[GenABEL-dev] Suggested change of default weight in GenABEL/ibs()

[Xia Shen]

How shall I provide a patch? Do I simply revise the ibs() code and submit to you the ibs.R file? 

Xia

On 03 Mar 2014, at 13:16, Yurii Aulchenko <yurii.aulchenko at gmail.com> wrote:

> I am voting for option 2; as for the version number - no strong opinion.
> 
> Xia, would you be willing to summarize this discussion as a feature
> request, or to provide a patch?
> 
> Best wishes,
> Yurii
> 
> ----------------------
> Yurii Aulchenko
> (sent from mobile device)
> 
>> On Mar 3, 2014, at 4:12 PM, "L.C. Karssen" <lennart at karssen.org> wrote:
>> 
>> Dear all,
>> 
>>> On 28-02-14 14:15, Yurii Aulchenko wrote:
>>> In principle I agree this is good idea, rarely "no" (default) option is
>>> used; but I am always worried to change defaults as this may destroy
>>> people pipelines.
>> 
>> How about issuing a warning? I see two options:
>> 1) Keep the current default and issue a warning when the user doesn't
>> specify a weight.
>> 2) Change the default and when ibs() is run and the weight argument is
>> not equal to 'freq', issue a warning saying that the default has changed
>> to freq.
>> 
>> Although I haven't used ibs() a lot, I think option 2 is best as it sets
>> a sane default.
>> 
>> Another thing to think about: when changing defaults, what do we do with
>> the version number. If we only change the minor number (the 8 in 1.8-0),
>> people will think not much has changed and this change in default
>> behaviour may go unnoticed.
>> 
>> 
>> Lennart.
>> 
>>> 
>>> We need third opinion :)
>>> 
>>> Best,
>>> Y
>>> 
>>> ----------------------
>>> Yurii Aulchenko
>>> (sent from mobile device)
>>> 
>>> On Feb 28, 2014, at 3:45 PM, Xia Shen <shenxia911 at gmail.com
>>> <mailto:shenxia911 at gmail.com>> wrote:
>>> 
>>>> Hi,
>>>> 
>>>> I suggest to change the default weight argument in the GenABEL/ibs()
>>>> function to be set to "freq" instead of "no". I have colleagues
>>>> constantly forget to set to "freq" and produce, what I would call,
>>>> "wrong" kinship matrix.
>>>> 
>>>> *Xia Shen*
>>>> PhD
>>>> 
>>>> Division of Computational Genetics
>>>> Department of Clinical Science
>>>> *Swedish University of Agricultural Sciences*
>>>> Uppsala, Sweden
>>>> 
>>>> www.shen.se <http://www.shen.se>
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> genabel-devel mailing list
>>>> genabel-devel at lists.r-forge.r-project.org
>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>> 
>>> 
>>> _______________________________________________
>>> genabel-devel mailing list
>>> genabel-devel at lists.r-forge.r-project.org
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>> 
>> 
>> --
>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>> L.C. Karssen
>> Utrecht
>> The Netherlands
>> 
>> lennart at karssen.org
>> http://blog.karssen.org
>> GPG key ID: A88F554A
>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>> 
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel