Links to Zika virus paper
I will try to handle any other replies off-list to keep the list on-topic, but wanted to reinforce my opine on this topic. My co-author & I believed so strongly in the need to ensure R & R package author work was properly acknowledged that we managed to get Wiley to allow 2 pages of package citations in our book, Data-Driven Security. Virtually everything (with a small fraction of exceptions) I produce in my cybersecurity research is owed to a cadre of coders &| scientists who have contributed R packages to make it possible. #ty. Y'all rock ;-)
On Thu, Apr 21, 2016 at 8:00 AM, Roman Lu?trik <roman.lustrik at gmail.com> wrote:
Bob opens up an interesting topic, perhaps not really fit for this mailing list, of which packages to cite. Most packages load dependencies. Should these dependencies be cited? How do you handle this issue in citing packages? Cheers, Roman On Thu, Apr 21, 2016 at 1:29 PM, boB Rudis <bob at rudis.net> wrote:
Agreed it was great to see "Each of the 300 individual models was
fitted using the gbm.step subroutine in the dismo package in the R
statistical programming environment (Elith et al. 2008)" in there and
also agreed that the following should have made it into the citations
(assuming only library(dismo) was done which is a terrible assumption
:-). Many thanks to Roger, Edzer (et al) as well. Critial,
foundational work which made this paper possible.
@Manual{R-base,
title = {R: A Language and Environment for Statistical Computing},
author = {{R Core Team}},
organization = {R Foundation for Statistical Computing},
address = {Vienna, Austria},
year = {2016},
url = {https://www.R-project.org/},
}
@Manual{R-dismo,
title = {dismo: Species Distribution Modeling},
author = {Robert J. Hijmans and Steven Phillips and John Leathwick
and Jane Elith},
year = {2015},
note = {R package version 1.0-12},
url = {https://CRAN.R-project.org/package=dismo},
}
@Manual{R-raster,
title = {raster: Geographic Data Analysis and Modeling},
author = {Robert J. Hijmans},
year = {2015},
note = {R package version 2.5-2},
url = {https://CRAN.R-project.org/package=raster},
}
@Manual{R-sp,
title = {sp: Classes and Methods for Spatial Data},
author = {Edzer Pebesma and Roger Bivand},
year = {2015},
note = {R package version 1.2-1},
url = {https://CRAN.R-project.org/package=sp},
}
On Thu, Apr 21, 2016 at 4:43 AM, Barry Rowlingson
<b.rowlingson at lancaster.ac.uk> wrote:
On Thu, Apr 21, 2016 at 8:19 AM, Roger Bivand <Roger.Bivand at nhh.no> wrote:
Why we do what we do: Congratulations to Robert Hijmans and others maintaining the dismo package: https://cran.r-project.org/web/packages/dismo/index.html which is the computational basis for: http://elifesciences.org/content/5/e15272v1 and reported on in: http://www.bbc.com/news/health-36090650
Great stuff, but sadly I don't see the either R itself or the dismo package cited in the journal article - the one mention of dismo gets a reference to a paper (Elith, J., J. R. Leathwick & T. Hastie (2008) A working guide to boosted regression trees. J Anim Ecol, 77, 802-13) and nothing else. *sigh* Barry
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