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

Katharina May may.katharina at googlemail.com
Sun Feb 2 18:52:03 CET 2014

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.

Many thanks once again,


R Code Example
 #retrieve xylemRohWeekXnn2011 test data frame
 eval( expr =         parse( text =

 xylemRohWeekXnn.fit.bam  <- bam(sensor1 ~ sensor2 + s(site, bs="re")
+ s(site, NthSampling, bs="re") ,  data=xylemRohWeekXnn2011,

 #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)

My current Session Information (sessionInfo() Output - also confirming
that the problem exists on both Windows and Mac OS X):
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

[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

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

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