5, 20, 50%, or 'available' > > >>>> - Current build status -- errors or warnings on some or all > > >>>> platforms > > >>>> - Developer activity -- commits in the last 6 months > > >>>> - Historical presence -- years in Bioconductor > > >>>> > > >>>> Obviously the metrics are imperfect, so constructive feedback > > >>>> welcome -- we think the above capture in a more-or-less > > >>>> objective > > >>>> and computable way the major axes influencing use and > > >>>> usability. > > >>>> > > >>>> We initially intend to prominently display 'shields' (small > > >>>> graphical icons) on package landing pages. > > >>>> > > >>>> Thanks in advance for your comments, > > >>>> > > >>>> Martin Morgan > > >>>> Bioconductor > > >>>> -- > > >>>> Computational Biology / Fred Hutchinson Cancer Research Center > > >>>> 1100 Fairview Ave. N. > > >>>> PO Box 19024 Seattle, WA 98109 > > >>>> > > >>>> Location: Arnold Building M1 B861 > > >>>> Phone: (206) 667-2793 > > >>>> > > >>>> _______________________________________________ > > >>>> Bioc-devel@r-project.org mailing list > > >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > >>> > > >>> _______________________________________________ > > >>> Bioc-devel@r-project.org mailing list > > >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > >>> > > >>> _______________________________________________ > > >>> Bioc-devel@r-project.org mailing list > > >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > >> > > >> _______________________________________________ > > >> Bioc-devel@r-project.org mailing list > > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > >> > > > > > > _______________________________________________ > > > Bioc-devel@r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
