Good points. I think Levi hit on the direct reuse argument (via inheritance and composition), and, you're right, interoperability is another big one.
On Wed, Oct 18, 2017 at 10:26 AM, Ryan Thompson <r...@thompsonclan.org> wrote: > I think the main reason for reusing/subclassing core classes that users can > appreciate is that it makes it much easier for users to integrate multiple > packages into a single workflow. Only the most basic of pipelines uses just > a single Bioconductor package. For instance, an "edgeR" pipeline obviously > uses the edgeR package, but it likely also uses several other packages, > like sva, RUV, variancePartition, etc. The more these different packages > operate on the same core data structures, the less work the user has to do > to use them together. And to bring that back around to an incentive for > developers, making your package interoperate with other packages more > easily means that users will be more likely to use your package. > > On Tue, Oct 17, 2017 at 4:55 PM Levi Waldron <lwaldron.resea...@gmail.com> > wrote: > > > I'm putting together a presentation with a demo on why Bioconductor > > developers should re-use and extend core classes whenever possible. It > > includes a demo of some real-life consequences from two packages I use a > > lot, metagenomeSeq and phyloseq. These are far from the only examples, > many > > Bioconductor packages have created new classes from scratch, and I think > as > > a community we should greatly reduce that practice. I would welcome any > > feedback: > > > > https://www.slideshare.net/LeviWaldron/why-reuse-core-classes > > > > (sorry the slides are a little Frankenstein - in the interest of speed I > > made part of it in Powerpoint and part in Beamer, and used pdftk to > > concatenate these! In practice I would do the Beamer part as a live-demo, > > and take advantage of some animations in PPT) > > > > > > -- > > Levi Waldron > > http://www.waldronlab.org > > Assistant Professor of Biostatistics CUNY School of Public Health > > US: +1 646-364-9616 <(646)%20364-9616> > > Skype: > > levi.waldron > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
