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
