[R] package mgcv - predict with bam: Error in X[ind, ] : subscript out of bounds

[David Winsemius]

On Feb 2, 2014, at 9:52 AM, Katharina May wrote:

> Hi Simon,
> 
> thank you for your reply, I really appreciate any help to understand
> the problem here...
> Unluckily the package upgrade didn't help with this issue.
> An example reproducing the error, and a current sessionInfo() Output
> can be found below.

I suppose there may be an error of sorts,  but have you considered the fact that solving the error might not gain you admittance into heaven? Look at the RHS of the model:

sensor2 + s(site, bs = "re")
 
... and think about the fact that you are "smoothing" a factor variable. 

> str(gapData)
'data.frame':	2304 obs. of  5 variables:
 $ sensor1    : num  NA NA NA NA NA NA NA NA NA NA ...
 $ site       : Factor w/ 9 levels "KRB","NP.FOR",..: 3 3 3 3 3 3 3 3 3 3 ...
 $ NthSampling: int  7489 7490 7491 7492 7493 7494 7495 7496 7497 7498 ...
 $ YDay       : num  53 53 53 53 53 53 53 53 53 53 ...
 $ sensor2    : num  0.567 0.566 0.567 0.567 0.569 ...

I'm having trouble making any sense of how that might work. It is, of course, possible to just do this:

xylemRohWeekXnnSite.fit <-
predict.gam(xylemRohWeekXnn.fit.bam, type="response", se=F)

That gives predictions for the original dataset.

But I think the error might be helpful in alerting one to the problems with the model.

-- 
David.
> 
> Many thanks once again,
> 
>       Katharina
> 
> 
> R Code Example
> <snip>
> library(RCurl)
> library(mgcv)
> #retrieve xylemRohWeekXnn2011 test data frame
> eval( expr =         parse( text =
> getURL("https://webdisk.ads.mwn.de/Handlers/AnonymousDownload.ashx?folder=1a7cbaa4&path=xylemRohWeekXnn2011.R")
> ))
> 
> xylemRohWeekXnn.fit.bam  <- bam(sensor1 ~ sensor2 + s(site, bs="re")
> + s(site, NthSampling, bs="re") ,  data=xylemRohWeekXnn2011,
> na.action=na.omit)
> 
> #subset data containing gaps for predicting
> gapData <- xylemRohWeekXnn2011[is.na(xylemRohWeekXnn2011[,2]) &
> !is.na(xylemRohWeekXnn2011[,11]),c(2:3,6:7, 11)]
> 
> xylemRohWeekXnnSite.fit <-
> predict.gam(xylemRohWeekXnn.fit.bam,gapData, type="response", se=F)
> </snap>
> 
> 
> 
> My current Session Information (sessionInfo() Output - also confirming
> that the problem exists on both Windows and Mac OS X):
> <snip>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] mgcv_1.7-28    nlme_3.1-113   RCurl_1.95-4.1 bitops_1.0-6
> 
> loaded via a namespace (and not attached):
> [1] grid_3.0.2      lattice_0.20-24 Matrix_1.1-2    tools_3.0.2
> </snap>
> 
> 
> 
> 
> On 31/01/14 12:57, Simon Wood wrote:
>> 
>> Hi Katharina,
>> 
>> Could you try upgrading to mgcv_1.7-28, please? There was an occasional
>> problem to do with matching factor levels, which is fixed, but I'm not
>> very confident that is what is going on.
>> 
>> If upgrading doesn't work, is there any chance you could send me a small
>> example dataset and code that produces the error, and I'll look at it?
>> 
>> best,
>> Simon
>> 
>> --
>> Simon Wood, Mathematical Science, University of Bath BA2 7AY UK
>> +44 (0)1225 386603               http://people.bath.ac.uk/sw283
> 
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David Winsemius
Alameda, CA, USA