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

[Yurii Aulchenko]

Please have a look at

http://genabel.r-forge.r-project.org

----------------------
Yurii Aulchenko
(sent from mobile device)

> On Mar 5, 2014, at 4:53 PM, Xia Shen <shenxia911 at gmail.com> wrote:
>
> 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>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
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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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>>>
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>