Henrik, While I proposed the idea for the shields/badges Dan gets all the credit for the implementation.
As far as your (implied) idea of a coverage badge, the thought had occurred to us! Jim On Wed, May 20, 2015 at 1:34 PM, Henrik Bengtsson <henrik.bengts...@ucsf.edu > wrote: > So, lots of things are happening in a few months: Jim Hester starts > working at Bioconductor, we get Bioc shields/badges, Jim's covr > package is released on CRAN, snare drum, ... am I to eager if I > already now start wishing for a hi-hat as well? > > /Henrik > > On Tue, May 19, 2015 at 12:47 PM, Dan Tenenbaum <dtene...@fredhutch.org> > wrote: > > > > > > ----- Original Message ----- > >> From: "Leonardo Collado Torres" <lcoll...@jhu.edu> > >> To: "Dan Tenenbaum" <dtene...@fredhutch.org> > >> Cc: "Jim Hester" <james.f.hes...@gmail.com>, bioc-devel@r-project.org > >> Sent: Tuesday, May 19, 2015 12:37:18 PM > >> Subject: Re: [Bioc-devel] Use and Usability metrics / shields > >> > >> Regarding the 'posts' tag, I can see that it includes a "closed > >> questions" component. For example, > >> http://www.bioconductor.org/packages/release/bioc/html/derfinder.html > >> is 3/1/9/0 right now meaning that 0 questions are closed. From > >> https://support.bioconductor.org/info/faq/, only moderators can close > >> questions. That seems like quite a bit of work for the moderators. So > >> maybe it would be best to drop the "closed questions" component. Or > >> alternatively, can the author of a package moderate the posts that > >> have a tag corresponding to their package? > >> > > > > Perhaps the wording is wrong; what 'closed' is supposed to mean is that > the original poster has accepted an answer. I'll change 'closed' to > 'accepted'. > > > > > >> As for 'build: warnings', it seems like it will show for some devel > >> packages all the time. For example, > >> http://www.bioconductor.org/packages/devel/bioc/html/regionReport.html > >> always has a warning in the Windows build machine due to a mismatch > >> in > >> the version of Rtools installed. > > > > This is a bug in devtools and may have already been fixed (but not yet > propagated to CRAN). > > IMO this should be reflected in the build shield. > > > > Dan > > > > > >> > >> I do like these changes and the addition of shields =) > >> > >> > >> On Thu, May 14, 2015 at 10:56 AM, Dan Tenenbaum > >> <dtene...@fredhutch.org> wrote: > >> > > >> > ----- Original Message ----- > >> >> From: "Jim Hester" <james.f.hes...@gmail.com> > >> >> To: "Martin Morgan" <mtmor...@fredhutch.org> > >> >> Cc: bioc-devel@r-project.org > >> >> Sent: Thursday, May 14, 2015 7:53:03 AM > >> >> Subject: Re: [Bioc-devel] Use and Usability metrics / shields > >> >> > >> >> The common shield convention is to use blue or orange when the > >> >> information > >> >> is not qualitatively good or bad, but the color choice is just > >> >> subjective > >> >> in the end. > >> > > >> > It does seem though that we should indicate the non-changing nature > >> > of these shields with some kind of color change. Perhaps we can > >> > come up with one that works with the other design elements on the > >> > page. > >> > > >> > BTW, the 'posts' tag does change color; if there are 0 posts tagged > >> > with a package name, the shield is yellow; otherwise it's green. > >> > > >> > Dan > >> > > >> > > >> >> > >> >> On Thu, May 14, 2015 at 10:47 AM, Martin Morgan > >> >> <mtmor...@fredhutch.org> > >> >> wrote: > >> >> > >> >> > On 05/10/2015 11:39 AM, COMMO Frederic 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? > >> >> >> > >> >> >> > >> >> > Thanks for these suggestions. > >> >> > > >> >> > I like the idea of linking into the scientific literature, > >> >> > initially as > >> >> > part of the 'Citation' section on each landing page rather than > >> >> > as > >> >> > a shield > >> >> > (maybe a shield in the long term). As Wolfgang mentions it is a > >> >> > little more > >> >> > challenging than a one-liner to match the information available > >> >> > from a > >> >> > CITATION file (or automatically generated) to an appropriate > >> >> > search > >> >> > in > >> >> > PubMed, and because citations are an important formal metric it > >> >> > seems > >> >> > important to get this more-or-less right. > >> >> > > >> >> > For what it's worth the more-or-less continuous stream of papers > >> >> > citing > >> >> > 'Biocondcutor' are listed at > >> >> > > >> >> > http://bioconductor.org/help/publications/ > >> >> > > >> >> > The links in the 'Literature Search' box query various resources > >> >> > for use > >> >> > of the term 'Bioconductor'. > >> >> > > >> >> > We have so far kept the distinction between 'available' and > >> >> > 'build', > >> >> > partly because builds sometimes fail for transient (e.g., > >> >> > connectivity) > >> >> > reasons or, in devel, because of an incomplete check-in that > >> >> > does > >> >> > not > >> >> > compromise the end-user availability and functionality of the > >> >> > version > >> >> > available via biocLite(). > >> >> > > >> >> > It's kind of amusing that (a) most of the information was > >> >> > already > >> >> > available, often on the landing page (like the links to build > >> >> > reports that > >> >> > Henrik mentions, or years in bioc), so the shields are serving > >> >> > just > >> >> > to > >> >> > emphasize these; and (b) the 'green' implies some-how 'good', > >> >> > but > >> >> > many of > >> >> > the shields (e.g., years in Bioc, posts, commits, downloads) are > >> >> > actually > >> >> > never not green. Maybe these shields should be white? > >> >> > > >> >> > Thanks again for the feedback; initial response seems to be > >> >> > positive. > >> >> > > >> >> > Martin > >> >> > > >> >> > > >> >> > 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 > >> >> >> > >> >> >> > >> >> > > >> >> > -- > >> >> > 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 > >> >> > > >> >> > >> >> [[alternative HTML version deleted]] > >> >> > >> >> _______________________________________________ > >> >> 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
