[R-pkg-devel] UseR! Session: Navigating the jungle of R packages.

Sat Feb 11 18:40:05 CET 2017

Hello,

Jumping in here because those of us in the population genetics community have semi-recently tried to tackle some of these issues of giving users a clear sense of how R packages can work together in an analysis [0]. 
We created a website [1] that hosts vignettes openly contributed and curated by those in the population genetics community directly to a GitHub repository [2]. 

In our community we saw that the Task Views were good for getting a sense of what packages were out there and their general applications, but it was not clear as to how the packages interoperated or even where to start. Vignettes on the other hand, provide great examples of how to get started, but only focus on a single package. The website takes a hybrid approach between Task Views, package vignettes, and user forums as the resources on the site are community submitted and reproducible via continuous integration with an up-to-date docker container [3]. 

I just thought y'all might be interested in hearing how we have attempted to address these issues.

Cheers,
Zhian N. Kamvar

[0]: https://github.com/NESCent/r-popgen-hackathon <https://github.com/NESCent/r-popgen-hackathon>
[1]: http://popgen.nescent.org/ <http://popgen.nescent.org/>
[2]: https://github.com/NESCent/popgenInfo#readme <https://github.com/NESCent/popgenInfo#readme>
[3]: https://hub.docker.com/r/hlapp/rpopgen/ <https://hub.docker.com/r/hlapp/rpopgen/>

> On Feb 11, 2017, at 07:39 , J C Nash <profjcnash at gmail.com> wrote:
> 
> Certainly Google can be useful, but it can also be infuriatingly time-wasting when one needs to sort out related tools that do slightly different things. Then good, up-to-date task views are important, and wrappers such as I and some others are trying to develop can be a way to ease the chore of applying the tools or changing between related ones where there isn't enough information on which is best.
> 
> Perhaps Jim, Spencer, and I (others welcome!) can come up with some small examples to show where Google / sos / other search tools and the task views (Julia?) can be illustrated to provide guidance. After all, the purpose of the UseR! session is to try to develop improved ways to access R's packages.
> 
> Cheers, John Nash
> 
> On 2017-02-10 05:26 PM, Jim Lemon wrote:
>> This discussion started me thinking about searching for a function or
>> package, as many questions on the R help list indicate the that poster
>> couldn't find (or hasn't searched for) what they want. I don't think I
>> have ever used task views. If I haven't got a clue where to look for
>> something, I use Google. I can't recall an occasion when I didn't get
>> an answer, even if it was that what I wanted didn't exist. Perhaps we
>> should ask why Google is so good at answering uninformed questions, in
>> particular about R. I'm not the only person on the help list who
>> advises the clueless to try Google.
>> 
>> Jim
>> 
>> 
>> On Sat, Feb 11, 2017 at 3:51 AM, Ben Bolker <bbolker at gmail.com> wrote:
>>>  I definitely read the task views and advise others to do so.  I
>>> don't know how representative my little corner of the world is,
>>> though.
>>> 
>>>  I have an embryonic task view on mixed models at
>>> https://github.com/bbolker/mixedmodels-misc/blob/master/MixedModels.ctv
>>> but the perfect is the enemy of the good ...
>>> 
>>> 
>>> On Fri, Feb 10, 2017 at 9:56 AM, J C Nash <profjcnash at gmail.com> wrote:
>>>> We'd be more than happy to have you contribute directly. The goal is not
>>>> just an
>>>> information session, but to get some movement to ways to make the package
>>>> collection(s)
>>>> easier to use effectively. Note to selves: "effectively" is important -- we
>>>> could make
>>>> things easy by only recommending a few packages.
>>>> 
>>>> Best, JN
>>>> 
>>>> 
>>>> On 2017-02-10 09:29 AM, Michael Dewey wrote:
>>>>> 
>>>>> Dear all
>>>>> 
>>>>> That seems an interesting session. I am the maintainer of one of the CRAN
>>>>> Task Views (MetaAnalysis) and will attend
>>>>> unless I am successful in the draw for Wimbledon tickets.
>>>>> 
>>>>> Just in case I strike lucky one question I would have raised from the
>>>>> floor if I were there would have been "Does anyone
>>>>> read the Task Views?". Since I started mine I have received only a couple
>>>>> of suggestions for additions including a very
>>>>> abrupt one about a package which had been included for months but whose
>>>>> author clearly did not read before writing. So I
>>>>> would ask whether we need to focus much energy on the Task Views.
>>>>> 
>>>>> So, maybe see you there, maybe not.
>>>>> 
>>>>> 
>>>>> On 16/01/2017 14:57, ProfJCNash wrote:
>>>>>> 
>>>>>> Navigating the Jungle of R Packages
>>>>>> 
>>>>>> The R ecosystem has many packages in various collections,
>>>>>> especially CRAN, Bioconductor, and GitHub. While this
>>>>>> richness of choice speaks to the popularity and
>>>>>> importance of R, the large number of contributed packages
>>>>>> makes it difficult for users to find appropriate tools for
>>>>>> their work.
>>>>>> 
>>>>>> A session on this subject has been approved for UseR! in
>>>>>> Brussels. The tentative structure is three short
>>>>>> introductory presentations, followed by discussion or
>>>>>> planning work to improve the tools available to help
>>>>>> users find the best R package and function for their needs.
>>>>>> 
>>>>>> The currently proposed topics are
>>>>>> 
>>>>>> - wrapper packages that allow diverse tools that perform
>>>>>>  similar functions to be accessed by unified calls
>>>>>> 
>>>>>> - collaborative mechanisms to create and update Task Views
>>>>>> 
>>>>>> - search and sort tools to find packages.
>>>>>> 
>>>>>> At the time of writing we have tentative presenters for
>>>>>> the topics, but welcome others. We hope these presentations
>>>>>> at useR! 2017 will be part of a larger discussion that will
>>>>>> contribute to an increased team effort after the conference
>>>>>> to improve the the support for R users in these areas.
>>>>>> 
>>>>>> 
>>>>>> John Nash, Julia Silge, Spencer Graves
>>>>>> 
>>>>>> ______________________________________________
>>>>>> R-package-devel at r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>>>> 
>>>>> 
>>>> 
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> 
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