[R] mgcv bam() with grouped binomial data

[Simon Wood]

Hi Casey,

any chance that you could send me the data off list (under a strict 
undertaking to not use it for anything but this de-bugging of course)? I 
can't immediately reproduce the problem by simulating similar, but it 
certainly looks like a bug.

best,
Simon

On 02/02/2012 01:54 AM, Casey Olives wrote:
> Hi Simon,
>
> Thanks for your response. I am now running mgcv 1.7-13 on R-2.14. Having fixed this error, I now encounter the following when fitting this model
>
> Error in qr.qty(qrx, yn) : 'qr' and 'y' must have the same number of rows
> Calls: bam ->  bgam.fit ->  qr.update ->  qr.qty ->  qr.qty
>
> bam(cbind(group0, temp)~1+ as.factor(AGEcat) + HSMF+BachMF+income.cpi+poverty+tobacco+tax+CigSalesPerCap+blacks+hisp+asian+native +s( year.centered , by= fips , bs='cr', k=8) +s( fips , bs='re'), gamma=1.6, family=binomial(link="logit"), data=data
>
> My sense is that the error is coming from the term
>
> s( year.centered , by= fips , bs='cr', k=8)
>
> as if I run the same model with
>
> s( year.centered, bs='cr', k=8)
>
> I don't get the error. Thus, something about trying to fit these smooths by fips id is causing the error.
>
> Do you have any ideas on what might be happening? I recognize it is hard to know without seeing the data....
>
> Thanks again
> Casey
>
> -----Original Message-----
> From: Simon Wood [mailto:s.wood at bath.ac.uk]
> Sent: Tuesday, January 31, 2012 2:17 AM
> To: Casey Olives
> Cc: 'r-help at r-project.org'
> Subject: Re: [R] mgcv bam() with grouped binomial data
>
> upgrade to the current mgcv version (see last item in changeLog for mgcv
> 1.7-12)
>
> On 01/30/2012 10:04 PM, Casey Olives wrote:
>> Hello,
>>
>> I'm trying to use the bam() function in the R mgcv package for a large set of grouped binary data. However, I have found that this function does not take data in the format of cbind(numerator, denominator) on the left hand side of the formula. As an example, consider the following
>>
>> dat1<- data.frame(id=rep(1:6, each=3), num=rbinom(18, size=10, prob=0.8), den=rbinom(18, size=5, prob=0.5), x=rnorm(18))
>> m1.1<- gam(cbind(num, den) ~ x+s(id, bs="re"), data=dat1, family=binomial)
>> m2.1<- bam(cbind(num, den) ~x+ s(id, bs="re"), data=dat1, family=binomial)
>>
>> Running the above results in
>>
>>> dat1<- data.frame(id=rep(1:6, each=3), num=rbinom(18, size=10, prob=0.8), den=rbinom(18, size=5, prob=0.5), x=rnorm(18))
>>> m1.1<- gam(cbind(num, den) ~ x+s(id, bs="re"), data=dat1, family=binomial)
>>> m2.1<- bam(cbind(num, den) ~x+ s(id, bs="re"), data=dat1, family=binomial)
>> Error in dev.resids(y, mu, weights) :
>>     argument mu must be a numeric vector of length 1 or length 36
>>
>> Is this a known issue? If so, is there a way to handle it?
>>
>> Thank you,
>>
>> Casey
>>
>>
>> 	[[alternative HTML version deleted]]
>>
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>