[Bioc-devel] Use and Usability metrics / shields

[Dan Tenenbaum]

----- Original Message -----
> From: "Wolfgang Huber" <whuber at embl.de>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: bioc-devel at 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.

Dan




> 	Cheers
> 	Wolfgang
> 
> > On May 13, 2015, at 21:36 GMT+2, Dan Tenenbaum
> > <dtenenba at fredhutch.org> wrote:
> > 
> > 
> > 
> > ----- Original Message -----
> >> From: "Henrik Bengtsson" <henrik.bengtsson at ucsf.edu>
> >> To: "COMMO Frederic" <Frederic.COMMO at gustaveroussy.fr>
> >> Cc: bioc-devel at 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.COMMO at 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-bounces at r-project.org] de la part de
> >>> Wolfgang Huber [whuber at embl.de]
> >>> Date d'envoi : samedi 9 mai 2015 19:57
> >>> À : Martin Morgan
> >>> Cc: bioc-devel at 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
> >>>> <mtmorgan at 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 at r-project.org mailing list
> >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>> 
> >>> _______________________________________________
> >>> Bioc-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>> 
> >>> _______________________________________________
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> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> 
> >> _______________________________________________
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> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> 
> > 
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