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

[L.C. Karssen]

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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-- 
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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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