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

Katharina May may.katharina at googlemail.com
Thu Jan 30 13:20:10 CET 2014

Dear R-Community,

I`m trying to apply the mgcv package to fill gaps in sensor data from
different sites (9 sites, 2 sensors per site) and do the filling on a
site-wise level.
Based on http://r.789695.n4.nabble.com/mgcv-gamm-predict-to-reflect-random-s-effects-td3622738.html
my model looks like this:
 xylemRohWeekXnn.fit.bam  <- bam(sensor1 ~ sensor2 + s(site, bs="re")
+ s(site, NthSampling, bs="re") ,  data=xylemRohWeekXnn2011,

However, than I try to use predict, I get an error:
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)
Error in X[ind, ] : subscript out of bounds

I was hoping that someone might be able to provide a quick hint on if
there is an obvious problem or mistake  within my model
I attached the sessionInfo() Output below and the xylemRohWeekXnn2011
dump can be downloaded here:
I`m appreciating any help and hints!

Thank you very much, Katharina

R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252
[4] LC_NUMERIC=C                    LC_TIME=German_Germany.1252

attached base packages:
[1] splines   stats     graphics  grDevices utils     datasets
methods   base

other attached packages:
 [1] mgcv_1.7-27     plyr_1.8        ggplot2_0.9.3.1 lattice_0.20-24
gdata_2.13.2    nlme_3.1-113
 [7] zoo_1.7-10      xlsx_0.5.5      xlsxjars_0.5.0  rJava_0.9-6

loaded via a namespace (and not attached):
 [1] colorspace_1.2-4   dichromat_2.0-0    digest_0.6.4
grid_3.0.2         gtable_0.1.2
 [6] gtools_3.2.1       labeling_0.2       MASS_7.3-29
Matrix_1.1-2       munsell_0.4.2
[11] proto_0.3-10       RColorBrewer_1.0-5 reshape2_1.2.2
scales_0.2.3       stringr_0.6.2
[16] tools_3.0.2

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