[R] mgcv bam() with grouped binomial data

[Casey Olives]

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
>
>
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