Links to Zika virus paper

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Links to Zika virus paper

Roger Bivand
Administrator
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

this morning.

Roger

--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; fax +47 55 95 91 00
e-mail: [hidden email]
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
http://depsy.org/person/434412

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Roger Bivand
Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway
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Re: Links to Zika virus paper

Barry Rowlingson
On Thu, Apr 21, 2016 at 8:19 AM, Roger Bivand <[hidden email]> 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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Re: Links to Zika virus paper

boB Rudis
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
<[hidden email]> wrote:

> On Thu, Apr 21, 2016 at 8:19 AM, Roger Bivand <[hidden email]> 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
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo

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Re: Links to Zika virus paper

Roman Luštrik
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 <[hidden email]> 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
> <[hidden email]> wrote:
> > On Thu, Apr 21, 2016 at 8:19 AM, Roger Bivand <[hidden email]>
> 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
> >
> > _______________________________________________
> > R-sig-Geo mailing list
> > [hidden email]
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>



--
In God we trust, all others bring data.

        [[alternative HTML version deleted]]

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Re: Links to Zika virus paper

boB Rudis
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 Luštrik <[hidden email]> 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 <[hidden email]> 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
>> <[hidden email]> wrote:
>> > On Thu, Apr 21, 2016 at 8:19 AM, Roger Bivand <[hidden email]>
>> > 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
>> >
>> > _______________________________________________
>> > R-sig-Geo mailing list
>> > [hidden email]
>> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> [hidden email]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
>
>
>
> --
> In God we trust, all others bring data.

_______________________________________________
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