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

[L.C. Karssen]

Hi Xia,

Glad to hear you want to take on the task of writing a patch.

On 05-03-14 13:53, Xia Shen wrote:
> How shall I provide a patch? Do I simply revise the ibs() code and submit to you the ibs.R file? 

That's the basic idea. Technical instructions can be found at
http://genabel.r-forge.r-project.org/tutHowToPatch.html.

In steps:
- Check out the current code from SVN (our version control system)
- Change the code until you think the bug is fixed
- Test the changed function
- Send the changes to the original file(s) as a patch to the mailing list.
- We will review the code, and if approved, will commit it to SVN.

When writing code, please follow our coding style guidelines at
http://genabel.r-forge.r-project.org/codingstyle.html


If you need any help, let us know.


Lennart.


> 
> 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
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>>>
>>> _______________________________________________
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> 

-- 
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L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
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