[GenABEL-dev] descriptives.traits by.var bugs.

[pirastu at burlo.trieste.it]

Sorry, I took a better look and the problem and it is sligthly different,
in fact it's not the script but the dataset.
Basically all of the controls are missing the variable age and the t.test
crushes and gives out that error.
I think a check should be added to avoid this from happening, meanwhile
I've posted a reply on the forum on how to get results anyways.

Best

Nicola



> I've just looked at the problem
>
> [#1259] descriptives.trait with by.var argument does not work
>
> here's the problem he's had : descriptives.trait(data=test, by = bt)
>
> and it's the same you mentioned about sex, so actually it does fix it.
>
> Best
>
> Nicola
>
>> Nicola,
>>
>> many thanks for this!
>>
>> Questions: we have few 'by.var' args bugs filed in at
>>
>> https://r-forge.r-project.org/search/?type_of_search=full&group_id=505&atid=0&words=by.var&Search=Search
>>
>> I think your suggestions take direct care of
>>
>> [#1185] descriptives.trait with missings in by.var argument
>> [#1184] descriptives.trait can not see the variable in by.var argument
>> unless full path specified
>>
>> correct?
>>
>> did you try to see if it would address
>>
>> [#1259] descriptives.trait with by.var argument does not work
>> (contributed by Richard Ahn)
>>
>> as well?
>>
>> best wishes, and thanks a lot!
>>
>> Yurii
>>
>>
>> On Mon, Mar 7, 2011 at 2:36 PM,  <pirastu at burlo.trieste.it> wrote:
>>> Dear all,
>>>
>>> I'm new to the group so I'm not sure I'm doing this correctly, so if
>>> I'm
>>> not please tell me so.
>>> Anyways I think I found how to fix the problems with
>>> descriptives.traits:
>>>
>>> 1) descriptives.trait with missings in by.var argument
>>>
>>>   this line is causing the problem
>>>
>>>   if (!is.numeric(ctrao) | all(ctrao == svar))
>>>
>>> it should be like this:
>>>
>>> if (!is.numeric(ctrao) | all(ctrao == svar,na.rm=T))
>>>
>>>
>>> 2)  descriptives.trait can not see the variable in by.var argument
>>> unless
>>> full path specified.
>>>
>>> the line
>>> svar <- by.var
>>>
>>> and could be modified with these 3 lines:
>>>
>>> if(is.character(by.var) & length(by.var)==1){ svar <- data[,by.var]}
>>> #in
>>> this case by.var should be specified as ie. "sex"
>>>
>>> if(is.vector(by.var)){ svar <- by.var }# in this case by.var should be
>>> like phdata(ge03d2ex)$sex
>>>
>>> if(is.formula(by.var)){ svar <- data[,as.character(by.var)[2]]} #in
>>> this
>>> case by.var should have the form ie. ~sex
>>>
>>>
>>> I hope I could be of help. Sorry if I did not do things the right way.
>>>
>>> Best
>>>
>>> Nicola
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
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>>>
>>
>
>
>