authorship and citation

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Re: authorship and citation

hadley wickham
On Tue, Oct 6, 2015 at 4:58 PM, Adrian Dușa <[hidden email]> wrote:

> Hi Gabriel,
>
> On Tue, Oct 6, 2015 at 10:59 PM, Gabriel Becker <[hidden email]>
> wrote:
>
>> [...]
>>
>> At the very least, this is seems to be a flagrant violation of the
>> *spirit* of the CRAN policy, which AFAIK is intended to enforce
>> acknowledgement of the contributions of all copyright holders in the
>> package. The fact that you are trying to bypass the policy by suggesting
>> users use an unofficial citation which would not comply with the policy
>> while maintaining an official one which complies, but which you don't want
>> users to see  is probably a suggestion that you shouldn't do that.
>>
>
>
> But that is the very point: I read the CRAN policies twice, and there is no
> official guideline on how to compile the citation.
> Regarding the Source packages, the policies mention:
>
> ######
> The ownership of copyright and intellectual property rights of all
> components of the package must be clear and unambiguous (including from the
> authors specification in the DESCRIPTION file). Where code is copied (or
> derived) from the work of others (including from R itself), care must be
> taken that any copyright/license statements are preserved and authorship is
> not misrepresented.
> Preferably, an ‘Authors@R’ would be used with ‘ctb’ roles for the authors
> of such code. Alternatively, the ‘Author’ field should list these authors
> as contributors.
>
> Where copyrights are held by an entity other than the package authors, this
> should preferably be indicated via ‘cph’ roles in the ‘Authors@R’ field, or
> using a ‘Copyright’ field (if necessary referring to an inst/COPYRIGHTS
> file).
>
> Trademarks must be respected.
> ######
>
> Now, that requirement is already met: the former author is still in the
> authors' list. So the contribution of the former author is duly
> acknowledged, but the fundamental issue of my question related to the
> citation file, for which the CRAN policies doesn't offer any other
> information.
>
> If the spirit of the CRAN policies is to enforce citing each and every one
> of the authors, then I don't understand why the citation from package Rcmdr
> meets this spirit, while my suggestion doesn't.

I'd recommend that you read
https://cran.r-project.org/web/packages/shiny/DESCRIPTION and compare
it to citation("shiny"). Authors, but not contributors, all listed in
the citation.

Hadley

--
http://had.co.nz/

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Re: authorship and citation

Gabriel Becker
Hadley,

With all due respect, I'm not sure what exactly your deliniation between
author and contributor is, but from what I can tell I don't agree with it.

>From the blogpost regarding your new purrr package:

"Purrr wouldn’t be possible without Lionel Henry
<https://github.com/lionel->. He wrote a lot of the package and his
insightful comments ..."

And yet he is listed as a contributor in the DESCRIPTION file, and thus in
your view not worthy of being in the citation even as a non-first author?
That does not jive with what I understand to be "standard practice" with
regard to software-related publications, and it certainly isn't what I
would choose to do in that situation.

Best,
~G

On Wed, Oct 7, 2015 at 4:59 AM, Hadley Wickham <[hidden email]> wrote:

> On Tue, Oct 6, 2015 at 4:58 PM, Adrian Dușa <[hidden email]> wrote:
> > Hi Gabriel,
> >
> > On Tue, Oct 6, 2015 at 10:59 PM, Gabriel Becker <[hidden email]>
> > wrote:
> >
> >> [...]
> >>
> >> At the very least, this is seems to be a flagrant violation of the
> >> *spirit* of the CRAN policy, which AFAIK is intended to enforce
> >> acknowledgement of the contributions of all copyright holders in the
> >> package. The fact that you are trying to bypass the policy by suggesting
> >> users use an unofficial citation which would not comply with the policy
> >> while maintaining an official one which complies, but which you don't
> want
> >> users to see  is probably a suggestion that you shouldn't do that.
> >>
> >
> >
> > But that is the very point: I read the CRAN policies twice, and there is
> no
> > official guideline on how to compile the citation.
> > Regarding the Source packages, the policies mention:
> >
> > ######
> > The ownership of copyright and intellectual property rights of all
> > components of the package must be clear and unambiguous (including from
> the
> > authors specification in the DESCRIPTION file). Where code is copied (or
> > derived) from the work of others (including from R itself), care must be
> > taken that any copyright/license statements are preserved and authorship
> is
> > not misrepresented.
> > Preferably, an ‘Authors@R’ would be used with ‘ctb’ roles for the
> authors
> > of such code. Alternatively, the ‘Author’ field should list these authors
> > as contributors.
> >
> > Where copyrights are held by an entity other than the package authors,
> this
> > should preferably be indicated via ‘cph’ roles in the ‘Authors@R’
> field, or
> > using a ‘Copyright’ field (if necessary referring to an inst/COPYRIGHTS
> > file).
> >
> > Trademarks must be respected.
> > ######
> >
> > Now, that requirement is already met: the former author is still in the
> > authors' list. So the contribution of the former author is duly
> > acknowledged, but the fundamental issue of my question related to the
> > citation file, for which the CRAN policies doesn't offer any other
> > information.
> >
> > If the spirit of the CRAN policies is to enforce citing each and every
> one
> > of the authors, then I don't understand why the citation from package
> Rcmdr
> > meets this spirit, while my suggestion doesn't.
>
> I'd recommend that you read
> https://cran.r-project.org/web/packages/shiny/DESCRIPTION and compare
> it to citation("shiny"). Authors, but not contributors, all listed in
> the citation.
>
> Hadley
>
> --
> http://had.co.nz/
>



--
Gabriel Becker, PhD
Computational Biologist
Bioinformatics and Computational Biology
Genentech, Inc.

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Re: authorship and citation

Spencer Graves-3
An example from the sos package:  Its DESCRIPTION file says Author:
Spencer Graves, Sundar Dorai-Raj, and Romain Francois.  However, the
package includes a findFn function, whose help file includes an
Author(s) section, which reads, "Spencer Graves, Sundar Dorai-Raj,
Romain Francois.  Duncan Murdoch suggested the "???" alias for "findFn"
and contributed the code for it.  Special thanks to Jonathan Baron and
Andy Liaw. Baron maintains the RSiteSearch data base. Liaw and Baron
created the RSiteSearch function in the utils package."


Another example:  The "Author" of the Ecdat package is Yves Croissant
<[hidden email]>.  I'm the Maintainer.  At some
point, I may add my name to the list of Authors but I certainly would
never remove Yves' name.  That package is, I think, exclusively data
sets.  I added functions, which I later spun off into a separate Edfun
package;  I'm listed as the Author and Maintainer of that.


Another example that may help you:  The "distr" package has several
companion packages:  distrDoc, distrEx, distrSim, distrTEst, distrTeach,
distrMod, and distrEllipse.  I haven't checked, but each package could
have a separate and different list of authors.


Hope this helps.
Spencer


On 10/7/2015 9:23 AM, Gabriel Becker wrote:

> Hadley,
>
> With all due respect, I'm not sure what exactly your deliniation between
> author and contributor is, but from what I can tell I don't agree with it.
>
> >From the blogpost regarding your new purrr package:
>
> "Purrr wouldn’t be possible without Lionel Henry
> <https://github.com/lionel->. He wrote a lot of the package and his
> insightful comments ..."
>
> And yet he is listed as a contributor in the DESCRIPTION file, and thus in
> your view not worthy of being in the citation even as a non-first author?
> That does not jive with what I understand to be "standard practice" with
> regard to software-related publications, and it certainly isn't what I
> would choose to do in that situation.
>
> Best,
> ~G
>
> On Wed, Oct 7, 2015 at 4:59 AM, Hadley Wickham <[hidden email]> wrote:
>
>> On Tue, Oct 6, 2015 at 4:58 PM, Adrian Dușa <[hidden email]> wrote:
>>> Hi Gabriel,
>>>
>>> On Tue, Oct 6, 2015 at 10:59 PM, Gabriel Becker <[hidden email]>
>>> wrote:
>>>
>>>> [...]
>>>>
>>>> At the very least, this is seems to be a flagrant violation of the
>>>> *spirit* of the CRAN policy, which AFAIK is intended to enforce
>>>> acknowledgement of the contributions of all copyright holders in the
>>>> package. The fact that you are trying to bypass the policy by suggesting
>>>> users use an unofficial citation which would not comply with the policy
>>>> while maintaining an official one which complies, but which you don't
>> want
>>>> users to see  is probably a suggestion that you shouldn't do that.
>>>>
>>>
>>> But that is the very point: I read the CRAN policies twice, and there is
>> no
>>> official guideline on how to compile the citation.
>>> Regarding the Source packages, the policies mention:
>>>
>>> ######
>>> The ownership of copyright and intellectual property rights of all
>>> components of the package must be clear and unambiguous (including from
>> the
>>> authors specification in the DESCRIPTION file). Where code is copied (or
>>> derived) from the work of others (including from R itself), care must be
>>> taken that any copyright/license statements are preserved and authorship
>> is
>>> not misrepresented.
>>> Preferably, an ‘Authors@R’ would be used with ‘ctb’ roles for the
>> authors
>>> of such code. Alternatively, the ‘Author’ field should list these authors
>>> as contributors.
>>>
>>> Where copyrights are held by an entity other than the package authors,
>> this
>>> should preferably be indicated via ‘cph’ roles in the ‘Authors@R’
>> field, or
>>> using a ‘Copyright’ field (if necessary referring to an inst/COPYRIGHTS
>>> file).
>>>
>>> Trademarks must be respected.
>>> ######
>>>
>>> Now, that requirement is already met: the former author is still in the
>>> authors' list. So the contribution of the former author is duly
>>> acknowledged, but the fundamental issue of my question related to the
>>> citation file, for which the CRAN policies doesn't offer any other
>>> information.
>>>
>>> If the spirit of the CRAN policies is to enforce citing each and every
>> one
>>> of the authors, then I don't understand why the citation from package
>> Rcmdr
>>> meets this spirit, while my suggestion doesn't.
>> I'd recommend that you read
>> https://cran.r-project.org/web/packages/shiny/DESCRIPTION and compare
>> it to citation("shiny"). Authors, but not contributors, all listed in
>> the citation.
>>
>> Hadley
>>
>> --
>> http://had.co.nz/
>>
>
>

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Re: authorship and citation

Tim Keitt-3
On Wed, Oct 7, 2015 at 11:29 AM, Spencer Graves <[hidden email]
> wrote:

> Another example:  The "Author" of the Ecdat package is Yves Croissant <
> [hidden email]>.  I'm the Maintainer.  At some
> point, I may add my name to the list of Authors but I certainly would never
> remove Yves' name.  That package is, I think, exclusively data sets.  I
> added functions, which I later spun off into a separate Edfun package;  I'm
> listed as the Author and Maintainer of that.
>

This reminded me of something I have always found curious about roles
listed in the DESCRIPTION file. Since there is no "maintainer" role in this
list: http://www.loc.gov/marc/relators/relaterm.html, which was used to get
the role names, you will be listed as the "creator" of the package when you
list yourself as maintainer even if you did not initiate the package or
even contribute code.

THK

http://www.keittlab.org/

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Re: authorship and citation

Duncan Murdoch-2
On 07/10/2015 1:39 PM, Tim Keitt wrote:

> On Wed, Oct 7, 2015 at 11:29 AM, Spencer Graves <[hidden email]
>> wrote:
>
>> Another example:  The "Author" of the Ecdat package is Yves Croissant <
>> [hidden email]>.  I'm the Maintainer.  At some
>> point, I may add my name to the list of Authors but I certainly would never
>> remove Yves' name.  That package is, I think, exclusively data sets.  I
>> added functions, which I later spun off into a separate Edfun package;  I'm
>> listed as the Author and Maintainer of that.
>>
>
> This reminded me of something I have always found curious about roles
> listed in the DESCRIPTION file. Since there is no "maintainer" role in this
> list: http://www.loc.gov/marc/relators/relaterm.html, which was used to get
> the role names, you will be listed as the "creator" of the package when you
> list yourself as maintainer even if you did not initiate the package or
> even contribute code.
>

I think it was easier to (ab)use that role than to get a "Maintainer"
role added to the standard ones.  The description of "creator" is

"A person or organization responsible for the intellectual or artistic
content of a resource"

The usual English meaning of "creator" would be close to

"A person or organization originally responsible for the intellectual or
artistic content of a resource"

R's use of it is close to

"A person or organization currently responsible for the intellectual or
artistic content of a resource"

Duncan Murdoch

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Re: authorship and citation

Tim Keitt-3
On Wed, Oct 7, 2015 at 2:39 PM, Duncan Murdoch <[hidden email]>
wrote:

> I think it was easier to (ab)use that role than to get a "Maintainer"
> role added to the standard ones.
>

Why bother with the relators list at all?

THK

http://www.keittlab.org/

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Re: MARC creator role (was: authorship and citation)

Achim Zeileis-4
On Wed, 7 Oct 2015, Tim Keitt wrote:

> On Wed, Oct 7, 2015 at 2:39 PM, Duncan Murdoch <[hidden email]>
> wrote:
>
>> I think it was easier to (ab)use that role than to get a "Maintainer"
>> role added to the standard ones.

Also note that the "creator" in the MARC vocabulary is with respect to a
_resource_ - which is different from the creation of a _work_ by an
"author".

In the case of the CRAN repository, the individual resources are the
packages. And the maintainer is the person who is responsible for a
package (aka resource) being made available (aka created) on CRAN. Also,
the maintainer is the contact responsible for the resource.

Therefore, using the "author" role for those who have created the code
(aka work) and the "creator" role for those who have created the (CRAN)
package (aka resource) seemed appropriate.

> Why bother with the relators list at all?

Certainly, it is better to use a standard vocabulary than creating a new
domain-specific vocabulary to facilitate communication of the information
outside the domain. Therefore, both the "person" and the "bibentry"
objects try to follow models that were well established rather than
starting out from scratch.

> THK
>
> http://www.keittlab.org/
>
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>
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>

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Re: authorship and citation

Stephen Ellison
In reply to this post by hadley wickham

> > I read the CRAN policies twice, and there
> > is no official guideline on how to compile the citation.

The policies are about copyright and IP, not credited authorship. There's overlap but they are not the same thing.

You can see whether someone is a copyright holder by referring to the license you had and whether there is any of their content remaining. But that might not mean they are package 'authors'. If you reuse code verbatim from another package's function, you _must_ note the copyright - but that does not necessarily make the original author of the code a co-author of your package (though I would expect to see at least an acknowledgement in the particular function's help page). And not all 'authors' need necessarily provide code - they could, for example, have developed the core maths the code implements. Of itself, that does not confer copyright in any part of the package code or help text, but it's very likely they'd deserve credit as co-authors.

Common sense would suggest to me that if you are in doubt about whether someone should be on your author list (as opposed to copyright owner list) in a package's citation, you should probably ask them. And if you are considering removing an author, you should very definitely be in doubt because there was a reason they were there.

The answers you get from different contributors might be different so it would not be surprising if packages differed in the extent to which they cited contributions or added acknowledgements. In essence, though, if everybody feels fairly treated by the citations within a package, there's no reason for anyone else to complain about it, and if someone feels they have not been properly credited they can - and should - contact the maintainer and say so.

So ask before removing someone from your citation. If they say 'no', don’t remove them.

S Ellison


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Re: authorship and citation

Prof Brian Ripley
S Ellison posted:

(quoting someone else, it appears)

>>> I read the CRAN policies twice, and there
>>> is no official guideline on how to compile the citation.

And once again Dr Ellison is not attributing quotes: that is clearly
covered by the posting guide.  Including:

Take care when you quote other people’s comments ...
     The original authorship and meaning should always be clear.

> The policies are about copyright and IP, not credited authorship.

Hmm, people keep saying things like that, but it is not correct.  The
right to be identified as an author is an IP right: in some
jurisdictions it is called a 'moral right' (and there are others).


--
Brian D. Ripley,                  [hidden email]
Emeritus Professor of Applied Statistics, University of Oxford
1 South Parks Road, Oxford OX1 3TG, UK

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