It should also be pointed out that reference classes classes are rarely
needed and can easily be used for the wrong reasons (e.g. performance?).
The pass-by-reference semantic they provide can fire back. Most of the
time objects don't need and should not have pass-by-reference semantic,
only *some* of their slots.
Nice slides Levi!
H.
On 10/17/2017 10:04 PM, Michael Lawrence wrote:
If Biocondutor integration is important, then reference classes
(setRefClass) are preferable, since they fully integrate with the rest of
S4, including class hierarchies and method dispatch. It's important not to
be confused by the R6 branding. It's (sort of) an alternative to S4, not an
evolution of it.
Does R now have more HDF5 interfaces or more OOP frameworks?
Michael
On Tue, Oct 17, 2017 at 5:16 PM, Vincent Carey <st...@channing.harvard.edu>
wrote:
I found it a very congenial presentation.
One related issue -- perhaps -- a new HDF5 interface package, that is
based on R6!
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_hhoeflin_hdf5r&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=7p6EBgpmq8k2A5GFXnzr1xAeSglBWSTiCKL7PRFVWZ4&s=vmpy2qtzBGi5DFekbDE1qkhGv0M7xO2rWFLc0QhcKno&e=
Core class consciousness is surely worthy of promotion. But what about OOP
methodology? I personally am happy with S4. I believe there are some
packages
that use setRefClass ... any guidance on this?
On Tue, Oct 17, 2017 at 7:54 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://urldefense.proofpoint.com/v2/url?u=https-3A__www.slideshare.net_LeviWaldron_why-2Dreuse-2Dcore-2Dclasses&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=7p6EBgpmq8k2A5GFXnzr1xAeSglBWSTiCKL7PRFVWZ4&s=yHRWnacXXrnqXO4MhBRdET7vTRtXXqUyttaU7pb-hjQ&e=
(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
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.waldronlab.org&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=7p6EBgpmq8k2A5GFXnzr1xAeSglBWSTiCKL7PRFVWZ4&s=Cme7IjGc4Z0ZBhjX5BXbB8rmp7Jz9igM5hzVrYZTk3A&e=
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616 Skype:
levi.waldron
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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