R help - May 2012 - GAM, how to set qr=TRUE

Hello,

I don't understand what went wrong or how to fix this. How do I set qr=TRUE
for gam?

When I produce a fit using gam like this:

fit = gam(y~s(x),data=as.data.frame(l_yx),family=family,control
list(keepData=T))

...then try to use predict:
(see #1 below in the traceback() )
> traceback()
6: stop("lm object does not have a proper 'qr' component.\n Rank
zero or
should not have used lm(.., qr=FALSE).") at #81
5: qr.lm(object) at #81
4: summary.glm(object, dispersion = dispersion) at #81
3: summary(object, dispersion = dispersion) at #81
2: predict.glm(fit, data.frame(x = xx), type = "response", se.fit = T,
       col = prediction_col, lty = prediction_ln) at #81
1: predict(fit, data.frame(x = xx), type = "response", se.fit = T,
       col = prediction_col, lty = prediction_ln) at #81

...I get this error:

Error in qr.lm(object) : lm object does not have a proper 'qr'
component.
 Rank zero or should not have used lm(.., qr=FALSE).

I read this post: http://tolstoy.newcastle.edu.au/R/devel/06/04/5133.html

So I tried adding qr=T to the gam call but it didn't make any difference.
This is how I did it:

fit = gam(y~s(x),data=as.data.frame(l_yx),family=family,control
list(keepData=T),qr=T)

Its all very strange because I've produced fits with this data may times
before with no issues (and never having to do anything with the qr
parameter. I don't understand why this is coming up or how to fix it.

PS - I don't think this matters, but I am calling a script called
FunctionGamFit.r like this:
err = system(paste('"C:\\Program
Files\\R\\R-2.14.1\\bin\\R.exe"', 'CMD
BATCH FunctionGamFit.r'), wait = T)
...to produce the fit.

Thanks for any help!

ben

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Which version of gam are you using (i.e. which package and version number?)

prediction with fitted gam objects should call predict.gam, and I'm not 
quite sure why this is not happening here (you do have the mgcv or gam 
loaded while trying to predict, I suppose?).

On 03/05/12 22:56, Ben quant wrote:
> Hello,
>
> I don't understand what went wrong or how to fix this. How do I set
qr=TRUE
> for gam?
>
> When I produce a fit using gam like this:
>
> fit = gam(y~s(x),data=as.data.frame(l_yx),family=family,control >
list(keepData=T))
>
> ...then try to use predict:
> (see #1 below in the traceback() )
>
>> traceback()
> 6: stop("lm object does not have a proper 'qr' component.\n
Rank zero or
> should not have used lm(.., qr=FALSE).") at #81
> 5: qr.lm(object) at #81
> 4: summary.glm(object, dispersion = dispersion) at #81
> 3: summary(object, dispersion = dispersion) at #81
> 2: predict.glm(fit, data.frame(x = xx), type = "response", se.fit
= T,
>         col = prediction_col, lty = prediction_ln) at #81
> 1: predict(fit, data.frame(x = xx), type = "response", se.fit =
T,
>         col = prediction_col, lty = prediction_ln) at #81
>
> ...I get this error:
>
> Error in qr.lm(object) : lm object does not have a proper 'qr'
component.
>   Rank zero or should not have used lm(.., qr=FALSE).
>
> I read this post: http://tolstoy.newcastle.edu.au/R/devel/06/04/5133.html
>
> So I tried adding qr=T to the gam call but it didn't make any
difference.
> This is how I did it:
>
> fit = gam(y~s(x),data=as.data.frame(l_yx),family=family,control >
list(keepData=T),qr=T)
>
> Its all very strange because I've produced fits with this data may
times
> before with no issues (and never having to do anything with the qr
> parameter. I don't understand why this is coming up or how to fix it.
>
> PS - I don't think this matters, but I am calling a script called
> FunctionGamFit.r like this:
> err = system(paste('"C:\\Program
Files\\R\\R-2.14.1\\bin\\R.exe"', 'CMD
> BATCH FunctionGamFit.r'), wait = T)
> ...to produce the fit.
>
> Thanks for any help!
>
> ben
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
Simon Wood, Mathematical Science, University of Bath BA2 7AY UK
+44 (0)1225 386603               http://people.bath.ac.uk/sw283

Solution: have package mgcv loaded when you predict...not just for the fit.
:) Silly mistake...

Thanks Simon!

Ben

On Thu, May 3, 2012 at 3:56 PM, Ben quant <ccquant@gmail.com> wrote:
> Hello,
>
> I don't understand what went wrong or how to fix this. How do I set
> qr=TRUE for gam?
>
> When I produce a fit using gam like this:
>
> fit = gam(y~s(x),data=as.data.frame(l_yx),family=family,control >
list(keepData=T))
>
> ...then try to use predict:
> (see #1 below in the traceback() )
>
> > traceback()
> 6: stop("lm object does not have a proper 'qr' component.\n
Rank zero or
> should not have used lm(.., qr=FALSE).") at #81
> 5: qr.lm(object) at #81
> 4: summary.glm(object, dispersion = dispersion) at #81
> 3: summary(object, dispersion = dispersion) at #81
> 2: predict.glm(fit, data.frame(x = xx), type = "response", se.fit
= T,
>        col = prediction_col, lty = prediction_ln) at #81
> 1: predict(fit, data.frame(x = xx), type = "response", se.fit =
T,
>        col = prediction_col, lty = prediction_ln) at #81
>
> ...I get this error:
>
> Error in qr.lm(object) : lm object does not have a proper 'qr'
component.
>  Rank zero or should not have used lm(.., qr=FALSE).
>
> I read this post: http://tolstoy.newcastle.edu.au/R/devel/06/04/5133.html
>
> So I tried adding qr=T to the gam call but it didn't make any
difference.
> This is how I did it:
>
> fit = gam(y~s(x),data=as.data.frame(l_yx),family=family,control >
list(keepData=T),qr=T)
>
> Its all very strange because I've produced fits with this data may
times
> before with no issues (and never having to do anything with the qr
> parameter. I don't understand why this is coming up or how to fix it.
>
> PS - I don't think this matters, but I am calling a script called
> FunctionGamFit.r like this:
> err = system(paste('"C:\\Program
Files\\R\\R-2.14.1\\bin\\R.exe"', 'CMD
> BATCH FunctionGamFit.r'), wait = T)
> ...to produce the fit.
>
> Thanks for any help!
>
> ben
>
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